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adrenal gland code (Julia Schaepe) #2

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36 changes: 36 additions & 0 deletions EAID_000003/README.md
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# Adrenal Gland ENCODE single-cell analysis
Contact information: [email protected]

Integrated analysis for the following ENCODE 10x multiome adrenal gland experiments:
- ENCSR194KHA (scATAC)
- ENCSR420EWQ (scATAC)
- ENCSR693GAD (scATAC)
- ENCSR726IPC (snRNA)
- ENCSR362YDM (snRNA)
- ENCSR724KET (snRNA)

The samples are referred to in the analysis as:
- W62 (ENCSR693GAD, ENCSR724KET)
- W64 (ENCSR420EWQ, ENCSR362YDM)
- W73 (ENCSR194KHA, ENCSR726IPC)

Analysis steps in the code:
1. Loading scATAC data for each sample and creating arrow files with ArchR.
2. Filtering scATAC data with a minTSS of 5 and minFrags of 3,162 and outputting cell barcodes that pass.
3. Loading snRNA data with Seurat.
4. Filtering snRNA data with number RNA reads between 1,000 and 30,000 and percent of mitochondrial reads less than 10%.
5. Additional filtering of snRNA for only cells that pass scATAC QC.
6. Integrating snRNA datasets with scTransform and performing dimensionality reduction and clustering.
7. Visualizing snRNA data.

Required packages:
- library(ArchR), version 1.0.1
- library(Seurat), version 4.0.6
- library(dplyr)
- library(patchwork)
- library(ggplot2)
- library(sctransform)

Installation instructions:
1. Install ArchR following instructions here: https://www.archrproject.com/
2. Install Seurat following instructions here: https://satijalab.org/seurat/articles/install.html
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This folder contains the following files:
- adrenal_multiome_processing: the code used to import, filter, process and visualize all samples
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This folder contains relevant visualizations of the data.

Each sample (W62, W64, W73) has the following quality control figures:
- ATAC_QC: pre-filtered TSS Enrichment versus unique fragments
- filtered_ATAC_QC: post-filtering TSS Enrichment versus unique fragments
- ATAC_frags: pre-filtered fragment size distribution
- RNA_QC: pre-filtered unique RNA counts, RNA counts, percent mitochondrial

The final integrated and labeled dataset has the following figures:
- UMAP: UMAP labeled by cluster
- UMAP_nolegend: UMAP labeled by cluster without legend
- marker_expression: dotplot of marker gene expression by cluster
- cluster_ratios: barplot of cluster proportions across each sample

