title: spleen leukemic T cells, WT0 treated with BCAT1 inhibitor (ERG-245), rep3

value: BCAT1 inhibitor (ERG-245)


title: spleen leukemic T cells, WT0 treated with BCAT1 inhibitor (ERG-245),  rep2

status: Public on Sep 01 2024

type: SRA

city: Padova

first: Erich

last: Piovan

address: via Gattamelata 64

department: Surgery, Oncology and Gastroenterology

country: Italy

institute: University of Padova

library_source: transcriptomic

data_processing:
reads were trimmed for adapter sequences using trimgalore
trimmed reads were mapped to the genome using the STAR algorithm with default settings
The number of fragments overlapping genes were counted using featureCountsin Subread software packages
differential analysis was performed using DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: spleen

growth_protocol: deltaE-NOTCH1  transduced BM progenitor cells (GFP+Lineage-cKit+Sca1+) from Bcat1 KO and Bcat1 WT  were transplanted into lethally irradiated C57BL/6J hosts .

extract_protocol:
Total RNA was isolated from the cells using the Qiagen RNeasy Mini Kit (Qiagen, cat# 74104)
2 ug of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594)

treatment_protocol: deltaE-NOTCH1 leukemia bearing mice were injected i.p. with three doses of ERG245 (30mg/kg) at 8 h intervals or vehicle (PBS)

tag: tissue

value: spleen

tag: cell type

value: mouse primary tumour spleen leukemic T cells

tag: genotype

value: BCAT1 WT

tag: treatment


title: NEWBV25

type: genomic

city: Tartu

first: Alena

last: Kushniarevich

address: Riia 23b

department: Institute of Genomics

country: Estonia

institute: UNIVERSITY OF TARTU

description: Genomic DNA extracted from blood was genotyped using InfiniumOmniExpress-24v1.2 (Illumina).

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on an iSCAN System (Illumina).

data_processing:
Image data was analyzed using Genomestudio 2.0.5 (Illumina).
Genotype: AA,AB,BB,or NC (no call)

label: Biotin (C, G), Dinitrophenyl (A, T)

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master, according to the manufacturer's protocol. After incubation the amplified DNA was fragmented with fragmentation mix, precipitated with isopropanol and precipitation mix and resuspended in hybridization buffer.

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: project

tag: samplewell

tag: population

value: Kalmyk Buzav

tag: geographic location

value: Russia


title: HCT-116 cells, Control-3

type: RNA

city: Taipei City

first: Sukanya

last: Unson

address: No. 250, Wuxing Street, Xinyi District

department: Cancer biology and drug discovery

country: Taiwan

institute: Taipei medical university

hyb_protocol: Followed nCounter PanCancer Progression Panel protocol.

scan_protocol: Raw counts of mRNA were counted using the NanoString nCounter SPRINT Profiler Instrument.

data_processing:
Data were quantified, normalized and analyzed using the NanoString nSolver software analysis vers.4.0.
Gene Expression CodeSet profiling 770 genes; All data was normalized to internal reference controls (740 endogenous genes + 30 housekeeping genes).
Technical and biological normalization of the raw counts of each gene was performed using the NanoString nSolver software analysis vers.4.0.

label: Fluorescent barcode-labeled hybridization probes

source_name: Large intestine; Colon

growth_protocol: HCT-116 cells were seeded in six-well plates overnight at a density of 10^5 cells/well

extract_protocol: Total RNA was isolated using the TRIzol reagent

treatment_protocol: Cells were treated with heteronemin, tetrac, or their combination for 24 h.

value: Large intestine; Colon

value: Epithelial, Carcinoma

tag: cell line

value: Control


title: MG4

value: Mongol Derbet

value: Mongolia


title: SK442, ASA treatment

city: Chicago

first: Sonia

middle: S

last: Kupfer

state: IL

department: Human Genetics

country: USA

institute: University of Chicago

data_processing:
RNA-seq equence alignment and gene expression value estimation was performed using RSEM (v.1.3.1) using the STAR aligner in paired-end mode.
RNA-seq differential expression analysis was performed with the R package DESeq2 (v1.30.1) after first filtering for protein coding biotype and using DESeq's independent filtering.
Assembly: transcriptome reference was generated from the 1000genomes Phase2 Reference Genome Sequence (hs37d5) and transcript annotations from the Gencode comprehensive gene annotation GTF (Release 29)
Supplementary files format and content: RSEM output files of transcript level abundances in tab-delimited plain text format

source_name: colonic organoid

growth_protocol: Organoids were derived using a protocol adapted from Sato et al 2011

extract_protocol:
RNA-seq: mRNA was isolated from cells using the RNeasy® Plus Mini Kit (Qiagen) according to the manufacturer’s protocol.
RNA-seq libraries were prepared using Illumina mRNA TruSeq kits as protocolled by Illumina.

treatment_protocol: Organoids were treated with either 3mM ASA or vehicle control (0.1% DMSO) for 24 hours.

value: colonic organoid

tag: Sex

value: F

tag: age

tag: ethnicity

value: AA

value: ASA


title: SK440, DMSO control

value: M

value: DMSO


title: SK442, DMSO control


title: NEWBV34


title: spleen leukemic T cells, WT0 treated with BCAT1 inhibitor (ERG-245), rep1

value: BCAT1 inhibitor (ERG-245)


title: pre_28

city: shihezi

first: lanying

last: gu

address: shibei 4th road

country: China

institute: shihezi university

library_source: genomic

data_processing:
Raw data filtration    Adapter sequences were trimmed by using cutadapt. The parameter settings used was “ -a AGATCGGAAGAGC -m 35 -n 2”.    Sequence alignment    The cleaned reads were mapped back to genome using BSMAP software version 2.90 (Xi & Li, 2009). The parameter settings used was “-n 0 -v 0.08 -g 1”. Methylation ratios were extracted from BSMAP output (SAM) using a Python script (methratio.py) which is distributed with the BSMAP package. Only unique mapped reads were used to calculate methylation ratios. Only cytosines in a CpG context with sufficient sequencing depth (greater than or equal to 5x coverage) were retained for further analysis.    DMR detection    Differentially methylated regions (DMRs) were detected using metilene (Jühling et al., 2016) in de-novo mode among CpG sites with at least 5x coverage. The parameter settings used was “--mincpgs 5 --minMethDiff 0.1 --mtc 1 -X 1 -Y 1 -v 0.7”. Then detected DMR were filtered according to the standard: (1) Q-value must be less than 0.05; (2) methylation level difference must be greater than 0.1; (3) CpG number contained in DMR must be greater than 5; (4) the length of the DMR must be greater than 50bp.
Assembly: susScr11
Supplementary files format and content: bedgraph flies include methylation level for each C cite in each samples

organism: Sus scrofa

source_name: Blood

extract_protocol:
DNA was extracted from blood samples of pig using a DNA extraction Kit(Beijing, China, Tiangen Biochemical Technology Co., Ltd., DP304-03)
About 1µg of genomic DNA mixed with unmethylated lambda DNA was digested by MspI enzyme for 16 hours at 37℃. After digestion, the libraries were constructed as the Illumina Pair-End protocol with some modifications. Briefly, purified digested DNA was subsequently treated with a mix of T4 DNA polymerase, Klenow Fragment and T4 polynucleotide kinase to repair, blunt and phosphorylate ends. After that, the blunt DNA were 3’ adenylated using Klenow Fragment (3’-5’ exo-) and following with ligation to adaptors synthesized with 5’-methylcytosine instead of cytosine using T4 DNA Ligase. After each step, the DNA was purified using MinElute PCR Purification Kit (Qiagen). ZYMO EZ DNA Methylation-Gold Kit™ was employed to convert unmethylated cytosine into uracil according to the instructions. Finally, PCR was carried out in a final reaction volume of 50µl consisting of 20µl adapter ligated DNA, 4µl 2.5mM dNTP, 5µl 10×buffer, 0.5µl JumpStart™ Taq DNA Polymerase, 2µl PCR primers and 18.5µl water and the following thermal cycling program was 94°C 1 min, 12cycles of 94 °C 10s, 62°C 30s, 72°C 30 then prolong with 5min at 72°C and products could be hold at 12°C. Before analysis with Illumina sequencing platform, the size selected library was analyzed by the Bioanalyzer analysis system (Agilent, Santa Clara, USA) and quantified by the real time PCR.

