title: 8hDMSO

description: Neuro 2 A cells were incubated for 8 hours with drug-free DMSO.

data_processing:
alignment to reference genome
Tophat 2.0.8, samtools-0.1.7, bowtie 2.1.0
Identification of differentially expressed genes
cufflinks
Assembly: mm9

source_name: Neuro 2A cells

growth_protocol: Minimal Essential Medium (MEM) supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
TRIzol™ Reagent, invitrogene, Dynabeads mRNA Purification Kit
SuperScript II Reverse Transcriptase (Invitrogen), T4 DNA polymerase (Promega), QIAquick PCR Purification Kit (Quiagen), DNAase I enzyme (New England Biolabs), End-It DNA End-Repair Kit (Epicentre Biotechnologies), QIAquick MinElute PCR Purification Kit (Qiagen), Illumina Genomic DNA Sequencing Kit, Size selection via Gel Extraction

treatment_protocol: 16h starvation in serum free MEM supplemented with 0.1% Bovine Serum Albumin (BSA), followed by addition of HU210 (dissolved in DMS) in a final volumn of 2.0uM or drug-free DMSO for 2, 4,6 or 8h.

value: drug-free DMSO

tag: time point

value: 8 hours


title: Blood cells from CLL patient 76

status: Public on Oct 11 2022

type: SRA

city: Montpellier

first: Jerome

last: Moreaux

address: 141 rue de la Cardonille

department: Institute of Human Genetics

country: France

institute: CNRS-UM

description: RNA-seq expression data from blood cells of CLL patient

library_source: transcriptomic

data_processing:
Assembly: RNA-seq read pairs were mapped to the reference human GRCh37 genome using the STAR aligner
The expression level of each gene was summarized and normalized using the DESeq2 R/Bioconductor package. Differential expression analysis was performed using the DESeq2 pipeline. p-values were adjusted to control the global FDR across all comparisons with the default option of the DESeq2 package.

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Total RNAs, including small RNAs, were extracted using the PAXgene Blood miRNA Kit (Qiagen, Courtaboeuf, France), according to the manufacturer’s instruction.
The RNA-seq library preparation was completed with 150 ng of input RNA using the Illumina TrueSeq Stranded mRNA Library Prep Kit.
Paired-end RNA-seq was performed with an Illumina NextSeq sequencing instrument

treatment_protocol: Blood was collected befor treatment in PAXgene blood RNA tubes

tag: tissue

value: Blood

tag: cell type

value: Blood cells from CLL patient


title: 8hHU210

city: New York

first: Jens

last: Hansen

state: NY

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Neuro 2 A cells were stimulated for 8 hours with 2uM HU210 (stock solution in DMSO).

organism: Mus musculus

tag: treatment

value: HU210 in DMSO


title: Blood cells from CLL patient 74


title: 295_ST_

city: Boston

first: Yinglu

last: Zhou

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
fastq files were aligned to version 97 of human reference genome GRCm38 using the Salmon.
Low read counts gene and sample filtering
Expression data was normalized using the VOOM with LOESS fit, and Combat-seq function in the Limma package in R
Assembly: version 97 of human reference genome GRCm38
Supplementary files format and content: Normalized RNA-seq

source_name: Prostate Stroma from RP

extract_protocol:
For each case, FFPE blocks with stroma-enriched (>60%) areas adjacent to tumor and benign areas distant from the tumor (another prostate quadrant or lobe in a separate FFPE block) were selected. Besides the identification of tumor- and benign-adjacent stroma areas for sampling, pathologists (G.N.F., M.L.) determined the Gleason score in the nearby tumor and annotated cribriform patterns and other histologic features. Stroma-enriched regions of interest (ROIs) adjacent to the tumor or benign glands were manually circled on slides. Tissue edges and ROIs were outlined on a parafilm strip and transferred onto the corresponding FFPE block.
Libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols.

tag: gleason score

tag: lethal

value: No

tag: cribriform

value: Non-Cribriform

tag: used in analysis

value: Yes


title: 296_ST_

value: Cribriform


title: 6hDMSO

description: Neuro 2 A cells were incubated for 6 hours with drug-free DMSO.

value: 6 hours


title: tumor_controltumorbearing_L9_L2

city: Candiolo

first: Luigia

last: Pace

address: Strada Provinciale, 142 -KM 3.95

country: Italy

institute: Italian Institute for Genomic Medicine

library_source: transcriptomic single cell

data_processing:
Single-cell sequencing files (base calls) were demultiplexed with bcl2fastq2 v.2.20.0.422 with default parameters for paired-end sequencing
FASTQ files were aligned to GRCm38 mouse (mm10) genome using STAR v.2.7.3a
Transcript-per-million (TMP) counts were obtained by processing the alignment results with RSEM v.1.3.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files of transcript expression quantification obtained via RSEM

source_name: tumor

extract_protocol:
Dextramer-Adpgk+ CD8+ T cells were FACS sorted from draining lymph nodes and tumors, harvested from non-treated tumor bearing mice, treated with αPD-1, and αPD-1 combined with GAd. Neoepitope specific- CD8+ T cells were sorted into 384-well plates, containing lyses buffer and immediately frozen.
Single cell library preparation was done as previously described (Picelli et al., 2014).

value: Adpgk+ CD8+ T cell

value: tumor

tag: strain

tag: age

value: 6-10 weeks old


title: tumor_controltumorbearing_L8_L2


title: Blood cells from CLL patient 75


title: 6hHU210

description: Neuro 2 A cells were stimulated for 6 hours with 2uM HU210 (stock solution in DMSO).


title: Blood cells from CLL patient 72


title: 295_SN_


title: 4hDMSO

description: Neuro 2 A cells were incubated for 4 hours with drug-free DMSO.

value: 4 hours


title: Blood cells from CLL patient 73


title: Blood cells from CLL patient 77


title: tumor_controltumorbearing_L7_L2


title: 294_ST_


title: tumor_controltumorbearing_L6_L2


title: 4hHU210

description: Neuro 2 A cells were stimulated for 4 hours with 2uM HU210 (stock solution in DMSO).


title: 2hDMSO

description: Neuro 2 A cells were incubated for 2 hours with drug-free DMSO.

value: 2 hours


title: tumor_controltumorbearing_L5_L2


title: Blood cells from CLL patient 70


title: 294_SN_


title: Blood cells from CLL patient 71


title: 292_ST_


title: tumor_controltumorbearing_L4_L2


title: 2hHU210

description: Neuro 2 A cells were stimulated for 2 hours with 2uM HU210 (stock solution in DMS).


title: 292_SN_


title: tumor_controltumorbearing_L3_L2


title: MCF7 cells p300 inhibitor  replicate 3

city: Eggenstein-Leopoldshafen

first: Christine

last: Blattner

address: Hermann-von-Helmholtz-Platz 1

department: IBCS-BIP

country: Germany

institute: KIT

data_processing:
Data were processed by Novogene
Assembly: hg38
Supplementary files format and content: xls file gene_count contains gene counts for each sample; xls file: gene_fkpm contains normalized gene counts

growth_protocol: MCF7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and pen/strep in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TriFast (peqLab) according to the manufacturer's protocol
Libraries were prepared by Novogene.

tag: cell line

value: breast cancer

tag: genotype

value: wild type


title: 291_ST_


title: Blood cells from CLL patient 67


title: tumor_controltumorbearing_L2_L2


title: MCF7 cells CRISPR/Cas9 KO2 replicate 3

value: TRIM25 KO

value: 0.1% DMSO


title: Blood cells from CLL patient 68

value: Blood


title: tumor_aPD1.GAd_L23_L2


title: 291_SN_


title: 290_ST_GS4


title: Blood cells from CLL patient 66

value: Blood cells from CLL patient


title: 290_ST_GS3


title: MCF7 cells Non-targeted control replicate 3


title: Blood cells from CLL patient 65


title: tumor_aPD1.GAd_L22_L2


title: MCF7 cells p300 inhibitor  replicate 2


title: Blood cells from CLL patient 64


title: tumor_aPD1.GAd_L21_L2


title: MCF7 cells CRISPR/Cas9 KO2 replicate 2


title: tumor_aPD1.GAd_L20_L2


title: Blood cells from CLL patient 69


title: Blood cells from CLL patient 63


title: tumor_controltumorbearing_L1_L2


title: 288_ST_


title: 289_ST_


title: 287_SN_


title: MCF7 cells CRISPR/Cas9 KO1 replicate 2


title: MCF7 cells Non-targeted control replicate 2


title: tumor_aPD1.GAd_L19_L2


title: Blood cells from CLL patient 61


title: tumor_aPD1.GAd_L18_L2


title: 286_ST_


title: MCF7 cells p300 inhibitor  replicate 1


title: tumor_aPD1.GAd_L17_L2


title: Blood cells from CLL patient 60


title: 286_SN_


title: MCF7 cells CRISPR/Cas9 KO2 replicate 1


title: 285_SN_


title: MCF7 cells CRISPR/Cas9 KO1 replicate 1


title: Blood cells from CLL patient 59


title: Blood cells from CLL patient 58


title: MCF7 cells Non-targeted control replicate 1


title: Blood cells from CLL patient 57


title: tumor_controltumorbearing_L13_L2


title: 283_SN_


title: Blood cells from CLL patient 62


title: 283_ST_


title: tumor_controltumorbearing_L12_L2


title: 282_ST_


title: Blood cells from CLL patient 56


title: tumor_controltumorbearing_L11_L2


title: htNSC batch 11 DIV 34

city: Seoul

first: Yanuar

middle: Alan

last: Sulistio

address: Wangsimni-ro 222

department: Biomedical Science

country: South Korea

institute: Hanyang University

data_processing:
Adapter trimmed using trimmomatic
Reference mapping using HISAT2 with hg19 as reference genome
Transcript count and gene count were called using StringTie
Assembly: hg19
Supplementary files format and content: csv file of read count matrix

source_name: h9 hESC

growth_protocol: hPSC maintained in matrigel + mTSER1 media, htNSC obtained from differentiating hPSC through organoid stage

extract_protocol:
TriZol
TruSeq Stranded mRNA Sample Preparation Guide

value: h9 hESC

value: hNSC

tag: divisions

value: DIV 34


title: htNSC batch 12 DIV 27

value: DIV 27


title: htNSC batch 13 DIV 20

value: DIV 20


title: Blood cells from CLL patient 55


title: AG09908R1 hiPSC

value: hPSC


title: tumor_controltumorbearing_L10_L2

value: Adpgk+ CD8+ T cell


title: tumor_controltumorbearing_K8_L2

value: tumor


title: tumor_controltumorbearing_L14_L2

value: 6-10 weeks old


title: tumor_controltumorbearing_K9_L2


title: 284_ST_

value: Yes

value: Non-Cribriform


title: 282_SN_


title: 281_ST_

value: No


title: 280_ST_


title: h9 hESC


title: Blood cells from CLL patient 53


title: 280_SN_


title: 279_ST_


title: Blood cells from CLL patient 51


title: Blood cells from CLL patient 52


title: CMC11 hiPSC


title: tumor_controltumorbearing_K7_L2


title: tumor_controltumorbearing_K6_L2


title: Blood cells from CLL patient 54


title: Blood cells from CLL patient 50


title: tumor_controltumorbearing_K5_L2


title: Blood cells from CLL patient 48


title: 275_ST_


title: Blood cells from CLL patient 47


title: MET.macrophage.3

city: Baltimore

first: Peter

middle: C

last: Searson

state: MD

address: 3400 North Charles Street

institute: Johns Hopkins University

data_processing:
alignment and quantification to GRCh38 using Rsubread
Fragments Per Kilobasee of transcript per Million fragments mapped (FPKM) was calculated for each gene as outlined in Trapnell et al., Nature Biotechnology, 2010.
Normalization using variance stabilizing regularized logarithm transformation (rlog) using DESeq2.
Assembly: GRCh38
Supplementary files format and content: FPKMs

source_name: iBMEC-PM-RFP

growth_protocol: Cell culture was conducted at 5% CO2 and 37 °C.  iBMECs were differentiated using sequential treatment of iPSC colonies with unconditioned media without bFGF (for six days) and endothelial media (for two days). iBMECs were seeded onto cylindrical microvessel constructs coated with 50 µg mL-1 human placental collagen IV and 25 µg mL-1 fibronectin from human plasma in endothelial media supplemented with ROCK inhibitor (10 µM Y27632).  After 24 h, media was switched to basal medium.  Unconditioned media without bFGF: DMEM/F12 supplemented with 20% knockout serum replacement, 1% non-essential amino acids, 0.5% GlutaMAX, and 0.836 μM beta-mercaptoethanol. Endothelial media: human endothelial cell serum-free medium supplemented with 1% human platelet poor derived serum, 2 ng mL-1 bFGF, and 10 mM all-trans retinoic acid. Basal media: human endothelial serum-free medium supplemented with 1% human platelet poor derived serum, 1% penicillin-streptomycin.

