title: ATAC-seq MCF-7 DMSO

data_processing:
Nextera adapters (-a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT ) were removed from the fastq files using Atropos (v1.1.28) {Didion, 2017}
Trimmed reads were mapped to the human reference GRCh38 using BWA mem v0.7.17 {Li, 2009} with default settings
Aligned bam files were filtered with bamtools {Barnett, 2011} to remove a) reads with more than 4 mismatches b) reads that are not in FR orientation within 2kb on the same chromosome.
Peaks of open chromatin were identified using Genrich v0.6 {Gaspar, 2020} in ATAC-seq mode (-j) to adjust for Tn5 shift, using its internal PCR duplicate remover (-r), ignoring mitochondrial (-e chrM) and black-listed regions (-E).
The union of peaks between conditions was identified with bedtools v2.29.2 (merge -d 10) and reads in each peak were quantified with featureCounts (subRead v2.0.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cells were thawed quickly in a 37 °C rock bath and 900 μl of ice-cold PBS supplemented with Roche Complete Mini Protease inhibitor was added immediately. Cells were split into two 1.5-ml Eppendorf DNA lo-bind tubes to serve as technical replicates. Cells were centrifuged at 500g for 5 min at 4 °C, washed once in PBS with protease inhibitor, centrifuged at 500g for 5 min at 4 °C and supernatant was removed completely using two separate pipetting steps with extreme caution taken to avoid resuspension (for example, smooth and consistent aspiration). The transposition reaction consisted of 20-μL total volume of the following mixture (10 μl 2× TD Buffer, 1 or 0.5 μl TDEnzyme, 0.1 μl of 2% digitonin, 0.2 μl of 10% Tween 20, 0.2 μl of 10% NP40, 6.6 μl of 1× PBS and 2.3 μl of nuclease-free water).
Tagmented DNA was purified by QIAGEN MinElute Clean up Kit, PCR amplified and libraries were purified with 1.2X volume of AMPure XP beads. DNA bound to the beads was washed twice in 80% ethanol and eluted in 20 μl of water. Indexed fragments were checked in concentration by qPCR, profiled by Bioanalyzer, equimolarly pooled and sequenced on an Illumina Hi-Seq 4000 with 2 samples multiplexed per lane.


title: RNA-seq MCF7 5nM CPI-1612_rep1

status: Public on Mar 04 2022

type: SRA

city: Cambridge

first: David

last: Mayhew

state: MA

address: 500 Technology Square, Suite 700

country: USA

institute: Foghorn Therapeutics

description: RNAseq MCF7 cpi_1612_5nm-1

library_source: transcriptomic

data_processing:
Isoform expression of Ensembl transcripts (GRCh38 release 99) was calculated with Salmon version 0.11.3 {Patro, 2017}.
Gene-level counts were then imported into R using tximport {Soneson, 2015}
Differential expression analysis was performed with DESeq2 v1.30.0  {Love, 2014} to analyze for differences between conditions, and the set of differentially expressed genes were filtered only for the genes with a |fold-change| of 1.5 and a Benjamini-Hochberg FDR adjusted P values less than or equal to 0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene-level counts as a csv

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Cells were grown in DMEM + 10%FBS at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted after 3 days using TRIzol (Invitrogen).
RNA-Seq analysis was performed with polyA selection and standard library construction

treatment_protocol: Cells were treated with CPI-1612 and/or Fulvestrant for six hours.

tag: treatment

tag: cell line


title: A549_24h_ Hpx_rep1

city: Liverpool

first: Sonia

last: Rocha

address: Crown Street

country: United Kingdom

institute: University of Liverool

data_processing:
Reads in fastq files were trimmed for adaptors using Cutadapt and low quality score using Sickle. Reads were aligned to the human genome version hg38 (GRCh38, Ensembl) using and the resulting binary alignment mapped (bam) files were indexed using Samtools.
Read counts for each transcript (GRCh38, Ensembl) were generated using Subread (featureCounts)
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file with transcript count data

molecule: total RNA

growth_protocol: HeLa and A549 cells were maintained in DMEM supplemented with 10% v/v FBS, 2 mM L-glutamine, 50 units/mL penicillin and 50 μg/mL streptomycin at 5% CO2 and 37 °C. Cells were cultured for no more than 30 passages and routinely tested for mycoplasma contamination using MycoAlert Mycoplasma Detection Kit .

extract_protocol:
Qiagen RNeasy kit
Dual-indexed, strand specific RNA-seq libraries were generated using NEBNext polyA selection and Ultra Directional RNA library preparation kits

treatment_protocol: Cells were transfected with 27 nM of small interfering RNA (siRNA) oligonucleotides (Eurofins) for 48h using Interferin (Polyplus) transfection reagent according to manufacturer’s instructions. Hypoxia treatments were performed by incubating cells in an InvivO2 300 Hypoxia Workstation (Baker Ruskinn) at 1% O2, 5% CO2 and 37 °C.

value: 1percent oxygen (hypoxia)

tag: time point


title: A549_24h_ Hpx_rep3


title: A549_Control_rep3

value: Control

value: 0 h


title: A549_24h_ Hpx_rep2


title: A549_Control_rep2


title: A549_Control_rep1


title: HeLa_24h_ Hpx_rep2

source_name: HeLa

value: HeLa


title: RNA-seq MCF7 DMSO_rep1

description: RNAseq MCF7 dmso-1

value: DMSO


title: HeLa_24h_ Hpx_rep3


title: HeLa_24h_ Hpx_rep1


title: ATAC-seq MCF-7 50nM CPI-1612

library_source: genomic

molecule: genomic DNA

growth_protocol: MCF-7 cells were grown in DMEM + 10%FBS at 37°C and 5% CO2.

treatment_protocol: Cells were treated with 50 nM CPI-1612 or DMSO for six hours.


title: HeLa_1h_ Hpx_rep3

value: 1 h


title: HeLa_1h_ Hpx_rep2


title: HeLa_1h_ Hpx_rep1


title: HeLa_Control_rep3


title: HeLa_Control_rep2


title: HeLa_Control_rep1


title: MSC_2_EACTD, RNAseq

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

data_processing:
RNAseq reads were trimmed using Trimgalore version 0.6.4 . Trimmed reads were aligned on both the Human genome and transcriptome assembly Hg19 with STAR version 2.5.0a.
Transcript quantification was done using rsem version 1.3.0 . A matrix of the rsem counts is given as a supplementary file.
Genes were filtered based on the rule of 1 count per million (cpm) in at least 1 sample. Library sizes were scaled using TMM normalization and log-transformed with limma voom function. Normalized data was corrected for batch effect using removeBatchEffect function (limma). Unwanted variation was removed using RUVr (RUVseq package version 1.24.0)
Differential expression was computed on the log-transformed TMM-scaled values using limma by fitting a linear model on the selected samples. Batch and RUVr-computed factors were added in the design matrix.
Genome_build: hg19
Supplementary_files_format_and_content: CCS_project_RNAseq_counts_matrix.xlsx

source_name: Primary cell culture

growth_protocol: DTC1 and SUCCS1 were cultured in RPMI-1640 medium supplemented with 10% and 1% Pen/Strep as suspension cells in Ultra-low attachment flasks. HpMSCs were cultured in IMDM medium supplemented with 10%, 1% MEM NEAA, 1% Pen/Strep and 10 ng/ml PDGF-BB as adherent cells.

extract_protocol:
Total RNA was extracted with the Rneasy mini kit according to the manufacturer's instructions (Qiagen) and minimum 100ng used for library preparation.
Sequencing mRNA libraries were prepared using the TruSeq mRNA stranded kit (Illumina cat. no. 20020595) according to the manufacturer's instructions.

treatment_protocol: As indicated in the Characteristics "treatment" column above.

tag: cell type

value: Bone marrow derived pediatric MSCs

value: Infected with C-term V5-tagged EWSR1-ATF1

value: MSC


title: MSC_2_EANTD, RNAseq

value: Infected with N-term V5-tagged EWSR1-ATF1


title: MSC_2_pLIV, RNAseq

value: Infected with empty pLIV vector


title: CBTTC_5294

city: St. Petersburg

first: Rudrmani

last: Pokhrel

state: United States

address: 600 Fifth Street S.

department: Oncology

institute: Johns Hopkins All Children’s Hospital

data_processing:
Demultiplexing:  bcl2fastq v2.20
Filtering and QC: FastP v0.20.1
Mapping to Genome: STAR v2.4.2a
Gene Count Matrix:  featureCounts v2.0.1
Differential Analysis: DESeq2 v1.34.0
Genome_build: Human 38 (GRCh38.p13)
Supplementary_files_format_and_content: CSV file of 2D matrix of gene count vs samples

source_name: Cerebrospinal fluid

extract_protocol:
CSF (0.2 mL) was mixed with 1 ml of QIAzol (Qiagen, Hilden, Germany) and incubated for 5 min at room temperature. Next, 0.4 ml of chloroform was added and mixed. The aqueous phase was obtained by centrifugation at 14,000 x g for 15 min at 4°C, and RNAs were isolated using the miRNeasy Mini kit (Qiagen) according to the manufacturer’s protocol.
To perform library generation with the NuGen Ovation Solo system, the purified RNAs were concentrated using a RNA Clean & Concentrator (Zymo Research Corp), and libraries were prepared according to the manufacturer's instructions. The quantification of libraries was estimated using a KAPA library quantification kit (Roche Sequencing and Life Science, Wilmington, MA).

tag: disease

value: Medulloblastoma

tag: sub group

value: not available


title: Primary_AFH2, RNAseq

source_name: Primary tumor tissue

value: Untreated

tag: tissue

value: Angiomatoid fibrous histiocytoma


title: Chetan_8292


title: Primary_AFH1, RNAseq


title: CBTTC_4509


title: 5.FS2-shRras2

type: RNA

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

description: Rras2(Q72L) knockdown (sh#89) fibrosarcoma cells

hyb_protocol: Clariom S arrays (Affymetrix) under standard conditions

scan_protocol: Standard Affymetrix protocol

data_processing: Upon microarray hybridization, the raw data was normalized with RMA using R (v.3.6.3).

label: biotin

organism: Mus musculus

source_name: Fibrosarcoma (Rras2(Q72L))

label_protocol: Total RNA was quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA) and used (2.3 mg/sample) to generated labeled cRNA probes according to the manufacturer's instructions (Affymetrix).

growth_protocol: These cells were grown in DMEM supplemented with 10% fetal bovine serum, 1% L-glutamine, penicillin (10 μg/mL), and streptomycin (100 μg/mL)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Rras2(Q72L) fibrosarcoma cells were transduced with either pLKO or Rras2-directed shRNA vectors

tag: strain

tag: genotype

value: Fibrosarcoma


title: 6.FS2-shRras2


title: 3.FS2-pLKO

description: pLKO control of Rras2(Q72L) fibrosarcoma cells

value: pLKO


title: CBTTC_6289


title: Primary_CCS3, RNAseq

value: Soft tissue clear cell sarcoma


title: 1.FS2-pLKO


title: 2.FS2-pLKO


title: CBTTC_2173


title: 4.FS2-shRras2


title: CBTTC_3459


title: Primary_CCS1, RNAseq


title: Primary_CCS2, RNAseq


title: Chetan_8104


title: SUCCS1_siCTRL_96h_1, RNAseq

source_name: Cell line

value: Derived from the pleural effusion of a 16 year old Caucasian girl with a heel CCS tumor

value: Transfected with CTRL siRNA

value: SU-CCS-1 (RRID:CVCL_B470)


title: Chetan_9637-4


title: Chetan_88425


title: CBTTC_5459


title: SUCCS1_siEA_96h_1, RNAseq

value: Transfected with siRNA targeting EWSR1-ATF1 fusion transcript


title: Chetan_8045-2


title: DTC1_siEA_96h_2, RNAseq

value: Derived from malignant pleural effusion of a patient with a chest wall CCS tumor

value: DTC1 (CVCL_0J31)


title: DTC1_siEA_96h_3, RNAseq


title: CBTTC_6054


title: DTC1_siCTRL_96h_3, RNAseq


title: DTC1_siCTRL_96h_2, RNAseq


title: DTC1_siCTRL_96h_1, RNAseq


title: CBTTC_6785


title: CBTTC_7286


title: SUCCS1_siEA_96h_HiChIP

data_processing:
Library strategy: HiChIP-seq
HiChIP paired-end reads were aligned to hg19 genomes using HiC-Pro (version: 2.7.6) with defalt parameters.
Hichipper (version: 0.7.7) was used for loop calling by H3K27ac ChIP-seq peaks (qvalue <= 0.00001) with parameter: --max-dist 100000000 --read-length 100.
.hic format processed files were generated by hicpro2juicebox.sh from HiC-Pro.
Genome_build: hg19
Supplementary_files_format_and_content: .hic contact matrix files and .bedpe loop files. Only the loops with more than 5 reads are kept in the files.