value: Blood


title: SK440, ASA treatment


title: spleen leukemic T cells, WT0 control (PBS treated), rep3

value: spleen

value: mouse primary tumour spleen leukemic T cells

value: PBS


title: spleen leukemic T cells, WT0 control (PBS treated), rep2

value: BCAT1 WT


title: MG91


title: KBV140

value: Kalmyk Buzav

value: Russia


title: pre_0


title: MIX treatment, biological replicate 4

city: New York

first: Anna

last: Podlesny-Drabiniok

state: NY

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Reads QC FastQC v0.11.8
Adapter trimming Cutadapt v2.6
Alignment to the human genome STAR v2.5.3a
Assembly: hg38
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

growth_protocol: THP-1 monocytic leukemia line was differentiated to THP-1 macrophages for 72h in 25ng/ml 12-phorbol 13-myristate acetate (PMA).

extract_protocol:
Rneasy Mini column (Qiagen), according to the manufacturer's protocol
TruSeq RNA Sample Prep Kit v2, according to the manufacturer's protocol

treatment_protocol: THP-1 macrophages were treated with 20ng/ml IL-4, 25ng/ml M-CSF, 50ng/ml TGF-β and 100ng/ml IL-34 for 2-3 days and cells were collected. Four groups were obtained: 3F (IL34, TGFb, MCSF), IL4 (IL4), MIX (3F + IL4) and non-treated

value: THP-1 macrophages

value: WT

value: mix of 3F and IL4


title: SK430, DMSO control

value: colonic organoid


title: spleen leukemic T cells, WT0 control (PBS treated), rep1


title: HCT-116 cells, Control-1

label_protocol: Followed nCounter PanCancer Progression Panel protocol.

value: Large intestine; Colon

value: Epithelial, Carcinoma

value: Control


title: KT70

value: Kalmyk Torgut


title: MG2

value: Mongol Derbet

value: Mongolia


title: MIX treatment, biological replicate 2


title: KT33


title: KT60


title: MIX treatment, biological replicate 3


title: SK430, ASA treatment

value: M

value: AA

value: ASA


title: S-V9-Ab E0771 bio rep 1

city: Iowa City

first: Michael

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

data_processing:
Data were processed using the SpaceRanger pipeline (version 2.0.1) from 10X in "count" mode
Assembly: GRCh38
Supplementary files format and content: feature by barcode matrix
Supplementary files format and content: visium image file

source_name: Primary tumor

growth_protocol: C57BL/6-derived mammary tumor cells E0771 (5x105cells/mouse) were orthotopically injected into mammary fats of C57BL/6 mice (8-10 weeks old).

extract_protocol:
Fresh tumor tissues were removed and placed in a petri-dish and embedded with room temperature OCT without any bubbles on the tissue’s surface. The embedded samples were transferred into the cryo mold . The cryo mold containing OCT-embedded samples were put into the metal beaker with 2-methylbutane in a dewar of liquid nitrogen until the OCT was solidified. Sample cryosectioning, affixment to cDNA capture slide, H&E staining, tissue permeabilization, RNA capture, and cNDA synthesis were performed according to the 10 x Visium spatial transcriptomics’ introductions.
Libaries were prepared with 10x Genomics Visium Spatial Tissue Optimization Slides & Reagent Kit 4 slides(product code:1000193), Visium Spatial Gene Expression Slides & Reagent Kit 4 rxns(product code:1000187), and Dual index KitTT Set A 96 rxns(product code:1000215)
Spatial Transcriptomics

treatment_protocol: After tumor injection, mice were randomly divided into two groups. The mice in antibody treatment group were treated with antibody (twice/week) start from the third day post-tumor injection. Mice treated with same volume of PBS were used as control group.

value: Primary tumor


title: HCT-116 cells, Control-2


title: MIX treatment, biological replicate 1


title: Control E0771 bio rep 2

value: PBS


title: KH19

value: Kalmyk Khoshut


title: KBV194

value: Kalmyk Buzav

value: Russia


title: Control E0771 bio rep 1


title: 3F treatment, biological replicate 4

value: THP-1 macrophages

value: WT


title: SK426, DMSO control

value: colonic organoid

value: F

value: DMSO


title: 3F treatment, biological replicate 3


title: SK428, ASA treatment

value: EA


title: SK426, ASA treatment


title: S-V9-Ab E0771 bio rep 2


title: Smarca5_KO

city: Rehovot

first: Ziv

last: Shulman

address: 234 Herzl st.

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the cellranger-arc-2.0.2
Assembly: mm10
Supplementary files format and content: 10x counts: zipped folder of tab-separated values files and matrix files from cellranger-arc
Supplementary files format and content: 10x ATAC raw output: ATAC bam output from cellranger-arc. Can be converted to fastq using 10x bamtofastq
Supplementary files format and content: 10x ATAC fragments: tsv files contains peaks of open chromatin
Library strategy: scMultiome - RNA + ATAC

molecule: nuclear RNA

source_name: Lymph node

extract_protocol:
B cells were sorted into FACS wash buffer, and nuclei were isolated using the Chromium Nuclei Isolation Kit (10x Genomics) according to the manufacturer's instructions. Nuclei were counted using trypan blue and hemocytometer, and imaged at 40X magnification to assess their quality. Nuclei were diluted in nuclei buffer supplemented with 1 mM DTT and 1 U/µl RNAse inhibitor to a final concentration of 3700 nuclei/ul.
Nuclei were processed with the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics) according to the manufacturer’s protocol. Final libraries were quantified by qPCR with the NEB-next Library Quant Kit (New England Biolabs) and with Qubit and TapeStation. Sequencing was done with a Nova-Seq 6000 (Illumina) using two SP100 cycle kits (for the ATAC-seq library and for the gene expression library), allocating 25,000 read pairs per nucleus for the ATAC-seq library and 20,000 read pairs per nucleus for gene expression libraries.

value: Lymph node

value: B cells


title: SK422, DMSO control


title: 3F treatment, biological replicate 2


title: Smarca5_cntrl

description: 10x Genomics


title: 3F treatment, biological replicate 1


title: KSHM9

value: Kalmyk Derbet


title: KT9

value: Kalmyk Torgut


title: SK422, ASA treatment


title: Smar_KO3

description: MARS-seq bulk RNAseq

data_processing:
Reads were quality trimmed using cutadapt. Mapped to the genome using STAR.
Htseq count was used to create count matrix
Assembly: mm10
Supplementary files format and content: counts: xlsx file with counts per sample per gene

molecule: polyA RNA

extract_protocol:
mRNA was isolated using the Dynabeads mRNA direct kit according to the manufacturer’s instructions (Life Technologies).
A bulk adaptation of the massively parallel single-cell RNA sequencing protocol (MARS-seq) was used (Jaitin et al. Science 2014) to generate RNA-seq libraries for transcriptomic analysis.


title: Smar_KO2

description: MARS-seq bulk RNAseq


title: SK428, DMSO control


title: KIB20


title: Smar_KO1

description: MARS-seq bulk RNAseq


title: SK420, DMSO control


title: IL4 treatment, biological replicate 4


title: SK420, ASA treatment


title: KBV184


title: Smar_Cntrl6

description: MARS-seq bulk RNAseq


title: KSHM18


title: KSHM12


title: SK418, DMSO control


title: Smar_Cntrl5

description: MARS-seq bulk RNAseq


title: IL4 treatment, biological replicate 2


title: IL4 treatment, biological replicate 3


title: SK418, ASA treatment


title: IL4 treatment, biological replicate 1


title: KH15


title: Smar_Cntrl4

description: MARS-seq bulk RNAseq


title: no cytokines, biological replicate 4

value: non-treated


title: SK416, DMSO control


title: Smar_Cntrl3

description: MARS-seq bulk RNAseq


title: KH21


title: KBV185


title: no cytokines, biological replicate 3


title: SK416, ASA treatment

value: ASA


title: Smar_Cntrl2

description: MARS-seq bulk RNAseq


title: Smar_Cntrl1

description: MARS-seq bulk RNAseq


title: SK414, ASA treatment


title: BTEC_Au_rep3

city: Norman

first: Stefan

last: Wilhelm

state: Oklahoma

address: 173 Felgar Street

department: School of Biomedical Engineering

institute: University of Oklahoma

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. The gene hit counts were used for comparing gene expressions between groups of samples using DESeq2. The Wald test was used to generate p-values and log2 fold changes.
Assembly: Homo sapiens GRCh38 reference genome available on ENSEMBL
Supplementary files format and content: excel files; differential gene expression analyses of comparisons including BTEC vs MMEC, BTEC_Au vs MMEC_Au, BTEC_Au vs BTEC, and MMEC_Au vs MMEC.

