title: 15B_M_1062


title: 15B_M_1068

status: Public on Jun 16 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


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title: 14D_M_1493


title: 14D_M_1492


title: 14D_M_1481


title: 14D_M_1479


title: 14D_M_1474


title: 14D_M_1478


title: 14D_M_1476


title: 14D_M_1477


title: 14D_M_1468


title: 14D_M_1470


title: 14D_M_1471


title: 14D_M_1475


title: 14D_M_1472


title: 14D_M_1465


title: 14D_M_1469


title: 14D_M_1464


title: 14D_M_1467


title: 14D_M_1463


title: 14D_M_1207


title: 14D_M_1208


title: 14D_M_1462


title: 14D_M_1480


title: 14D_M_1206


title: 14D_M_1205


title: 14D_M_1204


title: 14D_M_1202


title: 14D_M_1201


title: 14D_M_1203


title: 14D_M_1466


title: 14D_M_1200


title: 14D_M_1473


title: 14D_M_1199


title: 14D_M_1196


title: 14D_M_1194


title: 14D_M_1197


title: 14D_M_1195


title: 14D_M_1189


title: 14D_M_1188


title: 14D_M_1193


title: 14D_M_1191


title: 14D_M_1187


title: 14D_M_1190


title: 14D_M_1186


title: 14D_M_1185


title: 14D_M_1184


title: 14D_M_1183


title: 14D_M_1182


title: 14D_M_1179


title: 14D_M_1181


title: 14D_M_1180


title: 14D_M_1178


title: 14D_M_1198


title: 14D_M_1176


title: 14D_M_1175


title: 14D_M_1177


title: 14D_M_1174


title: 14D_M_1173


title: 14D_M_1171


title: 14D_M_1168


title: 14D_M_1170


title: 14D_M_1169


title: 14D_M_1165


title: 14D_M_1166


title: 14D_M_1164


title: 14D_M_1163


title: 14D_M_1161


title: 14D_M_1159


title: 14D_M_1157


title: 14D_M_1154


title: 14D_M_1153


title: 14D_M_1152


title: 14D_M_1149


title: 14D_M_1172


title: 14D_M_1148


title: 14D_M_1167


title: 14D_M_1143


title: 14D_M_1144


title: 14D_M_1145


title: 14D_M_1147


title: 14D_M_1141


title: 14D_M_1142


title: 14D_M_1162


title: 14D_M_1160


title: 14D_M_1139


title: 14D_M_1138


title: 14D_M_1137


title: 14D_M_1158


title: 14D_M_1140


title: 14D_M_1135


title: 14D_M_1151


title: 14D_M_1133


title: 14D_M_1131


title: 14D_M_1155


title: 14D_M_1146


title: 14D_M_1129


title: 14D_M_1128


title: 14D_M_1127


title: 14D_M_1136


title: 14D_M_1156


title: 14D_M_1125


title: 14D_M_1122


title: 14D_M_1126


title: 14D_M_1124


title: 14D_M_1120


title: 14D_M_1119


title: 14D_M_1134


title: 14D_M_1118


title: 14D_M_1117


title: 14D_M_1113


title: 14D_M_1115


title: 14D_M_1114


title: 14D_M_1116


title: 14D_M_1111


title: 14D_M_1112


title: 14D_M_1109


title: 14D_M_1110


title: 14D_M_1132


title: 14D_M_1108


title: 14D_M_1107


title: 14D_M_1130


title: 14D_M_1105


title: 14D_M_1106


title: 14D_M_1103


title: 14D_M_1102


title: 14D_M_1123


title: 14D_M_1104


title: 14D_M_1101


title: 14D_M_1121


title: 14D_M_1099


title: 14D_M_1095


title: 14D_M_1097


title: 14D_M_1093


title: 14D_M_1100


title: 14D_M_1096


title: 14D_M_1091


title: 14D_M_1089


title: 14D_M_1092


title: 14D_M_1088


title: 14D_M_1086


title: 14D_M_1094


title: 14D_M_1087


title: 14D_M_1082


title: 14D_M_1080


title: 14D_M_1081


title: 14D_M_1083


title: 14D_M_1085


title: 14D_M_1084


title: 14D_M_1078


title: 14D_M_1098


title: 14D_M_1079


title: 14D_M_1074


title: 14D_M_1077


title: 14D_M_1076


title: 14D_M_1073


title: 14D_M_1072


title: 14D_M_1071


title: 14D_M_1075


title: 14D_M_1090


title: 14D_M_1068


title: 14D_M_1070


title: 14D_M_1067


title: 14D_M_1066


title: 14D_M_1064


title: 14D_M_1065


title: 14D_M_1063


title: 14D_M_1062


title: 14D_M_1069


title: 14D_M_1060


title: 14D_M_1061


title: 14D_M_1058


title: 14D_M_1059


title: 14D_M_1057


title: 14D_M_1051


title: 14D_M_1050


title: 14D_M_1053


title: 14D_M_1052


title: 14D_M_1048


title: 14D_M_1049


title: 14D_M_1047


title: 14D_M_1045


title: 14D_M_1044


title: 14D_M_1043


title: 14D_M_1046


title: 14D_M_1041


title: 14D_M_1042


title: 14D_M_1039


title: 14D_M_1040


title: 14D_M_1036


title: 14D_M_1033


title: 14D_M_1038


title: 14D_M_1037


title: 14D_M_1031


title: 14D_M_1034


title: 14D_M_1032


title: 14D_M_1029


title: 14D_M_1030


title: 14D_M_1035


title: 14D_M_1055


title: 14D_M_1054


title: 14D_M_1028


title: 14D_M_1056


title: 14D_M_1027


title: 14D_M_1026


title: 14D_M_1025


title: 14D_M_1024


title: 14D_M_1023


title: 14D_M_1022


title: shcbx8-2-2

city: Tianjin

first: Chenghao

last: Xuan

address: 22 Qixiangtai Road

country: China

institute: Tianjin Medical University

library_source: transcriptomic

data_processing:
Clean datas were mapped to the human genome (UCSC hg38) using Hisat2 (v2.2.1).
Each transcript expression level was quantified as transcript_count using StringTie (v2.2.1).
DEseq2(v1.34.0) was used to perform differential expression analysis.
Assembly: hg38
Supplementary files format and content: transcript_count.csv: comma-separated table file includes raw count for each example

molecule: total RNA

organism: Homo sapiens

source_name: lung

growth_protocol: A549 cells were cultured in Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum at 37 ℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The lentiviruses expressing control or shCBX8 shRNA were employed to infect A549 cells to obtain stable expression cells.

tag: tissue

value: lung

tag: cell line

tag: genotype

value: CBX8 knockdown


title: Platelet1

city: shanghai

first: Zhenyu

last: Shao

state: --- Select a state ---

address: Yueyang Road 320

department: Center for Excellence in Molecular Cell Science

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
For data processing, raw data were trimmed by Trim Galore (v0.5.0) with default settings.
Then, the clean data were mapped to the rCRS (NC_012920.1) or ChrM of mm10 mouse reference genome using Bismark (v0.20.1) with the parameters -X 2000 --score_min L,0,-0.6 or BS-Seeker2 (v2.1.8) with the parameter -m 3.
Duplicates were removed using Picard (v2.22.4). Bigwig files were generated using bedGraphToBigWig and visualized in Integrative Genomics Viewer(IGV).
Since we regarded sequencing depth as a relative concept and the vast majority of cytosines in mtDNA was sequenced far more than 50 times, we intentionally did not set a depth cutoff.
Assembly: Hg38
Supplementary files format and content: bigwig files for levels and sequencing depths of mtDNA-5mC

source_name: Platelet

extract_protocol:
Total DNA was extracted from cells or tissues using Phenol-chloroform DNA extraction protocol. If needed, enrichment of mtDNA was performed using TIANprep Mini Plasmid Kit (TIANGEN) according to the manufacturer’s instructions.
Briefly, 200-1000 ng genomic DNA was used for WGBS library construction. DNA was sonicated to ~250 bp fragments with the Diagenode Bioruptor Pico. Then DNA was subjected to end-repair, A-tailing, and ligation using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) and methylated adaptor (Roche) according to the manufacturer’s instructions. DNA was purified with VAHTS DNA Clean Beads. Subsequently, library was bisulfite modified using QIAGEN EpiTect Fast DNA Bisulfite Kit (59824) and amplified with KAPA2G Robust HotStart PCR Kits with dNTPs (Sigma-Aldrich). Library was finally subjected to 150 bp paired-end sequencing using the Illumina Novaseq6000 instrument.

tag: cell type

value: Platelet


title: Platelet2


title: shcbx8-2-1


title: shcbx8-1-1


title: 14D_M_1021


title: Control2

value: control


title: shcbx8-1-2


title: 14D_M_1020


title: Control1


title: 14D_M_1019


title: 14D_M_1017


title: 14D_M_1018


title: 14D_M_889


title: 14D_M_890


title: FBL mitochondrial RNA-seq

city: Palo Alto

first: Ji-Fan

last: Hu

state: California

address: 3801 Miranda Ave

institute: Stanford University

data_processing:
Filter raw data with fastp (version:v0.20.0)
The obtained clean reads were aligned to the human reference genome human (GRCh38.p13)  using the spliced mapping algorithm of StringTie.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.
Supplementary files format and content: Gene_Ontology_results.tar
Supplementary files format and content: KEGG_results.tar

source_name: FBL

growth_protocol: The H9 cells and iPSCs were cultured in mTESR1(STEMCELL, Cat.#85850) medium, in Matrigel (Corning, Cat.354277) precoated 6-well plate. The human fibroblasts were cultured in DMEM (Sigma, Cat.#D5796) supplemented with 10% FBS. All cells were cultured at 37 °C with 5% CO2.