growth_protocol: DTC1 and SUCCS1 were cultured in RPMI-1640 medium supplemented with 10% and 1% Pen/Strep as suspension cells in Ultra-low attachment flasks.

extract_protocol:
A detailed protocol is outlined in Methods. Briefly, cells were cross-linked with formaldehyde and nuclei washed and collected. Chromatin was digested using the MboI restriction enzyme, end-filled with incorporation of biotin-labelled dATP, subjected to proximity ligation, and proceeded with H3K27ac ChIP. ChIP DNA was purified and concentrated, and biotin pulldown performed with Dynabeads Streptavidin beads followed by magnetic separation.
Hi-ChIP sequencing libraries were prepared using the Next Gen DNA Library kit (Cat. no. #53216 and #53264) according to the manufacturer´s instructions, carrying out the reactions on bead-bound DNA followed by magnetic separation. Hi-ChIP library DNA was PCR amplified (8 cycles) and purified using AMPure XP beads.


title: CBTTC_4940


title: CBTTC_4956


title: DTC1_siCTRL_96h_1_2, RNAseq

value: Transfected with CTRL siRNA. Technical replicate.


title: DTC1_wt_HiChIP

value: untreated


title: MSC_2_empty_H3K4me3_1

data_processing:
The ChIPseq reads were first trimmed using Trimgalore
Trimmed reads were aligned on the human genome assembly hg19 with STAR version 2.5.0a, first taking all multiple matches for quality survey. Multiple matches, mitochondrial reads, as well as regions from the ENCODE Data Analysis Center (DAC) blacklisted regions (https://www.encodeproject.org/annotations/ENCSR636HFF/ , hg19 assembly) were then removed. A maximum of three redundant reads (i.e. reads with different IDs but mapping at the same genomic location) were kept for further analysis.
First, peaks were detected using MACS2 version 2.2.6 with an FDR of 1e-7 for ATF1_C and H3K4me3, and 1e-4 for EWSR1. In parallel, genomic enriched bins were extracted using the method described in : Renaud M, Praz V, Vieu E, Florens L, Washburn MP, L’Hôte P, et al. Gene duplication and neofunctionalization: POLR3G and POLR3GL. Genome Res. 2014;24: 37–51. 10.1101/gr.161570.113
To reduce the number of false-positives in the set, only the MACS2 peaks that intersected with the enriched genomic bins selected with the above-described method were considered for further analysis
CPM-normalized BigWig files were generated using bamCoverage (deepTools version 3.5.)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for genome browser, and bed files with peaks positions

extract_protocol:
Cells were cross-linked with formaldehyde, flash-frozen and processed for ChIP using Protein G beads. ChIP DNA was purified with AMPure XP beads.
ChIP DNA libraries were prepared using the Illumina TruSeq ChIP library preparation kit (Illumina cat. no. IP-202-1012 or IP-202-1024) according to the manufacturer's instructions and 200-500 bp fragments selected using AMPureXP beads.

value: Bone marrow derived pediatric MSCs

tag: chip antibody

value: H3K4me3 (#07-473, Millipore)

value: MSC


title: CBTTC_5235

value: Medulloblastoma

value: not available


title: CBTTC_5187

value: Group 4


title: CBTTC_5238


title: SUCCS1_siCTRL_96h_HiChIP

value: Transfected with non-targeting control siRNA


title: CBTTC_4188


title: MSC_2_EA_YS37mut_CTD_V5_1

value: V5 (#13202, Cell signaling)

value: Infected with C-term V5-tagged EWS(YS37)mut-ATF1


title: CBTTC_747


title: SUCCS1_wt_HiChIP

value: Derived from the pleural effusion of a 16 year old Caucasian girl with a heel CCS tumor


title: CBTTC_5463


title: MSC_2_EACTD_H3K4me3_2

value: Infected with C-term V5-tagged EWSR1-ATF1


title: CBTTC_4345

value: Group 3/4


title: CBTTC_3931


title: DTC1_siEA_96h_1_2, RNAseq

value: Transfected with siRNA targeting EWSR1-ATF1 fusion transcript. Technical replicate.


title: MSC_2_ATF1_CTD_V5_1

value: Infected with C-term V5-tagged ATF1


title: JHACH_2518


title: DTC1_wt_TFAP2A_1

value: Derived from malignant pleural effusion of a patient with a chest wall CCS tumor

value: TFAP2A (sc-12726, Santa Cruz)

value: DTC1 (CVCL_0J31)


title: DTC1_siEA_96h_1, RNAseq

value: Transfected with siRNA targeting EWSR1-ATF1 fusion transcript


title: CBTTC_7495


title: CBTTC_3949


title: Primary_CCS3_H3K4me3_1

value: H3K4me3 (#07-473, Millipore)

value: untreated

value: Soft tissue clear cell sarcoma


title: CBTTC_2169

value: Medulloblastoma


title: JHACH_1192


title: SUCCS1_wt_TFAP2A_1

value: SU-CCS-1 ATCC CRL-2971


title: CBTTC_4681

value: SHH


title: Primary_CCS3_H3K4me1_1

value: H3K4me1 (ab8895, Abcam)


title: Primary_CCS3_Input_1

value: none (Input)


title: Primary_CCS3_H3K27ac_1

value: H3K27ac (#39133, Active motif) (#39133, Active motif)


title: CBTTC_922


title: CBTTC_931


title: Primary_CCS1_Input_1


title: JHACH_6867


title: JHACH_1629

value: WNT


title: Primary_CCS1_H3K4me3_2


title: CBTTC_4221


title: Primary_CCS1_H3K4me1_2


title: CBTTC_2118


title: Primary_CCS2_Input_1


title: Primary_CCS1_ATF1_N_1

value: ATF1 N (A303-034A, Bethyl laboratories)


title: CBTTC_6781

value: Group 3/4


title: MSC_2_EA_YS37mut_CTD_H3K4me3_1

value: Bone marrow derived pediatric MSCs

value: Infected with C-term V5-tagged EWS(YS37)mut-ATF1

value: MSC


title: JHACH_2493


title: Primary_CCS1_ATF1_C_1

value: ATF1 C (LS-C351857, LS Bio)


title: CBTTC_3025


title: BioIVT_801

value: Normal


title: MSC_2_EACTD_V5_2

value: V5 (#13202, Cell signaling)

value: Infected with C-term V5-tagged EWSR1-ATF1


title: BioIVT_800


title: Primary_CCS2_H3K4me3_1

value: H3K4me3 (#07-473, Millipore)

value: untreated

value: Soft tissue clear cell sarcoma


title: Primary_AFH2_Input_1

value: Angiomatoid fibrous histiocytoma


title: Primary_AFH2_H3K4me3_1


title: Primary_CCS2_H3K4me1_1

value: H3K4me1 (ab8895, Abcam)


title: CBTTC_2934

value: Medulloblastoma


title: BioIVT_799


title: Primary_CCS2_H3K27ac_1

value: H3K27ac (#39133, Active motif) (#39133, Active motif)


title: BioIVT_798


title: BioIVT_797


title: Primary_AFH2_H3K4me1_1


title: Primary_AFH1_Input_1

value: none (Input)


title: Normal_CSF


title: Discovery_05681


title: Primary_AFH2_H3K27ac_1


title: Primary_AFH1_H3K4me1_1


title: Primary_AFH1_H3K4me3_1


title: Primary_AFH1_H3K27ac_1


title: Primary_CCS1_H3K27ac_2


title: Discovery_75288


title: Discovery_07360


title: SUCCS1_siCTL_96h_H3K4me1_1

value: Derived from the pleural effusion of a 16 year old CaucasiEAn girl with a heel CCS tumor

value: Transfected with CTRL siRNA

value: SU-CCS-1 ATCC CRL-2971


title: MSC_2_EANTD_p300_1

value: Bone marrow derived pediatric MSCs

value: p300 (#54062, Cell signaling)

value: Infected with N-term V5-tagged EWSR1-ATF1


title: MSC_2_empty_p300_1

value: Infected with empty pLIV vector

value: MSC


title: ALCAM-KD SP RPMI8226 cells rep3

city: Chengdu

first: Fangfang

last: Wang

address: Guoxuexiang NO.37

country: China

institute: West China Hospital, Sichuan University

data_processing:
Illumina Bcl2fastq (v2.17.1.14) software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by Cutadapt (V1.9.1), then aligned to whole genome via software Hisat2 (v2.0.1).
FPKM (Fragments Per Kilo bases per Million reads) to estimate gene expression levels was performed by HTSeq (v0.6.1)  and differential expression analysis used the DESeq2 Bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Cells were cultured in RPMI1640 medium containing 10% fetal bovine serum and 100 U penicillin / 0.1 mg/ml streptomycin.

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)
Next generation sequencing library preparations were constructed  using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (Vazyme, Cat No. NR603, China)

treatment_protocol: CTR-KD and ALCAM-KD RPMI8226 MM cell lines were established by infecting lentivirus carrying CTR or ALCAM shRNA

value: multiple myeloma (MM) cells

tag: cell population

value: SP

value: ALCAM-Knock down


title: ALCAM-KD SP RPMI8226 cells rep2


title: ALCAM-KD SP RPMI8226 cells rep1


title: DTC1_wt_p300_1

value: Derived from malignant pleural effusion of a patient with a chest wall CCS tumor

value: untreated

value: DTC1 (CVCL_0J31)


title: MSC_2_EACTD_p300_1

value: Infected with C-term V5-tagged EWSR1-ATF1


title: ALCAM-KD MP RPMI8226 cells rep3

value: MP


title: SUCCS1_wt_p300_1

value: Derived from the pleural effusion of a 16 year old Caucasian girl with a heel CCS tumor


title: CTR-KD SP RPMI8226 cells rep3

value: CTR-Knock down


title: SUCCS1_siEA_96h_H3K4me1_1

value: H3K4me1 (ab8895, Abcam)

value: Transfected with siRNA targeting EWSR1-ATF1 fusion transcript


title: SUCCS1_siEA_96h_Input_1

value: none (Input)

value: SU-CCS-1 ATCC CRL-2971


title: ALCAM-KD MP RPMI8226 cells rep1


title: SUCCS1_siEA_96h_ATF1_N_1

value: ATF1 N (A303-034A, Bethyl laboratories)


title: CTR-KD SP RPMI8226 cells rep2


title: CTR-KD SP RPMI8226 cells rep1


title: SUCCS1_siEA_96h_H3K4me3_1

value: H3K4me3 (#07-473, Millipore)


title: Discovery_07363

value: Normal


title: CTR-KD MP RPMI8226 cells rep2

value: multiple myeloma (MM) cells


title: CTR-KD MP RPMI8226 cells rep3


title: SUCCS1_siCTL_96h_ATF1_N_1

value: Transfected with CTRL siRNA


title: Discovery_07394


title: SUCCS1_siCTL_96h_ATF1_C_1

value: ATF1 C (LS-C351857, LS Bio)


title: SUCCS1_siCTL_96h_Input_1


title: BU #2

city: CLAYTON

first: Robin

middle: Mark

last: Hobbs

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Single cell (sc) RNA-seq processing was performed with Cell Ranger software (10x Genomics, Inc.).
Matrix files from Cell Ranger output were analysed using Seurat v3.2. Seurat objects of Control and BU-treated groups were built by loading matrix files using the “Read10X” function. Each dataset was filtered and cells with greater than 1000 genes expressed and less than 20% of reads mapped to the mitochondrial genome were retained.
The datasets were normalized using the “LogNormalize” function and scaled using a scale factor of 100,000.
The top 2000 highly variable genes were selected using the “FindVariableFeatures” function.
To account for variations among different batches, the datasets were aligned using canonical correlation analysis (CCA) with “FindIntegrationAnchors” and “IntegrateData” functions.
Dimensionality of data was reduced by principal component analysis (PCA) (30 components) and visualized with UMAP
Genome_build: GRCm39

source_name: Undifferentiated spermatogonia

growth_protocol: Adult WT mice (6-8 weeks) were either untreated or treated with busulfan (10mg/kg) and testis samples were harvested at day 10 post-busulfan

extract_protocol:
Sorted cells were resuspended at ~200 viable cells/ml in PBS containing 2% FBS prior to library preparation using a 10X Chromium controller
CTRL #1 and BU #1 (pooled from 3 mice for each group): Library construction was performed using a 10X Chromium controller with the Chromium Single Cell 3’ Reagent Kit V2. Both libraries were sequenced in one high-output lane of an Illumina NextSeq in single-read 150b format (115b effective read length)
CTRL #2 and BU #2 (pooled from 3 mice for each group): Library construction was performed using a 10X Chromium controller with the Chromium Single Cell 3’ Reagent Kit V3.1. Both libraries were sequenced in one high-output lane of an Illumina NextSeq.
single-cell RNA-seq (10x genomics)

treatment_protocol: A single dose of busulfan (10mg/kg) was given to the treatment group. Testis cell suspensions were prepared by a standard two step digestion protocol with collagenase and trypsin. Cells were sorted on a BD Influx Cell Sorter (BD Biosciences). The undifferentiated population was gated according to expression of E-cadherin and surface markers c-KIT and CD49f. E-cadherin is a well-established marker of undifferentiated spermatogonia plus cells at early differentiation stages. c-KIT marks differentiating spermatogonia and CD49f is enriched on functional stem cells. Undifferentiated cells were sorted as E-cadherin positive, CD49f positive, c-KIT negative.