source_name: breast tumor

growth_protocol: HMMECs and HBTECs were cultured on gelatin (CellBiologics, 6950) pre-coated flasks with complete human endothelial cell medium (CellBiologics, H1168) until reaching 80% confluency. Then the cells were cultured for another 5 days in conditioned media. The conditioned media were composed of 70% of the general complete endothelial cell media and 30 % of the basal media which were incubated with MCF-10a (for HMMECs) and MDA-MB-231 (for HBTECs) for 24 hours.

extract_protocol:
RNA was extracted using Rneasy Plus Mini Kit (Qiagen).
SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for library construction.

treatment_protocol: For the samples with gold nanoparticle incubation, cells were incubated with gold nanoparticles at a concentration of 0.16 nM in conditioned media for 24 hours.

value: breast tumor

value: human primary breast tumor-associated endothelial cell, HBTEC

value: endothelial cell

value: 24-hour incubation with gold nanoparticles


title: no cytokines, biological replicate 2


title: KT37

value: Russia


title: no cytokines, biological replicate 1

value: THP-1 macrophages


title: SK414, DMSO control


title: KDR275


title: KH9

value: Kalmyk Khoshut


title: isotype_1

description:
CUT & RUN
Smarca5_vs_isotype_1_peaks.narrowPeak

data_processing:
Reads were mapped using bowtie2. Peaks were called using MACS2 with isotype samples as background
Assembly: mm10
Supplementary files format and content: peaks files: narrow peaks output from MACS2 (except for isotype samples)
Library strategy: CUT & RUN

source_name: lymph nodes

extract_protocol:
Sorted B cells were subjected to the CUT&RUN protocol Version 3 (Janssens et al. 2019). B cells were added to a Concanavalin A-coated bead slurry that had been pre-incubated with CaCl2 and MnCl2 to activate the beads. The cells and beads were rotated for 10 minutes at room temperature to ensure that all cells were coated onto the beads. The cells of each mouse were divided into two samples. Tubes were then placed into a magnetic stand to remove the liquid, and the supernatants were discarded. The cell-bead mixtures were resuspended in 100 µl of antibody buffer containing 0.05% digitonin for permeabilization. Next, 1 µl of monoclonal rabbit-anti mouse SNF2H antibody (Abcam) or a rabbit monoclonal isotype antibody (Cell Signaling Technologies) were added to the permeabilized samples, and the mixture was incubated overnight on a rotator. The following day, the beads were washed twice and then incubated for one hour in 150 µl of digitonin-containing wash buffer with 700 ng/ml of pA/G-MNase (kindly provided by the lab of Steven Henikoff). After incubation, the beads were washed twice and resuspended in 100 µl of digitonin-containing wash buffer. The beads were then chilled to 0°C in a metal block resting in ice. Finally, 2 µl of 100 mM CaCl2 was added to activate the MNase activity, resulting in a final concentration of 2 mM. The reaction was stopped after 30 minutes. The bead-cell mixture was incubated for at least 30 minutes at 37°C to release restricted DNA fragments. Then, the tubes were placed into a magnetic stand, and the supernatants containing DNA fragments of interest were collected.
DNA fragments were used directly for library preparation, by performing joint end repair and poly A tailing, Truseq adapter ligation and PCR enrichment with the KAPA HiFi master mix (Roche) for 10-14 cycles. CUT and RUN libraries were then analyzed with a Nova-Seq 6000 sequencer (Illumina) using paired end sequencing.

value: lymph nodes

value: GC B


title: isotype_2

description:
CUT & RUN
Smarca5_vs_isotype_2_peaks.narrowPeak


title: SK408, DMSO control

value: colonic organoid

value: M

value: DMSO


title: Smarca5_2


title: BTEC_Au_rep1


title: BTEC_Au_rep2


title: KSS5

value: Kalmyk Xinjiang

value: China


title: KT4

value: Kalmyk Torgut


title: SK408, ASA treatment

value: EA


title: Smarca5_1


title: KBV177

value: Kalmyk Buzav


title: SK406, ASA treatment

value: AA

value: ASA


title: SK406, DMSO control


title: MMEC_Au_rep2

source_name: breast

value: breast

value: human primary mammary microvascular endothelial cell, HMMEC

value: endothelial cell


title: gWAT KO HFD_rep3

city: Seoul, Republic of Korea

first: Sumin

last: Lee

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
bcl2fastq2-v2.20.0 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.38. (Trimmomatic option : ILLUMINACLIP:[TruSeq3-PE-2.fa]:2:30:10:5:true ,LEADING:3 , TRAILING:3 , SLIDINGWINDOW:4:15, MINLEN:36)
To estimate expression levels, the RNA-Seq reads were mapped to Mus musculus genome (mm10) using HISAT2 version 2.1.0, which is capable of reporting split-read alignments across splice junctions and determined using StringTie version 1.3.4d software in default options.
The read count data of filtered genes was normalized by RLE (Relative Log Expression) normalization with DESeq2. The nbinomWaldTest function in DESeq2 was used to test for differential expression. The output prints foldChange, p-value and FDR values which corrected by the Benjamin-Hochberg procedure.  DEGs was determined by |fold change|>=2 and p-value <0.05. For DEGs, hierarchical clustering analysis was performed with complete linkage method and Euclidean distance as a measure of similarity.
Gene-enrichment analysis and KEGG pathway analysis for DEGs were also performed based on Gene Ontology (http://geneontology.org/) and KEGG pathway (https://www.genome.jp/kegg/) database respectively. All statistical analysis and visualization of differentially expressed genes was conducted using R.3.5.1 (www.r-project.org).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: gonadal white adipose tissue

growth_protocol: Mice were fed a NCD or HFD and were kept on a 12-h light/12-h dark cycle with free access to food and water at 22±1 °C.

extract_protocol:
RNA was isolated using Trizol reagent (Invitrogen) and processed as per manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit, according to the manufacturer’s protocol.

treatment_protocol: Mice were fed a NCD or HFD for 16 weeks at the age of 8 weeks.

value: gonadal white adipose tissue

tag: strain

value: male

value: miR-10a KO

value: 16 weeks of HFD feeding


title: SK402, DMSO control

value: colonic organoid

value: F


title: KBV173

value: Russia


title: gWAT KO HFD_rep2


title: KIB18

value: Kalmyk Derbet


title: SK402, ASA treatment


title: BTEC_rep2

value: breast tumor

value: human primary breast tumor-associated endothelial cell, HBTEC


title: gWAT WT HFD_rep3

value: Wild-type


title: KDR217


title: MMEC_rep2


title: KSS4

value: Kalmyk Xinjiang

value: China


title: SK400, DMSO control

value: EA

value: DMSO


title: SK398, DMSO control


title: SK400, ASA treatment

value: ASA


title: MMEC_Au_rep3

value: breast

value: human primary mammary microvascular endothelial cell, HMMEC

value: endothelial cell

value: 24-hour incubation with gold nanoparticles


title: BTEC_rep1


title: MMEC_rep1


title: gWAT WT HFD_rep2

value: gonadal white adipose tissue

value: male

value: 16 weeks of HFD feeding


title: SK398, ASA treatment

value: colonic organoid

value: F


title: KSS1


title: gWAT KO NCD_rep3

value: miR-10a KO

value: 16 weeks of NCD feeding


title: gWAT KO NCD_rep2


title: T3

city: Shanghai

first: Chuandong

last: Wang

address: 320 Yueyang Road

institute: SJTU

description:
T3
piRNA_raw_counts.txt

data_processing:
Blastn (2.9.0+) software was used to identify piRNAs and obtain the read count number quantitatively
According to the CPM value of each sample, violin and density charts were made to show the distribution of the CPM of each sample
Assembly: Ensembl_v107
Supplementary files format and content: mRNA FPKM values for each sample
Supplementary files format and content: piRNA CPM values for each sample

source_name: cell line

extract_protocol:
RNA was isolated from peripheral blood plasma using an EZ-press Serum/Plasma RNA Purification Kit (EZB Bioscience, #EZB-RN2).
RNA samples were treated with 3'-terminal ligation, reverse transcription primer hybridization, 5'-terminal ligation, cDNA single strand synthesis, library amplification

value: cell line

value: Lung cancer cells

value: WT

tag: disease

value: Lung cancer patient


title: MMEC_Au_rep1


title: T2

description:
T2
piRNA_raw_counts.txt


title: SK394, ASA treatment

value: M

value: AA


title: Myotube11

first: Pei

last: Zhu

address: 420 E. Superior St

department: Biochemistry and Molecular Genetics

institute: northwestern university

data_processing:
Sequence reads were trimmed for adaptor sequences using the Trimmomatic (v0.33) tool
The trimmed reads were mapped to the mm10 Mus musculus reference genome using STAR aligner (v2.5.2).
The number of alignments mapped to each gene was counted using RSEM (v1.3.3), followed by passing to DESeq2 using the tximport package
Differentially expressed genes (DEGs) were identified through the results function in DESeq2 and corrected for multiple testing (an adjusted P-value was generated using the Benjamini-Hochberg correction).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

source_name: primary myoblast-derived myotubes

growth_protocol: Primary myoblasts isolated from Bmal1-floxed mice were induced into myotube and maintained in DMEM supplemented with 2% horse serum and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using Direct-zol RNA MicroPrep kit (Zymo Research).
cDNA libraries were constructed from 1 μg of total RNA using the TruSeq stranded total RNA library preparation kit (Illumina 20020596).