extract_protocol: The mitochondria were isolated with Qproteome Mitochondria Isolation Kit (QIAGEN, Cat.#37612). The ribosomes were isolated by sucrose gradient ultracentrifugation, and the polyribosome fractions were determined by 260 nm absorbance.

treatment_protocol: Before sucrose gradient ultracentrifugation for ribosome isolation,  the cells were treated with 100 μg/ml cycloheximide for 15 min at 37 °C in PBS.

value: FBL

value: Fibroblasts

value: WT


title: FBL polyribosomal RNA-seq

molecule: polyA RNA


title: 14D_M_887


title: 14D_M_888


title: iPSC mitochondrial RNA-seq

source_name: iPSC

value: iPSC


title: FBL RNA-seq


title: 14D_M_886


title: 14D_M_885


title: iPSC polyribosomal RNA-seq


title: hTERT cells, MED12-G44 mutant colony-1, HIC

city: CHICAGO

first: MAZHAR

last: ADLI

state: IL

address: 303 E SUPERIOR STREET

department: OBGYN

institute: NORTHWESTERN UNIVERSITY

data_processing:
The mapping, filtering, and binning of the data were done using the runHiC(v0.8.6) pipeline.
First, the adapters of the Hi-C FASTQ files were trimmed using Trim Galore(v0.4.5), and then runHiC aligned the trimmed FASTQ files to the hg38 human reference genome with Burrows-Wheeler Aligner
Low-quality reads and PCR duplicates were removed. Read pairs were then used to couple aligned reads, and redundant PCR artifacts Read pairs aligned to the same restriction fragments were filtered out before the next stage
The binning stage binned the reads at 5-kb, 10-kb, 50-kb, 1-Mb, 10-Mb, and 50-Mb resolution and performed the ICE normalization at the same time. After the binning state, ICE normalized matrices .mcool files were generated for downstream analyses.
The compartment analysis for WT/Mut HiC was performed using cooltools. The A/B compartments PC1 values at 100-kb resolution were called using cooltools eigs-cis command
Assembly: GRCh38 human genome
Supplementary files format and content: hic file (highly compressed binary file) and Bigwig files for eigen vector

source_name: Uterus

growth_protocol: Human myometrial hTERT cells were maintained in DMEM/F-12  with 10% Fetal Bovine Serum and 1 % Penicillin–streptomycin . Cells were cultured and incubated at 37 °C in a humidified atmosphere of 5 % CO2 and 95 % air.

extract_protocol:
Approximate 1 million WT/Mut cells were harvested, counted, and fixed with 1% formaldehyde and quenched with 0.125 M glycine at room temperature
The Hi-C was performed using the Arima-HiC Kit (A510008, Arima Genomics) as instructed by the manufacturer
Hi-C libraries were generated using KAPA Library Quantification Kit (KAPA Biosystems) and quality-checked according to the manufacturer’s protocol

value: Uterus

value: hTERT uterine smooth muscle cell

value: Human myometrial  cells

value: MED12-G44 mutant


title: hTERT cells, MED12-WT, HIC

value: MED12 wild type


title: iPSC RNA-seq


title: H9 polyribosomal RNA-seq

value: Embryo stem cell


title: H9 mitochondrial RNA-seq


title: 14D_M_883


title: H9 RNA-seq


title: 14D_M_884


title: NC_2_Si

city: Changzhou

first: Sheng

last: Zhou

state: Jiangsu

address: 29 Xinlong Lane

institute: The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
Assembly: GRCH38
Supplementary files format and content: tab-delimited text files include RPKM and count values for each Sample
Supplementary files format and content: xlsx files include COUNT values for each Sample

source_name: cells

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).
The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: cells

value: Osteosarcoma cell

tag: treatment

value: siNC


title: 14D_M_882


title: 14D_M_880


title: NC_3_Si


title: Heterogeneity of therapy-resistant CML cells

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
bcl2fastq v2.20 (loaded by cellranger mkfastq (3.0.1)) software used for basecalling.
reads were aligned to refdata-cellranger-mm10-1.2.0 genome assembly using cellranger v3.0.1
Counting data of reference gene expression levels were generated by cellranger v3.0.1 (automatic identification of chemistry properties)
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Primary CML patient cells

growth_protocol: Patient derived primary cells were kept in QBSF60 medium

extract_protocol:
Dead cells were removed using kit and cells were resuspended in PBS
Cells encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3′ Reagent Kits v3 (1000075) according to manufacturer’s protocol (10x Genomics). The generated scRNA-seq libraries were sequenced on a HiSeq using a read structure of 28 bp for Read 1, 8 bp for Index 1, and 101 bp for Read 2.
Library preparation was performed using 10x Genomics Chromium Single Cell 3’ Solution with v3 chemistry following manufacturer protocols (10x Genomics).

treatment_protocol: Cells were treated with 5 uM Imatinib for 7 days in QBSF60

value: leukemic stem cells

value: imatinib


title: 14D_M_879


title: NC_1_Si


title: 14D_M_878


title: 14D_M_876


title: 14D_M_875


title: KPNA2_2_Si

value: KPNA2 knockdown


title: KPNA2_1_Si


title: 14D_M_870


title: 14D_M_872


title: 14D_M_877


title: 14D_M_874


title: 14D_M_873


title: 14D_M_871


title: KPNA2_3_Si


title: 14D_M_868


title: 14D_M_869


title: ADT-derived cDNA R1041_4-A

city: New York

first: Darwin

last: D'Souza

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

description:
ADT-derived cDNA
protein
paired-end
Illumina NovaSeq 6000
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Tumor, Normal, Lymph Node and PBMC

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the hg19 1.2.0 genome build and Ensembl 82 annotations.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: hg19 1.2.0
Supplementary files format and content: Processed counts from CellRanger in an R object, data_SingleCellExperiment_object.Rda; Additional metadata in “sample_annots.csv” and “full_HCC_cluster_annotation.csv”

source_name: Liver

extract_protocol:
Human tumor lesions and non-involved adjacent tissues were digested as described in the material and method. Briefly, samples received mechanical and enzymatic digestion, filtration and the cell suspension was enriched in immune cells using a Percoll gradient, followed by a RBC lysis. Lymph nodes were digested mechanically and enzymatically followed by RBC lysis. Blood samples were processed by Ficoll followed by RBC lysis.
Library was prepared using Chromium Single Cell 3ʹ v2 protocol/3ʹ  protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell associated protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell associated protocol (10x Genomics). For antibody-derived tagged library, we used the KAPA HiFI HotStart Library Amplification Kit (Roche) with the following primers and amplification program:
-CITE-seq library: amplification was performed at 95°C for 3’ followed by ten cycles at 95°C f¬¬or 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 primer as i7 primer (Illumina).
-HASH-seq library: amplification was performed at 95°C for 3’ followed by ten cycles 95°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGC-3’ TruSeq D701_s primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for both CITE- and HASH- seq library amplification.
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% HTO library before sequencing.
OTHER: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

value: Liver

value: Tumor, Normal, Lymph Node and PBMC

tag: library type

value: ADT

tag: antibodies/tags

value: see meta_features.csv located in supplementary files for Antibody name and barcode


title: T-cell Receptor R1041_3-T

description:
T-cell Receptor
TCR RNA
paired-end
Illumina NovaSeq 6000
TCR library: read1 file contains cell barcode and UMI; read2 file contains recepter sequence
Tumor, Normal, Lymph Node and PBMC