value: Testis

tag: age

value: Adult (6-8 weeks)


title: CTRL #2


title: SUCCS1_siCTL_96h_H3K27ac_1

value: H3K27ac (#39133, Active motif) (#39133, Active motif)


title: BU #1


title: SUCCS1_siCTL_96h_H3K4me3_1


title: CTRL #1


title: DTC1_siEA_96h_H3K4me3_1

value: Derived from malignant pleural effusion of a patient with a chest wall CCS tumor

value: DTC1 (CVCL_0J31)


title: DTC1_siEA_96h_H3K4me1_1


title: Red

city: Suita

first: Shugo

last: Sasaki

state: Osaka

address: 2-2 Yamadaoka, Suita-shi

department: Metabolic Medicine

country: Japan

institute: Osaka University

data_processing:
Following sequencing, data were analysed using publicly available software programs and R pipelines. First, cellranger mkfastq (10x Genomics) generates FASTQ files from the raw sequencing data. Next, cellranger count uses the FASTQ file to perform sequence alignment (mouse: GRCm38, human: GRCh38), filter sequences based on quality score, and generate single cell gene counts. For count alignment of the lineage-tracing transgenes, the mouse reference genome was annotated to include the GFP and Timer sequences. Cellranger aggr was used to combine data from multiple samples (Green1, Green2 and Red) and ensure all libraries have the same sequencing depth.
As minimal filtering is performed in cellranger, two additional R pipelines were used to filter out cells that did not meet the quality control standard. The first pipeline is Scater (https://bioconductor.org/packages/release/bioc/html/scater.html) and is a single cell analysis pipeline that places a great emphasis on quality control. For this analysis, cells were discarded based on counts (transcripts/cell), genes (genes/cell) and percentage mitochondrial DNA expression, greater than 3 standard deviation away from the mean. Low-abundance genes, which were expressed by less than 3 cells, were removed.
This QC dataset was then analyzed using the Seurat V2.0 and V3.0 pipeline (http://satijalab.org/seurat/), another R toolkit for single cell genomics. Seurat posed an additional filtering step that removed out cells with less than 500 genes. Seurat was then used for normalization, correcting cells by their library size, and linear dimensional reduction, removing uninteresting source of variations.
Finally, unsupervised shared nearest neighbor modularity optimization based clustering was performed using Seurat to group cells based on gene expression and to identify unique cell types within the populations.
Genome_build: Customize reference transcriptomes were made by adding the GFP and Timer sequences to GRCm38 mouse transcriptome.
Supplementary_files_format_and_content: Raw counts matrix removing out background barcodes(<1000 UMI counts) and excluding genes with 0 counts.

source_name: pancreatic β-lineage cells

growth_protocol: Ins1-GFP; Timer embryos were dissected at E16.5 and sorted for green+ and red+ cells. hESCs were differentiated using Nair et al. protocol.

extract_protocol:
The 10x Genomics ChromiumTM controller and Single Cell 3’ Reagent Kits v2 (Pleasanton, CA, USA) were used to generate single cell libraries. Briefly, cells were counted following FACS and cell suspensions were loaded for a targeted cell recovery of 1000-5000 cells per channel.The microfluidics platform was used to barcode single cells using Gel Bead-In-Emulsions (GEMs).
RT is performed within GEMs, resulting in barcoded cDNA from single cells. The full length, barcoded cDNA is PCR amplified followed by enzymatic fragmentation and SPRI double sided size selection for optimal cDNA size. End repair, A-tailing, Adaptor Ligation, and PCR are performed to generate the final libraries that have P5 and P7 primers compatible with Illumina sequencing. The libraries were pooled and sequenced using an Illumina NextSeq500 platform with a 150 cycle High Output v2 kit in paired-end format with 26 bp Read 1, 8 bp I5 Index, and 85 bp Read 2.

value: FACS sorted Green+Red+ E16.5 pancreatic Beta-lineage cells


title: ALCAM-KD MP RPMI8226 cells rep2

value: MP

value: ALCAM-Knock down


title: Green1

description: Green1 and Green2 samples were harvested from two different embryos

value: FACS sorted Green+ E16.5 pancreatic Beta-lineage cells


title: DTC1_siCTL_96h_H3K4me1_1

value: H3K4me1 (ab8895, Abcam)


title: Green2


title: DTC1_siEA_96h_ATF1_N_1

value: Transfected with siRNA targeting EWSR1-ATF1 fusion transcript


title: DTC1_siEA_96h_Input_1

value: none (Input)


title: SUCCS1_siEA_96h_H3K27ac_1

value: Derived from the pleural effusion of a 16 year old Caucasian girl with a heel CCS tumor

value: SU-CCS-1 ATCC CRL-2971


title: DTC1_siCTL_96h_ATF1_N_1

value: ATF1 N (A303-034A, Bethyl laboratories)


title: DTC1_siCTL_96h_Input_1

value: Transfected with CTRL siRNA


title: SUCCS1_siEA_96h_ATF1_C_1

value: ATF1 C (LS-C351857, LS Bio)


title: CTR-KD MP RPMI8226 cells rep1

value: multiple myeloma (MM) cells

value: CTR-Knock down


title: DTC1_siCTL_96h_H3K27ac_1

value: H3K27ac (#39133, Active motif) (#39133, Active motif)


title: DTC1_siCTL_96h_ATF1_C_1

value: Derived from malignant pleural effusion of a patient with a chest wall CCS tumor


title: MSC_2_EANTD_Input_1

value: Bone marrow derived pediatric MSCs

value: Infected with N-term V5-tagged EWSR1-ATF1

value: MSC


title: MSC_2_EANTD_ATF1_N_1


title: DTC1_siCTL_96h_H3K4me3_1

value: H3K4me3 (#07-473, Millipore)

value: DTC1 (CVCL_0J31)


title: MSC_2_EANTD_V5_1

value: V5 (#13202, Cell signaling)


title: MSC_2_EANTD_H3K27ac_1


title: MSC_2_EACTD_ATF1_N_1

value: Infected with C-term V5-tagged EWSR1-ATF1


title: NS+LPS_3

city: Regensburg

first: Patrick

last: Neubert

address: Franz-Josef-Strauß-Allee 11

department: Department of Clinical Microbiology and Hygiene

country: Germany

institute: University Hospital Regensburg

description: Gene expression NS + LPS, 24h, replicate 3

hyb_protocol: The hybridization procedure was performed according to the ‘One-Color Microarray-Based Gene Expression Analysis’ protocol (p/n G4140-90040) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System G2505C (Agilent Technologies, Santa Clara, CA, USA).

data_processing: The Agilent Feature Extraction Software (FES) 10.7.3.1 was used to read out and process the microarray image files.

source_name: NS + LPS, 24h, replicate 3

label_protocol: Sample labelling was performed as detailed in the ‘One-Color Microarray-Based Gene Expression Analysis’ protocol (p/n G4140-90040).

extract_protocol: Total RNA was extracted with Trifast® (PeqLab) according to the manufacturer’s instruction.


title: DTC1_siEA_96h_ATF1_C_1

value: Transfected with siRNA targeting EWSR1-ATF1 fusion transcript


title: HS+LPS_1

description: Gene expression HS + LPS, 24h, replicate 1

source_name: HS + LPS, 24h, replicate 1


title: MSC_2_EACTD_V5_1


title: NS_3

description: Gene expression NS, 24h, replicate 3

source_name: NS, 24h, replicate 3


title: NS+LPS_2

description: Gene expression NS + LPS, 24h, replicate 2

source_name: NS + LPS, 24h, replicate 2


title: HS+LPS_2

description: Gene expression HS + LPS, 24h, replicate 2

source_name: HS + LPS, 24h, replicate 2


title: MSC_2_EACTD_H3K27ac_1


title: HS_2

description: Gene expression HS, 24h, replicate 2

source_name: HS, 24h, replicate 2


title: HS_1

description: Gene expression HS, 24h, replicate 1

source_name: HS, 24h, replicate 1


title: MSC_2_empty_ATF1_N_1

value: Infected with empty pLIV vector


title: DTC1_siEA_96h_H3K27ac_1


title: HS+LPS_3

description: Gene expression HS + LPS, 24h, replicate 3

source_name: HS + LPS, 24h, replicate 3


title: HS_3

description: Gene expression HS, 24h, replicate 3

source_name: HS, 24h, replicate 3


title: BFC 8d-rep3

city: SAN ANTONIO

first: Sijia

last: He

state: Texas

address: 7703 Floyd Curl Dr.

institute: uthealth sa

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization,   Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization   Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station   450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s   instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix,   Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA,   US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene   Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing:
The data were analyzed using SBC Analysis System (SAS) provided by ShanghaiBio Corporation.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.1.2800.28061

source_name: Brown fat cell (differentiated)

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express   Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s   instructions to obtain biotin labeled cRNA.

growth_protocol: Brown adipocyte cell lines were maintained in growth medium (DMEM with 10% FBS and 1% Penicillin-Streptomycin). 3T3-L1 preadipocytes were maintained in growth medium (DMEM with 10% Fetal Calf Serum and 1% Penicillin-Streptomycin)

extract_protocol: Total RNA was extracted and purified using RNeasy Lipid Tissue Mini Kit  （Cat#74804，QIAGEN, GmBH, Germany) following the manufacturer’s instructions   and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer   2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: For brown cells, 2 days after confluence (day 0), differentiation was induced by adding IBMX (0.5 mM), indomethacin (125 µM), dexamethasone (1 µM), insulin (20 nM), and T3 (1 nM) and cultured for 3 days. Cells were then maintained in growth medium containing insulin (20 nM) and T3 (1 nM) until fully differentiated (day 8). For 3T3-L1 cells, at 2 days post confluence (day 0), differentiation was induced by adding IBMX (0.5 mM), dexamethasone (1 µM), and insulin (1 µg/mL) and cultured for 3 days. Cells were then cultured in growth medium contain insulin (1 µg/mL) for 2 more days followed by maintenance in the growth medium till harvest (day 10).