treatment_protocol: Primary myotubes were infected with Cre-expressing adenovirus or empty control virus for 48 hours, followed by exposed to normal oxygen levels (21%) or 1% oxygen for 6 hours, simulating post-surgery intramuscular hypoxia.

value: primary myoblast-derived myotubes

value: Bmal1 knockout

value: Hypoxia (1% O2 for 6h)


title: SK394, DMSO control

value: DMSO


title: Myotube12


title: gWAT KO HFD_rep1

value: gonadal white adipose tissue


title: T1

description:
T1
piRNA_raw_counts.txt


title: gWAT KO NCD_rep1

value: male


title: SK390, DMSO control


title: KH13

value: Kalmyk Khoshut

value: Russia


title: Myotube10


title: gWAT WT HFD_rep1

value: Wild-type

value: 16 weeks of HFD feeding


title: N3

description:
N3
piRNA_raw_counts.txt

value: Non-lung cancer patient


title: SK390, ASA treatment

value: colonic organoid

value: F

value: ASA


title: gWAT WT NCD_rep2

value: 16 weeks of NCD feeding


title: Myotube8

value: wildtype

value: Normoxia (21% O2)


title: SK382, DMSO control

value: M

value: EA


title: gWAT WT NCD_rep1


title: N2

description:
N2
piRNA_raw_counts.txt

value: cell line

value: Lung cancer cells

value: WT


title: Myotube7

value: primary myoblast-derived myotubes


title: SK382, ASA treatment


title: Myotube6

value: Bmal1 knockout

value: Hypoxia (1% O2 for 6h)


title: immune cell, rep4, scRNAseq

first: Yajing

last: Gao

address: Minhang district

institute: Fudan University

description: 10× Genomics

data_processing:
The Cell Ranger software pipeline (version 5.0.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
We processed the unique molecular identifier (UMI) count matrix using the R package Seurat
To remove low-quality cells and likely multiplet captures, which is a major concern in microdroplet-based experiments, a set of criteria were conducted
We applied DoubletFinder package (version 2.0.2) to identify potential doublet.
To obtain the normalized count, library size normalization was processed using NormalizeData function in Seurat
Assembly: mm10
Supplementary files format and content: Matrix table with RAW gene counts for every gene and every cell.
Supplementary files format and content: fastq.gz table for EAW reads.

source_name: section of the colon

extract_protocol:
Colons were digested and single cell suspensions obtained using 70-μm filters (BD, Franklin Lake, NJ, USA). After incubation with red blood cell lysis buffer, CD45+ immune cells were isolated by positive selection with anti-mouse CD45 magnetic beads (Miltenyi, Germany), according to the manufacturer’s instructions. Finally, cells were resuspended in complete RPMI-1640 medium, counted for viability, and then immediately subjected to library preparation.
ScRNA-Seq libraries were prepared using 10x Single Cell Genomics technology (10x Genomics, San Diego, CA, USA), according to the manufacturer’s instructions.

value: section of the colon

value: intestinal lamina propria leukocytes

tag: developmental stage

value: 10-weeks old

value: DSS


title: SK372, DMSO control

value: colonic organoid

value: F

value: DMSO


title: P3mouse_forelimb_3

city: Salt Lake City

first: Mai

last: Tran

state: UT

address: 201 President Circle

institute: University of Utah

description: raw original fastq files

data_processing:
Sequenced were trimmed for low quality sequence
trimmed sequence were mapped as described in the method section
normalized readcount were extracted for further differential gene expression analysis
Assembly: custom
Supplementary files format and content: tab-delimited read-count output of STAR

source_name: forelimb muscle

extract_protocol: NOT PROVIDED

value: forelimb muscle

value: normal


title: SK372, ASA treatment

value: ASA


title: immune cell, rep3, scRNAseq

description: 10× Genomics


title: immune cell, rep2, scRNAseq

description: 10× Genomics


title: Myotube5


title: P3mouse_forelimb_1

description: raw original fastq files


title: Myotube4


title: P3mouse_foot_3

description: raw original fastq files

source_name: hindfoot muscle

value: hindfoot muscle


title: gWAT WT NCD_rep3

value: gonadal white adipose tissue

value: male

value: Wild-type

value: 16 weeks of NCD feeding


title: immune cell, rep1, scRNAseq

description: 10× Genomics


title: SK358, ASA treatment

value: AA


title: Myotube3

value: primary myoblast-derived myotubes

value: wildtype

value: Normoxia (21% O2)


title: N1

description:
N1
piRNA_raw_counts.txt

value: cell line

value: Lung cancer cells

value: WT

value: Non-lung cancer patient


title: in vitro oocyte, polysomal RNA, rep1 [IVM-1 P]

city: Libechov

first: Michal

last: Dvoran

address: Rumburska 89

country: Czech Republic

institute: Institute of Animal Physiology and Genetics, CAS

description:
DGE IVM DO-IVO.xlsx
DGE IVM DO-IVM COC.xlsx

data_processing:
CLC Genomics Workbench v 22.0.0.
Sequence reads were trimmed
Trimmed sequence reads were mapped to GRCm39 by DRAGEN software (Illumina) pipeline
Read count extraction and normalization were performed using CLC Genomics benchwork
Assembly: GRCm39
Supplementary files format and content: excel files include RPKM values for each sample

source_name: ovarian

extract_protocol: RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

value: ovarian

value: germ cell

tag: sample group

value: in vitro oocyte, polysomal RNA

value: polysome fractionation


title: SK354, DMSO control

value: colonic organoid

value: F

value: EA

value: DMSO


title: P3mouse_foot_1

description: raw original fastq files

value: hindfoot muscle

value: normal


title: P3mouse_foot_2

description: raw original fastq files


title: Myotube2

value: primary myoblast-derived myotubes


title: SK354, ASA treatment

value: ASA


title: in vitro oocyte, polysomal RNA, rep3 [IVM-3 P]


title: Myotube9

value: wildtype

value: Normoxia (21% O2)


title: Myotube1


title: in vitro oocyte, polysomal RNA, rep2 [IVM-2 P]


title: SK358, DMSO control

value: AA


title: SK344, DMSO control

value: M


title: P0mouse_forelimb_2

description: trimmed fastq files

value: forelimb muscle


title: P0mouse_forelimb_3

description: trimmed fastq files


title: SK344, ASA treatment


title: SK340, DMSO control


title: TAMs, PLD2-KO, 2

city: Tsukuba

first: Kazuki

last: Hamada

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

data_processing:
CLC Genomics Workbench v 10.1.1
Assembly: mm10
Supplementary files format and content: bedGraph

source_name: tumor

extract_protocol:
Total RNA was extracted from whole bladders using a NucleoSpin RNA kit and from sorted cells using a TRIzol reagent. 500 ng total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an NEBNext Ultra Directional RNA Library Prep Kit following manufacturer's protocol.

value: tumor


title: in vitro cumulus-oocyte complex, polysomal RNA, rep1 [COC-1 P]

description:
DGE IVM COC-IVO.xlsx
DGE IVM DO-IVM COC.xlsx

value: ovarian

value: germ cell


title: TAMs, PLD2-KO, 3


title: TAMs, PLD2-KO, 1


title: P0mouse_forelimb_1

description: trimmed fastq files


title: in vitro cumulus-oocyte complex, polysomal RNA, rep2 [COC-2 P]

value: polysome fractionation


title: P0mouse_foot_3

description: trimmed fastq files


title: SK340, ASA treatment

value: colonic organoid


title: in vitro cumulus-oocyte complex, polysomal RNA, rep3 [COC-3 P]


title: in vitro cumulus-oocyte complex, polysomal RNA, rep4 [COC-4 P]


title: P0mouse_foot_2

description: trimmed fastq files


title: TAMs, WT, 3

value: WT


title: P0mouse_foot_1

description: trimmed fastq files


title: SK336, ASA treatment

value: EA


title: SK326, DMSO control

value: DMSO


title: in vivo oocyte, polysomal RNA, rep2 [IVO-2 P]

description:
DGE IVM COC-IVO.xlsx
DGE IVM DO-IVO.xlsx

value: in vivo oocyte, polysomal RNA


title: SK336, DMSO control


title: in vitro oocyte, polysomal RNA, rep4 [IVM-4 P]

value: in vitro oocyte, polysomal RNA


title: TAMs, WT, 1


title: LB12_LPS+HMO

city: San Diego

first: Nathan

middle: E.