value: TCR


title: ADT-derived cDNA R1041_3-A


title: 14D_M_866


title: 14D_M_867


title: T-cell Receptor R1041_5-T


title: T-cell Receptor R1041_4-T


title: ADT-derived cDNA R1041_2-A


title: ADT-derived cDNA R1041_5-A


title: T-cell Receptor R1041_1-T


title: 14D_M_865


title: 14D_M_863


title: 14D_M_881


title: 14D_M_861


title: 14D_M_862


title: ADT-derived cDNA R1040_6-A


title: 14D_M_864


title: T-cell Receptor R1041_2-T


title: 14D_M_856


title: T-cell Receptor R1040_6-T


title: ADT-derived cDNA R1041_1-A


title: 14D_M_857


title: 14D_M_853


title: 14D_M_859


title: T-cell Receptor R1040_5-T


title: 14D_M_860


title: 14D_M_852


title: T-cell Receptor R1040_4-T


title: ADT-derived cDNA R1040_5-A


title: 14D_M_858


title: 14D_M_855


title: 14D_M_854


title: 14D_M_850


title: 14D_M_849


title: 14D_M_847


title: ADT-derived cDNA R1040_4-A


title: T-cell Receptor R1040_3-T


title: 14D_M_845


title: 14D_M_848


title: T-cell Receptor R1040_2-T


title: ADT-derived cDNA R1040_2-A


title: 14D_M_846


title: T-cell Receptor R1040_1-T


title: ADT-derived cDNA R1040_3-A


title: 14D_M_851


title: 14D_M_842


title: 14D_M_843


title: ADT-derived cDNA R1040_1-A


title: T-cell Receptor R1039_6-T


title: 14D_M_844


title: 14D_M_840


title: 14D_M_839


title: 14D_M_841


title: 14D_M_834


title: 14D_M_833


title: 14D_M_835


title: ADT-derived cDNA R1039_5-A


title: 14D_M_831


title: T-cell Receptor R1039_5-T


title: ADT-derived cDNA R1039_3-A


title: T-cell Receptor R1039_4-T


title: 14D_M_837


title: 14D_M_830


title: 14D_M_763


title: T-cell Receptor R1039_3-T


title: 14D_M_832


title: ADT-derived cDNA R1039_4-A


title: ADT-derived cDNA R1039_2-A


title: 14D_M_829


title: 14D_M_828


title: T-cell Receptor R1039_1-T


title: ADT-derived cDNA R1039_6-A


title: 14D_M_836


title: 14D_M_838


title: ADT-derived cDNA R1039_1-A


title: 14D_M_762


title: 14D_M_761


title: 14D_M_758


title: T-cell Receptor R1038_5-T


title: 14D_M_757


title: 14D_M_759


title: HTO-derived cDNA R1038_5-H

description:
HTO-derived cDNA
protein
paired-end
Illumina NovaSeq 6000
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Tumor, Normal, Lymph Node and PBMC

value: HTO

value: see meta_features.csv located in supplementary files for Antibody name and barcode and meta_sample.csv in supplmentary files for Hashtag to sample mappings