value: differentiated brown adipocyte


title: NS_1

description: Gene expression NS, 24h, replicate 1

source_name: NS, 24h, replicate 1


title: BFC 8d-rep2


title: NS+LPS_1

description: Gene expression NS + LPS, 24h, replicate 1

source_name: NS + LPS, 24h, replicate 1


title: NS_2

description: Gene expression NS, 24h, replicate 2

source_name: NS, 24h, replicate 2


title: MSC_2_EACTD_Input_1

source_name: Primary cell culture

value: none (Input)


title: BFC 8d-rep1


title: BFC 0d-rep3

source_name: Brown fat cell (un-differentiated)

value: brown pre-adipocyte


title: BFC 0d-rep2


title: MSC_2_empty_V5_1


title: DTC1_wt_EWSR1_3

source_name: Cell line

value: EWSR1 N (sc-48404, Santa Cruz)

value: untreated


title: 3T3-L1 10d-rep3

source_name: 3T3-L1 cell (differentiated)

value: differentiated 3T3-L1 white adipocyte


title: MSC_2_empty_Input_1


title: DTC1_wt_EWSR1_2


title: DTC1_wt_Input_2


title: 3T3-L1 10d-rep1


title: HEL_5J20_DoxInduced_GFP_rep1

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie2 v2.2.6.
Peaks were called using MACS2
RPKM normalized bigwig files were generated using Deeptools 3.1.2
Genome_build: hg19
Supplementary_files_format_and_content: RPKM normalized bigwig files were generated using Deeptools 3.1.2, reads were elongated to 250bp

extract_protocol:
Cells were fixed in 1% formaldehyde, chromatine was sonicated using a Bioruptor Pico
Libraries were constructed using a custom protocol and NEXTFLEX adapters and barcodes

value: hematopoietic cells

value: anti-GFP antibody


title: HEL_5J20_DoxInduced_GFP_rep2


title: DTC1_wt_H3K4me3_2

value: Derived from malignant pleural effusion of a patient with a chest wall CCS tumor


title: HEL_5J20_DoxInduced_H3K27ac

source_name: hematopoietic cells

value: HEL_5J20 cell line

tag: agent

value: Dox

tag: antibody

value: ChIP using anti-H3K227ac antibody


title: 3T3-L1 0d-rep2

source_name: 3T3-L1 cell (un-differentiated)

value: 3T3-L1 white pre-adipocyte


title: DTC1_wt_H3K4me1_2

value: H3K4me1 (ab8895, Abcam)

value: DTC1 (CVCL_0J31)


title: BFC 0d-rep1


title: 3T3-L1 0d-rep3


title: HEL_5J20_NonInduced_H3K27ac


title: HEL_5J20_NonInduced_Input

value: sonicated Input chromatin


title: AMKL7_H3K27ac

value: patient derived AMKL cells


title: 3T3-L1 0d-rep1


title: HEL_5J20_DoxInduced_Input


title: DTC1_wt_ATF1_C_1

value: ATF1 C (LS-C351857, LS Bio)


title: DTC1_wt_H3K4me1_1


title: HEL_5J20_NonInduced_GFP


title: 3T3-L1 10d-rep2


title: DTC1_wt_H3K27ac_1

value: H3K27ac (#39133, Active motif) (#39133, Active motif)


title: AMKL7_Input


title: SUCCS1_wt_EWSR1_3

value: Derived from the pleural effusion of a 16 year old Caucasian girl with a heel CCS tumor

value: SU-CCS-1 (RRID:CVCL_B470)


title: DTC1_wt_ATF1_N_1

value: ATF1 N (A303-034A, Bethyl laboratories)

value: untreated


title: MSC_2_empty_H3K27ac_1

value: Bone marrow derived pediatric MSCs

value: Infected with empty pLIV vector

value: MSC


title: DTC1_wt_H3K27ac_2

value: Derived from malignant pleural effusion of a patient with a chest wall CCS tumor


title: Retina periphery P6

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the human reference genome (Gencode, human: GRCh38.p13, all regions, release 37) with RNA STAR (Dobin et al., 2013) using the corresponding Gencode main annotation file.
Two BAM files for each sample (one for each lane) were combined in one BAM file per sample using Merge BAM Files.
Reads mapped to the reference genome were counted with featureCounts (Liao et al., 2014) using the aforementioned annotation files.
The outputs of featureCounts were imported to RStudio (Version 1.4.1103, R Version 4.0.3).
Gene symbols were determined based on the ENSEMBL database (release 103, download on 03/23/2021) (Howe et al., 2021). Genes with 0 reads in all samples were removed from the anal-ysis. After principle component analysis (Love et al., 2014), normalized reads and differential gene expression were calculated using the R package DESeq2 (version 1.30.1) with default parameters (Benjamini-Hochberg adjusted p-values) (Love et al., 2014). Transcripts with log2 fold change (log2FC) > 2 or < -2 and adjusted p-value < 0.05 were considered as differentially expressed genes (DEG).
Genome_build: hg38

source_name: Retina periphery

extract_protocol:
Total RNA was extracted from FACS sorted cells stabilized in RNAprotect buffer ac-cording to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany). In brief, cells were stored and shipped in RNAprotect buffer at 2-8 °C. After pelleting by centrifugation for 5 minutes at 5,000 x g, RNAprotect was replaced by 350 µl RLT Plus buffer and the samples were homogenized by vortexing for 30 seconds. Genomic DNA contamina-tion was removed by using gDNA Eliminator spin columns. Next, one volume of 70 % ethanol was added and the samples were applied to RNeasy MinElute spin col-umns followed by several wash steps. Finally, the total RNA was eluted in 12 μl of nuclease-free water. Purity and integrity of the RNA were assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA). RNA isolation from FFPE retinal specimens was carried out as previously described (Lange et al., 2018;Schlecht et al., 2020a). Briefly, total RNA was extract-ed from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, Cali-fornia). Following DNAse I digestion using the Baseline-ZERO Kit (Epicentre, Madi-son, Wisconsin), the RNA concentration was quantified using the Qubit RNA HS Assay Kit on a Qubit Fluorometer (Life Technologies, Carlsbad, California). RNA quality was determined via the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, Massachusetts).
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from approx-imately 1 ng total-RNA. Double-stranded cDNA was amplified by LD PCR (12 cy-cles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and frag-mented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step, 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA Library Quantification Kit - Illumina/ABI Prism User Guide (Roche Sequencing Solutions, Inc., Pleasanton, CA, USA). Equimolar amounts of each library were sequenced on a NextSeq 500 instrument controlled by the NextSeq Control Software (NCS) v2.2.0, using two 75 Cycles High Output Kits with the dual index, single-read (SR) run parameters. Image analysis and base calling were done by the Real Time Analysis Software (RTA) v2.4.11. The resulting .bcl files were converted into .fastq files with the bcl2fastq v2.18 software. RNA extraction, library preparation and RNAseq were performed at the Genomics Core Facility “KFB - Center of Excellence for Fluorescent Bioanalytics” (University of Regensburg, Regensburg, Germany; www.kfb-regensburg.de). Retinal samples (FFPE) were sequenced using the 3' RNA sequencing method Massive Analysis of cDNA Ends (MACE) (Schlecht et al., 2020a;Wolf et al., 2020), which allows se-quencing of FFPE samples with high accuracy and without a significant impact of FFPE processing (Boneva et al., 2020a). Briefly, barcoded libraries comprising unique molecule identifiers were sequenced on the NextSeq 500 (Illumina) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers.

value: Retina periphery


title: DTC1_wt_ATF1_C_2


title: SUCCS1_wt_EWSR1_2

value: EWSR1 N (sc-48404, Santa Cruz)


title: DTC1_wt_H3K4me3_1

value: H3K4me3 (#07-473, Millipore)


title: Retina periphery P1


title: Non-classical Monocytes P9 FC2

source_name: Non-classical Monocytes

value: Non-classical Monocytes


title: Retina central P6

source_name: Retina central

value: Retina central


title: DTC1_wt_ATF1_N_2

value: DTC1 (CVCL_0J31)


title: SUCCS1_wt_Input_3

value: none (Input)


title: SUCCS1_wt_ATF1_N_2


title: SUCCS1_wt_ATF1_C_2

value: ATF1 C (LS-C351857, LS Bio)


title: Non-classical Monocytes P8 FC1


title: SUCCS1_wt_H3K4me1_2

value: H3K4me1 (ab8895, Abcam)


title: Retina central P1


title: Non-classical Monocytes P9 FC1


title: DTC1_wt_Input_1


title: SUCCS1_wt_Input_2

value: Derived from the pleural effusion of a 16 year old Caucasian girl with a heel CCS tumor


title: SUCCS1_wt_ATF1_N_1

value: SU-CCS-1 (RRID:CVCL_B470)


title: SUCCS1_wt_H3K4me3_2


title: SUCCS1_wt_H3K27ac_2

value: H3K27ac (#39133, Active motif) (#39133, Active motif)


title: Non-classical Monocytes P7 FC1


title: Non-classical Monocytes P8 FC2


title: Non-classical Monocytes P7 FC2


title: Non-classical Monocytes P2 FC1


title: Retina periphery P4


title: SUCCS1_wt_ATF1_C_1

value: untreated


title: SUCCS1_wt_Input_1


title: Non-classical Monocytes P1 FC2


title: SUCCS1_wt_H3K4me3_1


title: Non-classical Monocytes P1 FC1


title: SUCCS1_wt_H3K4me1_1


title: SUCCS1_wt_H3K27ac_1


title: Retina central P2


title: Intermediate Monocytes P9 FC2

source_name: Intermediate Monocytes

value: Intermediate Monocytes


title: Intermediate Monocytes P9 FC1


title: SUCCS1_siCTRL_96h_ATAC_2

data_processing:
The ATACseq reads were first trimmed using Trimgalore
Trimmed paired-end reads were aligned on the human genome assembly hg19 with STAR version 2.5.0a, first taking all multiple matches for quality survey. Multiple matches, mitochondrial reads, as well as regions from the ENCODE Data Analysis Center (DAC) blacklisted regions (https://www.encodeproject.org/annotations/ENCSR636HFF/ , hg19 assembly) were then removed. A maximum of three redundant reads were kept for further analysis. Fragments positions were shifted + 4 bp and − 5 bp for positive and negative strand respectively, to account for the 9-bp duplication created by DNA repair of the nick by Tn5 transposase.
First, peaks were detected using MACS2 version 2.2.6 with an FDR of 5.00e-02 and the --nomodel and BEDPE options. In parallel, genomic enriched bins were extracted using the method described in : Renaud M, Praz V, Vieu E, Florens L, Washburn MP, L’Hôte P, et al. Gene duplication and neofunctionalization: POLR3G and POLR3GL. Genome Res. 2014;24: 37–51. 10.1101/gr.161570.113
To reduce the number of false-positives in the set, only the MACS2 peaks that intersected with the enriched genomic bins selected with the above-described method were considered for further analysis
CPM-normalized BigWig files were generated using bamCoverage (deepTools version 3.5.)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

extract_protocol:
75 000 cells were collected and re-suspended in lysis buffer to swell cytoplasm. The nuclei preparation was lysed DNA was tagmented with Tn5 Transposase (Nextera DNA Sample prep kit, Illumina #15028212) for 30 min and purified.
Sequencing libraries were generated by 12 cycles of PCR amplification using NEBnext PCR mix (New England Biolabs) and custom Nextera primers.