last: Lewis

state: CA

address: 9500 Gilman Dr.

department: Pediatrics

institute: University of California, San Diego

description:
LPS+HMO
LB12

data_processing:
RNA-Seq quality was assessed using FastQC. Adapter sequences and low-quality bases were trimmed using Trimmomatic (Bolger et al. 2014).
Sequence alignment was accomplished using STAR (Dobin et al. 2013) against the Mouse genome (GCA_000001635.2) with default parameters.
HTSeq (Anders et al. 2015) was used to quantify the expression of each gene. We performed differential gene expression analysis using DESeq2 (Anders and Huber 2010).
Genome_build: Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample.

source_name: Macrophage

growth_protocol: All animals were housed and bred in vivaria approved by the Association for Assessment and Accreditation of Laboratory Animal Care located in the School of Medicine, UCSD, following standards and procedures approved by the UCSD Institutional Animal Care and Use Committee. Mice were weaned at 4 weeks, maintained on a 12-hour light cycle, and fed ad libitum with water and standard rodent chow (PicoLab® Rodent Diet 20 5053) or a Western diet (TD.88137, Envigo Teklad) containing 42 % kcal from fat.

extract_protocol:
Total RNA was isolated from homogenized tissue and cells and purified using E.Z.N.A. Hp Total RNA kit (Omega Tek) or RNeasy Mini kit (Qiagen) according to the manufacturer’s instructions. The quality and quantity of the total RNA was monitored and measured with NanoDrop (NanoDrop Technologies, Inc. Wilmington, DE). For quantitative PCR analysis, 5-10 ng of cDNA was used for real-time PCR with gene-specific primers (Supplemental Table 2) and TBP as a house keeping gene on a BioRad CFX96 Real-time PCR system (Bio Rad).
Transcriptomes of quiescent BMDM (PBS) were compared to BMDM incubated with either 3’SL or LPS alone and LPS and 3’SL together. RNA was extracted from cells and stranded RNA-Seq libraries were prepared from polyA enriched mRNA using the TruSeq Stranded mRNA library prep kit (Illumina). Library construction and sequencing was performed by the University of California San Diego (UCSD) Institute for Genomic Medicine.

treatment_protocol: Mice received 3’sialyllactose citrate in PBS (400 µg/injection) or PBS via subcutaneous injections twice daily for 6 weeks.

value: Macrophage

tag: intervention

value: LPS+HMO


title: in vivo oocyte, polysomal RNA, rep1 [IVO-1 P]

tag: tissue


title: SK326, ASA treatment

value: ASA


title: BBN_bladder, PLD2-KO, 16w-2

source_name: bladder

value: bladder


title: in vivo oocyte, polysomal RNA, rep3 [IVO-3 P]

tag: cell type


title: LB09_PBS

description:
PBS
LB09

value: PBS


title: BBN_bladder, PLD2-KO, 16w-3

tag: genotype


title: LB10_HMO

description:
HMO
LB10

value: HMO


title: LB11_LPS

description:
LPS
LB11

value: LPS


title: in vivo oocyte, polysomal RNA, rep4 [IVO-4 P]

tag: treatment


title: P3mouse_forelimb_2

description: raw original fastq files

value: forelimb muscle

value: normal


title: SK318, DMSO control

source_name: colonic organoid

value: M

value: AA


title: in vitro zygote, polysomal RNA, rep1 [IMZ-1 P]

description: DGE IMZ-IVZ.xlsx

value: ovarian

value: germ cell

value: in vitro zygote, polysomal RNA

value: polysome fractionation


title: SK318, ASA treatment

value: colonic organoid


title: BBN_bladder, WT, 16w-3

value: WT


title: TAMs, WT, 2

value: tumor


title: SK316, DMSO control

value: F

value: EA

value: DMSO


title: LB08_LPS+HMO

description:
LPS+HMO
LB08

value: Macrophage

value: LPS+HMO


title: in vitro zygote, polysomal RNA, rep2 [IMZ-2 P]

description: DGE IMZ-IVZ.xlsx


title: in vitro zygote, polysomal RNA, rep3 [IMZ-3 P]

description: DGE IMZ-IVZ.xlsx


title: LB07_LPS

description:
LPS
LB07

value: LPS


title: BBN_bladder, WT, 16w-2

value: bladder


title: in vitro zygote, polysomal RNA, rep4 [IMZ-4 P]

description: DGE IMZ-IVZ.xlsx


title: BBN_bladder, WT, 16w-1


title: SK306, DMSO control


title: bone marrow CLP (Lin-CD127+Flt3+) cells, wiltype (WT) 1

city: Bern

first: Interfaculty

last: Bioinformatics Unit

state: Bern

address: Baltzerstrasse 6

department: Interfaculty Bioinformatics Unit

country: Switzerland

institute: University of Bern

data_processing:
The quality of the RNA-seq data was assessed using fastqc v. 0.11.9and RSeQC v. 4.0.0 (Wang et al. 2012). The reads were mapped to the reference genome using HiSat2 v. 2.2.1(Kim et al. 2015). FeatureCounts v. 2.0.1(Liao et al. 2014)was used to count the number of reads overlapping with each gene as specified in the genome annotation (Mus_musculus.GRCm38.102).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file with raw gene counts for each sample

source_name: bone marrow

extract_protocol:
Total RNA from FACS sorted bone marrow CLP (Lin-CD127+Flt3+) cells were prepared using Picopure RNA isolation kit (ThermoFischer Scientific). The quality and concentration of total RNA was determined on Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Pico Assay. Samples with the RNA Index number (RIN) higher than 7 were used for library preparation.
RNA was reverse transcribed, and cDNA was amplified with SMART-Seq v2 or v4 (Takara). Libraries were prepared with Nextera XT (Illumina) according to manufacturer's instructions, as previously described (Rao TN , et al. JAK2-mutant hematopoietic cells display metabolic alterations that can be targeted to treat myeloproliferative neoplasms. Blood. 2019;134(21):1832-1846).

treatment_protocol: Sixteen weeks post-tamoxifen (TAM) treatment, total bone marrow cells were harvested from Wiltype (WT) and SclCre;JAK2-V617F (VF) mice.

value: bone marrow

value: bone marrow CLP (Lin-CD127+Flt3+) cells

value: Sixteen weeks post-tamoxifen (TAM)


title: LB06_HMO

description:
HMO
LB06

value: HMO


title: SK306, ASA treatment

data_processing:
RNA-seq equence alignment and gene expression value estimation was performed using RSEM (v.1.3.1) using the STAR aligner in paired-end mode.
RNA-seq differential expression analysis was performed with the R package DESeq2 (v1.30.1) after first filtering for protein coding biotype and using DESeq's independent filtering.
Assembly: transcriptome reference was generated from the 1000genomes Phase2 Reference Genome Sequence (hs37d5) and transcript annotations from the Gencode comprehensive gene annotation GTF (Release 29)
Supplementary files format and content: RSEM output files of transcript level abundances in tab-delimited plain text format

extract_protocol:
RNA-seq: mRNA was isolated from cells using the RNeasy® Plus Mini Kit (Qiagen) according to the manufacturer’s protocol.
RNA-seq libraries were prepared using Illumina mRNA TruSeq kits as protocolled by Illumina.