title: ADT-derived cDNA R1038_5-A


title: T-cell Receptor R1039_2-T


title: 14D_M_755


title: ADT-derived cDNA R1038_4-A


title: 14D_M_752


title: T-cell Receptor R1038_4-T


title: HTO-derived cDNA R1038_4-H


title: 14D_M_756


title: 14D_M_748


title: 14D_M_749


title: ADT-derived cDNA R1038_3-A


title: 14D_M_753


title: T-cell Receptor R1038_3-T


title: HTO-derived cDNA R1038_3-H


title: 14D_M_751


title: 14D_M_754


title: 14D_M_760


title: T-cell Receptor R1038_2-T


title: 14D_M_747


title: 14D_M_745


title: ADT-derived cDNA R1038_2-A


title: 14D_M_746


title: HTO-derived cDNA R1038_2-H


title: 14D_M_744


title: 14D_M_743


title: 14D_M_742


title: ADT-derived cDNA R1038_1-A


title: 14D_M_750


title: 14D_M_740


title: HTO-derived cDNA R1038_1-H


title: 14D_M_738


title: 14D_M_741


title: T-cell Receptor R1037_8-T


title: ADT-derived cDNA R1037_8-A


title: T-cell Receptor R1037_7-T


title: 14D_M_739


title: ADT-derived cDNA R1037_7-A


title: 14D_M_733


title: 14D_M_737


title: 14D_M_736


title: T-cell Receptor R1037_6-T


title: 14D_M_731


title: 14D_M_732


title: 14D_M_730


title: T-cell Receptor R1037_5-T


title: 14D_M_729


title: T-cell Receptor R1038_1-T


title: 14D_M_727


title: 14D_M_728


title: ADT-derived cDNA R1037_5-A


title: T-cell Receptor R1037_4-T


title: 14D_M_726


title: ADT-derived cDNA R1037_4-A


title: 14D_M_725


title: T-cell Receptor R1037_3-T


title: 14D_M_723


title: 14D_M_722


title: 14D_M_734


title: ADT-derived cDNA R1037_6-A


title: 14D_M_720


title: 14D_M_719


title: T-cell Receptor R1037_1-T


title: ADT-derived cDNA R1037_1-A


title: ADT-derived cDNA R1037_2-A


title: 14D_M_718


title: 14D_M_717


title: 14D_M_714


title: 14D_M_713


title: ADT-derived cDNA R1032_6-A


title: 14D_M_712


title: T-cell Receptor R1032_5-T


title: 14D_M_724


title: 14D_M_711


title: ADT-derived cDNA R1032_5-A


title: 14D_M_710


title: 14D_M_709


title: 14D_M_721


title: ADT-derived cDNA R1037_3-A


title: T-cell Receptor R1037_2-T


title: 14D_M_707


title: T-cell Receptor R1032_3-T


title: ADT-derived cDNA R1032_4-A


title: 14D_M_705


title: 14D_M_716


title: 14D_M_715


title: 14D_M_704


title: ADT-derived cDNA R1032_2-A


title: T-cell Receptor R1032_2-T


title: T-cell Receptor R1032_6-T


title: ADT-derived cDNA R1032_3-A


title: 14D_M_701


title: 14D_M_700


title: T-cell Receptor R1032_1-T


title: 14D_M_571


title: 14D_M_570


title: ADT-derived cDNA R1032_1-A


title: T-cell Receptor R1032_4-T


title: 14D_M_568


title: HTO-derived cDNA R1031_6-H


title: 14D_M_567


title: T-cell Receptor R1031_6-T


title: 14D_M_566


title: 14D_M_569


title: 14D_M_708


title: 14D_M_706


title: 14D_M_565


title: ADT-derived cDNA R1031_6-A


title: 14D_M_702


title: T-cell Receptor R1031_5-T


title: HTO-derived cDNA R1031_5-H


title: 14D_M_563


title: 14D_M_562


title: 14D_M_564


title: ADT-derived cDNA R1031_5-A


title: 14D_M_703


title: T-cell Receptor R1031_4-T


title: HTO-derived cDNA R1031_4-H


title: 14D_M_559


title: 14D_M_558


title: 14D_M_557


title: T-cell Receptor R1031_3-T


title: ADT-derived cDNA R1031_4-A


title: 14D_M_554


title: T-cell Receptor R1031_2-T


title: 14D_M_555


title: ADT-derived cDNA R1031_3-A


title: ADT-derived cDNA R1031_2-A


title: HTO-derived cDNA R1031_1-H


title: HTO-derived cDNA R1031_3-H


title: 14D_M_548


title: 14D_M_549


title: 14D_M_547


title: 14D_M_552


title: T-cell Receptor R1030_6-T


title: 14D_M_556


title: 14D_M_550


title: T-cell Receptor R1031_1-T


title: 14D_M_546


title: 14D_M_553


title: 14D_M_561


title: 14D_M_560


title: 14D_M_545


title: 14D_M_544


title: ADT-derived cDNA R1031_1-A


title: 14D_M_551


title: 14D_M_542


title: 14D_M_543


title: HTO-derived cDNA R1030_6-H


title: ADT-derived cDNA R1030_6-A


title: T-cell Receptor R1030_5-T


title: 14D_M_541


title: HTO-derived cDNA R1030_5-H


title: 14D_M_540


title: 14D_M_539


title: HTO-derived cDNA R1030_4-H


title: T-cell Receptor R1030_4-T


title: 14D_M_537


title: 14D_M_536


title: 14D_M_533


title: 14D_M_535


title: T-cell Receptor R1030_3-T


title: HTO-derived cDNA R1030_3-H


title: ADT-derived cDNA R1030_4-A


title: 14D_M_528


title: 14D_M_530


title: 14D_M_532


title: ADT-derived cDNA R1030_2-A


title: T-cell Receptor R1030_2-T


title: 14D_M_531


title: 14D_M_529


title: T-cell Receptor R1030_1-T


title: ADT-derived cDNA R1030_5-A


title: 14D_M_527


title: 14D_M_526


title: HTO-derived cDNA R1030_1-H


title: 14D_M_538


title: 14D_M_524


title: ADT-derived cDNA R1030_3-A


title: 14D_M_523


title: 14D_M_522


title: ADT-derived cDNA R1030_1-A


title: HTO-derived cDNA R1030_2-H


title: 14D_M_521


title: 14D_M_519


title: 14D_M_520


title: HTO-derived cDNA R1029_6-H


title: T-cell Receptor R1029_6-T


title: ADT-derived cDNA R1029_6-A


title: 14D_M_518


title: 14D_M_517


title: HTO-derived cDNA R1029_5-H


title: T-cell Receptor R1029_5-T


title: 14D_M_525


title: 14D_M_515


title: 14D_M_514


title: 14D_M_516


title: ADT-derived cDNA R1029_5-A


title: HTO-derived cDNA R1029_4-H


title: ADT-derived cDNA R1029_4-A


title: T-cell Receptor R1029_4-T


title: 14D_M_511


title: 14D_M_513


title: 14D_M_510


title: T-cell Receptor R1029_3-T


title: 14D_M_512


title: HTO-derived cDNA R1029_3-H


title: 14D_M_509


title: ADT-derived cDNA R1029_3-A


title: 14D_M_508


title: 14D_M_507


title: HTO-derived cDNA R1029_2-H


title: T-cell Receptor R1029_2-T


title: 14D_M_504


title: 14D_M_506


title: 14D_M_505


title: ADT-derived cDNA R1029_2-A


title: 14D_M_503


title: T-cell Receptor R1029_1-T


title: 14D_M_502


title: HTO-derived cDNA R1029_1-H


title: ADT-derived cDNA R1029_1-A


title: T-cell Receptor R1027_4-T


title: ADT-derived cDNA R1027_3-A


title: 14D_M_498


title: 14D_M_496


title: 14D_M_501


title: 14D_M_497


title: 14D_M_493


title: 14D_M_491


title: 14D_M_495


title: T-cell Receptor R1027_3-T


title: 14D_M_499


title: 14D_M_492


title: 14D_M_494


title: 14D_M_500


title: T-cell Receptor R1027_2-T


title: 14D_M_488


title: ADT-derived cDNA R1027_2-A


title: 14D_M_490


title: 14D_M_487


title: T-cell Receptor R1027_5-T


title: ADT-derived cDNA R1027_1-A


title: 14D_M_486


title: 14D_M_485


title: T-cell Receptor R1027_1-T


title: 14D_M_483


title: T-cell Receptor R1026_5-T


title: ADT-derived cDNA R1026_5-A


title: 14D_M_484


title: 14D_M_489


title: 14D_M_482


title: 14D_M_480


title: 14D_M_481


title: 14D_M_478


title: 14D_M_479


title: ADT-derived cDNA R1026_4-A


title: 14D_M_477


title: 14D_M_475


title: T-cell Receptor R1026_3-T


title: ADT-derived cDNA R1026_2-A


title: 14D_M_474


title: 14D_M_476


title: T-cell Receptor R1026_2-T


title: ADT-derived cDNA R1026_1-A


title: HTO-derived cDNA R1025_6-H


title: T-cell Receptor R1025_6-T


title: T-cell Receptor R1026_1-T


title: 14D_M_473


title: 14D_M_469


title: 14D_M_534


title: 14D_M_470


title: 14D_M_471


title: 14D_M_467


title: 14D_M_472


title: 14D_M_468


title: ADT-derived cDNA R1025_6-A


title: T-cell Receptor R1026_4-T


title: ADT-derived cDNA R1026_3-A


title: 14D_M_465


title: 14D_M_466


title: T-cell Receptor R1025_5-T


title: 14D_M_464


title: HTO-derived cDNA R1025_5-H


title: T-cell Receptor R1025_4-T


title: ADT-derived cDNA R1025_5-A


title: 14D_M_462


title: HTO-derived cDNA R1025_4-H


title: 14D_M_458


title: 14D_M_461


title: 14D_M_459


title: ADT-derived cDNA R1025_4-A


title: HTO-derived cDNA R1025_3-H


title: T-cell Receptor R1025_3-T


title: T-cell Receptor R1025_2-T


title: 14D_M_453


title: 14D_M_457


title: 14D_M_456


title: 14D_M_454


title: 14D_M_455


title: 14D_M_452


title: 14D_M_451


title: ADT-derived cDNA R1025_2-A


title: T-cell Receptor R1025_1-T


title: 14D_M_450


title: 14D_M_463


title: 14D_M_449


title: 14D_M_460


title: 14D_M_448


title: ADT-derived cDNA R1025_1-A


title: 14D_M_446


title: HTO-derived cDNA R1025_1-H


title: T-cell Receptor R1023_6-T


title: 14D_M_445


title: HTO-derived cDNA R1023_6-H


title: 14D_M_447


title: ADT-derived cDNA R1025_3-A


title: 14D_M_444


title: 14D_M_443


title: 14D_M_441


title: HTO-derived cDNA R1023_5-H


title: 14D_M_442


title: HTO-derived cDNA R1025_2-H


title: T-cell Receptor R1023_4-T


title: 14D_M_439


title: ADT-derived cDNA R1023_6-A


title: HTO-derived cDNA R1023_4-H


title: 14D_M_440


title: T-cell Receptor R1023_5-T


title: 14D_M_436


title: ADT-derived cDNA R1023_4-A


title: 14D_M_438


title: 14D_M_435


title: 14D_M_434


title: T-cell Receptor R1023_3-T


title: 14D_M_433


title: HTO-derived cDNA R1023_3-H


title: ADT-derived cDNA R1023_3-A


title: 14D_M_431


title: HTO-derived cDNA R1023_2-H


title: 14D_M_432


title: 14D_M_430


title: 14D_M_428


title: 14D_M_429


title: T-cell Receptor R1023_2-T


title: 14D_M_427


title: ADT-derived cDNA R1023_2-A


title: 14D_M_437


title: ADT-derived cDNA R1023_5-A


title: 14D_M_426


title: ADT-derived cDNA R1023_1-A


title: HTO-derived cDNA R1023_1-H


title: T-cell Receptor R1023_1-T


title: 14D_M_425


title: 14D_M_423


title: T-cell Receptor R1021_6-T


title: 14D_M_424


title: 14D_M_419


title: 14D_M_421


title: 14D_M_418


title: ADT-derived cDNA and HTO-derived cDNA R1021_6-F

description:
ADT-derived cDNA and HTO-derived cDNA
protein
paired-end
Illumina NovaSeq 6000
ADT and HTO
Tumor, Normal, Lymph Node and PBMC