value: Transfected with CTRL siRNA


title: SUCCS1_siEA_96h_ATAC_2

value: Transfected with siRNA targeting EWSR1-ATF1 fusion transcript


title: Intermediate Monocytes P8 FC2


title: SUCCS1_wt_ATAC_1


title: Intermediate Monocytes P8 FC1


title: MSC2_EA_NTD_ATAC_2

value: Bone marrow derived pediatric MSCs

value: Infected with N-term V5-tagged EWSR1-ATF1

value: MSC


title: Intermediate Monocytes P7 FC2


title: Intermediate Monocytes P7 FC1


title: Intermediate Monocytes P2 FC2


title: MSC2_EA_CTD_ATAC_2

value: Infected with C-term V5-tagged EWSR1-ATF1


title: Intermediate Monocytes P2 FC1


title: DTC1_wt_ATAC_2

value: Derived from malignant pleural effusion of a patient with a chest wall CCS tumor


title: Intermediate Monocytes P1 FC2


title: DTC1_siEA_96h_ATAC_2


title: DTC1_siCTRL_96h_ATAC_2


title: Classical Monocytes P9 FC2

source_name: Classical monocytes

value: Classical monocytes


title: Intermediate Monocytes P1 FC1


title: Non-classical Monocytes P2 FC2

value: Non-classical Monocytes


title: M07e_Input_sg7-2

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie2 v2.2.6
Peaks were called using MACS2
RPKM normalized bigwig files were generated using Deeptools 3.1.2
Genome_build: hg19
Supplementary_files_format_and_content: RPKM normalized bigwig files were generated using Deeptools 3.1.2, reads were elongated to 250bp

source_name: M07e cells infected with dCas9-KRAB and sg7, replicate 2

value: hematopoietic cells

value: sonicated Input chromatin

value: infected with dCas9-KRAB and sg7


title: Classical Monocytes P9 FC1


title: M07e_H3K9me3_sg7-2


title: Classical Monocytes P8 FC2


title: M07e_Input_sgR-2

source_name: M07e cells infected with dCas9-KRAB and sgRennilla, replicate 2

value: infected with dCas9-KRAB and sgRennilla


title: Classical Monocytes P8 FC1


title: M07e_H3K9me3_sg2-2

source_name: M07e cells infected with dCas9-KRAB and sg2, replicate 2

value: infected with dCas9-KRAB and sg2


title: Classical Monocytes P7 FC2


title: Classical Monocytes P7 FC1


title: M07e_H3K9me3_sgR-2


title: Classical Monocytes P5 FC2


title: M07e_H3K27ac_sg2-2


title: M07e_H3K27ac_sg7-2


title: M07e_H3K27ac_sgR-2


title: Classical Monocytes P5 FC1


title: Classical Monocytes P2 FC2


title: Classical Monocytes P1 FC2


title: M07e_Input_sg7-1

source_name: M07e cells infected with dCas9-KRAB and sg7, replicate 1


title: Classical Monocytes P2 FC1


title: M07e_Input_sg2-1

source_name: M07e cells infected with dCas9-KRAB and sg2, replicate 1


title: Classical Monocytes P1 FC1


title: M07e_Input_sgR-1

source_name: M07e cells infected with dCas9-KRAB and sgRennilla, replicate 1


title: MSC2_pLIV_ATAC_1

source_name: Primary cell culture

value: Infected with empty pLIV vector


title: M07e_H3K9me3_sg7-1


title: Retinal microglia P5 FC2

source_name: Retinal microglia

value: Retinal microglia


title: M07e_H3K27ac_sg7-1


title: M07e_H3K9me3_sg2-1


title: M07e_H3K9me3_sgR-1


title: Retinal microglia P6 FC1


title: Retinal microglia P5 FC1


title: M07e_Input_sg2-2


title: M07e_H3K27ac_sg2-1


title: LRG1_KO

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq Fastq reads were aligned with the reference genome (UCSC mouse genome build mm9) using TopHat2 default settings (Trapnell et al., 2012).
The BAM files obtained after alignment were processed using htseq-count to obtain the counts per gene in all samples (Anders et al., 2015).
Genome_build: UCSC mouse genome build mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: Liver tissue

extract_protocol:
RNA was harvested using Trizol reagent
Approximately 500ng Total RNA was used for RNA-seq library preparation by following TruSeq stranded mRNA-seq library preparation kit ( Cat. No: 20020595, Illumina, USA). Following mRNA enrichment by oligodT beads,  the RNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library for sequencing by 50bp singlle-end protocol with Illumina HiSeq 3000 platform.

treatment_protocol: For liver tissue samples, Lrg1 whole body knockout mice (Lrg1 KO)  and C57BL/6J wild type mice were fed with a diet containing 45% of calories from fat (Research Diets Inc., Cat. #D12451) starting at 8 weeks of age for 16 weeks, liver tissue were harvested, snap frozen in liquid nitrogen, kept in -80 degree celsius until RNA isolation.

value: High fat diet 16 weeks

value: liver

value: Lrg1 knockout

tag: Sex

value: male


title: Retinal microglia P4 FC2


title: WT

value: wild type


title: LRG1_treatment_rep3 [L_3]

growth_protocol: Primary hepatocyte samples were isolated from 4-month-old male wild type mice.

treatment_protocol: Cells were treated with PBS control or 20 μg/mL LRG1 protein for 16 hours before harvested for RNA isolation.

value: LRG1 16 hours

value: primary hepatocytes

tag: strain background


title: M07e_H3K27ac_sgR-1


title: LRG1_treatment_rep1 [L_1]


title: LRG1_treatment_rep2 [L_2]


title: Retinal microglia P4 FC1


title: Control_treatment_rep3 [Con_3]

value: PBS 16 hours


title: Retinal microglia P3 FC2


title: Control_treatment_rep2 [Con_2]


title: Control_treatment_rep1 [Con_1]


title: Retinal microglia P3 FC1


title: Undifferentiated spermatogonia, BU #4

data_processing:
Used RNAsik pipeline to bam, counts and gather different metrics on RNAseq data https://github.com/MonashBioinformaticsPlatform/RNAsik-pipe
Used Degust  to analysis table of counts, output form RNAsik. Degust is a webapp that uses either edgeR or limma-voom for differential gene analysis http://degust.erc.monash.edu
Genome_build: Mus_musculus.GRCm38.dna_sm.primary_assembly.fa
Supplementary_files_format_and_content: Raw counts file was generated by featureCounts, which than was uploaded to Degust

source_name: Testis

growth_protocol: Adult WT mice (6-8 weeks) were either untreated or treated with busulfan (10mg/kg) and testis samples were analysed at day 10 post-busulfan

extract_protocol:
Sorted cells were lysed in TRIzol LS reagent (Thermo Fisher Scientific) then RNA was purified and DNase treated using a Direct-zol RNA Microprep kit (Zymo Research).
Nugen SPIA libraries and Illumina HiSeq3000 sequencing: - Nugen RNA-Seq system V2 (SPIA Amplification) followed by Nugen Ultralow Library preparation. Illumina HiSeq3000 sequencing using 100bp PE reads

value: Undifferentiated spermatogonia

value: Testis

value: Adult (6-8 weeks)

value: busulfan


title: Undifferentiated spermatogonia, BU #2


title: Retinal microglia P1 FC2


title: Undifferentiated spermatogonia, BU #3


title: Retinal microglia P6 FC2


title: Patient 4

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 500 Newton Road

department: Dermatology

institute: University of Iowa

data_processing:
Basecalls were converted into FASTQs using the Illumina bcl2fastq software by the University of Iowa Genomics Division
10x data was processed with the Cell Ranger pipeline, version 3.1
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited tsv files for genes and cell barcodes, mtx single-cell expression matrix, csv of CDR3 contig sequences

source_name: CD45+ Immune Cells

extract_protocol:
Single-cell suspensions were processed with the Chromium Single Cell 5-prime Library & Gel Bead Kit and the 10x Genomics TCR Immunprofiling kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: Sezary Syndrome


title: Undifferentiated spermatogonia, CTRL #4

tag: treatment

value: control


title: Undifferentiated spermatogonia, BU #1


title: Patient 5


title: Patient 3


title: M07e_sg2_2

description:
pool of RNAseq libraries
M07e_CRISPRI_SEKIT_96h.txt

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
reads were aligned using Tophat v2.1.1
differential expression was assessed using Cuffdiff v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: Tab separated file containing FPKM values of each genes of the hg19 UCSC reference annotation

source_name: hematopoietic cells

extract_protocol:
Total RNA was extracted using Qiagen RNAEasy plus mini kit
PolyA+ RNA was isolated using Oligo dT beads and stranded libraries were prepared using a custom protocol and NEXTFlex adapters and barcodes

tag: cell line

value: M07e cell line

value: 96 hours post infection


title: Patient 2


title: Undifferentiated spermatogonia, CTRL #2


title: Undifferentiated spermatogonia, CTRL #3


title: TBE11581 -1um SNX-5422 replicate 3

city: Durham

first: Ria

last: Goswami

state: NC

address: 2 Genome Ct. MSRBII

department: Duke Human Vaccine Institute

institute: Duke University

description:
featureCounts_all_sample_SNX5422_dmso_raw_counts.txt
normalized_SNX5422_dmso_all_sample_count_data.csv
collapsed_filtered_normalized_SNX5422_dmso_all_sample_count_DE_data.csv

data_processing:
Adaptor trimming and post-trim quality check of raw sequencing fastq files with Trim Galore v0.6.6 (FastQC and Cutadapt wrapper script) with the following parameters: --quality 20 --length 20 --fastqc --gzip --paired
Alignment of sequencing reads to GRCh38 human reference genome with STAR v2.7.5 splice-aware aligner. Genome indexing was performed with the following configurations: --runMode genomeGenerate --genomeFastaFiles ${Homo_sapiens.GRCh38.primary_assembly}.fa --sjdbGTFfile ${Homo_sapiens.GRCh38}.gtf. Alignment was then performed with the following parameters: --runMode alignReads --outSAMtype BAM Unsorted --outFilterMultimapNmax 3 with the indexed genome directory and paired-end fastq files as input
Quantification of read alignment to genome features at the exon level was performed with featureCounts v2.0.1 with the parameters: -s 0 -t exon -g gene_id  -p --extraAttributes gene_name,gene_biotype -a ${Homo_sapiens.GRCh38}.gtf and input of all sample alignment bams
Normalization of raw counts was performed with DESeq2 v1.28.1 median of ratios method in R statistical programming environment v4.0.2.
Differential expression SNX5422 vs. DMSO was calculated with DESeq2 in R statistical programming environment while controlling for TBE sample. Technical and biologic replicates for each TBE sample were collapsed and only genes with mean counts greater than or equal to 15 across conditions and samples were kept. Shrunken LFC (log2 Fold change) was applied to aid visualization of ranking.
Genome_build: GRCh38
Supplementary_files_format_and_content: featureCounts_all_sample_SNX5422_dmso_raw_counts.txt is a table of features, attributes, and raw feature counts across all biologic samples and treatments as well as their technical sequencing replicates. Columns represented in the table are "Geneid": ENSEMBL ID, "Chr": chromosome feature is on, "Start": genomic start coordinates of feature component, "End": genomic stop coordinates of feature component, "Strand": +/- strand, "Length": total length of feature in nucleotides, "gene_name": gene symbol/common name from gtf file, "gene_biotype": ENSEMBL gene biotype classification from gtf file, {SAMPLES...}: raw counts for each sample
Supplementary_files_format_and_content: normalized_SNX5422_dmso_all_sample_count_data.csv is a ENSEMBL Gene_ID by sample matrix of DESeq2 normalized counts across all biologic samples and treatments as well as their technical sequencing replicates
Supplementary_files_format_and_content: collapsed_filtered_normalized_SNX5422_dmso_all_sample_count_DE_data.csv is a table of normalized, filtered counts collapsed to the level of TBE sample across treatments and the results for DE of SNX5422 vs. DMSO treated samples. Columns consist of "Gene_ID": ENSEMBL gene ID, "baseMean": average normalized expression value across all samples, "logFC": Log2 fold-change, "lfcSE": Standard error of log2 fold-change, "pvalue": statistical P-value, "padj": FDR corrected p-value, {SAMPLE...}: Normalized expression values across biologic and technical sequencing replicates for each TBE sample/treatment combination

source_name: human primary tracheobronchial epithelial cells

growth_protocol: Fully differentiated human TBE cells (EpiAirwayTM) from 3 independent donors with no reported respiratory disease or smoking history were obtained from MatTek (Ashland, MA). The cells were cultured at the air-liquid interface in 1 ml of AIR-100-MM culture medium (MatTek) in 6 well plates at 37°C in 5% CO2. Upon receipt of cells, the cultures were acclimated for 16-24hr prior to the start of experiments.

extract_protocol:
After 48hrs, cells were resuspended in TRIzol reagent (Thermo Fisher) and total RNA from the cells was extracted by phase separation with chloroform and subsequently using the RNeasy Mini Kit (Qiagen).
RNA-Seq libraries were prepared using TruSeq RNA library Prep Kit v2 (Illumina, Inc. USA). Before pooling and sequencing, fragment length distribution and library quality were assessed on a TapeStation 2200 (Agilent Technologies), and the libraries were validated by Qubit Fluorometers (Thermo Fisher).
All libraries were then pooled in a concentration at 4nM and sequenced on a NextSeq 500 Illumina sequencing platform system using NextSeq 500/550 High Output Kit v2.0 (150 cycles) (Illumina, Inc. USA).

treatment_protocol: Human TBE cells  were treated with 1µM SNX-5422 or 0.1% DMSO (drug-vehicle) added to the media on the basolateral side of the culture, in three biological replicates for 48hrs.