extract_protocol:
After 48 hours in the microvessel construct, iBMECs were washed with 1x PBS by perfusion of the lumen, and lysed using RLT buffer supplemented with β-mercaptoethanol, before isolating RNA using a RNeasy Mini Kit (Qiagen) with DNase I digestion (Qiagen).
RNA libraries were prepared using Takara SMART-seq v4.

treatment_protocol: The inclusion of cancer spheroids (JIMT-1) and macrophages (THP-1 differentiated via PMA) were conducted prior to the seeding of iBMECs, by suspending both in a 6 mg/mL collagen I gel supplemented with 1.5 mg/mL Matrigel that surrounds the microvessel construct.

value: iBMEC-PM-RFP

value: cancer spheroids and macrophages


title: MET.cancer.3

value: cancer spheroids


title: tumor_controltumorbearing_K4_L2


title: MET.control.3

value: control


title: tumor_controltumorbearing_K2_L2


title: tumor_controltumorbearing_K3_L2


title: Blood cells from CLL patient 45

value: Blood

value: Blood cells from CLL patient


title: MCF7 cells CRISPR/Cas9 KO1 replicate 3

value: breast cancer

value: TRIM25 KO

value: 0.1% DMSO


title: Blood cells from CLL patient 49


title: Blood cells from CLL patient 46


title: 270_ST_


title: 271_SN_


title: MET.cancer.2


title: Blood cells from CLL patient 44


title: MET.macrophage.1


title: tumor_controltumorbearing_K24_L2


title: 271_ST_


title: 272_ST_


title: MET.control.2


title: tumor_controltumorbearing_K23_L2


title: 269_ST_

value: Cribriform


title: MET.cancer.1


title: MET.control.1


title: 268_ST_


title: tumor_controltumorbearing_K22_L2


title: tumor_controltumorbearing_K20_L2


title: Blood cells from CLL patient 43


title: 276_ST_


title: MET.macrophage.2


title: tumor_controltumorbearing_K21_L2


title: 267_ST_


title: Blood cells from CLL patient 42


title: 265_ST_


title: 264_ST_


title: tumor_controltumorbearing_K17_L2


title: tumor_controltumorbearing_K18_L2


title: Blood cells from CLL patient 38


title: tumor_controltumorbearing_K19_L2


title: RT112, DMSO

city: New Haven

first: Karen

middle: S

last: Anderson

state: CT

address: 333 Cedar Street

department: Pharmacology

institute: Yale University

data_processing:
RNA-seq was performed by Illumina NovaSeq 6000. Base calling was performed using Illumina Casava v1.8.2 software used for base-calling on HiSeq 4000. The adaptor and bad quality reads were first trimmed out by trimmomatic v0.36 using the parameter "ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:8:TRUE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36". Then all reads were mapped and aligned to Ensembl GRCh38 using HISAT2 v2.2.1. The mapped and aligned reads were then sorted by samtools v1.15.1. Next, the transcriptome was assembled and gene expression abundance was calculated by stringtie v2.2.1. Finally, FKPM of each gene for each sample was calculated by Ballgown v2.26.0.
Assembly: Ensembl GRCh38
Supplementary files format and content: The processed data of all samples were combined into one single .csv file (All_gene_expression_with_Q_treatment.csv). This file contains the gene ID from the RNA-seq analysis, gene name, and FKPM calculation of each gene for each sample. Each column reprensents different samples and each row represents different genes.

molecule: polyA RNA

source_name: Urinary Bladder Cancer

growth_protocol: RT4 cells were cultured in McCoy's 5A media, +10% HI-FBS, 1x anti-anti. RT112 cells were cultured in DMEM media, +10% HI-FBS, 1x anti-anti, +2mM L-glutamine, +1x non-essential amino acid (NEAA). SW780 cells were cultured in DMEM, +10% HI-FBS, 1x anti-anti. All cells were cultured at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was extracted by TRIZol Plus RNA Purification kit (Invitrogen, #12183555) according to manufacturer's protocol and 1ug total RNA of each sample was used for library construction.
Library was constructed by TruSeq® Stranded mRNA Library Prep kit (Illumina, #20020594) following manufacturer's protocol

treatment_protocol: Cells were treated by DMSO or quisinostat (50nM for RT4, 10nM for RT112, and 25nM for SW780) for 2 days. Then RNA were extracted and RNA-seq were performed.

value: Urinary Bladder Cancer

value: Cancer cell line

value: FGFR3-TACC3 fusion

value: DMSO


title: SW780, DMSO

value: FGFR3-BAIBP2L1 fusion


title: RT4, 50nM quisinostat

value: 50nM quisinostat


title: 262_ST_

value: No

value: Non-Cribriform

value: Yes


title: tumor_controltumorbearing_K16_L2

value: Adpgk+ CD8+ T cell

value: tumor

value: 6-10 weeks old


title: Blood cells from CLL patient 40

value: Blood

value: Blood cells from CLL patient


title: Blood cells from CLL patient 36


title: SW780, 25nM quisinostat

value: 25nM quisinostat


title: tumor_controltumorbearing_K15_L2


title: 262_SN_


title: RT4, DMSO


title: tumor_controltumorbearing_K14_L2


title: Blood cells from CLL patient 35


title: tumor_controltumorbearing_K13_L2


title: Blood cells from CLL patient 34


title: 260_SN_


title: 261_SN_


title: Blood cells from CLL patient 39


title: RT112, 10nM quisinostat

value: 10nM quisinostat


title: Blood cells from CLL patient 41


title: 263_ST_

value: Cribriform


title: 259_ST_


title: Blood cells from CLL patient 33


title: Blood cells from CLL patient 32


title: tumor_controltumorbearing_K11_L2


title: 255_SN_


title: Blood cells from CLL patient 31


title: tumor_controltumorbearing_J9_L2


title: 253_ST_


title: tumor_controltumorbearing_K10_L2


title: Blood cells from CLL patient 30


title: Blood cells from CLL patient 29


title: 252_SN_


title: tumor_controltumorbearing_J8_L2


title: Blood cells from CLL patient 28


title: Blood cells from CLL patient 27


title: 251_ST_


title: 250_SN_


title: tumor_controltumorbearing_J7_L2


title: tumor_controltumorbearing_J6_L2


title: tumor_controltumorbearing_J5_L2


title: 248_ST_


title: tumor_controltumorbearing_K12_L2


title: 246_ST_


title: tumor_controltumorbearing_K1_L2


title: Blood cells from CLL patient 25


title: Blood cells from CLL patient 37


title: 245_ST_


title: Blood cells from CLL patient 26


title: tumor_controltumorbearing_J4_L2


title: tumor_controltumorbearing_J3_L2


title: Blood cells from CLL patient 24


title: 258_ST_


title: 242_ST_


title: Blood cells from CLL patient 23


title: tumor_controltumorbearing_J23_L2


title: 241_ST_


title: Blood cells from CLL patient 20


title: Blood cells from CLL patient 22


title: 240_ST_


title: 244_ST_


title: tumor_controltumorbearing_J2_L2


title: 239_SN_


title: Blood cells from CLL patient 17


title: tumor_controltumorbearing_J20_L2


title: tumor_controltumorbearing_J24_L2


title: Blood cells from CLL patient 18


title: Blood cells from CLL patient 16


title: Blood cells from CLL patient 21


title: 238_ST_


title: tumor_controltumorbearing_J18_L2


title: tumor_controltumorbearing_J22_L2


title: Blood cells from CLL patient 14


title: Blood cells from CLL patient 19


title: 240_SN_


title: 239_ST_


title: tumor_controltumorbearing_J21_L2


title: tumor_controltumorbearing_J1_L2


title: tumor_controltumorbearing_J19_L2


title: Blood cells from CLL patient 11


title: Blood cells from CLL patient 15


title: 234_ST_


title: 237_ST_


title: 237_SN_


title: 236_ST_


title: tumor_controltumorbearing_J12_L2


title: tumor_controltumorbearing_J15_L2


title: 235_ST_


title: 235_SN_


title: 232_ST_


title: Blood cells from CLL patient 7


title: Blood cells from CLL patient 10


title: tumor_controltumorbearing_J10_L2


title: tumor_controltumorbearing_J13_L2


title: tumor_controltumorbearing_J11_L2


title: Blood cells from CLL patient 13


title: 230_ST_


title: Blood cells from CLL patient 5


title: tumor_controltumorbearing_J17_L2


title: lymphnode_controltumorfree_I8_L2

source_name: lymph node

value: CD8+ T cell

value: lymph node


title: 231_SN_

value: Tumor Infiltrating Lymphocites


title: tumor_controltumorbearing_J14_L2


title: Blood cells from CLL patient 4


title: Blood cells from CLL patient 8


title: Blood cells from CLL patient 3


title: Blood cells from CLL patient 6


title: lymphnode_controltumorfree_I7_L2


title: tumor_controltumorbearing_J16_L2


title: 228_ST_


title: Blood cells from CLL patient 2


title: lymphnode_controltumorfree_I9_L2


title: Blood cells from CLL patient 12


title: 234_SN_


title: 231_ST_


title: 229_ST_


title: Blood cells from CLL patient 9


title: 226_ST_


title: 225_ST_


title: lymphnode_controltumorfree_I6_L2


title: 223_SN_


title: tumor_controltumorbearing_I23_L2


title: Blood cells from CLL patient 1


title: 226_SN_


title: 221_SN_


title: lymphnode_controltumorfree_I3_L2


title: tumor_controltumorbearing_I20_L2


title: lymphnode_controltumorfree_I2_L2


title: 221_ST_


title: 220_ST_


title: lymphnode_controltumorfree_I4_L2


title: tumor_controltumorbearing_I22_L2


title: 223_ST_GS4


title: lymphnode_controltumorfree_I1_L2


title: 218_ST_


title: 222_ST_


title: lymphnode_controltumorfree_I5_L2


title: tumor_controltumorbearing_I17_L2


title: R6

city: Guangzhou

first: Xueman

last: Chen

state: Guangdong

address: 107 Yanjiang West Road

country: China

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

data_processing:
Raw data (raw reads) of fastq format were processed through in-house Perl scripts.
Index of the reference genome was built using Bowtie2 v2.2.3.
Paired-end clean reads were aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM was then calculated to estimate the expression level of genes in each sample.
Assembly: hg38
Supplementary files format and content: Matrix files include FPKM values for each Sample

source_name: breast cancer tissue

extract_protocol:
RNA was harvested using Trizol (Invitrogen) according to the manufacturer’s instructions. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following the manufacturer’s recommendations.