value: ADT and HTO


title: HTO-derived cDNA R1021_6-H


title: T-cell Receptor R1021_5-T


title: 14D_M_417


title: 14D_M_416


title: T-cell Receptor R1021_4-T


title: ADT-derived cDNA and HTO-derived cDNA R1021_5-F


title: HTO-derived cDNA R1021_5-H


title: HTO-derived cDNA R1021_4-H


title: 14D_M_413


title: 14D_M_412


title: 14D_M_414


title: ADT-derived cDNA and HTO-derived cDNA R1021_4-F


title: 14D_M_410


title: T-cell Receptor R1021_3-T


title: 14D_M_409


title: 14D_M_408


title: 14D_M_420


title: ADT-derived cDNA and HTO-derived cDNA R1021_3-F


title: HTO-derived cDNA R1021_3-H


title: 14D_M_407


title: 14D_M_405


title: T-cell Receptor R1021_2-T


title: 14D_M_404


title: HTO-derived cDNA R1021_2-H


title: 14D_M_402


title: 14D_M_403


title: ADT-derived cDNA and HTO-derived cDNA R1021_2-F


title: 14D_M_415


title: 14D_M_401


title: 14D_M_400


title: HTO-derived cDNA R1021_1-H


title: 14D_M_411


title: 14D_M_396


title: 14D_M_397


title: 14D_M_399


title: 14D_M_398


title: ADT-derived cDNA and HTO-derived cDNA R1021_1-F


title: 14D_M_393


title: 14D_M_394


title: 14D_M_392


title: 14D_M_406


title: 14D_M_391


title: ADT-derived cDNA and HTO-derived cDNA R1017_6-F


title: 14D_M_389


title: T-cell Receptor R1021_1-T


title: T-cell Receptor R1017_5-T


title: 14D_M_390


title: 14D_M_385


title: 14D_M_388


title: ADT-derived cDNA and HTO-derived cDNA R1017_4-F


title: T-cell Receptor R1017_3-T


title: HTO-derived cDNA R1017_4-H


title: 14D_M_384


title: HTO-derived cDNA R1017_6-H


title: 14D_M_386


title: HTO-derived cDNA R1017_3-H


title: 14D_M_382


title: T-cell Receptor R1017_6-T


title: T-cell Receptor R1017_2-T


title: HTO-derived cDNA R1017_5-H


title: T-cell Receptor R1017_4-T


title: 14D_M_383


title: 14D_M_395


title: ADT-derived cDNA and HTO-derived cDNA R1017_2-F


title: 14D_M_381


title: 14D_M_315


title: 14D_M_316


title: T-cell Receptor R1017_1-T


title: ADT-derived cDNA and HTO-derived cDNA R1017_5-F


title: 14D_M_380


title: 14D_M_387


title: 14D_M_314


title: 14D_M_313


title: ADT-derived cDNA and HTO-derived cDNA R1017_1-F


title: 14D_M_312


title: 14D_M_309


title: 14D_M_310


title: HTO-derived cDNA R1017_1-H


title: 14D_M_307


title: T-cell Receptor R1014_6-T


title: HTO-derived cDNA R1014_6-H


title: ADT-derived cDNA and HTO-derived cDNA R1017_3-F


title: T-cell Receptor R1014_5-T


title: 14D_M_308


title: HTO-derived cDNA R1017_2-H


title: ADT-derived cDNA and HTO-derived cDNA R1014_6-F


title: 14D_M_305


title: HTO-derived cDNA R1014_5-H


title: 14D_M_304


title: 14D_M_302


title: 14D_M_306


title: 14D_M_303


title: ADT-derived cDNA and HTO-derived cDNA R1014_5-F


title: 14D_M_300


title: 14D_M_298


title: HTO-derived cDNA R1014_4-H


title: 14D_M_301


title: ADT-derived cDNA and HTO-derived cDNA R1014_4-F


title: 14D_M_299


title: T-cell Receptor R1014_3-T


title: HTO-derived cDNA R1014_3-H


title: 14D_M_311


title: 14D_M_297


title: 14D_M_296


title: 14D_M_294


title: HTO-derived cDNA R1014_2-H


title: T-cell Receptor R1014_2-T


title: T-cell Receptor R1014_4-T


title: ADT-derived cDNA and HTO-derived cDNA R1014_3-F


title: 14D_M_295


title: 14D_M_292


title: 14D_M_291


title: ADT-derived cDNA and HTO-derived cDNA R1014_2-F


title: 14D_M_293


title: T-cell Receptor R1014_1-T


title: 14D_M_288


title: 14D_M_289


title: 14D_M_290


title: HTO-derived cDNA R1012_6-H


title: T-cell Receptor R1012_6-T


title: 14D_M_284


title: HTO-derived cDNA R1014_1-H


title: 14D_M_287


title: 14D_M_283


title: 14D_M_286


title: T-cell Receptor R1012_5-T


title: ADT-derived cDNA and HTO-derived cDNA R1012_6-F


title: 14D_M_279


title: 14D_M_280


title: 14D_M_275


title: 14D_M_282


title: 14D_M_285


title: HTO-derived cDNA R1012_5-H


title: ADT-derived cDNA and HTO-derived cDNA R1012_5-F


title: HTO-derived cDNA R1012_3-H


title: 14D_M_278


title: 14D_M_281


title: T-cell Receptor R1012_4-T


title: 14D_M_277


title: HTO-derived cDNA R1012_4-H


title: T-cell Receptor R1012_3-T


title: 14D_M_269


title: ADT-derived cDNA and HTO-derived cDNA R1012_4-F


title: 14D_M_271


title: ADT-derived cDNA and HTO-derived cDNA R1014_1-F


title: T-cell Receptor R1012_2-T


title: 14D_M_273


title: 14D_M_268


title: 14D_M_267


title: ADT-derived cDNA and HTO-derived cDNA R1012_3-F


title: 14D_M_274


title: 14D_M_266


title: 14D_M_272


title: HTO-derived cDNA R1012_1-H


title: ADT-derived cDNA and HTO-derived cDNA R1012_2-F


title: 14D_M_270


title: 14D_M_276


title: T-cell Receptor R1012_1-T


title: ADT-derived cDNA and HTO-derived cDNA R1012_1-F


title: 14D_M_265


title: 14D_M_264


title: HTO-derived cDNA R1012_2-H


title: 14D_M_263


title: 14D_M_262


title: T-cell Receptor R1006_6-T


title: T-cell Receptor R1006_5-T


title: 14D_M_259


title: 14D_M_257


title: ADT-derived cDNA and HTO-derived cDNA R1006_5-AH


title: 14D_M_260


title: 14D_M_258


title: 14D_M_261


title: T-cell Receptor R1006_4-T


title: ADT-derived cDNA and HTO-derived cDNA R1006_6-AH


title: 14D_M_255


title: 14D_M_256


title: ADT-derived cDNA and HTO-derived cDNA R1006_4-AH


title: 14D_M_188


title: 14D_M_253


title: 14D_M_254


title: 14D_M_189


title: ADT-derived cDNA and HTO-derived cDNA R1006_3-AH


title: T-cell Receptor R1006_3-T


title: T-cell Receptor R1006_2-T


title: 14D_M_187


title: 14D_M_184


title: 14D_M_186


title: ADT-derived cDNA and HTO-derived cDNA R1006_2-AH


title: 14D_M_185


title: 14D_M_182


title: T-cell Receptor R1006_1-T


title: 14D_M_183


title: ADT-derived cDNA and HTO-derived cDNA R1006_1-AH


title: 14D_M_180


title: T-cell Receptor R1005_6-T


title: ADT-derived cDNA and HTO-derived cDNA R1005_6-AH


title: 14D_M_177


title: 14D_M_179


title: 14D_M_176


title: 14D_M_175


title: T-cell Receptor R1005_5-T


title: ADT-derived cDNA and HTO-derived cDNA R1005_5-AH


title: 14D_M_174


title: T-cell Receptor R1005_4-T


title: 14D_M_173


title: 14D_M_181


title: ADT-derived cDNA and HTO-derived cDNA R1005_4-AH


title: 14D_M_172


title: T-cell Receptor R1005_3-T


title: 14D_M_171


title: 14D_M_170


title: 14D_M_169


title: Group 2, rep 2,

type: RNA

city: Montreal

first: Gilles

last: Gouspillou

state: Québec

address: 141 Avenue du Président Kennedy

department: Département des sciences de l'activité physique

country: Canada

institute: UQAM

hyb_protocol: Affymetric protocol

scan_protocol: Affymetric protocol

data_processing: The Affymetric Clariom S microarrays were further analyzed using Affymetrix Expression Console with the Robust Multichip Analysis (SST-RMA) procedure. The gene-level differential expression was performed using the Affymetrix Transcriptome Anaylsis Console (TAC) Software using default parameters.                                                                                Array Type: Clariom_S_Mouse  Analysis Type: Expression (Gene)                                                                                Genome Version: mm10 (Mus musculus)  Annotation: Clariom_S_Mouse.r1.na36.mm10.a1.transcript.csv

label: biotin

source_name: 7_TA_CLP 1466 Atg7KO

label_protocol: Microarray was performed at the McGill University and Génome Québec Innovation Centre (Montréal, QC). Raw data were analyze using default parameters from the Transcriptome Analysis Console (TAC) 4.0.1 software (Affymetrix) using default parameters.

extract_protocol: Total RNA was isolated by Trizol, according to the manufacturer’s instructions.

tag: group

value: Setpic mice with ablation of Atg7 in skeletal muscle

value: tibialis anterior


title: Input_ChIP-seq in adipose tissue endothelial cells Input_N1ICD

city: Philadelphia

first: Tobias

last: Friedrich

state: Pennsylvania

address: 421 Curie Boulevard

institute: University of Pennsylvania

data_processing:
Raw fastq files were quality and adapter trimmed using TrimGalore v.0.6.4.
Trimmed fastq files were aligned using HISAT2 v.2.2.1 with parameter “--no-spliced-alignment”.
PCR duplicates were removed using Picard tools MarkDuplicates v.2.21.9.
RPKM normalized coverage tracks (bigWig) were generated using bamCoverage.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files

source_name: Adipose tissue endothelial cells

growth_protocol: Endothelial cells were grown at 37°C with 5% CO2 in EGM-2 medium (Lonza) supplemented with 1% penicillin/streptomycin.

extract_protocol:
ChIP was done essentially as previously described (Ferrante et al. NAR 2020, doi: 10.1093/nar/gkaa088)
Lybrary-prep kit: Diagenode MicropPlex Library Preparation kit v3 (C05010001).

treatment_protocol: Endothelial cells were infected with adenoviruses expressing N1ICD or GFP in EGM-2 medium for 24 hours. After 24 hours, cells were washed twice with PBS and fresh EGM-2 medium was added. Cells were cultured for an additional day in fresh medium.

tag: chip antibody

value: Adipose tissue endothelial cells were infected with adenoviruses expressing the N1ICD protein.


title: Group 2, rep 5,

source_name: 10_TA_CLP 1445  Atg7KO


title: ADT-derived cDNA and HTO-derived cDNA R1005_3-AH


title: Group 1, rep 4,

source_name: 4_TA_CLP 1177 Atg7ff

value: Setpic mice with intact Atg7


title: Group 1, rep 5,

source_name: 5_TA_CLP 1734 Atg7ff


title: J04_FFPE_031

city: Suita

first: Yoshiaki

last: Sota

state: Osaka

address: Yamadaoka 2-15

department: Breast and Endocrine Surgery

country: Japan

institute: Osaka University

hyb_protocol: FF tissues. Hybridization on U133 Plus 2.0 arrays overnight (17 h) according to the manufacturer's protocol. FFPE tissues. Hybridization on U133 Plus 2.0 arrays overnight (17‑20 h) according to the manufacturer's protocol.

scan_protocol: FF tissues. The hybridized DNA microarray was fluorescently stained with GeneChip Fluidics Station 450, and scanned using a GeneChip Scanner 3000. FFPE tissues. The hybridized DNA microarray was fluorescently stained using GeneChip Fluidics Station 450, and scanned using a GeneChip Scanner 3000 (both Affymetrix; Thermo Fisher Scientific, Inc.).

data_processing: Probe intensities were normalized with MAS5.

source_name: FFPE (Formalin-fixed paraffin-embedded) tumor

label_protocol:
FF tissues. Approximately 100 ng RNA (RNA integrity number >7) was used to generate second‑strand cDNA, and cRNA was amplified using the oligodeoxynucleotide ribosylthymine primers, then biotinylated and fragmented using the Gene Profiling Reagent kit (Affymetrix; Thermo Fisher Scientific, Inc.).
FFPE tissues. Second‑strand cDNA was generated using 70‑100 ng of RNA, and cDNA was amplified using the oligodeoxynucleotide ribosylthymine and random primers using an Ovation FFPE whole‑transcriptome amplification system (NuGEN Technologies, Inc.) according to the manufacturer's protocol. The cDNA was then biotinylated and fragmented using the Encore Biotin Module (NuGEN Technologies, Inc.).