value: Fully differentiated airway epithelial cells

value: 1uM SNX-5422-treated

tag: donor age, sex

value: 33, Female

tag: donor race

value: Caucasian

tag: smoking status

value: Non-smoker

tag: lung disease

value: None identified


title: Retinal microglia P1 FC1

tag: cell type

value: Retinal microglia


title: Undifferentiated spermatogonia, CTRL #1

tag: tissue

tag: strain


title: TBE11581 -1um SNX-5422 replicate 2


title: M07e_sg2_1

tag: time point


title: GlfT2_ATC_1

city: Shanghai

first: Hanmei

last: Liu

state: Shanghai

address: D507, School of Life Sciences, Fudan University, Yangpu District, Shanghai

department: School of Life Sciences

institute: Fudan University

data_processing:
Statistics and quality control of sequenced columns.（Raw data statistics ：Illumina platform；Quality control data statistics：SeqPrep (https://github.com/jstjohn/SeqPrep)； Sickle (https://github.com/najoshi/sickle)
Clean data (reads) after quality control was compared with the reference genome to obtain the mapped data (reads) for subsequent transcript assembly, expression calculation, etc. At the same time, the quality of the comparison results of the transcriptome sequencing was assessed.The analysis mainly included sequencing saturation, gene coverage, Reads distribution in different regions of the reference genome and Reads distribution in different chromosomes.【TopHat2 (http://ccb.jhu.edu/software/tophat/index.shtml) ；HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) 】
Transcriptome quality assessment
Based on the selected reference genome sequence, the StringTie or Cufflinks software is used to concatenate the Mapped Reads and compare the Mapped Reads with the original genome annotation information to find the original unannotated transcript and discover new transcripts and genes of the species, thus complementing and improving the original genome annotation information.
Expression statistics

source_name: Macrophage

growth_protocol: J-774A.1 macrophages were growth in DMEM medium (Gibco, 10% fatal bovine serum), 37 ℃， 5% CO2.

extract_protocol:
Murine macrophages (cell line J774A.1) infected by control and knock-down strains (MOI=5) 12 hours post infection were collected by TRIzol (Invitrogen), and transcriptome were purified.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Murine macrophages (J774A.1 cell line) were infected by knock-down strains with multiplicity of infection (MOI=5). Cells were washed with DMEM medium (Gibco, 10% fatal bovine serum) 3 times to remove extracellular bacteria 3h post infection. Remaining extracellular bacteria were killed off by penicillin (100U/mL) and streptomycin (100μg/mL) in medium. ATc concentration in the culture medium was maintained at 200 ng/mL during or after infection to ensure continued low expression of EmbA/GlfT2_KD stains. Cells were then incubated at 30℃ with 5% CO2 until further analysis.


title: EmbA_ATC_3


title: GlfT2_ATC_2


title: GlfT2_ATC_3


title: TBE11581 -1um SNX-5422 replicate 1


title: M07e_sgRen_2


title: EmbA_ATC_2


title: Patient 6


title: M07e_sgRen_1


title: EmbA_ATC_1


title: TBE11581 DMSO replicate 2

value: 0.1% DMSO treated


title: P962_ATC_3


title: P962_ATC_2


title: AMKL7_BM_sg2_2

description:
pool of RNAseq libraries
AMKL7_CRISPRI_SEKIT_48h.txt

value: patient derived AMKL cells

value: 48 hours post infection


title: TBE11581 DMSO replicate 1


title: AMKL7_BM_SgRen_2


title: AMKL7_BM_sg2_1


title: P962_ATC_1


title: TBE22 -1um SNX-5422  replicate 3

value: 35, Male


title: TBE22 -1um SNX-5422 replicate 2


title: TBE22 -1um SNX-5422 replicate 1


title: M07e sg7_2

description:
Stranded RNA-seq libraries done with barcoded TruSeq-like fork adapters (NEXTFlex) from polyA selected RNA from total extract.
M07e_CRISPRI_SEKIT_48h.txt


title: M07e sg7_1


title: TBE22 DMSO  replicate 3


title: HeLa cells with CM of hypoxic hDFs

type: protein

city: Seoul

first: Kyu-Hyun

last: Han

address: 81 Irwon-ro, Gangnam-gu

department: Division of Vascular Surgery

country: South Korea

institute: Samsung Medical Center, Sungkyunkwan University School of Medicine

description: HeLa with H-CM

hyb_protocol: Biotin labeled extract was hybridized with antibody-spotted slide for 2hr at room temperature. After hybridization, slide was washed with 1X wash buffer (Fullmoon Bio) and de-ionized water. Detection Buffer including Cy3-Streptavidin (fullmoon Bio) was treated for 20min at room temperature. And slide was washed with 1X wash buffer (Fullmoon Bio) and de-ionized water.

scan_protocol: Scanned on an GenePix 4100 scanner.

data_processing: GenePix Software (v 6.1) was used for data extraction.

molecule: protein

source_name: human cervical cancer cells

label_protocol: 50ug of protein extract was labeled with Biotin and label buffer (Fullmoon Bio).

growth_protocol: Human adult dermal fibroblasts (PromoCell GmbH, Heidelberg, Germany) and HeLa cells (ATCC, Manassas, VA, USA) were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Gibco, Grand Island, NY, USA) and 0.1% antibiotics (Gibco, Grand Island, NY, USA) at 37ºC in a 5% CO2 incubator (APM-30D; ASTEC, Fukuoka, Japan). An oxygen level of 21%, as the normoxic condition, and 1% O2, as the hypoxic condition, were applied to the culture of HDFs from passage 4 to passage 6. When the cell confluency of all cells reached 90%, the cells were passaged using 0.25% Trypsin-EDTA (Gibco, Grand Island, NY, USA).

extract_protocol: Cell pellet samples were homogenized with Extracting buffer (Fullmoon Bio). Debris was removed from Cell pellet extract with centrifuge.

treatment_protocol: Normoxic and hypoxic HDFs (2 × 105 cells) at passage 6 were cultured in 100-mm culture plates with complete medium. When cell confluency reached 90% on day 5, the medium was removed, and 1× phosphate-buffered saline (PBS) was added to wash the cells. Next, 6 mL of DMEM without FBS and antibiotics was added to the cells. After incubation for 24 h, the N-CM and H-CM were harvested and centrifuged at 300 g for 5 minutes. The supernatant was transferred to new 15-mL tubes and stored at −80ºC. HeLa cells (2 × 105) were cultured in 100-mm culture plates with complete medium. When cell confluency reached 90%, the culture medium was removed, and 1× PBS was added to wash the cells. After removing the PBS, 10 mL of N-CM or H-CM was applied to the cells for 24 h.

value: human cervical cancer cells

tag: oxygen condition

value: HeLa cells treated with CM of hypoxic hDFs


title: M07e sgGFP_2


title: TBE11581 DMSO  replicate 3


title: HeLa cells with CM of normoxic hDFs

description: HeLa with N-CM

value: HeLa cells treated with CM of normoxic hDFs


title: TBE22 DMSO replicate 1


title: CM of hypoxic hDFs [H-CM]

hyb_protocol: Drying the glass slide, Blocking and Incubations. Biotin labeled extract was hybridized with antibody-spotted slide for 2hr at room temperature. After hybridization, slide was washed with 1X wash buffer I and 1X wash buffer II and de-ionized water. Detection Buffer including Cy3-Streptavidin was treated for 2hr at room temperature in dark. And slide was washed with 1X wash buffer I, II and DW.

source_name: human adult dermal fibroblasts

label_protocol: 200ul of Media sample was labeled with Biotin and labeling buffer (Raybiotech). And re-Dialysis on 1XPBS.

growth_protocol: Human adult dermal fibroblasts (HDFs) (PromoCell GmbH, Heidelberg, Germany) were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Gibco, Grand Island, NY, USA) and 0.1% antibiotics (Gibco, Grand Island, NY, USA) at 37ºC in a 5% CO2 incubator (APM-30D; ASTEC, Fukuoka, Japan). An oxygen level of 21%, as the normoxic condition, and 1% O2, as the hypoxic condition, were applied to the culture of HDFs from passage 4 to passage 6. When the cell confluency of all cells reached 90%, the cells were passaged using 0.25% Trypsin-EDTA (Gibco, Grand Island, NY, USA).

extract_protocol: Debris was removed from cell supernatant with centifuge. And Dialysis on 1X PBS that using the dialysis tube.

treatment_protocol: Normoxic and hypoxic HDFs (2 × 105 cells) at passage 6 were cultured in 100-mm culture plates with complete medium. When cell confluency reached 90% on day 5, the medium was removed, and 1× phosphate-buffered saline (PBS) was added to wash the cells. Next, 6 mL of DMEM without FBS and antibiotics was added to the cells. After incubation for 24 h, the N-CM and H-CM were harvested and centrifuged at 300 g for 5 minutes. The supernatant was transferred to new 15-mL tubes and stored at −80ºC.

value: human adult dermal fibroblasts

value: conditioned medium of hypoxic hDFs


title: CM of normoxic hDFs [N-CM]

value: conditioned medium of normoxic hDFs


title: TBE20 -1um SNX-5422 replicate 2

value: Fully differentiated airway epithelial cells

value: 13, Male


title: TBE20 -1um SNX-5422 replicate 1

value: 1uM SNX-5422-treated


title: TBE20 -1um SNX-5422 replicate 3

value: Caucasian


title: CD34_H3K27ac_1

value: CD34+ cord blood cells

value: ChIP using anti-H3K227ac antibody


title: M07e sgGFP_1

value: M07e cell line


title: AMKL7_BM_sgRen


title: CD34_H3K27ac_2


title: M07e_2

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Analysis was done using ENCODE ATACseq pipeline https://github.com/kundajelab/atac-seq-pipeline
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files generated with bedGraphToBigWig tool (https://github.com/ENCODE-DCC/kentUtils) from scaled bedgraph generated by MACS2

source_name: CBFA2T3-GLIS2+ Acute Megakaryoblastic Leukemia cells

extract_protocol:
ATACseq libraries generated using standard protocol from Buenrostro et al Nat Methods. 2013 Dec;10(12):1213-8. doi: 10.1038/nmeth.2688
ATACseq libraries generated using standard protocol from Buenrostro et al Nat Methods. 2013 Dec;10(12):1213-8. doi: 10.1038/nmeth.2688

value: hematopoietic cells

value: untreated cells


title: TBE20 DMSO replicate 1

value: 0.1% DMSO treated

value: Non-smoker

value: None identified


title: M07e_1


title: CD34_Input_1

value: sonicated Input chromatin


title: TBE20 DMSO replicate 2


title: TBE22 DMSO replicate 2

value: 35, Male


title: AMKL7_2

value: patient derived AMKL cells


title: LNCAP_AKTI_SAL_rep3

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

description: Transcriptional profiling (RNA sequencing)

data_processing:
The first 4 nucleotides were removed from the sequenced reads using fastx_trimmer (FASTX Toolkit 0.0.13). The low quality nucleotides from the end of each read were removed using fastq_quality_trimmer (FASTX Toolkit 0.0.13) with -Q 33 -t 20 -l 25 parameters. Only the first sequenced read from the pair end (R1) was used for the downstream analysis.
The fastq files were mapped to the hg19 genome using tophat (v2.1.0) with the following parameters --bowtie1 --no-coverage-search -a 5.
The number of reads covered by each gene was calculated using htseq-count (0.11.2) with -s no -a 0 -t exon -m intersection-nonempty parameters and hg19 gencode.v19 annotation.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: Htseq-count text files.

source_name: LNCaP human PCa cell line

growth_protocol: Cells were cultured in 5% FBS DMEM.

extract_protocol:
Total RNA was isolated using peqGOLD TriFast (Peqlab, Erlangen, Germany) according to the manufacturer’s protocol.
Sequencing library was prepared using SMARTer® Stranded Total RNA Sample Prep Kit - HI Mammalian (TAKARA).

treatment_protocol: Cells were treated in DMEM for 72h with Akti and 1nM R1881 (SAL) or 1pM R1881 (LAL).