The integrated and labeled dataset before high ribosomal and putative doublet clusters are removed:
- presubset_UMAP: UMAP labeled by cluster
- presubset_UMAP_nolegend: UMAP labeled by cluster without legend
- presubset_marker_expression: dotplot of marker gene expression by cluster
- presubset_cluster_ratios: barplot of cluster proportions across each sample
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# Marker genes for lymphatic endothelial cells
# gene_id: ENSEMBL Gene ID
# gene_name: Common name of the gene
# avg_log2FC: Log2 fold-change of the average expression between the given cell type and the remaining cells (min 0.5)
# FDR: p-value-derived FDR value for gene
# is_enriched: A binary (0/1) value indicating whether the given gene is enriched for the cell type (FDR < 0.1)
gene_id gene_name avg_log2FC p_val_adj is_enriched
ENSG00000135218 CD36 12.1238367182524 5.45928209868212e-71 1.0
ENSG00000205038 PKHD1L1 8.018038158215651 4.55096609445152e-65 1.0
ENSG00000003436 TFPI 8.16926466889874 7.992672554270858e-61 1.0
ENSG00000110841 PPFIBP1 10.756348851231198 1.5349285081403696e-54 1.0
ENSG00000138722 MMRN1 9.541488144782749 3.327912448972249e-54 1.0
ENSG00000075213 SEMA3A 9.83659709847116 2.9954446850502594e-53 1.0
ENSG00000064989 CALCRL 3.32846556248751 1.0449220126344e-47 1.0
AC007319.1 9.11800189508779 3.35996755442131e-47 1.0
ENSG00000147459 DOCK5 3.5392485252132704 3.14017380855364e-46 1.0
ENSG00000173320 STOX2 1.36905569066564 1.0329158997610499e-45 1.0
ENSG00000189056 RELN 9.95432795495999 1.29031611935625e-45 1.0
ENSG00000188559 RALGAPA2 2.3448743542426898 2.2814705020925398e-45 1.0
ENSG00000184005 ST6GALNAC3 2.10856818470725 4.4293081204200405e-44 1.0
ENSG00000134215 VAV3 2.39422289041687 5.678788566285129e-39 1.0
ENSG00000150054 MPP7 8.91394653471308 7.716036099185779e-39 1.0
ENSG00000182022 CHST15 1.4039208668467098 1.0334249562478799e-38 1.0
ENSG00000185070 FLRT2 1.8439375925824601 2.94994318279986e-38 1.0
ENSG00000113448 PDE4D 1.7468179737972 1.2952692441077599e-33 1.0
ENSG00000150625 GPM6A 1.4497698508442198 1.0553110214285798e-32 1.0
ENSG00000111145 ELK3 2.2442542325512798 3.50996937833149e-32 1.0
ENSG00000166147 FBN1 13.150109247137499 6.62870021104212e-31 1.0
ENSG00000184349 EFNA5 8.91203501007748 1.25198280686909e-30 1.0
ENSG00000169946 ZFPM2 0.572102200777556 1.2786590785488399e-29 1.0
ENSG00000110328 GALNT18 1.98223949546534 2.6386961931013395e-28 1.0
ENSG00000198795 ZNF521 4.36298267417778 1.34382338840203e-26 1.0
ENSG00000120278 PLEKHG1 6.091429617587281 5.38474142676365e-26 1.0
ENSG00000249797 LINC02147 6.03486346582038 3.6577163715117294e-25 1.0
ENSG00000170365 SMAD1 12.4025523956793 1.77882874736368e-24 1.0
ENSG00000130396 AFDN 2.11250657942354 1.3671827351665097e-23 1.0
ENSG00000154175 ABI3BP 2.60516128370354 2.90561015109167e-23 1.0
ENSG00000088387 DOCK9 1.32482708621589 1.6869077224813199e-22 1.0
ENSG00000237238 BMS1P10 3.00408089859136 5.47602101680957e-22 1.0
ENSG00000118257 NRP2 8.40197953387496 6.944374064104979e-21 1.0
ENSG00000122644 ARL4A 11.3405694920835 1.82397687505661e-20 1.0
ENSG00000132334 PTPRE 3.2788855546468803 3.05620845265101e-19 1.0
ENSG00000117707 PROX1 17.5797997606754 3.4541897101138894e-19 1.0
ENSG00000137269 LRRC1 5.39927404678595 4.1769510476809397e-19 1.0
AC087633.2 4.3891615729349 2.54138699378039e-18 1.0
ENSG00000171408 PDE7B 2.83096237004029 2.8586301917883497e-18 1.0
ENSG00000137077 CCL21 7.41199730094427 4.24076029364218e-17 1.0