extract_protocol:
FF tissues. RNA was extracted from FF tumor tissues using Qiagen RNeasy Lipid Tissue Mini kits (Qiagen GmbH).
FFPE tissues. RNA was extracted from four consecutive sections (10 μm) of each FFPE tissue using RNeasy FFPE kits (Qiagen GmbH).

treatment_protocol: The patients agreed to have their research specimens cryopreserved for future use after undergoing radical breast cancer surgery. Adjuvant treatments are unknown.

value: breast cancer


title: Group 2, rep 3,

source_name: 8_TA_CLP 1439 Atg7KO


title: 14D_M_166


title: Group 2, rep 4,

source_name: 9_TA_CLP 1740 Atg7KO


title: 14D_M_167

source_name: C57BL/6J Male P56 Mouse Brain


title: T-cell Receptor R1005_2-T


title: Input_ChIP-seq in adipose tissue endothelial cells Input_GFP

value: Adipose tissue endothelial cells were infected with adenoviruses expressing the GFP protein.


title: ADT-derived cDNA and HTO-derived cDNA R1005_2-AH


title: Group 1, rep 3,

source_name: 3_TA_CLP 1747 Atg7ff


title: J04_FFPE_030

value: FFPE (Formalin-fixed paraffin-embedded) tumor


title: Group 1, rep 2,

source_name: 2_TA_CLP 1468 Atg7ff


title: J04_FFPE_029


title: J04_FFPE_027


title: J04_FFPE_028


title: 14D_M_165


title: Group 2, rep 1,

source_name: 6-TA_CLP 1372 Atg7KO


title: Group 1, rep 1,

source_name: 1_TA_CLP 1465 Atg7 ff


title: J04_FFPE_026


title: 14D_M_168


title: J04_FFPE_025


title: J04_FFPE_024


title: ChIP-seq in adipose tissue endothelial cells H3K27ac_N1ICD_Rep2

value: H3K27ac:Diagenode pAb-174-050


title: J04_FFPE_023


title: T-cell Receptor R1005_1-T


title: ChIP-seq in adipose tissue endothelial cells H3K27ac_N1ICD_Rep1


title: ChIP-seq in adipose tissue endothelial cells H3K27ac_GFP_Rep1


title: 14D_M_163


title: ChIP-seq in adipose tissue endothelial cells H3K27ac_GFP_Rep2


title: J04_FFPE_022


title: 14D_M_162


title: ADT-derived cDNA and HTO-derived cDNA R1005_1-AH


title: hTERT cells, Spheroid-MED12-G44 mutant colony-2, rep-3

data_processing:
RNA-seq reads were aligned to the GRCh38 human genome assembly (Ensembl release 102) using the STAR aligner (v2.7.5).
BAM files were converted into bigwig files using bam coverage/DeepTools(v3.5.1)  (bin size 1, normalized BPM, effectiveGenomeSize 2913022398).
Gene exon counts were found using featureCounts (Subread package, v1.6.1, settings: -g gene_id -t exon -p -s 2)
Assembly: GRCh38 human genome assembly (Ensembl release 102)
Supplementary files format and content: tab-delimited text files include exon count values for each Sample
Supplementary files format and content: Bigwig files of RNA-seq for each Sample

source_name: Uterus

growth_protocol:
Human myometrial hTERT cells were maintained in DMEM/F-12  with 10% Fetal Bovine Serum and 1 % Penicillin–streptomycin . Cells were cultured and incubated at 37 °C in a humidified atmosphere of 5 % CO2 and 95 % air.
Cells were seeded (3000 cells per well) on Corning ultra-low attachment plate, 96 wells (#4515) for spheroid formation. Total RNA was harvested on 6th day after seeding.

extract_protocol:
Total RNA was isolated using the Zymo research Quick RNA miniprep kit utilizing the on-column DNAse treatment according to the manufacturer’s instructions (#R1054).500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEBNext #E7490) and NEBNext® Ultra™ Directional RNA Library Prep Kit (NEBNext #E7420)  following manufacturer's protocols.

value: Uterus

value: Human myometrial cells

value: MED12-G44 mutant


title: hTERT cells, Spheroid-MED12-WT, rep-1

value: MED12 wild type


title: ADT-derived cDNA and HTO-derived cDNA R1004_6-AH

value: Liver

value: Tumor, Normal, Lymph Node and PBMC


title: hTERT cells, Spheroid-MED12-WT, rep-2


title: 14D_M_159


title: 14D_M_160


title: 14D_M_158


title: T-cell Receptor R1004_5-T

value: TCR


title: J04_FFPE_020


title: 14D_M_164


title: 14D_M_157


title: hTERT cells, Spheroid-MED12-G44 mutant colony-2, rep-2


title: J04_FFPE_021


title: J04_FFPE_017


title: 14D_M_156


title: hTERT cells, Spheroid-MED12-G44 mutant colony-2, rep-1


title: hTERT cells, Spheroid-MED12-G44 mutant colony-1, rep-3


title: T-cell Receptor R1004_6-T


title: T-cell Receptor R1004_4-T


title: 14D_M_155


title: hTERT cells, Spheroid-MED12-G44 mutant colony-1, rep-2


title: J04_FFPE_016


title: 14D_M_154


title: J04_FFPE_014


title: 14D_M_153


title: J04_FFPE_018


title: J04_FFPE_019


title: hTERT cells, Spheroid-MED12-G44 mutant colony-1, rep-1


title: J04_FFPE_013


title: J04_FFPE_015


title: J04_FFPE_012


title: ADT-derived cDNA and HTO-derived cDNA R1004_4-AH

value: see meta_features.csv located in supplementary files for Antibody name and barcode and meta_sample.csv in supplmentary files for Hashtag to sample mappings


title: J04_FFPE_010


title: 14D_M_152


title: ADT-derived cDNA and HTO-derived cDNA R1004_5-AH

value: ADT and HTO


title: T-cell Receptor R1004_3-T


title: 14D_M_150


title: hTERT cells, MED12-WT, rep-1

data_processing:
RNA-seq reads were aligned to the GRCh38 human genome assembly (Ensembl release 102) using the STAR aligner (v2.7.5)  with default settings
BAM files were converted into bigwig files using bam coverage/DeepTools(v3.5.1)  (bin size 1, normalized BPM, effectiveGenomeSize 2913022398).
Gene exon counts were found using featureCounts (Subread package, v1.6.1, settings: -g gene_id -t exon -p -s 2)
Assembly: GRCh38 human genome assembly (Ensembl release 102)
Supplementary files format and content: tab-delimited text files include exon count values for each Sample
Supplementary files format and content: Bigwig files of RNA-seq for each Sample

extract_protocol:
Total RNA was isolated using the Zymo research Quick RNA miniprep kit utilizing the on-column DNAse treatment according to the manufacturer’s instructions (#R1054).750 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEBNext #E7490) and NEBNext® Ultra™ Directional RNA Library Prep Kit (NEBNext #E7420)  following manufacturer's protocols.

value: hTERT uterine smooth muscle cell

value: Human myometrial  cells


title: hTERT cells, MED12-WT, rep-2


title: 14D_M_149


title: 14D_M_151


title: hTERT cells, MED12-WT, rep-3


title: J04_FFPE_011


title: ADT-derived cDNA and HTO-derived cDNA R1004_3-AH


title: J04_FFPE_009


title: hTERT cells, MED12-KO, rep-3

value: MED12 knock-out


title: T-cell Receptor R1004_2-T


title: hTERT cells, MED12-KO, rep-2


title: 14D_M_147


title: ADT-derived cDNA and HTO-derived cDNA R1004_2-AH


title: 14D_M_148


title: hTERT cells, MED12-KO, rep-1


title: T-cell Receptor R1004_1-T


title: 14D_M_146


title: hTERT cells, MED12-G44 mutant colony-2, rep-3


title: J04_FFPE_007


title: J04_FFPE_008


title: J04_FFPE_006


title: 14D_M_145


title: hTERT cells, MED12-G44 mutant colony-2, rep-1


title: 14D_M_144


title: hTERT cells, MED12-G44 mutant colony-1, rep-1


title: hTERT cells, MED12-G44 mutant colony-1, rep-3


title: J04_FFPE_004


title: J04_FFPE_003


title: J04_FFPE_005


title: J04_FFPE_002


title: 14D_M_143


title: T-cell Receptor R1003_6-T


title: ADT-derived cDNA and HTO-derived cDNA R1003_6-AH


title: hTERT cells, MED12-G44 mutant colony-2, rep-2


title: hTERT cells, MED12-WT input, anti-Rabbit IgG(NBP1-72763, Novusbio)

data_processing:
library strategy: CUT&Tag
Reads were aligned to the hg38 reference genome using Bowtie2. .
Then, PCR duplicates and blacklisted regions were removed using Picard tools (“Picard Toolkit.” 2019. Broad Institute, GitHub Repository.https://broadinstitute.github.io/picard/ ) and bedtools, respectively
Bigwig files were generated using deepTools  to visualize CUT&Tag tracks. Peak calling was performed using MACS2 with default settings.
Assembly: GRCh38 human genome
Supplementary files format and content: bigWig for each sample and narrowPeak for each sample (except for Input sample)