value: LNCaP

value: Prostate cancer cell line

value: 1nM R1881 & Akti


title: Sample 47: Genomic DNA from cardiac left ventricle

type: genomic

city: New York

first: Veli

middle: K

last: Topkara

state: NY

department: Cardiology

institute: Columbia University

hyb_protocol: Standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BMIQ normalization, batch correction, and merged on common 450K and Infinium EPIC probes

label: Cy3, Cy5

source_name: cardiac left ventricle

label_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k or EPIC Beadchip using standard Illumina protocol

extract_protocol: Genomic DNA was extracted and purified from Human Left Ventricle samples using Qiagen DNeasy Kit according to standard instructions

value: cardiac left ventricle

tag: age

tag: gender

value: Male

tag: race/ethnicity

value: White

tag: hf etiology

value: Non-Ischemic

tag: lvad status

value: pre-LVAD


title: Sample 46: Genomic DNA from cardiac left ventricle

value: Ischemic


title: AMKL7_1

value: hematopoietic cells


title: Sample 45: Genomic DNA from cardiac left ventricle

value: Black


title: Sample 48: Genomic DNA from cardiac left ventricle


title: Sample 49: Genomic DNA from cardiac left ventricle

value: Female


title: Sample 44: Genomic DNA from cardiac left ventricle


title: Sample 51: Genomic DNA from cardiac left ventricle


title: CD34_Input_2

value: CD34+ cord blood cells

tag: antibody


title: TBE20 DMSO replicate 3

value: Fully differentiated airway epithelial cells

tag: treatment

value: 0.1% DMSO treated

value: 13, Male

value: Caucasian

value: Non-smoker

value: None identified


title: LNCAP_AKTI_SAL_rep1

tag: cell line

value: LNCaP

value: Prostate cancer cell line

value: 1nM R1881 & Akti


title: 16 [miRNA-Seq]

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

data_processing:
filtering of data performed by BGI
mapping done by BGI using Bowtie2
sRNA classification and prediction done by BGI
Supplementary_files_format_and_content: Matrix table with raw counts and TPM values for every small RNA and every sample

source_name: iWAT

growth_protocol: 4-day expansion after isolation and FACS sorting

extract_protocol:
miRNeasy Mini Kit
done by company BGI

treatment_protocol: no treatment

value: mesenchymal stromal cells


title: Sample 43: Genomic DNA from cardiac left ventricle

value: cardiac left ventricle

value: Male

value: Hispanic


title: 15 [miRNA-Seq]


title: LNCAP_AKTI_rep3

value: Akti


title: Sample 50: Genomic DNA from cardiac left ventricle

value: Black

value: Non-Ischemic

value: pre-LVAD


title: Sample 40: Genomic DNA from cardiac left ventricle

value: White

value: Ischemic


title: M07e_sg2

value: M07e cell line

value: hematopoietic cells

value: CRISPRI expressing cells


title: M07e_sg5


title: LNCAP_AKTI_rep2


title: Sample 37: Genomic DNA from cardiac left ventricle


title: Sample 41: Genomic DNA from cardiac left ventricle


title: 14 [miRNA-Seq]


title: Sample 42: Genomic DNA from cardiac left ventricle


title: LNCAP_AKTI_SAL_rep2


title: 8 [miRNA-Seq]

source_name: pancreas


title: M07e_sg8


title: LNCAP_AKTI_rep1


title: M07e_sgRen


title: LNCAP_AKTI_LAL_rep3

value: 1pM R1881 & Akti


title: 13 [miRNA-Seq]


title: M07e_sg7


title: LNCAP_AKTI_LAL_rep2

value: LNCaP


title: Sample 39: Genomic DNA from cardiac left ventricle

value: Female


title: Sample 38: Genomic DNA from cardiac left ventricle


title: 6 [miRNA-Seq]


title: EM-seq of mouse NAc Drd2-MSN biological replicate 1

city: Tallahassee

first: Jian

last: Feng

state: FL

address: 319 Stadium Dr

department: biological science

institute: Florida State University

description: Sample 3 EM-seq with Replicate 1

data_processing:
library stategy: enzymatic conversion-based method Enzymatic Methyl-seq (EM-seq)
Trim Galore 0.6.4 and Cutadapt 1.18 were used to  remove the low-quality sequences (Quality Phred score <20) and artificial adaptor se-quences. We trimmed an additional 18 bp from 5’ end and 4 bp from 3’ end for both reads of AM-seq libraries. For both reads of EM-seq libraries, we trimmed 8 bp from 5’ end and 4 bp from 3’ end according to the positional base content bias result by FastQC. Read-pairs with any one read less than 20 bp were removed.
Processed reads were mapped to mouse reference genome of mm10 by Bismark (Krueger et. al, 2011). After deduplication and removal of unconverted reads, the bam files were used for methylation base calling using "bismark_methylation_extractor --CX --buffer_size 16G  --gzip --parallel 8 -p --bedGraph". The methylation profiling of each cytosine in genomic context was generated by  "coverage2cytosine  --gzip  --coverage_threshold 1 "
Genome_build: mm10
Supplementary_files_format_and_content: Methylation coverage file with cytosine context information by "coverage2cytosine" of Bismark. Columns for left to right are : <chromosome>  <position>  <strand>  <count methylated>  <count non-methylated>  <C-context>  <trinucleotide context>.

source_name: nucleus accumbens

growth_protocol: Male D2-eGFP mice (Gong et al., 2003) were born and raised in a controlled laboratory condition under a 12-hour reverse light/dark lighting cycle at 22-25°C. Pups were weaned at postnatal day 21 and were group-housed with up to 4 mice per cage with ad libitum access to food and water. All mice used in this study were of a C56BL/6J genetic background.

extract_protocol:
we followed the recommended mannul of NEBNext Enzymatic Methyl-seq kit.
libraries were sequenced on Illumina Novaseq 6000 S1 flow cell with 30% spike-in of whole-genome sequencing libraries

treatment_protocol: Mouse brains were immediately removed after cervical dislocation and decapitation, and then sectioned in a stainless steel brain matrix (1 mm intervals) on ice. Four micro-punches of NAc were collected from each brain by a 14-gauge blunt-tip pipetting needle and minced into small pieces in ice-cold Hibernate A -Ca medium (Brainbits, # HA-CA500) plus B27 supplement (Fisher scientific, #17504044). The minced tissue was then incubated in Hibernate A -Ca medium with 20 unit/ml papain (Worthington, #LK003176), 5% trehalose (Acros organics, # AC30987), and 0.1 mg/ml DNase (Worthington, #LK003170) at 37°C for 30 min with 700 rpm agitation. After being washed by Hibernate A-Ca medium with 1% BSA, the tissue was triturated to cell suspension. After passing through a 70um cell strainer, the suspension was sorted on a FACS Aria SORP (BD) using a 100uM nozzle, and the GFP-positive cells were collected in ice-cold 1X PBS buffer with 1% BSA

value: D2 medium spiny neurons

value: nucleus accumbens

tag: library stategy

tag: biological sample


title: EM-seq of mouse NAc Drd2-MSN biological replicate 2

description: Sample 4 EM-seq with Replicate 2

value: enzymatic conversion-based method Enzymatic Methyl-seq (EM-seq)


title: C42_AKTI_SAL_rep3

source_name: C4-2 human PCa cell line

value: Prostate cancer cell line

value: 1nM R1881 & Akti


title: Sample 34: Genomic DNA from cardiac left ventricle

value: cardiac left ventricle

value: Male


title: Sample 36: Genomic DNA from cardiac left ventricle

value: Asian

value: Non-Ischemic


title: C42_AKTI_SAL_rep2


title: 5 [miRNA-Seq]

value: mesenchymal stromal cells


title: Bisulfite sequencing of mouse NAc Drd2-MSN biological replicate 2

description: Sample 2 AM-seq with Replicate 2

data_processing:
library stategy: sodium bisulfite-based Accel-NGS Methyl-Seq (AM-seq)
Trim Galore 0.6.4 and Cutadapt 1.18 were used to  remove the low-quality sequences (Quality Phred score <20) and artificial adaptor se-quences. We trimmed an additional 18 bp from 5’ end and 4 bp from 3’ end for both reads of AM-seq libraries. For both reads of EM-seq libraries, we trimmed 8 bp from 5’ end and 4 bp from 3’ end according to the positional base content bias result by FastQC. Read-pairs with any one read less than 20 bp were removed.
Processed reads were mapped to mouse reference genome of mm10 by Bismark (Krueger et. al, 2011). After deduplication and removal of unconverted reads, the bam files were used for methylation base calling using "bismark_methylation_extractor --CX --buffer_size 16G  --gzip --parallel 8 -p --bedGraph". The methylation profiling of each cytosine in genomic context was generated by  "coverage2cytosine  --gzip  --coverage_threshold 1 "
Genome_build: mm10
Supplementary_files_format_and_content: Methylation coverage file with cytosine context information by "coverage2cytosine" of Bismark. Columns for left to right are : <chromosome>  <position>  <strand>  <count methylated>  <count non-methylated>  <C-context>  <trinucleotide context>.

extract_protocol:
we followed the recommended mannul of Accel-NGS Methyl-Seq DNA Library Kit.
libraries were sequenced on Illumina Novaseq 6000 S1 flow cell with 30% spike-in of whole-genome sequencing libraries


title: 16

data_processing:
adapters and low-quality reads have been filtered by BGI
reads have been aligned to reference using STAR
FPKM values for transcripts were determind by STRINGTIE
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Matrix table with FPKM transcript values for every transcript and every sample


title: C42_AKTI_SAL_rep1


title: C42_AKTI_rep3

value: Akti


title: Bisulfite sequencing of mouse NAc Drd2-MSN biological replicate 1

description: Sample 1 AM-seq with Replicate 1

value: sodium bisulfite-based Accel-NGS Methyl-Seq (AM-seq)


title: 15


title: 15/R50t: Fetal Ovary Late Gestation_rep10

city: Adelaide

first: Katja

last: Hummitzsch

state: SA

address: Level 5, North Tce/George Street

department: Obstetrics& Gynaecology

institute: The University of Adelaide

description: RNA from whole fetal ovary

data_processing:
pre-alignment QA/QC and base trimming in Partek Flow, version 8
alignment using STAR 2.7.3a aligner for bovine genome ARS-UCD1.2 and Partek E/M annotation model in Partek Flow, version 8
filter counts and normalized counts were determined in Partek Flow, version 8
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each gene and each sample

organism: Bos taurus

source_name: fetal ovary

extract_protocol:
Fetal ovaries were removed from fetuses, flash frozen on dry ice, and RNA was harvested using Trizol reagent (including homogenisation).
Single-end Poly A-selection mRNA libraries (~35m reads per sample) were created using the Nugen Universal Plus mRNA-Seq library kit from Tecan (Mannedorf, Switzerland) and sequenced with an Illumina Nextseq 500 using single read 75bp (v2.0) sequencing chemistry (Illumina Inc., San Diego, CA, USA). Two sequencing runs, with 10 samples per run, were performed and sample 15/R43t was used as internal control in both runs.