treatment_protocol: Breast cancer with adjuvant aromatase inhibitor (AI) treatment

value: breast cancer tissue

value: AI-resistant

value: aromatase inhibitor treatment


title: 219_SN_

value: No


title: 227_ST_

value: Non-Cribriform


title: 216_ST_

value: Yes


title: tumor_controltumorbearing_I18_L2

value: Adpgk+ CD8+ T cell


title: 217_ST_


title: 215_ST_


title: R7


title: tumor_controltumorbearing_I21_L2

value: tumor


title: R4


title: tumor_controltumorbearing_I19_L2

value: 6-10 weeks old


title: 214_SN_


title: lymphnode_controltumorfree_I14_L2


title: lymphnode_controltumorfree_I13_L2


title: R3


title: tumor_controltumorbearing_I16_L2


title: tumor_controltumorbearing_I24_L2


title: 212_SN_


title: lymphnode_controltumorfree_I12_L2


title: 212_ST_


title: 214_ST_


title: 211_ST_


title: R1


title: lymphnode_controltumorfree_I15_L2


title: lymphnode_controltumorfree_I11_L2


title: tumor_aPD1.GAd_H9_L1


title: S7

value: AI-sensitive


title: tumor_aPD1.GAd_H24_L1


title: 210_ST_


title: lymphnode_controltumorfree_I10_L2


title: S4


title: R2


title: 213_ST_


title: S3


title: R5


title: S6


title: 206_ST_


title: tumor_aPD1.GAd_G22_L1


title: S1


title: S5


title: tumor_aPD1.GAd_H21_L1


title: 208_ST_


title: tumor_aPD1.GAd_E24_L1


title: tumor_aPD1.GAd_H18_L1


title: 205_ST_


title: TOP3A+TOP1MT-3

city: Newcastle upon Tyne

first: Thomas

middle: Joseph

last: Nicholls

address: Framlington Place

department: Wellcome Centre for Mitochondrial Research

country: United Kingdom

institute: Newcastle University

data_processing:
Reads were quantified against transcripts using Salmon (version 1.3.0)
Gene level counts were obtained from transcript level counts using the R package tximport (version 3.13)
Assembly: GRCh38
Supplementary files format and content: Processed data file count_table.txt is a tab-delimited text file containing a matrix of gene level counts. Rows are features (ensembl gene Ids) and columns are  samples

source_name: HeLa cells

growth_protocol: Dulbeccos Modified Eagle medium with 10% FBS and 100 U/ml penicillin and 100 µg/ml streptomycin

extract_protocol:
RNA prepared using Qiagen Rneasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Three biological replicates each were reverse transfected with ctrl siRNA, TOP3A siRNA, TOP1MT siRNA or TOP3A + TOP1MT siRNAs and re-transfected after 72 hours for a total of six days of transfection

tag: genotype/variation

value: TOP3A and TOP1MT siRNA double knockdown


title: 204_ST_


title: 202_ST_


title: tumor_aPD1_D21_L2


title: 203_ST_


title: TOP3A+TOP1MT-1


title: TOP3A+TOP1MT-2


title: TOP1MT-3

value: TOP1MT siRNA knockdown


title: tumor_aPD1.GAd_B24_L1


title: 200_ST_


title: tumor_aPD1.GAd_B22_L1


title: tumor_aPD1.GAd_C16_L1


title: TOP1MT-1


title: 201_ST_


title: 199_SN_


title: 201_SN_


title: TOP1MT-2


title: tumor_aPD1.GAd_C22_L1


title: tumor_aPD1.GAd_B21_L1


title: S2


title: tumor_aPD1.GAd_A22_L1


title: tumor_aPD1.GAd_A21_L1


title: 199_ST_


title: 198_ST_


title: TOP3A-2

value: TOP3A siRNA knockdown


title: TOP3A-1


title: ctrl-3

value: ctrl siRNA transfected


title: 198_SN_


title: tumor_aPD1.GAd_A20_L1


title: ctrl-2


title: 197_ST_


title: tumor_aPD1.GAd_A17_L1


title: tumor_aPD1.GAd_A19_L1


title: 197_SN_


title: ctrl-1


title: lymphnode_controltumorfree_A15_L2

value: CD8+ T cell


title: 195_ST_


title: lesional skin RNA expression compared with univovled skin control 2 [BN4]

city: Klong Luang

first: Onjira

last: Jumlongpim

state: Pathumthanii

address: Chulabhorn international college of medicine, 99 Moo 18

department: Dermatology

country: Thailand

institute: Chulabhorn International College of Medicine, Thammasat University

description:
processed data file:
Uninvovled_Expression_Profile.hg19.transcript.xlsx

data_processing:
The NGS was carried out using NovaSeq 6000 S4 Reagent Kit on the NovaSeq 6000 System according to the user guide (Illumina Inc., San Diego, CA, USA) with 100 bp paired-end reads.
Trimmed reads were mapped to referent genome with HISAT2, splice-aware aligner
The transcripts were assembled by StringTie with aligned reads
The Fragments Per Kilobase of Transcript Per Million Mapped Reads (FPKM) value was used as a normalization value.
the read counts to statically analyze the differentially expressed genes (DEGs) using the edgeR Bioconductor statistical library version 3.13 on RStudio
Supplementary_files_format_and_content: The table shows the transcripts with their read raw count (xlsx file)

source_name: Uninvoled skin

growth_protocol: no

extract_protocol:
Total RNAs were extracted from each skin biopsy of the volunteers (LN skin, n = 3; UN skin, n = 2) using TRIzol Reagent (Ambion, Austin, Tx, USA) according to the manufacturer’s instruction. The next-generation sequencing (NGS) was carried out by a commercial company (Macrogen, Seoul, Korea). Briefly, RNA quality was qualified by an Agilent 2100 bioanalyzer (RIN>7).
Libraries for these sequencing were constructed using SMARTer Universal Low Input RNA Kit, TruSeq RNA Sample Prep Kit v2 (pair-end). The cDNAs were checked for the quantity and quality by the bioanalyzer.

treatment_protocol: no

tag: tissue donor

value: Untreated patient with moderate to severe psoriasis vulgaris

tag: type

value: Whole skin biopsy, punch

tag: volunteer

value: Normal phenotypic skin, 10 cm away from lesional skin

tag: test

value: Control


title: lymphnode_controltumorfree_A10_L1

tag: tissue

value: lymph node


title: 196_SN_


title: 195_SN_

value: No


title: TOP3A-3


title: lesional skin RNA expression compared with univovled skin control 1 [BN1]


title: lesional skin RNA expression compared with univovled skin test 1 [BL1]

description:
processed data file:
Lesional skin_Expression_Profile.hg19.transcript.xlsx

source_name: lesional skin

value: center of plaque lesion

value: test


title: 193_SN_

value: Cribriform

value: Yes


title: minus 2 hr rep 8

city: Eugene

first: Amy

middle: K

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

data_processing:
Single-end 50 bp reads were mapped with with bowtie (Langmead 2010) using the following command: bowtie --best --chunkmbs 256 -k 1 -m 2 -S -p 2. HTseq was used to count reads mapping to genes (Anders et al. 2015) using version WS210 of the C. elegans genome obtained from Maxwell et al. (Maxwell et al. 2012).
Count tables were used to detect differential expression in R using edgeR (Robinson et al. 2010). Prior to differential expression analysis, count tables were filtered first to include only genes with counts per million (CPM) greater than one across four libraries. This resulted in 16,699 genes for further analysis. The edgeR glm functionality was used to fit a GLM, and a likelihood ratio test was performed for each gene; this ANOVA-like test was used to detect any differences across the twelve time points.
Genome_build: WS210
Supplementary_files_format_and_content: Count files for each library; these are the non-normalized input into edgeR for differential expression analysis. An excel final with edgeR output from differential expression analysis is also included.

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: Well-fed N2 was maintained on OP50 at 20°C. For each biological replicate, 20 large (10 cm) NGM plates with gravid adults were hypochlorite treated to obtain over 200,000 embryos. Embryos were resuspended in S-basal at a density of 1 embryo/uL in an Erlenmeyer flask at 20°C in a shaker at 180 rpm. Time points used in the time series are 12 hours offset from hypochlorite treatment and signify when worms have begun hatching and are thus undergoing L1 arrest. L1 larvae hatch approximately 12 hours after hypochlorite treatment, and this is considered 0 hr. At least 10,000 L1s were collected per time point. For days 8 and 12, the number of L1s collected was doubled and quadrupled, respectively, to account for lethality at later time points. To collect samples, L1s in S-basal were first spun down at 3,000 rpm, and S-basal was aspirated off down to less than 100 uL. The pellet and residual S-basal was transferred to a 1.5 mL Eppendorf tube using a glass pipet. Samples were flash frozen in liquid nitrogen and stored at -80°C until RNA isolation.

extract_protocol:
RNA was extracted using TRIzol Reagent (Thermo-Fisher Scientific) using the manufacturer’s protocol with some exceptions. 100 mL of sand (Sigma-Aldrich) was included to aid homogenization. Sand was first prepared by washing two times in 1 M HCl, washed eight times in RNAse-free water (to a neutral pH), and baked to dry.
Libraries were prepared for sequencing using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, E7530) with 100 ng of starting RNA per library and 14 cycles of PCR. Libraries were sequenced using Illumina HiSeq 4000.

tag: developmental stage

value: L1 larvae

tag: time point (hours)

value: minus 2 hr


title: 193_ST_

tag: gleason score


title: lesional skin RNA expression compared with univovled skin test 2 [BL3]

value: Untreated patinet with modertate to severe psoriasis vulgaris


title: lesional skin RNA expression compared with univovled skin test 2 [BL4]


title: 194_ST_

tag: lethal

value: Non-Cribriform


title: 192_ST_

tag: cribriform


title: epithelial_normal_day4rep2

city: Charleston

first: Lu

last: Han

address: 86 Jonathan Lucas St

institute: Medical University of South Carolina

data_processing:
Initial quantification and QC was done in CellRanger; transcript set augmented with tdTomato, CRE, and FlipO
Using the R package Seurat, individual samples were processed, filtering cells with too much MT content (> 20%) or too few detected features (< 200)
Also in Seurat, integration anchors selected, all samples integrated, scaled, and clustered
Assembly: GRCm38
Supplementary files format and content: Rdata files containing Seurat objects with the integrated sample sets