extract_protocol:
Cells were  harvested and counted to obtain 100,000 cells for each sample. Benchtop CUT&Tag  V.2 protocol was slightly modified to profile genome-wide H3K27ac and extract protocol described in the methods.
Library preparation was performed as described in Benchtop CUT&Tag V.2 protocol

value: anti-Rabbit IgG(NBP1-72763, Novusbio)


title: hTERT cells, MED12-G44 mutant colony-1, rep-2


title: T-cell Receptor R1003_5-T


title: 14D_M_140


title: J04_FFPE_001

value: breast cancer


title: hTERT cells, MED12-WT, H3K27ac (ab4729, Abcam) , rep -2

value: H3K27ac (ab4729, Abcam)


title: 14D_M_141


title: ADT-derived cDNA and HTO-derived cDNA R1004_1-AH


title: J04_FF_030

source_name: FF (fresh frozen) tumor

value: FF (fresh frozen) tumor


title: J04_FF_031


title: hTERT cells, MED12-WT, H3K27ac (ab4729, Abcam) , rep -1


title: 14D_M_142


title: J04_FF_029


title: 14D_M_138


title: 14D_M_139


title: ADT-derived cDNA and HTO-derived cDNA R1003_5-AH


title: 14D_M_137


title: T-cell Receptor R1003_4-T


title: 14D_M_136


title: hTERT cells, MED12-G44 mutant colony-1, H3K27ac (ab4729, Abcam) , rep -2


title: 14D_M_135


title: ADT-derived cDNA and HTO-derived cDNA R1003_4-AH


title: J04_FF_027


title: 5648 SP IµBCL6

city: London

first: Alan

last: Ramsay

state: -- Select One --

address: Great Maze Pond

country: United Kingdom

institute: King's College London

data_processing:
Automated concatenation of the fastq files from separate sequencing lanes in Partek
Read trimming using Trimgalore (v0.4.4)
Filtering of mitochondrial and ribosomal RNA using Bowtie2 (v2.2.5)
Read mapping to reference genome using STAR (v2.5.3a)
Filtering of duplicate reads using Picard (v2.17.11)
Gene expression quantification using Partek E/M against Gencode M23 annotation
Genome_build: GRCm38
Supplementary_files_format_and_content: text file in tab-separated value format

source_name: spleen

growth_protocol: Not applicable

extract_protocol:
FRCs were sorted in Agencourt RNAdvance Cell v2 Total RNA lysis buffer. mRNA was extracted using Agencourt RNAdvance Cell v2 Total RNA extraction magnetic kit
SMARTSeqV4-protocol with Ovation RNA-Seq System V2 library preparation kit

treatment_protocol: Not applicable

value: flow sorted FRCs (gating on CD45-, CD31-, PDPN+ cells)

value: spleen

tag: mouse id

value: age >16 months

value: flow sorted FRCs


title: 5613 SP IµBCL6


title: J04_FF_028


title: T-cell Receptor R1003_3-T

source_name: Liver


title: 5925 SP WT

value: WT


title: J04_FF_026


title: 5915 SP WT


title: 14D_M_132


title: J04_FF_025


title: 5804 SP IµBCL6


title: ADT-derived cDNA and HTO-derived cDNA R1003_3-AH

value: Liver


title: hTERT cells, MED12-G44 mutant colony-1, H3K27ac (ab4729, Abcam) , rep -1

value: Uterus

value: MED12-G44 mutant


title: J04_FF_022


title: 14D_M_130


title: 5909 SP WT


title: 5847 SP WT


title: J04_FF_021


title: 14D_M_129


title: J04_FF_023


title: 14D_M_134


title: J04_FF_024


title: J04_FF_019


title: J04_FF_020


title: ADT-derived cDNA and HTO-derived cDNA R1003_2-AH

value: Tumor, Normal, Lymph Node and PBMC

value: see meta_features.csv located in supplementary files for Antibody name and barcode and meta_sample.csv in supplmentary files for Hashtag to sample mappings


title: 14D_M_133


title: 14D_M_128


title: 14D_M_127


title: 5794 SP WT


title: T-cell Receptor R1003_2-T

value: TCR


title: 14D_M_131


title: 6009 LN IµBCL6

source_name: lymph nodes

value: lymph nodes


title: J04_FF_018


title: 5648 LN IµBCL6


title: Hepatocyte fraction RNAseq from group B #1

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

institute: Yale University

data_processing:
Raw sequencing reads were aligned to the human–mouse combined genome with STAR (https://doi.org/10.1093/bioinformatics/bts635), annotated and counted with HTSeq (https://doi.org/10.1093/bioinformatics/btu638), normalized using DESeq2 (https://doi.org/10.1186/s13059-014-0550-8) and graphed using the Broad Institute Morpheus web tool.
Differential expression analysis was performed with DESeq2.
Corresponding pathway enrichment analysis of differentially expressed human genes was achieved using geneontology (http://geneontology.org/docs/go-enrichment-analysis/).
Assembly: hg19 + mm10
Supplementary files format and content: Read count tables in .xlsx format

source_name: humanized liver hepatocytes

growth_protocol: Standard mouse housing conditions, hepatocyte isolation from freshly isolated liver tissue

extract_protocol:
RNA isolation from hepatocytes with Trizol
Poly-A

treatment_protocol: No treatment of mice

value: BALB/c

value: humanized liver tissue with human hepatocytes and human NPCs (group B)

value: 18 weeks

value: MISTRG-Fah-/-


title: T-cell Receptor R1001_6-T


title: 5613 LN IµBCL6


title: 5804 LN IµBCL6


title: T-cell Receptor R1003_1-T


title: 5970 LN IµBCL6


title: ADT-derived cDNA and HTO-derived cDNA R1001_6-AH

value: ADT and HTO


title: J04_FF_016

value: FF (fresh frozen) tumor

value: breast cancer


title: J04_FF_014


title: Total liver tissue

source_name: Liver tissue

growth_protocol: Standard mouse housing conditions,snap frozen total liver tissue

extract_protocol:
RNA isolation with Trizol
poly-A

value: humanized liver tissue


title: J04_FF_017


title: J04_FF_015


title: 5928 LN WT

value: flow sorted FRCs (gating on CD45-, CD31-, PDPN+ cells)

value: age >16 months

value: flow sorted FRCs


title: 4011 LN IµBCL6


title: Hepatocyte fraction RNAseq from group B #2


title: MP_Bulk_RNA_replicate_2

city: Seoul

first: Joonyub

last: Lee

state: Seoul

address: 222, Banpo-daero, Seocho-gu

country: South Korea

institute: Seoul St. Mary's hospital

description: TruSeqstrandedmRNA

data_processing:
Fastq files were mapped to GRCm38/mm10 using STAR
The mapped reads were counted by using RSEM
Assembly: mm10
Supplementary files format and content: Raw counts for each Sample

source_name: Pancreatic islets

extract_protocol:
RNA was extracted by using Trizol (Invitrogen, 15596026)
TruSeq Stranded mRNA kit (RS-122-9004DOC)

value: Pancreatic islets

value: Wild type (C57BL/6J )

value: no treatment


title: MP_Bulk_RNA_replicate_1

description: TruSeqstrandedmRNA


title: ADT-derived cDNA and HTO-derived cDNA R1003_1-AH

value: Liver

value: Tumor, Normal, Lymph Node and PBMC

value: see meta_features.csv located in supplementary files for Antibody name and barcode and meta_sample.csv in supplmentary files for Hashtag to sample mappings


title: J04_FF_012


title: 5848 LN WT

value: lymph nodes

value: WT


title: Hepatocyte fraction RNAseq from group A #2

value: BALB/c

value: humanized liver tissue with human hepatocytes (group A)

value: 18 weeks


title: ADT-derived cDNA and HTO-derived cDNA R1001_5-AH

value: ADT and HTO


title: 4012 LN IµBCL6


title: J04_FF_011

value: FF (fresh frozen) tumor

value: breast cancer


title: Hepatocyte fraction RNAseq from group A #1

value: MISTRG-Fah-/-


title: J04_FF_010


title: Virgin_Bulk_RNA_replicate_2

description: TruSeqstrandedmRNA


title: T-cell Receptor R1001_5-T

value: TCR


title: 5925 LN WT

value: flow sorted FRCs (gating on CD45-, CD31-, PDPN+ cells)

value: age >16 months

value: flow sorted FRCs


title: J04_FF_009


title: T-cell Receptor R1001_4-T


title: 5915 LN WT


title: MP_S961_Bulk_RNA_replicate_4

description: TruSeqstrandedmRNA

value: Pancreatic islets

value: Wild type (C57BL/6J )


title: J04_FF_008


title: Virgin_Bulk_RNA_replicate_1

description: TruSeqstrandedmRNA

value: no treatment


title: J04_FF_013


title: 5909 LN WT


title: ADT-derived cDNA and HTO-derived cDNA R1001_4-AH

value: Liver

value: Tumor, Normal, Lymph Node and PBMC

value: see meta_features.csv located in supplementary files for Antibody name and barcode and meta_sample.csv in supplmentary files for Hashtag to sample mappings