value: AA

value: ASA


title: BBN_bladder, PLD2-KO, 16w-1


title: LB05_PBS

description:
PBS
LB05

value: PBS


title: bone marrow CLP (Lin-CD127+Flt3+) cells, wiltype (WT) 2


title: in vivo zygote, polysomal RNA, rep2 [IVZ-2 P]

description: DGE IMZ-IVZ.xlsx

value: ovarian

value: germ cell

value: in vivo zygote, polysomal RNA

value: polysome fractionation


title: SK304, DMSO control

value: colonic organoid

value: F


title: bone marrow CLP (Lin-CD127+Flt3+) cells, SclCre;JAK2-V617F 1 (SF1) 3


title: LB03_LPS

description:
LPS
LB03

value: Macrophage


title: in vivo zygote, polysomal RNA, rep3 [IVZ-3 P]

description: DGE IMZ-IVZ.xlsx


title: LB04_LPS+HMO

description:
LPS+HMO
LB04

value: LPS+HMO


title: LB02_HMO

description:
HMO
LB02


title: SK304, ASA treatment


title: SK302, DMSO control

value: DMSO


title: in vivo zygote, polysomal RNA, rep4 [IVZ-4 P]

description: DGE IMZ-IVZ.xlsx


title: bone marrow CLP (Lin-CD127+Flt3+) cells, SclCre;JAK2-V617F 1 (SF1) 1


title: LB01_PBS

description:
PBS
LB01


title: SK316, ASA treatment

value: EA


title: in vitro oocyte, total RNA, rep1 [IVM-1 T]

description:
DGE IVM DO-IVO T.xlsx
DGE IVM DO-IVM COC T.xlsx

value: in vitro oocyte, total RNA

value: RNA isolation


title: SK302, ASA treatment


title: D7_YKL

city: Dallas

first: Jialiang

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads obtained from scRNA-seq experiments were demultiplexed, aligned to the mouse genome, version mm10 (with tdTomato gene inserted), and collapsed into unique molecular identifiers (UMIs) with the Cellranger toolkit (10´ Genomics, version 3.1.0). The Seurat object was made with the count matrix for quality control, normalization, clustering, and identification of differentially expressed genes.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Callus tissue

extract_protocol:
Seven days post-operation, callus tissue was meticulously harvested. A dissection approach was employed, deliberately avoiding the bone marrow to minimize hematopoietic cell carryover. The callus material was subjected to collagenase digestion (0.2% collagenase type I, 35°C/15 min/500 rpm) to obtain a single-cell suspension.
Single cells were encapsulated into emulsion droplets using a Chromium Controller (10´ Genomics, Pleasanton, CA, USA). scRNA-seq libraries were constructed using Chromium Single-Cell 3’ v3 Reagent Kit according to the manufacturer’s protocol.

value: Callus tissue

value: YKL


title: in vitro oocyte, total RNA, rep2 [IVM-2 T]


title: in vivo zygote, polysomal RNA, rep1 [IVZ-1 P]

description: DGE IMZ-IVZ.xlsx


title: CRISPRa_Doxo_Rep1

city: palo alto

first: Chun

last: Liu

address: 1291 Welch Road BMI building, 3200-CVI Rm

institute: stanford

data_processing:
Sequencing reads were aligned to the expected library sequences using Bowtie (v1.0.0) and read counts were processed using Python scripts from https://github.com/mhorlbeck/ScreenProcessing.
Assembly: no genome build and assembly needed
Supplementary files format and content: raw counts as CSV file
Library strategy: Pooled CRISPR screen-seq

source_name: stem cell

growth_protocol: iCMs were first transduced with the pooled lentiviral gRNA library (druggable sublibraries of hCRISPRi or a-v2) of either CRISPRi or CRISPRa machinery at an MOI of 0.3 (to ensure that each infected BFP+ iCM received only one gRNA) in RPMI+B27 medium. The gRNA lentivirus contained a puromycin resistance gene for antibiotic selection purposes. Two days after gRNA transduction, 1 μg/ml of puromycin was added for 24 hours to initiate antibiotic selection. Following this, RPMI+B27 medium was used to remove dead cells, and surviving iCMs were recovered for another three days. The lentiviral gRNA library-transfected iCMs were then replated onto Matrigel-coated plates in RPMI+B27 medium with 5% KOSR at a density of 100,000 cells/cm2 in 6-well plates. Similar to the step of gRNA transduction, iCMs were switched to RPMI+B27 medium the next day and maintained for another three days. The gRNA-transfected iCMs were subsequently transduced with either dCas9-KRAB or dCas9-VPR lentivirus at an MOI > 1.5 to ensure that every cell received dCas9 lentiviral particles (100% mCherry+).

extract_protocol:
Genomic DNA was then extracted using a QIAamp DNA Blood Mini Kit (Qiagen) from all surviving iCMs of both groups.
The gRNA-inserted regions were amplified by PCR prepare CRISPRi/a screen NGS sequencing libraries, which were sequenced on an Illumina HiSeq-4000 and analyzed as previously described (PMID: 27661255)

treatment_protocol: Two days later, iCMs were confirmed to be positive for both BFP and mCherry. Double-positive iCMs were treated with doxorubicin (0.5 μM) or DMSO (vehicle control) for 72 hours.

value: stem cell

value: human iPSC

value: differentiated cardiomyocyte

value: doxorubicin


title: CRISPRa_Doxo_Rep2


title: SK300, DMSO control

first: Sonia

institute: University of Chicago

value: M


title: D7_PTH

description: 10x Genomics

value: PTH


title: SK300, ASA treatment

value: ASA


title: D7_Ctrl

description: 10x Genomics

value: Control


title: in vitro oocyte, total RNA, rep4 [IVM-4 T]

value: ovarian

value: germ cell


title: bone marrow CLP (Lin-CD127+Flt3+) cells, SclCre;JAK2-V617F 1 (SF1) 2

value: bone marrow

value: bone marrow CLP (Lin-CD127+Flt3+) cells

value: Sixteen weeks post-tamoxifen (TAM)


title: in vitro cumulus-oocyte complex, total RNA, rep1 [COC-1 T]

description:
DGE IVM DO-IVM COC T.xlsx
DGE IVM COC-IVO T.xlsx


title: CRISPRa_Vehicle_Rep1

value: vehicle


title: in vitro oocyte, total RNA, rep3 [IVM-3 T]

value: in vitro oocyte, total RNA

value: RNA isolation


title: SK294, DMSO control

value: colonic organoid

value: AA

value: DMSO


title: in vitro cumulus-oocyte complex, total RNA, rep2 [COC-2 T]


title: SK288, ASA treatment

value: F

value: EA


title: CRISPRi_Doxo_Rep2

value: stem cell

value: human iPSC

value: differentiated cardiomyocyte

value: doxorubicin


title: CRISPRi_Vehicle_Rep2


title: SK288, DMSO control


title: in vitro cumulus-oocyte complex, total RNA, rep3 [COC-3 T]

value: ovarian


title: CRISPRi_Vehicle_Rep1


title: SK280, DMSO control


title: KMT2A::MLLT3+NRAS/G12D, rep4, ATAC-seq

city: Lund

middle: K

last: Hagström-Andersson

address: BMC C13

country: Sweden

institute: Lund University

data_processing:
Basecalling was performed using bcl2fastq (v2.15), raw reads were trimmed adapters using Trimmomatic (v0.39), quality control was performed using fastQC (v0.12.1).
Clean reads were aligned to the mouse genome mm9 using bowtie2 (v2.5.1) with parameters "-X 2000 --very-sensitive". Duplicates were removed using Picard (v2.6.0) MarkDuplicates. Mitochondrial alignments, inappropriate alignments, and low-quality (<Q30) alignments were filtered using Samtools (v1.9), filtered alignments were shifted +5bp/-4bp on forward and reverse strand respectively using ATACseqQC package (v1.8.5).
Peaks were called using MACS2 callpeak (v2.1.0) for each sample, the consensus peaks of all samples were generated from individual samples using BEDTools intersect (v2.26.0), and peaks located in ENCODE blacklisted regions were removed. Peaks were annotated using HOMER.
BigWig files were generated using deepTools bamCoverage (v3.5.1) with parameter of "--normalizeUsing CPM". Motif analysis was conducted using RGT HINT (v0.13.2). Reads count on consensus peaks were generated using BEDTools multicov (v2.26.0). Differential comparison analysis was performed using DESeq2 (v1.20.0). Hierarchical clustering, PCA, t-SNE analysis, heatmap, and volcano ploting were conducted in R (v3.5).
Assembly: mm9
Supplementary files format and content: tab-delimited text file of raw counts for each sample
Supplementary files format and content: narrowPeak

source_name: Bone marrow

extract_protocol:
Cryopreserved cells were thawed and lysed using the cold lysis buffer following ATAC-seq protocol.
Nuclei were collected and resuspended in the transposase reaction mix for transposition reaction, the transposed fragments were immediately purified using a Qiagen MinElute PCR Purification kit (Qiagen). The purified fragments were amplificated 10 cycles on a thermocycler. Libraries were purified using Agencourt AMPure XP beads (Beckman Coulter) following the Manufacturer's instructions. Library quality was examined using Agilent High sensitivity DNA assay (Agilent) and Qubit dsDNA High sensitivity assay kit (ThermoFisher).