source_name: normal pancreata

extract_protocol:
Normal pancreas: Dissociation media for normal pancreas is Collagenase P (1 mg/ml), Soybean Trypsin inhibitor (0.2 mg/ml), Dnase I (12 U/ml), HEPES (10 mM), Rock inhibitor Y (10 μM) in HBSS (with Ca2+). Pancreas was dissected, minced in Eppendorf tubes, and then transferred to a Miltenyi gentleMACS tube with 2.5ml of dissociation media. Dissociation was performed on a gentleMACS Dissociator using program 37m-TDK-1 for 15 min. For tumor-bearing pancreata: Dissociation media for tumor bearing pancreas was prepared using the Tumor Dissociation Kit (Miltenyi Biotec, 130-096-730). Pancreas was dissected and cut into small pieces using a razor blade. A full program of 37m-TDK-1 was used to dissociate the tumor. Similar procedures were then used for both normal and tumor pancreata. 15ml of cold DMEM+10% fetal bovine serum (FBS) dissociation mix was then filtered through a 70 μm and then a 100 μm membrane. Red blood cell lysis buffer was then added to the pellate and pipetted. After centrifuge, cells are suspended in FACS buffer (5% FBS, 10 μM Y, 20 mM HEPES, 5 mM MgCl2, 12 U/ml DNase I in PBS). After Fc block, cells were incubated with fluorophore conjugated antibodies (Extended Data Table 2). A BD FACS Aria machine was used to ether analyze or sort the cells.   Tumor pancreas: Dissociation media for tumor bearing pancreas was prepared using the Miltenyi gentleMACS tumor dissociation kit. Pancreas was dissected and cut into small pieces using a razor blade. A full program of 37m-TDK-1 was used to dissociate the tumor. Procedures after dissociation were the same as the normal pancreas.
After dissociation and staining, cells were sorted into three groups, Group 1. hematopoietic cells; Group 2. endothelial + epithelial cells; and Group 3. fibroblasts. A fraction of Group 1 cells was combined to Group 2. The fraction was calculated to achieve similar cell numbers of Group 1 and Group 2. For tumor samples, 4-5 mice were pooled to generate each replicate (n=2). For normal samples, 6 mice were pooled, sorted and split into 2 replicates (n=2).  Cells were resuspended in PBS and counted with trypan blue to evaluate viability.  To create a pool of hematopoietic and endothelial + epithelial cells, an equal ratio of cells were mixed from these two groups to establish the pool 1+2.  Library preparation and sequencing were completed at MCW’s Genomic Science and Precision Medicine Center with 10,000 cells aliquoted for groups 1+2 and 3, and were processed according to the Chromium Next GEM Single Cell 3’ Reagent Kits (10X Genomics, dual indexes). All samples passed quality control metrics with 13-16 cycles of PCR completed to amplify the libraries.  Final libraries were quantified and pooled by qPCR (Kapa Library Quantification Kit, Kapa Biosystems) and sequencing completed on the NovaSeq6000 (GSPMC at MCW) targeting 50,000 reads per cell per condition.

value: mixed

value: around 56 days

value: Isl1cre/+; R26Tomato/+

value: normal pancreata


title: fibroblast_normal_day4rep1


title: 191_ST_

tag: used in analysis


title: 190_SN_


title: epithelial_normal_day4rep1

tag: strain


title: fibroblast_PDAC_day2

source_name: tumor-bearing pancreata

tag: age

value: tumor-bearing pancreata


title: minus 2 hr rep 1


title: minus 2 hr rep 6


title: minus 2 hr rep 5


title: fibroblast_normal_day4rep2


title: Macrophage #3 Young

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description:
Single-cell RNA-seq
mRNA

data_processing:
Cell Ranger software version 3.0.2 was used for extracting fastq files, sequence alignment and UMI counts.
Genome_build: Mouse genome mm10
Supplementary_files_format_and_content: *_filtered_feature_bc_matrix.h5: Matrix files containing UMIs associated with a feature and a barcode. Includes only detected cell-associated barcodes.

source_name: Skeletal muscle

extract_protocol:
Macrophages were isolated from mouse skeletal muscle by FACS, and subjected to single-cell GEM (Gel Bead-in-Emulsion) generation with Chromium Controller (10x Genomics).
Single-cell libraries were prepared with 10x Genomics Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics Cat# PN-1000092) with Chip B (10x Genomics, Cat# PN-1000073) following the manufacturer’s protocol with Chromium Controller (10x Genomics).

tag: cell type

value: Skeletal muscle macrophages

value: 3 months


title: 9 hr rep 8

value: 9 hr


title: epithelial_PDAC_day3

tag: genotype


title: epithelial_PDAC_day2


title: 189_ST_

value: No


title: M. musculus, TA, CTX, scRNA-seq

city: Halifax

first: Adam

last: Johnston

state: NS

address: 1344 Summer Street

department: Medical Neuroscience

country: Canada

institute: Dalhousie University

data_processing:
Sequencing of cDNA libraries were performed on Illumina HiSeq 2500 using single-end reads of 91 bp length.
Raw reads were filtered and aligned to the mm10 assembly, followed by UMI counting and gene expression matrix creation using the cellranger analysis suite (10x Genomics).
Gene expression matrices were analyzed in R (v3.6.3) using the Seurat library (v3.1). Cells were removed from downstream analysis if they had less than 200 UMIs, greater than 2500 UMIs, or greater than 20% of UMIs mapping to the mitochondrial genome. Genes expressed in less than 3 cells were also removed. Control and CTX datasets were integrated using Seurat's canonical correlation analysis (CCA) method following normalization and variable gene selection. PCA, neighbourhood graph construction, and louvain clustering were performed on the integrated dataset. Differentially-expressed genes were determined using the wilcoxon rank sum test and Bonferroni correction.
Assembly: mm10
Supplementary files format and content: seu.rds.gz: gzipped processed Seurat object of integrated dataset with cluster annotations and normalized expression levels in rds format.
Supplementary files format and content: matrices.tar.gz: gzipped tarball of cellranger output gene expression matrices (raw and filtered) in market exchange (MEX) format.

source_name: Tibialis anterior muscle

extract_protocol:
Tibialis anterior muscle from 8-week-old mice were collected 5 days-post CTX or sham (PBS) injury (n = 5 biological replicates for each group). After manual dissociation of muscle tissue from blood vessels, fat, and connective tissue, samples were mulched in dissociation media (10mg/ml Collagenase D [Roche], 4.8U/ml Dispase II [Roche], and 10% horse serum in high-glucose DMEM) with fine scissors and incubated at 37°C for 45 minutes with agitation. Collagenase/dispase was inactivated with FBS, and the cells were filtered through a 40µm strainer and centrifuged for 10 minutes at 1000g at 4°C, washed in PBS, and underwent red blood cell lysis (Qiagen) and myofiber debris removal (Miltenyi Biotec, 130-109-398) using commercial kits following the manufacturer's instructions. Cell viability was >90% based on trypan blue staining in all samples. Biological replicates were then pooled and fixed in ice-cold methanol for 15 minutes on ice and stored at -80°C until single-cell RNA-sequencing.
Single-cell cDNA libraries were prepared using 10x Genomics methanol fixation protocol (CG000136 rev. E).

value: Tibialis anterior muscle

tag: treatment

value: CTX

tag: Sex

value: M


title: M. musculus, TA, PBS, scRNA-seq

value: PBS


title: 9 hr rep 6

value: L1 larvae


title: 188_SN_

value: Yes


title: Macrophage #3 Old

description:
Single-cell RNA-seq
mRNA

value: 23 months


title: 187_SN_


title: 9 hr rep 5


title: 9 hr rep 1


title: Macrophage #2 Young

description:
Single-cell RNA-seq
mRNA


title: fibroblast_PDAC_day3


title: 187_ST_

value: Non-Cribriform


title: Macrophage #2 Old

description:
Single-cell RNA-seq
mRNA


title: 185_ST_

value: Cribriform


title: 190_ST_


title: 192 hr (8 d) rep 6


title: 192 hr (8 d) rep 1


title: Cultured murine RUNX1/EVI1 leukemia cells - ERG + shEVI1.2658 - Replicate 3

city: Vienna

first: Florian

last: Andersch

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Institute of Molecular Pathology

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D), ERG + shEVI1.2568 (Day5 ON DOX) - Replicate 3

data_processing:
For murine Quant-seq (3’ mRNA-Seq) data, the six nucleotide long 5’ UMIs were attached to each read name with umi-tools (v1.0.0) (Smith et al., 2017), before trimming away the UMIs plus the next four nucleotides (UMI spacer), as well as 3’ adapters (stringency of 3) and bases with low quality (threshold of 25), using cutadapt (v1.18) (MARIN, 2011) and its wrapper tool trimgalore (v0.6.2).
Read quality control was performed with FastQC (v0.11.8) (Andrews, 2010).
The remaining reads were sample-wise aligned to the mouse (GRCm38.p6; GCA_000001635.8) reference genome.
Mapping and subsequent filtering of 3’ UTR mapped reads was performed with slamdunk (v0.4.3) (Neumann et al., 2019). 3’ UTR regions were assembled as described previously (Muhar et al., 2018).
Aligned and filtered reads were deduplicated with umi-tools (v1.0.0) (Smith et al., 2017), based on the mapping coordinate and the UMI attached to the read name, prior to quantifying read abundances within 3’ UTR regions using featureCounts (v2.0.1) (Liao et al., 2014).
Differential expression analysis was performed with DESeq2 (v1.30.1) (Love et al., 2014).
genome build: GRCm38
processed data files format and content: tab-delimited text files include abundance measurements as normalized count values for each Sample ...
For standard murine RNA-seq data, reads were processed using the Nextflow based nf-core/rna-seq pipeline (Ewels et al., 2020) using Illumina’s mouse iGenome (GRCm38) as reference and “reverse” as input parameter for strandedness. Default parameters were kept for each processing step.
Read trimming with trimgalore (v0.6.6)
Alignment and quantification with STAR (v2.6.1d) (Dobin et al., 2013) and salmon (v1.4.0) (Patro et al., 2017)
Differential expression analysis with DESeq2 (v1.28.0) (Love et al., 2014).
genome build: GRCm38
processed data files format and content: tab-delimited text files include abundance measurements as normalized count values for each Sample ...

source_name: Bone marrow

growth_protocol: Cell culture was maintained at 37ºC with 5% CO2, cells cultivated in RPMI 1640 (Gibco) supplemented with l-glutamine (4 mM, Gibco), sodium pyruvate (1 mM, Sigma-Aldrich), penicillin-streptomycin (100 U/ml & 100 µg/ml, Sigma-Aldrich) and 10% FBS (Gibco)

extract_protocol:
sorted IRFP670+/shRNA +  GFP/ERG expressing cells
Facility (RNA/Lexogen, Quant-seq), stranded

treatment_protocol: cells were co-transduced with a Dox-responsive shRNA expression vector and ERG expression vector, treated for 5 days with Dox (0.5 ug/ml) to induce shRNA expression.

tag: source

value: in vitro cultured leukemia cells

value: DOX-induced induction of  shEVI1.2568 (5 days) in the presence of ectopic ERG expression


title: db_mouse_4

type: RNA

city: Waurn Ponds

first: Sean

last: McGee

state: VIC

address: 75 Pigdons Rd

country: Australia

institute: Deakin University

description: Mouse 7

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately and scanned.

scan_protocol: Slides were scanned immediately after washing using the GenePix 4000B scanner (Molecular Devices) using one color scan setting for 1x44k array slides. Scan resolution was 5µm, Dye channel was set to Green and the laser set at 100% while the PMT was individually adjusted for each array to avoid excessive over saturation of individual features.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Protocol GE1-v5_95_Feb07 and Grid: 014868_D_F_20060807 was used as the base design file with manual adjustment to correct for misaligned grid. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Each microarray was normalised to the 75th percentile of Signal. Distribution calculated after exclusion of non-control features and features that met the following criteria: gProcSig/gProcSigErr > 2, GNumSatPix < 50, glsWellAboveBG =1. The resultant normalised values were then used to create the dataset and used for subsequent analysis.

label: biotin

source_name: Soleus skeletal muscle

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were quantified using with the Agilent 2100 bioanalyzer.