title: MP_S961_Bulk_RNA_replicate_3

description: TruSeqstrandedmRNA


title: MP_S961_Bulk_RNA_replicate_2

description: TruSeqstrandedmRNA


title: T-cell Receptor R1001_3-T


title: J04_FF_006


title: J04_FF_007


title: Virgin_S961_Bulk_RNA_replicate_3

description: TruSeqstrandedmRNA


title: ATAC-seq_D4_PF_FABP_3

city: Cincinnati

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

data_processing:
Transcripts were aligned to the indexed reference for mm10 with default settings using TopHat2 v2.1.1 (Kim et al. 2013).
Reads were filtered using bamtools using the following settings: -isDuplicate false -mapQuality “>10” (Barnett et al. 2011).
Transcript reads were counted post-alignment using StringTie (Pertea et al. 2015).
Differential expression testing was performed using edgeR v3.16.5 (Robinson and Smyth 2007; Robinson and Smyth 2008; Robinson et al. 2010; McCarthy et al. 2012; Zhou et al. 2014) and limma v3.30.13 (Ritchie et al. 2015) packages in R v3.3.2.
Low level genes were removed within each condition using median log2-transformed counts per gene per million mapped reads (cpm) of 1 and a union generated from those lists.
Differential expression testing was performed using a general linear model (GLM) framework. For comparing FAB and FAB+V, a covariate for replicate was included to correct for batch effect.
Sequencing reads were aligned to the mm10 genome using Bowtie2 v2.3.0 (Langmead and Salzberg 2012) and SAMtools v0.1.19 (Li et al. 2009; Li 2011).
Peak calling was performed using MACS2 callpeak (Zhang et al. 2008; Feng et al. 2012) using the settings --nomodel --shift -100 --extsize 200 -q 0.1 after pooling biological replicates.
A fold-enrichment track was generated using MACS2 using the bdgcmp function (-m FE) for visualization on the genome browser.
Following removal of ENCODE blacklist sites (Amemiya et al. 2019; ENCODE Project Consortium 2012), a union set of sites was generated by identifying summits that overlapped within 200bp and arbitrarily selecting the summit of highest positional value. Summits were then extended by 200bp in both directions to create the set of union sites.
Fold-enrichment scores were assigned to each site using the multiBigwigSummary function from deepTools (Ramírez et al. 2016).
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq_Compilation.txt contains all outputs related to the RNA-seq datasets, including TPM values for every biological replicate and differential expression testing. TSS_TAD.bed contains the TSS and TAD assignments. UnifiedATAC_Dataset.txt contains a list of the union sites, positional information, and fold-enrichment scores. edgeR_Results_FABVoverFAB.txt is the differential accessibility testing comparing the FAB+V and FAB conditions. All files "_summits_noBlacklist.bed" contain the summit calls from MACS2 following removal of ENCODE blacklist sites. All "_FE.bw" are bigWig files containing the MACS2 fold-enrichment scores.

source_name: mouse embryonic stem cells

growth_protocol: Bry-GFP and ZX1 ES cell lines were maintained in a serum- and feeder-free culture system (Ying et al. 2003; Gadue et al. 2006; Ying et al. 2008; Kattman et al. 2011). Neurobasal medium and DMEM/F12 (50%/50%; Thermo Fisher Scientific) were supplemented with N2 (Thermo Fisher Scientific), B27 (Thermo Fisher Scientific), 0.05% BSA (MilliporeSigma), 150mM mono-thioglycerol (MilliporeSigma), 1000unit Mouse LIF (MilliporeSigma), 1μM PD0325901 (Stemgent), 3μM CHIR99021 (Stemgent), L-glutamine (Life Technologies), penicillin-streptomycin (Thermo Fisher Scientific). PD0325901 and CHIR99021 were not added at 2 days prior to start differentiation. For differentiation start, ES cells were dissociated with trypLE express (Thermo Fisher Scientific) and cultured, at 1.0x105 cells/ml for 48hrs (Gadue et al. 2006; Kattman et al. 2011). In brief, IMDM and Ham’s F12 medium (75%/25%) were supplemented with N2, B27, BSA, L-glutamine, 0.5mM ascorbic acid (MilliporeSigma), 450mM mono-thioglycerol (MilliporeSigma), penicillin-streptomycin. The cells were differentiated in 10 cm petri-dishes (Becton Dickenson). The 48hr-old embryoid bodies (EBs) were dissociated with trypLE express and the cells were re-aggregated in StemPro-34 SFM medium (Thermo Fisher Scientific) in the present of L-glutamine, 200μg/ml human transferrin, 500μM ascorbic acid, 450μM mono-thioglycerol, 6ng/ml bFGF, 8ng/ml Activin A and 1ng/ml BMP4 for Bry+, PDGFRα+ and Flk1+ mesoderm induction. 5ng/ml VEGF was treated at D2 for bipotential mesoderm induction. Human Activin A, human BMP4, mouse VEGF, human bFGF were purchased from R&D systems. For hematopoietic lineage and cardiac lineage induction, sorted cells were cultured in StemPro-34 SF medium, supplemented with 2 mM L-glutamine, 1 mM ascorbic acid (MilliporeSigma), and 10 ng/ml bFGF (Kattman et al. 2006; Kattman et al. 2011). 2×105/ml sorted cells were seeded into individual wells of a 48-well flat bottom plate (Becton Dickenson) coated with gelatin after sorting.

extract_protocol:
Total RNA was extracted using NucleoSpin RNAII kit (Clonetech). ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) was performed as previously described (Buenrostro et al. 2015).
For RNA-seq, library preparation was performed by the University of Chicago Genomics Facility using the Illumina TruSeq RNA Sample prep kit v2 (Part #RS-122-2001). Library fragments were approximately 275bps in length and were quantitated using the Agilent Bio-analyzer 2100 and pooled in equimolar amounts. Single-ended, 51bp sequencing was performed on the Illumina HiSeq2500 in Rapid Run Mode by the University of Chicago Facility. For ATAC-seq, libraries were amplified and normalized with the Illumina Nextera DNA Library prep kit (FC-121–1031) according to the manufacturer's protocols. Libraries were quantitated using the Agilent Bioanalyzer, pooled in equimolar amounts, and sequenced with 50-bp single-end reads on the Illumina HiSeq following the manufacturer's protocols through the Genomics Core Facility at the University of Chicago.

value: mouse embryonic stem cells

tag: day

value: Day 4

value: FAB+P

tag: sort

value: P+F+


title: ADT-derived cDNA and HTO-derived cDNA R1001_3-AH

value: ADT and HTO


title: ATAC-seq_D4_PF_FABP_2


title: T-cell Receptor R1001_2-T


title: ATAC-seq_D4_PF_FABP_4


title: 8379

data_processing:
The quality of the data in the fastq files from the human samples was evaluated using FastqQC.
STAR(v2.5.2b) was used trim the reads on the fly using the clip3pAdapterSequence option.
STAR(v2.5.2b) was used to align the reads to the reference human genome with two pass mapping multi-sample setting.
STAR(v2.5.2b) was used to obtain read counts for the genes annotated in GENCODE (v24) using the quantmode GeneCounts option.
Assembly: GRCh38
Supplementary files format and content: text file in tab-separated value format with read counts from STAR

source_name: passage 3 lymph node FRCs

growth_protocol: Lymph node FRCs were cultured up to passage 3.

extract_protocol:
FRCs were lysed using trizol and RNA extracted using  RNeasy Micro Kit from Qiagen
TruSeq stranded mRNA kit (Illumina)

treatment_protocol: Healthy lymph node FRCs were co-cultured with reactive LN B cells (primary or cell lines) for 48h using transwell (pore size 0.4µm)

value: passage 3 lymph node FRCs

value: 48h conditioning with primary reactive lymph node B cells using transwell (pore size 0.4µm)


title: 8603


title: Virgin_S961_Bulk_RNA_replicate_2

description: TruSeqstrandedmRNA


title: ATAC-seq_D4_PF_FABV_5

value: FAB+V


title: ATAC-seq_D4_PF_FABP_1


title: J04_FF_004

value: FF (fresh frozen) tumor

value: breast cancer


title: ATAC-seq_D4_PF_FABV_4


title: Virgin_S961_Bulk_RNA_replicate_1

description: TruSeqstrandedmRNA


title: J04_FF_005


title: J04_FF_003


title: ADT-derived cDNA and HTO-derived cDNA R1001_2-AH


title: J04_FF_001


title: T-cell Receptor R1001_1-T

value: TCR


title: 8979


title: J04_FF_002


title: ATAC-seq_D4_PF_FAB_4

value: FAB


title: MP_S961_Bulk_RNA_replicate_1

description: TruSeqstrandedmRNA

value: Pancreatic islets

value: Wild type (C57BL/6J )


title: 111BCL

value: 48h conditioning with reactive B cell line using transwell (pore size 0.4µm)


title: ATAC-seq_D4_PF_FAB_3


title: HB6391


title: ATAC-seq_D4_PF_FAB_2


title: JY


title: ATAC-seq_D4_PF_FAB_1