ENSG00000037280 FLT4 4.50904528656588 6.475414527579261e-17 1.0
ENSG00000153993 SEMA3D 3.72012273781482 8.788985488324411e-16 1.0
ENSG00000064692 SNCAIP 6.6593822138625 2.54802987327974e-15 1.0
ENSG00000128052 KDR 4.77433817630435 2.56986703267756e-15 1.0
ENSG00000168785 TSPAN5 6.48459031006561 1.03062937565072e-14 1.0
ENSG00000175048 ZDHHC14 2.66810443234464 6.49495949392301e-14 1.0
ENSG00000142192 APP 3.10252062918967 1.09219286925237e-13 1.0
ENSG00000115306 SPTBN1 0.753106482654193 1.84261128570877e-13 1.0
ENSG00000112769 LAMA4 6.3786238323122095 6.70035806974255e-13 1.0
AC083837.2 6.08935236064346 1.28628410490072e-12 1.0
ENSG00000273079 GRIN2B 7.280020505491559 1.31273728967325e-12 1.0
ENSG00000154529 CNTNAP3B 3.2290803380472406 2.623463975284e-12 1.0
ENSG00000189152 GRAPL 3.55519378840975 2.72675453030446e-11 1.0
ENSG00000071242 RPS6KA2 0.9952376956983641 3.27575860679221e-11 1.0
ENSG00000124440 HIF3A 3.9788460565122596 3.8226719381716e-11 1.0
ENSG00000011105 TSPAN9 7.99800952124487 4.7339023986094e-11 1.0
ENSG00000152284 TCF7L1 6.274766696226 1.25142976345521e-10 1.0
ENSG00000018408 WWTR1 1.54497321126213 1.55471370795619e-10 1.0
ENSG00000251003 ZFPM2-AS1 1.44860638938508 2.2363515448779998e-10 1.0
ENSG00000152104 PTPN14 1.09243325180977 6.18058506137498e-10 1.0
ENSG00000126785 RHOJ 0.9817370998573591 1.18296491094485e-09 1.0
ENSG00000135363 LMO2 4.3252203249367005 2.5289228258827e-09 1.0
AMYH02020865.1 4.08052527765652 4.372918431986e-09 1.0
ENSG00000114698 PLSCR4 1.28707298972181 5.7752394275781295e-09 1.0
ENSG00000143774 GUK1 3.2761065623857997 6.68491726388964e-09 1.0
ENSG00000129595 EPB41L4A 4.92002789999091 7.37758527398538e-09 1.0
ENSG00000144668 ITGA9 9.3284585454726 8.62049525132589e-09 1.0
ENSG00000169851 PCDH7 0.728349311193227 1.2493996287691201e-08 1.0
ENSG00000010810 FYN 2.7175957434459597 2.76972658949148e-08 1.0
ENSG00000154783 FGD5 4.21334117332578 3.01015441260889e-08 1.0
ENSG00000066027 PPP2R5A 3.86107096028821 3.9264776292599395e-08 1.0
ENSG00000103335 PIEZO1 2.04382362634315 7.00488734835658e-08 1.0
ENSG00000168497 CAVIN2 3.14957032205392 8.15001320661955e-08 1.0
ENSG00000167447 SMG8 0.90068539081652 8.62680849101813e-08 1.0
ENSG00000182718 ANXA2 0.565034986049826 2.1233247697780399e-07 1.0
ENSG00000017427 IGF1 4.87980867387524 3.59509832839431e-07 1.0
ENSG00000183580 FBXL7 3.24842120314441 4.74861867558846e-07 1.0
ENSG00000173210 ABLIM3 7.7727179732962695 2.46890847632578e-06 1.0
ENSG00000116117 PARD3B 1.1845656631758101 3.49707622950417e-06 1.0
ENSG00000131196 NFATC1 1.4982117016441296 4.4384543591323e-06 1.0
ENSG00000124831 LRRFIP1 2.5288543054442596 4.85929831706451e-06 1.0
ENSG00000139926 FRMD6 7.2610823747312105 8.27915363405892e-06 1.0
ENSG00000164687 FABP5 5.05994907392585 1.1809749378496902e-05 1.0
ENSG00000104432 IL7 6.50967728194661 1.91808516195247e-05 1.0
ENSG00000122417 ODF2L 1.4954777005174398 1.9894470137816603e-05 1.0
ENSG00000137449 CPEB2 4.74750931259739 2.1139479277341398e-05 1.0
ENSG00000250305 TRMT9B 5.14989572740795 2.48030522711006e-05 1.0
ENSG00000146592 CREB5 1.49938236038131 6.232848346946179e-05 1.0
ENSG00000226476 LINC01748 0.552357241081747 6.96179842216047e-05 1.0
ENSG00000126883 NUP214 2.04271434254663 7.218359862437579e-05 1.0
ENSG00000091136 LAMB1 5.89634502263556 7.737949344234409e-05 1.0
ENSG00000183808 RBM12B 1.46328654836272 0.00011665793453746299 1.0
ENSG00000114861 FOXP1 0.643204342142115 0.000218266474237173 1.0
ENSG00000106100 NOD1 3.08489505895177 0.00025033160393927 1.0