growth_protocol: Mouse C2C12 myoblasts (ATCC) expressing pIRES neo3 HDAC4 (wild-type, human) and pIRES hyg3 HDAC5 (wild-type, human) or empty plasmids were produced by transfection of plasmids with Lipofectamine LTX and PLUS reagent (Life Technologies). Stable expression was achieved by multiple rounds of antibiotic selection (500ug/mL Hygromycin B and 500ug/mL Geneticin; Invitrogen). Cells were maintained in growth media consisting of MEM alpha (1g/L glucose; Invitrogen), 10% foetal bovine serum (FBS; In Vitro Technologies) and antibiotic-antimycotic (100units/mL penicillin, 100µg/mL streptomycin and 0.25µg/mL Amphotericin B; Life Technologies), with the addition of selection antibiotics, at 37°C in 10% CO2. Male db/db mice (C57BL6J db +/+) and heterozygous littermates (control, db -/+) were were group housed with a 12hr light/dark cycle, temperature 21± 3°C, humidity: 30-70%. Animals had ad libitum access to standard rodent chow and water.

extract_protocol: Total RNA was extracted from C2C12 myoblasts using RNeasy spin columns (Qiagen). Total RNA was extracted from soleus muscle using Trizol and RNeasy spin columns (Qiagen). RNA quality and quantity was determined using an Agilent Bioanalyser and RNA 600 Nano Assay kit (Agilent).

treatment_protocol: Cells were seeded into 6-well plates and were harvested 48 hr later at ~80% confluency.  At 12 weeks of age, mice were fasted for 5 hr prior to humane killing by cervical dislocation for rapid excision of tissues, which were snap frozen in liquid nitrogen.

value: Soleus skeletal muscle

tag: plasmid

tag: antibiotic resistance

value: male

value: 12 weeks


title: 192 hr (8 d) rep 5


title: Macrophage #1 Old

description:
Single-cell RNA-seq
mRNA

value: Skeletal muscle macrophages


title: Cultured murine RUNX1/EVI1 leukemia cells - ERG + shEVI1.2658 - Replicate 2

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D), ERG + shEVI1.2568 (Day5 ON DOX) - Replicate 2


title: 181_SN_

source_name: Prostate Stroma from RP


title: Macrophage #1 Young

description:
Single-cell RNA-seq
mRNA

value: 3 months


title: 182_ST_

value: No


title: db_mouse_2

description: Mouse 5


title: 6 hr rep 8

value: 6 hr


title: 181_ST_


title: db_mouse_3

description: Mouse 6


title: Cultured murine RUNX1/EVI1 leukemia cells - ERG + shEVI1.2658 - Replicate 1

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D), ERG + shEVI1.2568 (Day5 ON DOX) - Replicate 1


title: 192 hr (8 d) rep 8


title: Cultured murine RUNX1/EVI1 leukemia cells - ERG + shRen.713 - Replicate 3

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D), ERG + shRen.713 (Day5 ON DOX) - Replicate 3

value: DOX-induced induction of  shRen.713 ctrl (5 days) in the presence of ectopic ERG expression


title: 180_ST_


title: db_mouse_1

description: Mouse 4


title: Con_mouse_3

description: Mouse 3


title: Con_mouse_1

description: Mouse 1


title: Cultured murine RUNX1/EVI1 leukemia cells - ERG + shRen.713 - Replicate 2

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D), ERG + shRen.713 (Day5 ON DOX) - Replicate 2


title: Con_mouse_2

description: Mouse 2


title: 183_ST_


title: 6 hr rep 5


title: 179_ST_


title: 6 hr rep 6


title: HDAC4&5_6

description: Cell 12

source_name: C2C12 myoblasts

value: C2C12 myoblasts

value: HDAC4 and HDAC5

value: Hygromycin and geneticin


title: HDAC4&5_5

description: Cell 11


title: 6 hr rep 1

value: L1 larvae


title: 4 hr rep 8

value: 4 hr


title: Cultured murine RUNX1/EVI1 leukemia cells - empty vector + shEVI1.2658 - Replicate 3

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D) - empty vector + shEVI1.2568 (Day5 ON DOX) - Replicate 3

extract_protocol:
sorted IRFP670+/shRNA +  GFP/emptyvector expressing cells
Facility (RNA/Lexogen, Quant-seq), stranded

treatment_protocol: cells were co-transduced with a Dox-responsive shRNA expression vector and empty control vector, treated for 5 days with Dox (0.5 ug/ml) to induce shRNA expression.

value: DOX-induced induction of  shEVI1.2568 (5 days) in the presence of ectopic empty vector expression


title: 178_ST_GS4

value: Non-Cribriform

value: Yes


title: Cultured murine RUNX1/EVI1 leukemia cells - ERG + shRen.713 - Replicate 1

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D), ERG + shRen.713 (Day5 ON DOX) - Replicate 1

value: in vitro cultured leukemia cells


title: pPIN2::TRH1-YFP root tips rep3

city: Athens

first: Stamatis

last: Rigas

state: Attiki

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

data_processing:
Raw reads were filtered into clean reads and aligned to the Arabidopsis genome (TAIR10).
RNA-seq data were analyzed using SOAPnuke (version v.1.5.2) with parameters ‘‘-l 20 -q 0.4 -n 0.1 –Q2’’ and the HISAT2 pipeline (version 2.0.4) with parameters ‘‘–phred64 –sensitive –no-discordant –no-mixed -I 1 -X 1000’’.
Clean reads were mapped to reference with Bowtie2 (version v2.2.5).
Gene expression level was calculated with RSEM with default parameters.
Analysis of differential gene expression was performed with DEseq2 with parameters ‘‘Fold Change ≥ 2.00 and Adjusted Pvalue ≤ 0.05’’
Genome_build: Arabidopsis genome reference (TAIR10)
Supplementary_files_format_and_content: Excel files with gene expression values and log2FoldChange between samples as generated by DEseq2

organism: Arabidopsis thaliana

source_name: Arabidopsis 1mm root tips

growth_protocol: Arabidopsis thaliana seeds were surface-sterilized and sown in 120×120 mm2 Petri dishes containing 0.5×Murashige and Skoog (MS) medium (Duchefa, Haarlem, the Netherlands), pH 5.7, supplemented with 1% sucrose and solidified with 0.4% phytagel (Sigma, Gillingham, UK). After 48h of stratification at 4oC, seedlings were positioned to grow vertically for 2–6 days after germination at 22oC in a Fitotron (Weiss Gallenkamp, Loughborough, UK) growth chamber under a long-day photoperiod with 16h of light and 8h of darkness per day and 100 μmol m−2s−1 light intensity.

extract_protocol:
~1 mm sections of root tips from trh1, pPIN1::TRH1-YFP and pPIN2::TRH1-YFP transgenic lines were collected for RNA-Seq analysis. Total RNA was extracted using the Direct-zol RNA Miniprep (Zymo research, Irvine CA, USA) kit with an on-column DNase treatment according to the manufacturer’s instructions. The quantity and integrity of RNA were assessed using a NanoDrop ND-1000 spectrophotometer (Thermo Fischer Scientific, Waltham, MA, USA) and agarose gel electrophoresis.
RNA-seq libraries were generated using the TruSeq Low Input kit according to the manufacturer’s instructions (Illumina).
Sequencing was performed on BGISEQ-500 platform instrument at BGI (Beijing Genomics Institute) in three biological replicates for each sample.

value: 1mm root tips


title: HDAC4&5_4

description: Cell 10


title: Cultured murine RUNX1/EVI1 leukemia cells - empty vector + shEVI1.2658 - Replicate 2

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D) - empty vector + shEVI1.2568 (Day5 ON DOX) - Replicate 2


title: HDAC4&5_3

description: Cell 9


title: 4 hr rep 6


title: pPIN2::TRH1-YFP root tips rep2


title: HDAC4&5_2

description: Cell 8


title: Cultured murine RUNX1/EVI1 leukemia cells - empty vector + shEVI1.2658 - Replicate 1

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D) - empty vector + shEVI1.2568 (Day5 ON DOX) - Replicate 1


title: pPIN2::TRH1-YFP root tips rep1


title: 4 hr rep 1


title: 96 hr (4 d) rep 8

value: 96 hr


title: Cultured murine RUNX1/EVI1 leukemia cells - empty vector + shRen.713 - Replicate 2

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D) - empty vector + shRen.713 (Day5 ON DOX) - Replicate 2

value: DOX-induced induction of  shRen.713 ctrl (5 days) in the presence of ectopic empty vector expression


title: pPIN1::TRH1-YFP root tips rep3


title: pPIN1::TRH1-YFP root tips rep1


title: pPIN1::TRH1-YFP root tips rep2


title: 96 hr (4 d) rep 6


title: 96 hr (4 d) rep 5


title: trh1 root tips rep3


title: 96 hr (4 d) rep 1


title: Cultured murine RUNX1/EVI1 leukemia cells - shEVI1.2658 - Replicate 3

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D) - shEVI1.2568 (Day3 ON DOX)- Replicate 3

extract_protocol:
sorrted GFP+/shRNA expressing cells
Facility (RNA/Lexogen, Quant-seq), stranded

treatment_protocol: cells treated with Dox (0.5 ug/ml) for 3 days to induce shRNA expression

value: DOX-induced induction of shEVI1.2568 (3 days)


title: WT_6

description: Cell 6

value: Empty


title: WT_3

description: Cell 3


title: WT_4

description: Cell 4


title: Cultured murine RUNX1/EVI1 leukemia cells - shEVI1.2658 - Replicate 2

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D) - shEVI1.2568 (Day3 ON DOX)- Replicate 2


title: WT_5

description: Cell 5


title: 2 hr rep 8

value: 2 hr


title: trh1 root tips rep2


title: Cultured murine RUNX1/EVI1 leukemia cells - shEVI1.2658 - Replicate 1

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D) - shEVI1.2568 (Day3 ON DOX)- Replicate 1


title: 4 hr rep 5


title: Cultured murine RUNX1/EVI1 leukemia cells - empty vector + shRen.713 - Replicate 1

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D) - empty vector + shRen.713 (Day5 ON DOX) - Replicate 1


title: trh1 root tips rep1


title: Cultured murine RUNX1/EVI1 leukemia cells - empty vector + shRen.713 - Replicate 3

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D) - empty vector + shRen.713 (Day5 ON DOX) - Replicate 3


title: 2 hr rep 6


title: 2 hr rep 5


title: 2 hr rep 1


title: Cultured murine RUNX1/EVI1 leukemia cells - shRen.713 - Replicate 3

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D) - shRen.713 (Day3 ON DOX)- Replicate 3

value: DOX-induced induction of shRen713 (3 days)


title: 7

city: Chongqing

first: Jin

last: Wu

state: 重庆

address: Gaotanyan Street

institute: Army Medical University

description:
human breast cancer
human Luminal breast cancer cell line
Processed data file is on GSM5934178

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Transcript abundance was calculated using STRINGTIE
Differential expression analysis was performed using DESeq2
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Human breast cancer cell lines MCF-7 (luminal breast cancer), SKBR3 (HER2+ breast cancer) and MDA-MB-231 (triple negative breast cancer) were purchased from ATCC. All cell lines were authenticated by profiling of short tandem repeat analysis. MCF-7 was cultured in DMEM (Gibco, USA) supplemented with 10% fetal bovine serum (FBS, Gibco, USA), penicillin (100 U/mL, Gibco, USA) and streptomycin (100 μg/mL, Gibco, USA). SKBR3 were cultured in McCoy’s 5A medium (McCoy's 5A, Gibco, USA) with 10% FBS, penicillin (100 U/mL, Gibco, USA) and streptomycin (100 μg/mL, Gibco, USA). MDA-MB-231 were cultured in Leibovitz's L-15 medium with 10% FBS, penicillin (100 U/mL, Gibco, USA) and streptomycin (100 μg/mL, Gibco, USA). Cells were incubated in a humidified atmosphere containing 5% CO2 at 37 °C and checked regularly for mycoplasma infection.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Performed by Sangon Biotech Co., Ltd. (Shanghai, China) in accordance with standard Illumina protocols.