value: Bone marrow

value: KMT2A::MLLT3, NRAS/G12D


title: KMT2A::MLLT3+NRAS/G12D, rep2, ATAC-seq


title: CRISPRi_Doxo_Rep1


title: SK280, ASA treatment

last: Kupfer

value: ASA


title: in vivo oocyte, total RNA, rep1 [IVO-1 T]

description:
DGE IVM DO-IVO T.xlsx
DGE IVM COC-IVO T.xlsx

value: germ cell

value: in vivo oocyte, total RNA


title: SK294, ASA treatment

value: M


title: CRISPRa_Vehicle_Rep2

value: vehicle


title: Father_3_A

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

data_processing:
RNA-seq mapping and quantification were performed with STAR using GENCODEv25 for annotation, featureCounts for gene counts.
Assembly: hg38
Supplementary files format and content: gene counts per sample, csv format

extract_protocol:
RNA was extracted with the Qiagen RNeasy Micro Kit
RS-122-2201 RNA TruSeq Stranded tRNA

treatment_protocol: Blood mononuclear blood cells were separated by centrifugation at 400gx30min over Ficoll-Hypaque. Human erythroblasts were obtained by culturing blood mononuclear cells (106 cells/mL) for 10-15 days in Iscove's modified Dulbecco's medium (IMDM) containing fetal bovine serum (FBS, 20%), SCF (10 ng/mL), EPO (1U/mL), interleukin-3 (IL-3, 1ng/mL), dexamethasone (Dex, 10−6 M) and estradiol (10−6 M), as described. Selected experiments were conducted in parallel cultures supplemented with growth factors plus and minus Dex. Day 8-12 proliferating erythroblasts (Prol) were collected and induced to differentiate (Diff) by culture for 4 additional days with EPO (3U/mL) and human recombinant insulin (10ng/mL).

tag: mutation


title: in vivo oocyte, total RNA, rep2 [IVO-2 T]

value: RNA isolation


title: SK278, DMSO control

city: Chicago

value: colonic organoid

value: AA


title: KMT2A::MLLT3+NRAS/G12D, rep1, ATAC-seq

first: Anna


title: Mother_3_A


title: SK278, ASA treatment


title: KMT2A::MLLT3+FLT3/N676K, rep3, ATAC-seq

value: KMT2A::MLLT3, FLT3/N676K


title: wt lungs, M.tb-infected, 7days

city: Wuhan

first: Bing

last: Yang

state: Hubei

address: No.1 Shizishan Street, Hongshan District

department: College of Vetirinary Medicine

institute: Huazhong Agricultural University

description: 10x Genomics

data_processing:
Primary analysis, including demultiplexing, barcode processing, alignment, and gene counting were performed using the 10X Genomics CellRanger software (10X Genomics).
Assembly: mm10
Supplementary files format and content: table-separated values files and matrix files

source_name: lung

extract_protocol:
Lungs were aseptically removed and homogenized in PBS containing DNase Ⅰ (EN401; Vazyme) and type Ⅰ collagenase (17100017; ThermoFisher), and incubated at 37℃ for 60 min. The homogenates were filtered through a 70μm cell strainer and centrifuged at 1500 rpm for 5 min. Red blood cells were lysed using red blood lysing buffer, and cells were pelleted and resuspended in RPMI-1640 medium for library preparation.
The single-cell suspension derived from dissociated lung tissues was analyzed for viability, and loaded onto the 10X Genomics Chromium Single Cell Controller at a concentration of one thousand cells per microliter. Next, the cell suspension, reagents, and 10x Genomics gel beads were encapsulated into individual nanoliter-sized Gelbeads in Emulsion (GEMs) and then reverse transcription of poly-adenylated mRNA was performed inside each droplet. The cDNA and VDJ-enriched libraries were completed in a single bulk reaction using the 10X Genomics Chromium NextGEM Single Cell 50 v 1.1 and V(D)J Reagent Kits. 50,000 or 5,000 sequencing reads per cell for scRNA-seq or VDJ libraries, respectively, were generated on the Illumina NextSeq 500 instrument.

value: lung

value: wild type

value: bacterium infection


title: Patient_3

value: 2.5 Mb on the BCL11A gene


title: KMT2A::MLLT3+NRAS/G12D, rep3, ATAC-seq


title: in vivo oocyte, total RNA, rep3 [IVO-3 T]


title: KMT2A::MLLT3+FLT3/N676K, rep2, ATAC-seq


title: SK276, DMSO control

value: DMSO


title: KMT2A::MLLT3+FLT3/N676K, rep1, ATAC-seq


title: SK276, ASA treatment


title: Father_2


title: in vitro cumulus-oocyte complex, total RNA, rep4 [COC-4 T]

value: ovarian


title: in vitro zygote, total RNA, rep1 [IMZ-1 T]

description: DGE IMZ-IVZ T.xlsx

value: in vitro zygote, total RNA


title: Mother_2


title: SK274, DMSO control

value: F

value: EA


title: in vitro zygote, total RNA, rep2 [IMZ-2 T]

description: DGE IMZ-IVZ T.xlsx

value: germ cell


title: KMT2A::MLLT3+FLT3/ITD, rep4, ATAC-seq

value: Bone marrow

value: KMT2A::MLLT3, FLT3/ITD


title: KMT2A::MLLT3+FLT3/N676K, rep4, ATAC-seq


title: in vitro zygote, total RNA, rep3 [IMZ-3 T]

description: DGE IMZ-IVZ T.xlsx


title: Patient_2

value: 642 kb on the BCL11A gene


title: KMT2A::MLLT3+FLT3/ITD, rep3, ATAC-seq


title: in vitro zygote, total RNA, rep4 [IMZ-4 T]

description: DGE IMZ-IVZ T.xlsx

value: RNA isolation


title: Mother_1_A


title: SK274, ASA treatment

value: colonic organoid

value: ASA


title: SK272, DMSO control


title: in vivo oocyte, total RNA, rep4 [IVO-4 T]

value: in vivo oocyte, total RNA


title: Patient_1_A

value: 3.5 Mb deletion downstream to BCL11A


title: SK272, ASA treatment


title: KMT2A::MLLT3+FLT3/ITD, rep1, ATAC-seq


title: LNCaP_ETV5, ETV5, ChIP

city: Pohang

first: Jongeun

address: 77 Cheongam-ro

institute: POSTECH

data_processing:
The quality of the sequencing reads was confirmed using FastQC (v0.11.9) analysis.
Low quality and adapter sequences were trimmed using ‘Trim Galore’ (v 0.6.8).
Trimmed reads were aligned to hg38 genome (GENCODE v36) using ‘Bowtie2’ (v 0.11.9). PCR duplicated reads were removed using ‘Sambamba markdup’ (v 0.8.2).
ETV5-enriched peaks were identified using ‘MACS2 callpeak’ (v 2.2.6) on the following parameter: ‘-f BAMPE --gsize hs -q 0.1’.
BigWig track files were created using ‘bamCoverage’ in ‘DeepTools’ package (v 3.5.1) normalized with Reads Per Genome Coverage (RPGC).
Assembly: hg38
Supplementary files format and content: bigWig files

source_name: LNCaP

extract_protocol:
Cells were fixed 1% formaldehyde for 20 minutes. After cell lysis, chromatin was sonicated using a Bioruptor Pico sonicator (Diagenode).
ChIP-seq library construction was performed using the NEBNext ChIP-Seq Library Prep Master Mix Set (NEB, E6240) following the manufacturer’s instruction with modifications. The libraries were sequenced using the Illumina HiSeq4000 platform with 100 bp paired-end reads.

value: LNCaP

value: Prostate carcinoma cells

value: ETV5 overexpression

tag: chip antibody


title: KMT2A::MLLT3, rep4, ATAC-seq


title: in vivo zygote, total RNA, rep2 [IVZ-2 T]

description: DGE IMZ-IVZ T.xlsx

value: in vivo zygote, total RNA


title: SK266, DMSO control

value: M

value: DMSO


title: SK266, ASA treatment


title: LNCaP_ETV5, Input


title: KMT2A::MLLT3, rep3, ATAC-seq


title: in vivo zygote, total RNA, rep3 [IVZ-3 T]

description: DGE IMZ-IVZ T.xlsx

value: ovarian


title: LNCaP_CON, ETV5, ChIP

value: WT


title: KMT2A::MLLT3, rep2, ATAC-seq


title: SK254, DMSO control

value: F

value: EA


title: in vivo zygote, total RNA, rep4 [IVZ-4 T]

description: DGE IMZ-IVZ T.xlsx

value: germ cell


title: LNCaP_CON, Input


title: SK254, ASA treatment


title: KMT2A::MLLT3, rep1, ATAC-seq

value: Bone marrow


title: KMT2A::MLLT3+FLT3/ITD, rep2, ATAC-seq

value: KMT2A::MLLT3, FLT3/ITD


title: SK252, DMSO control

value: colonic organoid

value: AA


title: Aged glomeruli rep2 [scRNA-seq]

city: South San Francisco

first: Andrey

last: Shaw

state: California

address: 1 DNA Way

institute: Genentech

data_processing:
Fastq files were processed with 10X Cell Ranger pipeline v6.0.1
Cells with fewer than 500 genes expressed or more than 5,000 genes expressed and  more than 12% mitochondrial content were filtered out. Features (genes) where value <= 0.0 in at least 99.5% of the cells were excluded. Initial cell count: 33,323 cells, after QA/QC: 22,840 cells were analyzed (7,161 young, 15,679 aged). Data were analyzed and visualized using Partek®Flow® (https://www.partek.com/partek-flow/).
Assembly: GRCm38
Supplementary files format and content: Tab-separated barcode, gene, and count matrix files.