value: fetal ovary

tag: crown-rump-length [cm]

tag: gestational age [days]


title: C42_AKTI_rep2

tag: cell type


title: 15/R49t: Fetal Ovary Late Gestation_rep9

description: RNA from whole fetal ovary

tag: tissue


title: 14

tag: strain


title: 13


title: 7 [miRNA-Seq]


title: 15/R38t: Fetal Ovary Late Gestation_rep8

description: RNA from whole fetal ovary


title: Sample 31: Genomic DNA from cardiac left ventricle

value: White

value: pre-LVAD


title: Sample 35: Genomic DNA from cardiac left ventricle

value: Black


title: Sample 33: Genomic DNA from cardiac left ventricle

value: Female


title: Sample 30: Genomic DNA from cardiac left ventricle

value: Ischemic


title: Sample 32: Genomic DNA from cardiac left ventricle


title: 15/R35t: Fetal Ovary Late Gestation_rep7

description: RNA from whole fetal ovary


title: 8


title: Sample 29: Genomic DNA from cardiac left ventricle


title: C42_AKTI_LAL_rep2

value: 1pM R1881 & Akti


title: 15/R47t: Fetal Ovary Late Gestation_rep6

description: RNA from whole fetal ovary


title: C42_AKTI_rep1


title: 7


title: 6


title: C42_AKTI_LAL_rep1


title: 15/R33t: Fetal Ovary Late Gestation_rep5

description: RNA from whole fetal ovary


title: Sample 27: Genomic DNA from cardiac left ventricle


title: Sample 26: Genomic DNA from cardiac left ventricle

value: Hispanic


title: C42_AKTI_LAL_rep3

value: Prostate cancer cell line


title: 15/R45t: Fetal Ovary Late Gestation_rep4

description: RNA from whole fetal ovary


title: N-CWS-Exos2  [6-Y2]

city: Yiwu

first: Qiang

last: Sun

state: Zhejiang

address: No. N1, Shangcheng Avenue

institute: Zhejiang University

data_processing:
fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads. STAR software (v2.7.9a) was used to align the high-quality clean reads to the human reference genome (hg38).
DCC software (v0.5.0) was used to identified circRNAs and calculate the raw junction reads as the circRNA expression profile. DESeq2 software (v1.30.1) was used to normalize and calculate the fold change and Pvalue between two groups. Ensembl human GTF gene annotation database (v104) and circBase database were used to annotating the circRNA by circAnno software
Genome_build: hg38
Supplementary_files_format_and_content: circRNA expression profile

source_name: HUVEC

growth_protocol: HUVECs were cultivated in Dulbecco’s Modified Eagle’s Medium

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: treated in  high glucose treatment(25 mM) and MSC-EXOs for 24h

value: HUVEC

value: high glucose treatment(25mM)

value: treated in MSC-CWS-Exos for 24h

tag: molecule type

value: circ DNA


title: 5


title: 15/R1t: Fetal Ovary Late Gestation_rep3

description: RNA from whole fetal ovary


title: N-CWS-Exos1  [5-Y1]


title: 4T1-GPD2 KO_rep3

first: Sean

last: Oh

address: Gwanakro

institute: Seoul National University

data_processing:
Before the data analysis, the adapter sequence was removed by the Trimmomatic 0.38 program.
HISAT2 (version 2.1.0) program was used for the reference genome mapping with genomic DNA reference UCSC mm10.
Transcript assembly was performed through StringTie (version 1.3.4d) program with the reference-based aligned reads information.
Further DEG (Differentially Expressed Genes) analysis was performed with the significant DEG results selected under these conditions: |fc|>=2 & exactTest raw p-value<0.05.
With the significant gene lists, gene-set enrichment analysis (GSEA) was conducted based on KEGG database (http://www.genome.jp/kegg/).
Genome_build: UCSC mm10.
Supplementary_files_format_and_content: The FPKM (Fragments Per Kilobase of transcript per Million mapped reads) value was used for extracting expression profile.

source_name: 4T1 cell line

growth_protocol: Grow 4T1 breast cancer cell line in RPMI growth medium

extract_protocol:
Total RNA was extracted from the cells using easy-spin Total RNA Extraction Kit (#17221, iNtRON Biotechnology Inc., Seongnam, Korea).
RNA samples were proceeded for library construction according to TruSeq Stranded mRNA Sample Preparation Guide (Part #15031047 Rev. E).
For the quality of data on Illumina sequencing platforms, the libraries were quantified by qPCR according to the Illumina qPCR Quantification Protocol Guide.

treatment_protocol: 4T1 cells were treated with GPD2 gRNA and CRISPR/Cas9 containing vector.

value: BALB/c

value: breast cancer cell

tag: genotype


title: LNCAP_SAL_rep3

data_processing:
The first 4 nucleotide was removed from the sequenced reads using fastx_trimmer (FASTX Toolkit 0.0.13). The low quality nucleotides from the end of each read was removed using fastq_quality_trimmer (FASTX Toolkit 0.0.13) with -Q 33 -t 20 -l 25 parameters. Only the first sequenced read form the pair end (R1) was used for the downstream analysis.
The fastq files were mapped to the hg19 genome using tophat (v2.1.0) with the following parameters --bowtie1 --no-coverage-search -a 5.
The number of reads covered by each gene was calculated using htseq-count (0.11.2) with -s no -a 0 -t exon -m intersection-nonempty parameters and hg19 gencode.v19 annotation.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: HTSeq-count text files.

treatment_protocol: Cells were treated in DMEM for 72h with DMSO or 1nM R1881(SAL) or 1pM R1881(LAL).

value: LNCaP


title: ES1

description: ES1 and ES2 are data from one sample which is sequenced twice to obtain enough reads

data_processing:
Following sequencing, data were analysed using publicly available software programs and R pipelines. First, cellranger mkfastq (10x Genomics) generates FASTQ files from the raw sequencing data. Next, cellranger count uses the FASTQ file to perform sequence alignment (mouse: GRCm38, human: GRCh38), filter sequences based on quality score, and generate single cell gene counts. For count alignment of the lineage-tracing transgenes, the mouse reference genome was annotated to include the GFP and Timer sequences. Cellranger aggr was used to combine data from multiple samples (Green1, Green2 and Red) and ensure all libraries have the same sequencing depth.
As minimal filtering is performed in cellranger, two additional R pipelines were used to filter out cells that did not meet the quality control standard. The first pipeline is Scater (https://bioconductor.org/packages/release/bioc/html/scater.html) and is a single cell analysis pipeline that places a great emphasis on quality control. For this analysis, cells were discarded based on counts (transcripts/cell), genes (genes/cell) and percentage mitochondrial DNA expression, greater than 3 standard deviation away from the mean. Low-abundance genes, which were expressed by less than 3 cells, were removed.
This QC dataset was then analyzed using the Seurat V2.0 and V3.0 pipeline (http://satijalab.org/seurat/), another R toolkit for single cell genomics. Seurat posed an additional filtering step that removed out cells with less than 500 genes. Seurat was then used for normalization, correcting cells by their library size, and linear dimensional reduction, removing uninteresting source of variations.
Finally, unsupervised shared nearest neighbor modularity optimization based clustering was performed using Seurat to group cells based on gene expression and to identify unique cell types within the populations.
Genome_build: Customize reference transcriptomes were made by adding the GFP and Timer sequences to GRCm38 mouse transcriptome.
Supplementary_files_format_and_content: Raw counts matrix removing out background barcodes(<1000 UMI counts) and excluding genes with 0 counts.

source_name: hESC-derived β-like cells

extract_protocol:
The 10x Genomics ChromiumTM controller and Single Cell 3’ Reagent Kits v2 (Pleasanton, CA, USA) were used to generate single cell libraries. Briefly, cells were counted following FACS and cell suspensions were loaded for a targeted cell recovery of 1000-5000 cells per channel.The microfluidics platform was used to barcode single cells using Gel Bead-In-Emulsions (GEMs).
RT is performed within GEMs, resulting in barcoded cDNA from single cells. The full length, barcoded cDNA is PCR amplified followed by enzymatic fragmentation and SPRI double sided size selection for optimal cDNA size. End repair, A-tailing, Adaptor Ligation, and PCR are performed to generate the final libraries that have P5 and P7 primers compatible with Illumina sequencing. The libraries were pooled and sequenced using an Illumina NextSeq500 platform with a 150 cycle High Output v2 kit in paired-end format with 26 bp Read 1, 8 bp I5 Index, and 85 bp Read 2.

tag: age

value: Day 27

value: CyT49 parental hESC line

value: hESC-derived Beta-like cells


title: 4T1-GPD2 KO_rep2


title: LNCAP_SAL_rep1


title: Sample 24: Genomic DNA from cardiac left ventricle

value: cardiac left ventricle

tag: gender

value: White

value: pre-LVAD


title: Sample 23: Genomic DNA from cardiac left ventricle

value: Unknown

tag: race/ethnicity

value: Non-Failing


title: Sample 22: Genomic DNA from cardiac left ventricle

tag: hf etiology


title: MSC-EXOs1  [3-W1]

value: high glucose treatment(25 mM)

value: treated in MSC-EXOs for 24h


title: Sample 28: Genomic DNA from cardiac left ventricle

value: Male

value: Ischemic

tag: lvad status


title: 15/R2t: Fetal Ovary Late Gestation_rep1

description: RNA from whole fetal ovary

value: fetal ovary


title: 15/R43t: Fetal Ovary Early Gestation_rep9 [technical repeat - 2 raw files for this sample]

description: RNA from whole fetal ovary


title: LNCAP_SAL_rep2

value: Prostate cancer cell line


title: LNCAP_LAL_rep3


title: 4T1-WT_rep3

value: BALB/c

value: wildtype


title: Sample 25: Genomic DNA from cardiac left ventricle

value: Female

value: Black

value: Non-Ischemic


title: 15/R44t: Fetal Ovary Late Gestation_rep2

description: RNA from whole fetal ovary


title: MSC-EXOs2  [4-W2]

value: HUVEC

value: circ DNA


title: HG2  [2-G2]

value: untreated


title: Sample 20: Genomic DNA from cardiac left ventricle

value: cardiac left ventricle


title: 4T1-GPD2 KO_rep1

value: breast cancer cell


title: ES2

value: Day 27

value: CyT49 parental hESC line

value: hESC-derived Beta-like cells


title: 15/R51t: Fetal Ovary Early Gestation_rep8

description: RNA from whole fetal ovary


title: HG1  [1-G1]

value: high glucose treatment(25 mM)


title: LNCAP_LAL_rep2

value: LNCaP


title: 15/R42t: Fetal Ovary Early Gestation_rep7

description: RNA from whole fetal ovary

value: fetal ovary


title: High_2

city: Oxford

first: Alun

last: Vaughan-Jackson

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

data_processing:
Raw pair-end reads (150bp) were pre-processed using fastp 0.20.1 software with following additional parameters: --trim_poly_x, --correction, --detect_adapter_for_pe
Salmon 1.3.0 selective alignment was used for transcript mapping to a full decoy-aware transcriptome using the Gencode version 34 reference human transcriptome and GRCh38 primary assembly genome. Optional parameters used: --validateMappings, --seqBias, --gcBias, --dumpEq
The counts were imported, scaled to the average transcript length over samples and the library size (‘LengthScaledTPM’), and summarised to the gene level using the tximport package (v.1.16.0)
Lowly expressed genes with length-scaled abundance estimates less than 10 in 3 samples were filtered out with the default filtering function in the edgeR package
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon quantification files (quant.sf) for each sample with transcript length , effective length , estimated abundances and TPM values

source_name: Macrophages plated at high density, cultured in OXM

growth_protocol: Differentiation of iPSC into iPSC-Macs was carried out as previously described (Vaughan-  Jackson et al., 2021; van Wilgenburg et al., 2013) culturing in OXM medium and with the final 7 day  differentiation occurring with cells plated at stated densities.

extract_protocol:
Lysates were passed through QIAshredder columns (QIAGEN) and the total RNA extracted using a QIAGEN RNeasy Mini kit, according to the manufacturer’s protocol using on-column DNase treatment (QIAGEN). RNA samples were eluted in 50 µL of RNase-free water. The quantity and quality of RNA was measured by Nanodrop and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies), with measured RNA integrity (RIN) values ≥8.8.The mRNA fraction was selected from the total RNA for each sample before conversion to cDNA.
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

value: iPSC-derived macrophages

tag: batch

tag: rin

tag: density

value: high


title: High_3


title: 4T1-WT_rep1

value: BALB/c

tag: cell line

value: wildtype


title: LNCAP_LAL_rep1

value: Prostate cancer cell line

tag: treatment


title: Fibril Sedentary (FS, n = 4)

city: Matsumoto

first: Xiaoran

last: Cui

address: 3-1-1 Asahi

institute: Shinshu University

data_processing:
Basecalls performed using Illumina Nova6000 p150
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by fastp(Version 0.23.2)
Indexes of the reference genome was built using STAR   and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used   the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result   for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each   gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM,   Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing   depth and gene length for the reads count at the same time, and is currently the most commonly   used method for estimating gene expression levels (Mortazavi et al., 2008)
Genome_build: mm10
Supplementary_files_format_and_content: txt files include FPKM values for each Sample
Supplementary_files_format_and_content: txt files include rawcounts for each Sample

source_name: Liver

extract_protocol:
10 mg liver samples taken from each mouse and stored at -80 ̊ C were homogenized in TRIzol RNA isolation reagent (Invitrogen-Thermo Fisher, Tokyo Japan) and then pooled in 4 sample tubes (VS, VI, FS and FI groups, N = 4). The sample tubes were sent to Novogene (Nagoya, Japan) for analysis. Total RNA was extracted, and RNA purity and integrity were confirmed by Novogene.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AKR/J

value: Liver

value: post 16-week training (26-week-old)

value: Apoa2c congenic mic


title: Fibril Interval exercise (FI, n = 4)


title: 15/R41t: Fetal Ovary Early Gestation_rep5

description: RNA from whole fetal ovary

tag: crown-rump-length [cm]