treatment_protocol: The epirubicin-resistant variants of MCF-7,SKBR3 or MDA-MA-231 cells were generated by pulse selection. Cells were exposed to respective the ninety percent maximal inhibitory concentration (IC90) value of epirubicin  for 4 h, once a week for 10 weeks.

tag: cell line

value: untreated

value: human Luminal breast cancer cell line


title: Cultured murine RUNX1/EVI1 leukemia cells - shRen.713 - Replicate 2

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D) - shRen.713 (Day3 ON DOX)- Replicate 2


title: D

description:
human breast cancer
epirubicin-resistant human HER2+ breast cancer cell line

value: The epirubicin-resistant variants of SKBR3 cells were generated by pulse selection. Cells were exposed to respective the ninety percent maximal inhibitory concentration (IC90) value of epirubicin  for 4 h, once a week for 10 weeks.


title: C

description:
human breast cancer
human HER2+ breast cancer cell line
Processed data file is on GSM5934176

value: human HER2+ breast cancer cell line


title: HDAC4&5_1

description: Cell 7

value: C2C12 myoblasts

value: HDAC4 and HDAC5

value: Hygromycin and geneticin


title: KO 5

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

institute: Monash University

data_processing:
The libraries were aligned to the GRCm38/mm10 genome using Rsubread_2.2.6; only uniquely mapped read-pairs were allowed. The mapped read-pairs in each library were assigned to the NCBI RefSeq gene annotation for mm10 (build 38.1) by using featureCounts.
Genes were excluded from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in at least 5 libraries. Counts were quantile normalized, precision weighted with the “voom” function of the limma package and converted to log2 counts per kilobase per million(log2 FKPM).
A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.05 or less.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file, Supp_Raw_Counts.txt, includes raw read counts for genes in all the libraries.

source_name: Liver tumor (pancreatic cancer origin)

extract_protocol:
KPC tumors from livers of WT and HCK knock-out mice were removed and flash frozen on dry ice. RNA extraction on tumor samples was performed using the RN-easy Mini Plus kit (Qiagen).
RNA was submitted to the Australian Genome Research Facility (AGRF) for sequencing on the Illumina NovaSeq 6000 platform with v1 200 cycle chemistry (100 bp paired-end). The Illumina TruSeq Stranded Total RNA Library Prep workflow with Ribo-Zero Gold was used to process the samples as per the manufacturer’s instructions.

value: HCK knock-out (KO)

tag: tissue

value: Liver tumor (pancreatic cancer origin)

tag: time point

value: 3 weeks after intrasplenic tumor cell injection


title: Wapl delta; Nipbl delta, rep6 [CT22]

city: Bethesda

first: Apratim

last: Mitra

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

institute: NICHD

data_processing:
Reads were trimmed to remove adapters using cutAdapt v2.4 and mapped to the mouse genome mm10 (GRCm38.p6) using STAR v2.5.3a.
The mapped reads were then counted using the featureCounts command of subread v1.6.4.
Sequencing and alignment quality was assessed using MultiQC v1.9.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts; The first column (Geneid) contains ENSEMBL IDs, the second column (gene_name) contains gene symbols. The remaining columns contain individual samples.

organism: Mus

source_name: whole brain

extract_protocol:
Total RNA was extracted from snap-frozen, whole brain tissue of female, E17.5 embryos using Tri-Pure isolation reagent (Sigma-Aldrich 11667165001) and Qiagen RNeasy Micro kit (Qiagen 74004)with on-column DNase I treatment (Qiagen 74004). Thermo Fisher NANODROP 2000c was used to evaluate purity and yield, and RNAs were stored at -70°C. Samples with RNA integrity numbers > 9.0 as determined using an Agilent BioAnalyzer were purified by oligo-d(T).
Libraries were prepared using RNA Sample Prep V2 kit (Illumina) and sequenced on an Illumina HiSeq2500 platform to generate 101 bp paired-end reads.

value: female

value: whole brain

value: Wapl +/delta; Nipbl +/delta


title: 48 hr (2 d) rep 8

tag: developmental stage

value: L1 larvae

tag: time point (hours)

value: 48 hr


title: B

description:
human breast cancer
epirubicin-resistant human triple negative breast cancer cell line

value: The epirubicin-resistant variants of MDA-MB-231 cells were generated by pulse selection. Cells were exposed to respective the ninety percent maximal inhibitory concentration (IC90) value of epirubicin  for 4 h, once a week for 10 weeks.


title: 48 hr (2 d) rep 6


title: WT_2

description: Cell 2

value: Empty


title: A

description:
human breast cancer
human triple negative breast cancer cell line
Processed data file is on GSM5934174

value: untreated


title: Wapl delta; Nipbl delta, rep5 [CT21]


title: Cultured murine RUNX1/EVI1 leukemia cells - shRen.713 - Replicate 1

description: Quant-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D) - shRen.713 (Day3 ON DOX)- Replicate 1

value: in vitro cultured leukemia cells

value: DOX-induced induction of shRen713 (3 days)


title: 7C

description:
human breast cancer
epirubicin-resistant human Luminal breast cancer cell line

value: The epirubicin-resistant variants of MCF-7 cells were generated by pulse selection. Cells were exposed to respective the ninety percent maximal inhibitory concentration (IC90) value of epirubicin  for 4 h, once a week for 10 weeks.


title: A549_Glu5.5

city: Taipei

first: Ting-Jing

last: Shen

address: 10F, No. 250, Wu-Xing Street

country: Taiwan

institute: Taipei Medical University

description: Gene expression data of A5.5

hyb_protocol: Samples were hybridized with Clariom™ S Array human (Affymetrix) and scanned at the NHRI Microarray Core Facility.

scan_protocol: GeneChips were scanned using GeneChip scanner 3000 7G (Affymatrix), GeneChip® Command Console® Software.

data_processing: The data were analyzed using Affymetrix Expression Console™ Software (version 1.4) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options.

source_name: ATCC

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: A549 cells were maintained in DMEM containing  5.5 mM glucose, 10% heat-inactivated FBS (Biological Industries), 1% Penicillin-Streptomycin and 1% sodium pyruvate at 37°C in 5% CO2.

extract_protocol: RNA was extracted by TriZol reagent according to manufacturer's instructions. One microgram of RNA from each sample was processed with the QIAGEN miRNeasy mini kit (QIAGEN, Hilden, Germany).

treatment_protocol: A549 cells were treated with for DMEM containing 5.5 or 25 mM and then collected at 48 hours post-stimulation

value: lung epithelial cells

tag: agent

value: 5.5 mM glucose


title: KO 3


title: 48 hr (2 d) rep 5


title: Wapl delta; Nipbl delta, rep4 [CT20]

value: Wapl delta/+; Nipbl +/delta


title: Wapl delta; Nipbl delta, rep3 [CT19]


title: PANC-1 cell line shHDAC5 #3 (arachidonic acid metabolism)

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

description: PANC-1 cell line shHDAC5 #3

data_processing:
Basecalls performed using Hisat2 v2.0.5
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the hg19.featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg19
Supplementary_files_format_and_content: text file include gene name, position,log2(Fold_change),p-value,q-value for each Sample
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read-counts and FPKM values for each Sample.

source_name: PANC-1 cells

extract_protocol:
RNA was harvested using Trizol reagent(Life Technologies). Illumina NEB Ultra directional RNA library Prep Kit was used with 1 ug of total RNA for the construction sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First   Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.


title: WT_1

description: Cell 1

value: C2C12 myoblasts

value: Hygromycin and geneticin


title: Wapl delta; Nipbl delta, rep2 [CT18]


title: PANC-1 cell line shHDAC5 #2 (arachidonic acid metabolism)

description: PANC-1 cell line shHDAC5 #2


title: 48 hr (2 d) rep 1


title: 24 hr (1 d) rep 8

value: 24 hr


title: PANC-1 cell line shHDAC5 #1 (arachidonic acid metabolism)

description: PANC-1 cell line shHDAC5 #1


title: A549_Glu25

description: Gene expression data of A25

value: 25 mM glucose


title: Wapl delta; Nipbl delta, rep1 [CT17]

value: female

value: whole brain


title: WT 5

value: Wild-type (WT)

value: Liver tumor (pancreatic cancer origin)

value: 3 weeks after intrasplenic tumor cell injection


title: PANC-1 cell line shControl #3 (arachidonic acid metabolism)

description: PANC-1 cell line shControl #3

value: shControl


title: PANC-1 cell line shControl #2 (arachidonic acid metabolism)

description: PANC-1 cell line shControl #2


title: PANC-1 cell line shControl #1 (arachidonic acid metabolism)

description: PANC-1 cell line shControl #1


title: Nipbl delta, rep1 [CT13]

value: Wapl +/+; Nipbl +/delta


title: WT 2


title: Nipbl delta, rep3 [CT15]


title: KO 4

value: HCK knock-out (KO)


title: WT 4


title: WT 1


title: 24 hr (1 d) rep 1

value: L1 larvae


title: Nipbl delta, rep2 [CT14]


title: 12 hr rep 8

value: 12 hr


title: KO 2


title: WT 3


title: 786-O cell line sh-CBX7 #2

data_processing:
Basecalls performed using Hisat2 v2.0.5
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the hg19.featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg19
Supplementary_files_format_and_content: text file include gene name, position,log2(Fold_change),p-value,q-value for each Sample
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read-counts values for each Sample.

source_name: 786-O cell line sh-CBX7

value: renal cancer cell line


title: male_distal sciatic_nerve part_rep_3

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

description: 24 h post surgery

data_processing:
FASTQ files were filtered to remove low-quality bases, TruSeq dual-index adapter sequences, and unpaired reads using Trimmomatic (Version 0.39)
Transcript-level quantification was performed using Salmon (Version 1.5.2) in quasi-mapping mode using the Gencode mouse genome. To correct for systematic biases commonly present in RNA-seq data, both -seqBias and -gcBias features were used.
RNA-seq quantification data quality was assessed using MultiQC (Version 1.9).
Genome_build: GENCODE M27 (05.05.21)
Supplementary_files_format_and_content: Salmon quant.sf format consisting Entrez IDs, Length, EffectiveLength, abundance measurements (TPM) and number of reads mapping to each transcript (NumReads)

source_name: left sciatic nerve, distal part

growth_protocol: Female and male C57BL6/J mice (6-8 weeks old, Jackson Labs) were randomly assigned to groups (n =6/group). The mice were housed in a temperature-controlled room (∼22 °C), on a 12-h light/dark cycle, and free access to food and water.

extract_protocol:
Tissues were submerged in 500 µl RNAlater Stabilization Solution to preserve RNA integrity, placed at 4C overnight, then transferred for storage at -20C.
RNA purification. Tissues from 2 animals were pooled to obtain at least 500 ng of total RNAs. Tissues were transferred in Trizol solution and disrupted by mechanical homogenization. Total RNAs were purified using RNeasy RNA purification reagents. RNA concentrations and quality were determined using Nanodrop absorbance ratios at 260/280nm and 260/230nm. RNA integrity was determined using Agilent Bioanalyzer Nano RNA chip. 500 ng of total RNA samples (3 replicates/group) with RIN≥7.0 were used for RNA-seq.
RNA-seq. mRNA libraries were generated following TruSeq Stranded mRNA library preparation protocol (Illumina). In brief, the Poly-A enriched mRNAs were purified using poly-T oligo coupled magnetic beads, followed by mRNA fragmentation, first and second strands synthesis, cleaning on AMPure XP beads, and 3’-adenylation. Barcoded libraries were constructed by ligation of TruSeq dual-index adapters. The quality of RNAseq libraries was validated using qPCR. Libraries were sized on Agilent Bioanalyzer DNA high sensitivity chip and normalized. RNA-seq was performed using the paired-end 100 cycle program on the NovaSeq 6000 system
Sequencing was conducted until at least 50 million paired-end reads per sample were acquired. Base calls were recorded and converted to FASTQ files containing sequencing reads and the corresponding quality scores using Illumina software.