ENSG00000164828 SUN1 0.557687459108359 0.000257566644083382 1.0
ENSG00000214415 GNAT3 8.873086916872449 0.000279411277111107 1.0
ENSG00000145337 PYURF 1.3728341795529 0.000371900508829265 1.0
ENSG00000156313 RPGR 13.6898203656264 0.000401581903916939 1.0
ENSG00000134046 MBD2 1.08071511191674 0.000510284549384743 1.0
ENSG00000198108 CHSY3 2.6041966229793103 0.000518159033656076 1.0
ENSG00000184232 OAF 2.4173717324302 0.000911633226058641 1.0
ENSG00000255693 LINC02389 3.2450756596893298 0.0009191317093997641 1.0
ENSG00000068615 REEP1 9.2397011264696 0.00102852335469121 1.0
ENSG00000282230 ADAM9 2.68787412992467 0.00117675282530566 1.0
ENSG00000168615 ADAM9 2.68787412992467 0.00117675282530566 1.0
ENSG00000091409 ITGA6 3.21528054871373 0.00139652224543756 1.0
ENSG00000117758 STX12 1.02758156413636 0.00140243566264464 1.0
ENSG00000198478 SH3BGRL2 15.087972437846 0.00205020580463704 1.0
ENSG00000128833 MYO5C 0.7223935067000491 0.0027221487201458698 1.0
ENSG00000196781 TLE1 9.114286405855971 0.00273850987760517 1.0
ENSG00000171988 JMJD1C 0.543708018312058 0.00341537204943883 1.0
ENSG00000107581 EIF3A 1.3088231337516398 0.00460582481366418 1.0
AC093157.1 4.465034916878429 0.00502453951258457 1.0
ENSG00000197261 C6orf141 6.91747468363911 0.00578291905198978 1.0
ENSG00000136938 ANP32B 1.28688701219185 0.006112026673838179 1.0
ENSG00000012983 MAP4K5 2.08667001571883 0.00697238421762178 1.0
ENSG00000137845 ADAM10 5.255218988527861 0.00817412015812652 1.0
ENSG00000197694 SPTAN1 10.5341251748302 0.00856991880158293 1.0
AC087257.2 4.5228299718831195 0.0101024046778357 1.0
ENSG00000281324 LRP6 2.1913723262231297 0.0107105634323057 1.0
ENSG00000070018 LRP6 2.1913723262231297 0.0107105634323057 1.0
ENSG00000101596 SMCHD1 0.6435080911035761 0.0159832168352904 1.0
ENSG00000138398 PPIG 1.84322004792995 0.0181921526180277 1.0
ENSG00000134470 IL15RA 5.251660988589331 0.0207848923400707 1.0
ENSG00000234948 LINC01524 7.27602690790493 0.021748285589801998 1.0
ENSG00000152661 GJA1 0.611266505979989 0.0224197436794614 1.0
AC073073.2 4.49686435249277 0.0230644688359195 1.0
ENSG00000144810 COL8A1 2.7565781752050205 0.0235041655920919 1.0
ENSG00000128656 CHN1 5.85718294156088 0.0245333293498968 1.0
ENSG00000171595 DNAI2 1.6735042275015102 0.0259041856991294 1.0
ENSG00000135974 C2orf49 1.25348991204289 0.0270146641583737 1.0
ENSG00000234545 FAM133B 2.46650745367826 0.0359081834689002 1.0
ENSG00000166484 MAPK7 6.12408904429438 0.0445983158179986 1.0
ENSG00000104388 RAB2A 0.501751593450913 0.0500840346842785 1.0
ENSG00000197747 S100A10 1.5015479160817502 0.0501533796659979 1.0
ENSG00000132819 RBM38 9.05232696047652 0.0504235692663329 1.0
ENSG00000151923 TIAL1 1.69286839446042 0.0504917420182491 1.0
AC004862.1 2.55984952487377 0.0513695606260124 1.0
ENSG00000136146 MED4 0.6600020268129411 0.0535925943646257 1.0
ENSG00000113282 CLINT1 1.08241651698274 0.0574652148788209 1.0
ENSG00000182704 TSKU 4.27121167108028 0.0614153894908254 1.0
ENSG00000277443 MARCKS 1.95349449731427 0.0702435640806778 1.0
ENSG00000176102 CSTF3 1.9955783024745 0.0796891512477257 1.0
ENSG00000282665 ERICH1 1.83280044708447 0.0824656329425297 1.0
ENSG00000104714 ERICH1 1.83280044708447 0.0824656329425297 1.0
ENSG00000143155 TIPRL 3.55234675355102 0.093419525833444 1.0
ENSG00000008441 NFIX 2.84261958995086 0.09578736230333901 1.0
ENSG00000144747 TMF1 1.4631395270556498 0.0970687629166707 1.0
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