treatment_protocol: All procedures were conducted between 8 and 12 daytime. Under isoflurane anesthesia, the left sciatic nerve was exposed at the mid-thigh level using sterile surgical scissors without transection (sham). The muscle was then sutured, and the skin stapled. At 24 h after surgery, sciatic nerves were collected for RNA isolation. All animal procedures were performed in agreement with the Policy on Humane Care and Use of Laboratory Animals and the protocol approved by the Institutional Animal Care and Use Committee at the VA San Diego Healthcare System.

value: male

value: axotomy


title: 12 hr rep 6


title: 24 hr (1 d) rep 5


title: Wapl delta, rep5 [CT10]

value: Wapl +/delta; Nipbl +/+


title: 12 hr rep 5


title: 12 hr rep1


title: 786-O cell line sh-CBX7 #3


title: 288 hr  (12 d) rep 8


title: Wapl delta, rep7 [CT12]


title: Wapl delta, rep6 [CT11]


title: KO 1


title: 786-O cell line sh-CBX7 #1


title: Wapl delta, rep3 [CT8]


title: 786-O cell line sh-Control #3

source_name: 786-O cell line sh-Control

value: sh-Control


title: Wapl delta, rep4 [CT9]


title: male_distal sciatic_nerve part_rep_2

description: 24 h post surgery


title: male_distal sciatic_nerve part_rep_1

description: 24 h post surgery


title: 786-O cell line sh-Control #2


title: 786-O cell line sh-Control #1


title: 288 hr (12 d) rep 6

source_name: L1 larvae


title: Wapl delta, rep2 [CT7]

value: Wapl delta/+; Nipbl +/+


title: 24 hr (1 d) rep 6

value: 24 hr


title: female_distal sciatic_nerve part_rep_3

description: 24 h post surgery

value: female


title: female_distal sciatic_nerve part_rep_2

description: 24 h post surgery


title: Wapl delta, rep1 [CT6]

value: whole brain


title: cultured mouse embryonic dermal LEC, Dot1l overexpression

city: Seoul

first: Kwonho

last: Hong

address: 120 Neungdong

institute: Konkuk university

data_processing:
Adapter sequences in the raw reads were trimmed with skewer (v0.2.2) with –L 75 and –e options specified.
The skewer output reads were aligned to the mm10 UCSC mouse reference genome using a STAR read aligner (v2.7.9a).
Quantification of the mapped reads was performed using VERSE (v0.1.5) with –S option.
Assembly: mm10
Supplementary files format and content: tab delimited text file of VERSE output of each sample

source_name: cultured mouse embryonic dermal LEC

growth_protocol: Cultured embryonic yolk sac BECs (CRL-2581, ATCC)  and cultured mouse embryonic dermal LECs (C57-6064L, Cell Biologics) and were used for viral transduction. Each cell line was maintained according to the manufacturer’s instructions.

extract_protocol: Total RNAs isolated from BECs and LECs were used to prepare an RNA-Seq library using the ScriptSeq v2 kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Dot1l overexpression vector with lentiviral packaging vectors [psPAX2 (cat. #12260, Addgene) and pMD2.G (cat. #12259, Addgene) vectors] were transfected into HEK293T cells to produce lentiviral particles. Once ECs reached approximately 50% confluence, viral particles were added to BECs and LECs for Dot1l overexpression. Control ECs were transduced with empty lentivirus.

value: cultured mouse embryonic dermal LEC

value: LEC

value: Dot1l OE


title: female_distal sciatic_nerve part_rep_1

description: 24 h post surgery


title: cultured mouse embryonic dermal LEC

value: wild type


title: 0 hr rep 8

value: 0 hr


title: 288 hr (12 d) rep 1


title: cultured mouse embryonic yolk sac BEC, Dot1l overexpression

source_name: cultured mouse embryonic yolk sac BEC

value: cultured mouse embryonic yolk sac BEC

value: BEC


title: 0 hr rep 6

value: L1 larvae


title: Trx2 KO

city: West Haven

first: Francesc

last: Lopez

department: Department of Genetics

institute: Yale University

description: Trx2 KO

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to mm10 mouse genome by Cellranger (v3.0.2).
The cell ranger output was processed in R using Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Read count matrix was formated by mtx. Barcodes and genes were provided by tsv format. Metadata file was provided as tab-separated format. Average expression per cluster was provided in Excel format (Cluster_averages_expression_SCT.xlsx).

source_name: Retina endothelial cells

extract_protocol: Chromium™ Single Cell 3’ Reagent Kits

treatment_protocol: Endothelial cell-specific deletion of the nuclear genes encoded mitocondrial proteins

tag: strain background

value: Retina endothelial cells

tag: genotype/variation

value: Trx2 KO


title: cultured mouse embryonic yolk sac BEC


title: WT, rep3 [CT3]

value: Wapl +/+; Nipbl +/+


title: 0 hr rep 5

extract_protocol:
RNA was extracted using TRIzol Reagent (Thermo-Fisher Scientific) using the manufacturer’s protocol with some exceptions. 100 mL of sand (Sigma-Aldrich) was included to aid homogenization. Sand was first prepared by washing two times in 1 M HCl, washed eight times in RNAse-free water (to a neutral pH), and baked to dry.
Libraries were prepared for sequencing using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, E7530) with 100 ng of starting RNA per library and 14 cycles of PCR. Libraries were sequenced using Illumina HiSeq 4000.

tag: strain


title: Tfam KO

description: Tfam KO

value: Tfam KO


title: E15.5 mouse skin BEC, Dot1l knock-out

source_name: E15.5 mouse skin

value: E15.5 mouse skin

value: Dot1l KO


title: WT, rep2 [CT2]

tag: age


title: 0 hr rep 1


title: 288 hr 12 d) rep 5


title: WT

description: WT

tag: cell type

value: WT


title: WT, rep1 [CT1]

value: female

tag: genotype


title: E15.5 mouse skin BEC


title: WT, rep5 [CT5]

value: whole brain


title: Cox10 KO

description: Cox10 KO

value: Cox10 KO


title: WT, rep4 [CT4]


title: cHL biopsy, 28R

status: Public on Oct 10 2022

city: TOULOUSE

first: Pauline

last: Gravelle

address: 1 Avenue Irène Joliot Curie

department: Anatomy-Pathology

institute: IUCT-ONCOPOLE

hyb_protocol: In brief, 5 μL of each sample were mixed with 8 μL of the hybridization cocktail (4 μL of the reporter codeset and 4 μL of hybridization buffer).Two μL of the capture codeset were added; the solution was mixed and spun down. It was then hybridized in a 65°C thermocycler (Veriti Thermal Cycler, Applied Biosystems, Foster City, CA, USA) for 16 hours.

scan_protocol: Hybridized samples were analyzed on the nCounter NanoString Preparation Station us-ing the high-sensitivity protocol, whereby excess capture and reporter probes were washed away and ternary target probe complexes were immobilized on a streptavidin-coated cartridge. Samples were scanned at maximum resolution on the nCounter Dig-ital Analyzer (NanoString Technologies, Seattle, WA).

data_processing:
Data were analyzed using ROSALIND® (https://rosalind.onramp.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, identity heatmaps, and sample Multidimensional Scaling (MDS) plots were generated as part of the QC step. Housekeeping probes used for normalization were se-lected based on the geNorm algorithm as implemented in the NormqPCR R library. Fold changes and p-values were calculated using nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment was performed using the Benjamini-Hochberg method of es-timating false discovery rates (FDR). Hypergeometric distribution was used to analyze the enrichment of pathways. The topGO R library was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including REACTOME. Further analyzes were performed and figures were generated with Graphpad Prism 9.0.0 and R v3.6.3, using Rstudio v1.2.5033. Hierarchical clustering and heatmaps were generated with the pheatmap package. Volcano plots were obtained using the EnhancedVolcano package. Lastly, the correlation matrix was created with the corrplot package.
normalized count after housekeeping genes normalization

label: biotin tag

source_name: lymph node

label_protocol: biotin tag

extract_protocol: RNA from each sample was extracted using the High Pure FFPET RNA Isolation Kit (Roche), following the manufacturer’s protocol. For each RNA extraction, the tumor con-tent was confirmed through histopathological evaluation performed by a certified pathologist. All 66 biological samples passed quantification and quality controls (QC) using the Agilent Bioanalyzer (BA) (2100 Bioanalyzer Instrument, Santa Clara, CA, USA).

tag: individual

value: patient 28

value: lymph node

tag: treatment

value: BEACOPP

value: EBVpos

tag: prognosis

value: relapse

tag: ann arbor stage


title: cHL biopsy, 29R

value: patient 29

value: ABVD


title: cHL biopsy, 19R2

value: patient 19

value: other

value: EBVneg


title: cHL biopsy, 3R

value: patient 3


title: cHL biopsy, 30R

value: patient 30


title: cHL biopsy, 7D

value: patient 7

value: DIAG


title: cHL biopsy, 13D

value: patient 13


title: cHL biopsy, 10D

value: patient 10


title: cHL biopsy, 10R


title: EyeBank_cultured_hCFs_monoculture_Exos_hCECs_rep1

city: Québec

first: Gaëtan

last: Le-Bel

state: Quebec

address: Local H2-00, Hôpital du Saint-Sacrement,1050 Chemin Sainte-Foy

institute: CUO-Recherche

description: Gene expression of hCFs cultivated in monoculture until they reached confluence with hCECs exosomes

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Data were analyzed using the ArrayStar V4.1 (DNASTAR, Madison, WI) software. All data generated from the array were also analyzed by RMA (Robust Multiarray Analysis) for background correction of the raw values. They were then transformed in log2 base and quantile normalized before a linear model was fitted to the normalized data in order to obtain an expression measure for each probe set.

source_name: Primary human corneal fibroblasts

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA (hCECs monoculture) or 100 ng RNA (hCECs from hTECs) using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions

growth_protocol: To isolate hCECs and hCFs, post-mortem corneas were incubated with dispase in HEPES buffer overnight at 4 °C to separate the epithelium from the stroma. The stroma was then cut into small pieces and incubated with collagenase H until the ECM was fully digested by the enzyme. hCECs were treated with trypsin for 15 min at 37 °C to separate the cells from each other. hCECs were grown in DH medium (Dulbecco–Vogt modification of Eagle's medium with Ham's F12 in a 3:1 ratio supplemented with 5% FetalClone II serum, 5 μg/mL of insulin, 0.4 μg/mL of hydrocortisone, 10 ng/mL of epidermal growth factor, 0.212 mg/mL of isoproterenol hydrochloride, antibiotics (100 IU/mL of penicillin, and 25 μg/mL of gentamycin) on lethally irradiated human fibroblasts feeder layers (iHFL) until they reached confluence. hCFs were grown in DME medium (Dulbecco–Vogt modification of Eagle's medium supplemented with 10% fetal calf serum and antibiotics). All cells were grown under 8% CO2 at 37°C and culture medium was changed every 2 or 3 days. To isolate hCEnCs, the Descemet membrane was carefully peeled off and incubated overnight in culture medium at 37°C. It was then digested with EDTA 0.02% buffered solution for 1 hour. Cells were detached by pipetting up and down with a flamed-polished pipette. hCEnCs were then seeded on fibronectin/collagen (FNC)-coated plastic culture dishes and grown until they reached confluence in a proliferation medium (Opti-MEM-I medium supplemented with 8% fetal bovine serum, 5 ng/ml epidermal growth factor, 0.08% chondroitin sulfate, 20 μg/mL ascorbic acid and 100 IU/mL of penicillin and 100 μg/mL of streptomycin). The culture medium was then replaced with a maturation medium (Opti-MEM-I medium supplemented with 8% fetal bovine serum and penicillin/streptomycin) when hCEnCs reached confluence, and were grown further for an additional 7 to 28 days.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Cat#74104)

treatment_protocol: 800-100 ug of exosomes were added to cell cultures for a incubation of 48h before harvesting cells. Vehicle alone (HBS) was used for controls.

tag: exosomes

value: hCECs exosomes

value: 26 days


title: EyeBank_cultured_hCFs_monoculture_Exos_hCFs_rep1

description: Gene expression of hCFs cultivated in monoculture until they reached confluence with hCFs exosomes

value: hCFS exosomes


title: EyeBank_cultured_hCEnCs_monoculture_Exos_hCEnCs_rep1

description: Gene expression of hCEnCs cultivated in monoculture until they reached confluence and maturation with hCECs exosomes

source_name: Primary human corneal endothelial cells

value: hCEnCs exosomes


title: EyeBank_cultured_hCEnCs_monoculture_Exos_hCFs_rep1

description: Gene expression of hCEnCs cultivated in monoculture until they reached confluence and maturation with hCFs exosomes


title: EyeBank_cultured_hCEnCs_monoculture_Exos_hCECs_rep1

description: Gene expression of hCEnCs cultivated in monoculture until they reached confluence and maturation with hCEnCs exosomes


title: cHL biopsy, 19D

value: lymph node


title: EyeBank_cultured_hCFs_monoculture_Exos_hCEnCs_rep1

description: Gene expression of hCFs cultivated in monoculture until they reached confluence with hCEnCs exosomes


title: EyeBank_cultured_hCFs_monoculture_CTRL_HBS_rep1

description: Gene expression of hCFs cultivated in monoculture until they reached confluence


title: EyeBank_cultured_hCECs_monoculture_Exos_hCFs_rep1

description: Gene expression of hCECs cultivated in monoculture until they reached near-confluence with hCFs exosomes

source_name: Primary human corneal epithelial cells


title: cHL biopsy, 12D

value: patient 12

value: relapse


title: cHL biopsy, 6R

value: patient 6

value: ABVD


title: EyeBank_cultured_hCEnCs_monoculture_CTRL_HBS_rep1

description: Gene expression of hCEnCs cultivated in monoculture until they reached confluence and maturation


title: EyeBank_cultured_hCECs_monoculture_Exos_hCEnCs_rep1

description: Gene expression of hCECs cultivated in monoculture until they reached near-confluence with hCEnCs exosomes


title: EyeBank_cultured_hCECs_monoculture_CTRL_HBS_rep1

description: Gene expression of hCECs cultivated in monoculture until they reached near-confluence


title: EyeBank_cultured_hCECs_monoculture_Exos_hCECs_rep1

description: Gene expression of hCECs cultivated in monoculture until they reached near-confluence with hCECs exosomes


title: cHL biopsy, 3D

value: BEACOPP


title: cHL biopsy, 23D

value: patient 23

value: EBVpos


title: cHL biopsy, 12R

value: EBVneg


title: cHL biopsy, 19R3

value: patient 19

value: other


title: cHL biopsy, 26R

value: patient 26


title: cHL biopsy, 24R

value: patient 24


title: cHL biopsy, 19R


title: cHL biopsy, 13R

value: patient 13


title: cHL biopsy, 18R

value: patient 18


title: cHL biopsy, 16R

value: patient 16


title: cHL biopsy, 8D

value: patient 8

value: DIAG


title: cHL biopsy, 4R

value: patient 4

value: lymph node


title: cHL biopsy, 27R

value: patient 27

value: relapse


title: cHL biopsy, 6D

value: patient 6

value: ABVD


title: cHL biopsy, 16D


title: cHL biopsy, 2R

value: patient 2


title: cHL biopsy, 20R

value: patient 20

value: EBVneg


title: cHL biopsy, 18D


title: cHL biopsy, 2D


title: cHL biopsy, 21R

value: patient 21


title: cHL biopsy, 1R

value: patient 1


title: cHL biopsy, 21D


title: cHL biopsy, 25R

value: patient 25


title: cHL biopsy, 17D

value: patient 17


title: cHL biopsy, 35D

value: patient 35

value: EBVpos


title: cHL biopsy, 8R

value: patient 8


title: cHL biopsy, 11D

value: patient 11

value: other

value: DIAG


title: cHL biopsy, 17R

value: lymph node


title: cHL biopsy, 22D

value: patient 22

value: relapse


title: cHL biopsy, 22R

value: ABVD


title: cHL biopsy, 41D

value: patient 41

value: BEACOPP


title: cHL biopsy, 42D

value: patient 42


title: cHL biopsy, 40D

value: patient 40

value: EBVneg


title: cHL biopsy, 34D

value: patient 34


title: cHL biopsy, 39D

value: patient 39


title: cHL biopsy, 31D

value: patient 31


title: cHL biopsy, 33D

value: patient 33


title: cHL biopsy, 38D

value: patient 38


title: cHL biopsy, 20D

value: patient 20


title: cHL biopsy, 4D

value: patient 4

value: other


title: cHL biopsy, 32D

value: patient 32

value: lymph node

value: DIAG


title: cHL biopsy, 37D

value: patient 37


title: cHL biopsy, 36D

value: patient 36

value: ABVD

value: EBVpos


title: cHL biopsy, 14R

value: patient 14

value: relapse


title: cHL biopsy, 5R

value: patient 5

value: BEACOPP

value: EBVneg


title: cHL biopsy, 5D


title: cHL biopsy, 11R

value: patient 11


title: cHL biopsy, 1D

value: patient 1


title: cHL biopsy, 9R

value: patient 9


title: CR012_Cambridge_HEK293_IgG

city: Lund

first: Ninoslav

last: Pandiloski

address: Sölvegatan 17

country: Sweden

institute: Lund University

library_source: genomic

data_processing:
library strategy: CUT&RUN-seq
Paired-end reads (2x150) were aligned to the hg38 genome using bowtie2 v. 2.3.4.2 (--local–very-sensitive-local --no-unal –no-mixed –no-discordant –phred33 -I 10 -X 700)
Reads were trimmed and de-duplicated with Picard (http://broadinstitute.github.io/picard/)
SAM files were converted to bam files with samtools (Langmead and Salzberg, 2012; Li et al., 2009). The BAM files were filtered according to alignment quality (MAPQ>10) using samtools (samtools view -bq 10 {BAM} > {FILTERED_BAM}) (Langmead and Salzberg, 2012; Li et al., 2009).
Normalized bigwig coverage tracks were made with bamCoverage (deepTools)  (Ramirez et al., 2014), with RPKM normalization.
Assembly: GRCh38
Supplementary files format and content: Bigwigs of filtered alignments for genome browser visualization, normalized with RPKM

molecule: genomic DNA

growth_protocol: 293 T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
CUT&RUN was done on 250,000 cells per condition following the protocol of Henikoff and colleagues (Skene et al, 2018). DNA was purified by the Nucleospin PCR clean-up kit (Macherey-Nagel). Antibodies were: rabbit anti-H3K9me3 (ab8898, 1:100 dilution) and guinea pig anti rabbit IgG (CSB-PA00150E1Gp, 1:100 dilution)
Illumina sequencing libraries were prepared using the Hyperprep kit (KAPA) with unique dual-indexed adapters (KAPA) following the manufacturer's instructions

treatment_protocol: Lentivirus for KAP1 complementation was produced by transfecting HEK23T cells in 6-well plates with 0.6 µg pMD2.G, 1.2 µg p8.91 and 1.2 µg KAP1 pHRSIN (WT or CCmut) using FuGENE 6 (Promega). Virus-containing supernatant was collected 48 h post-transfection, filtered through a 0.45 µm PVDF membrane and used to infect KAP1 KO HEK239T cells. Transduced cells were selected with 200 µg ml-1 hygromycin.

tag: cell line

value: Human embryonic kidney cells

value: WT

tag: antibody


title: CR012_Cambridge_Kap1KO_H3K9me3

value: rabbit anti-H3K9me3 (ab8898, 1:100 dilution)


title: CR012_Cambridge_HEK293_H3K9me3


title: cHL biopsy, 15R

value: patient 15

tag: tissue

value: lymph node


title: cHL biopsy, 15D

value: DIAG


title: CR012_Cambridge_WTcomp_H3K9me3

value: KO-WTcomplement


title: CR012_Cambridge_Kap1KO_IgG

value: guinea pig anti rabbit IgG (CSB-PA00150E1Gp, 1:100 dilution)


title: 4_ChIPseq_KO-WTcomp_rep2

data_processing:
Single-end reads (75nt) were aligned to the hg38 genome using bowtie2 v. 2.3.4.2(bowtie2 --phred33 --very-sensitive --no-unal --phred33 -I 10 -X 700 -U {FASTQ} -S {SAM})
The BAM files were filtered according to alignment quality (MAPQ>10) using samtools (samtools view -bq 10 {BAM} > {FILTERED_BAM}) (Langmead and Salzberg, 2012; Li et al., 2009).
ChIP-seq coverage plots were made with bamCoverage (deepTools)  (Ramirez et al., 2014), with RPKM normalization.
Assembly: GRCh38
Supplementary files format and content: Bigwigs of filtered alignments for genome browser visualization, normalized with RPKM

extract_protocol:
For each HEK293T cell sample, 107 cells grown in 10-cm plates were fixed for 15 min at room temperature with 1% formaldehyde, added directly to the DMEM media (GIBCO). The 10x formaldehyde stock solution was freshly prepared with molecular biology-grade reagents and contained 11% formaldehyde (Sigma-Aldrich, cat. no. F-8775), 50 mM HEPES pH 7.9, 0.1 M NaCl, and 1 mM EDTA. Fixation was quenched by adding 120 mM glycine (Sigma cat. no. G-7403) from a 20x stock solution and incubating for 5 min at room temperature. The cells were washed twice by centrifugation (800 g, 4˚C, 10 min) and resuspension in PBS, 0.5% IGEPAL CA-630 (Sigma-Aldrich, cat. no. I-8896), 0.1 mM phenylmethylsulfonyl fluoride (PMSF). Cell pellets were then frozen and shipped in dry ice to Active Motif for chromatin preparation, immunoprecipitation with anti-KAP1 antibody (Abcam cat. no. ab10483 RRID:AB_297222)
ChIP-Seq libraries were generated by Active Motif from the ChIP-DNA using a custom Illumina library type on an automated  system (Apollo 342, Wafergen Biosystems/Takara).

value: Human embryonic kidney cell

value: KO-WTcomp

tag: chip antibody


title: 6_ChIPseq_KO-CCmutComp_rep2

value: KO-CCmutComp

value: anti-KAP1 antibody (Abcam cat. no. ab10483 RRID:AB_297222)


title: 3_ChIPseq_KO-WTcomp_rep1


title: 5_ChIPseq_KO-CCmutComp_rep1


title: 0_ChIPseq_HEK293-Pooled_input


title: 2_ChIPseq_KAP1-KO_rep2


title: CR012_Cambridge_CCmutComp_H3K9me3

value: KO-CCmutant complement


title: cHL biopsy, 9D

value: ABVD

value: EBVpos

value: relapse


title: 1_ChIPseq_KAP1-KO_rep1