source_name: Kidney

extract_protocol:
Mice were perfused transcardially with 10 ml of RPMI with 200 ul of M-450 Dynabeads (Thermo Fisher Scientific, 14013). Kidneys were immediately extracted and minced using a razor blade, then transferred to 5 ml digestion buffer with LiberaseTM (1.5 U/ml; 5401127001, Millipore Sigma) and DNaseI (100 U/ml; D4527, Millipore Sigma) in RPMI-1640, and incubated for enzymatic digestion (37⁰C, 800 rpm, 20 min). Following digestion, samples were sieved via a 100 μm and a 70 μm MACS® SmartStrainers (130-098-463, 130-098-462, Miltenyi Biotec), and 30 ml ice-cold 10% FBS in RPMI-1640 were added to stop digestion. Samples were washed twice with 30 ml ice-cold RPMI-1640 and glomeruli were isolated using a magnetic separator (DynaMag-2, Thermo Fisher Scientific, 12321D). Glomeruli were dissociated in 1 ml digestion buffer with Trypsin (0.5% wt/vol; Thermo Fisher Scientific, 15090046), Dispase II (2 U/ml; Roche, 04942078001), Collagenase D (2 U/ml; Roche, 11088866001), and DNAse I (10 U/ml; D4527, Millipore Sigma), in RPMI-1640, and incubated for enzymatic digestion (37⁰C, 800 rpm, 40-60 min). Samples were kept on ice until further processing. Cell counts and viability were determined before further analyses and viability was determined at >95% viable cells.
Samples were kept on ice and immediately processed. Sample processing for scRNA-seq was done using Chromium Next GEM Single Cell 3’ Kit v3.1 (1000269, 10X Genomics) according to manufacturer’s instructions. Cell concentration was used to calculate the volume of single-cell suspension needed in the reverse transcription master mix, aiming to achieve approximately 8000 cells per sample. cDNA and libraries were prepared according to manufacturer’s instructions (10X Genomics). Sequencing reads were processed through 10X Genomics Cell Ranger (v.3.1.0) and aligned to GRCm38.

treatment_protocol: no treatment

value: Kidney

value: aged

value: whole tissue


title: in vivo zygote, total RNA, rep1 [IVZ-1 T]

description: DGE IMZ-IVZ T.xlsx

value: RNA isolation


title: Liver, fed, rep2

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

data_processing:
Fastqs were aligned to the mm10 reference genome (refdata-gex-mm10-2020-A) using cellranger (v6.0).
Ambient RNA was removed from the count matrix using SoupX.
Assembly: mm10
Supplementary files format and content: barcodes.tsv (Cell barcodes in tabular format)
Supplementary files format and content: genes.tsv (Genes from reference in tabular format)
Supplementary files format and content: matrix.mtx (Counts for each cell and gene in tabular format)

source_name: Liver

extract_protocol:
50 mg of flash frozen liver from 8 mice per group were pooled. Samples were dounced in a glass tissue grinder set (Corning) in ice-cold Nuclei EZ Prep buffer (Sigma) 24 times with pestle A and then 24 times with pestle B, incubated on ice for 5 min, passed successively through a 100 μm and then 40 μm filter, and finally centrifuged (500xg for 5 min at 4ºC; deceleration set to 5). The resulting nuclear pellet was washed twice in 1 ml EZ Prep Buffer; twice in 1mL of 1x ST (5mM Tris, 73mM NaCl, 0.5mM CaCl2, 10.5mM MgCl2, and 25u/mL RNase inhibitor); resuspended in 1-2 mL of 1x ST; and filtered through a 40 μm FlowMi cell strainer (Millipore Sigma).
Nuclei were counted, adjusted to a concentration of 700-1200 nuclei/uL, and loaded onto a 10X genomics controller (10X v3.1 chemistry). Two nuclear preps (each representing 8 livers) per group were analyzed.

value: Liver

value: fed


title: FNE1 cells overexpressed with E6E7 and YapS127A_rep3

city: boston

first: Jiyuan

state: Massachusetts

address: 55 fruit st.

institute: Mass Gen Hospital

data_processing:
Reads were aligned with HISAT2 and assembled and quantified with Cufflinks.
Assembly: GRCh38
Supplementary files format and content: csv including raw count matix

growth_protocol: FT190 cells were cultured in DMEM/F12 medium with 2% Ultroser™ G serum substitute (Pall Corporation)

extract_protocol:
Total RNA was extracted by combining the TRIzol protocol (Invitrogen; Carlsbad, CA) with the QIAGEN RNeasy mini kit (QIAGEN, Carlsbad, CA). Briefly, 1x107 cells were lysed with 0.65ml TRIzol reagent for 10 minutes at room temperature before adding 300ul chloroform. The mixture was vortexed for 15 seconds, kept static for 3 minutes, and then centrifuged samples at 12,000 rpm for 3 min at room temperature. The supernatant was carefully transferred into another DNase/RNase-free centrifuge tube, mixed well with an equal volume of 70% ethanol by pipetting, and loaded to the RNeasy Mini spin column provided in the QIAGEN RNeasy mini kit. The column with samples was kept static for 2 minutes before centrifuging for 15 s at 12,000rpm. Discard the flow-through. After washing, the spin column was placed in a new 2 ml collection tube and dried by spinning at 15,000 rpm for 5 min. RNA on the membrane will be eluted with 40μl RNase-free water (supplied in kit).
High-quality libraries were prepared following Illumina Stranded mRNA Prep Manual

treatment_protocol: FNE1 cells were cultured to 40% confluent and then transfected with retrovirus-based empty control vector (MXIV), or vectors expressing wild type of YAP1 (YAP), or constitutively active YAP1 (YAPS127A, a replacement of Serine at residue 127 with Alanine resulting in the constitutive activation of YAP1 protein [66]). All transfected cells were selected with G418 (200-400μg/ml). YAP1 expression in these cells was confirmed by RT-PCR and Western blot.

value: non-ciliated human fallopian tube epithelial cells immortalized by telomerase component hTERT

value: transfected with retrovirus


title: FNE1 cells overexpressed with E6E7 and YapS127A_rep2


title: SK252, ASA treatment

value: ASA


title: Liver, fasted, rep2

value: fasted


title: Young glomeruli rep2 [scRNA-seq]

value: young


title: SK250, DMSO control

value: F

value: EA

value: DMSO


title: Young glomeruli rep1 [scRNA-seq]


title: Liver, fed, rep1


title: FNE1 cells overexpressed with E6E7_rep3

value: FNE1 cells overexpressed with E6E7_rep3


title: SK250, ASA treatment

value: colonic organoid


title: Liver, fasted, rep1


title: FNE1 cells overexpressed with E6E7_rep2

value: FNE1 cells overexpressed with E6E7_rep2


title: Tbx3 KO liver #7

first: Hao

institute: UTSW

data_processing:
Alignment, quantification, and differential analysis were performed using the QBRC_BulkRnaSeqDE pipeline (https://github.com/QBRC/QBRC_BulkRnaSeqDE).
Briefly, Alignment of reads to human reference genome (GRCh38) was done using (v2.7.2b) [REF: https://pubmed.ncbi.nlm.nih.gov/23104886/].
FeatureCounts (v1.6.4) [REF: 24227677] was then used gene count quantification.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: liver

extract_protocol:
Total liver RNA was extracted using TRIzol reagent (Invitrogen #15596026) followed by purification using the RNeasy Mini kit (Qiagen #74014).
RNA-seq libraries were prepared with the SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara #634875)

treatment_protocol: 3 months of Western Diet

value: liver

value: C57BL/6; TetO-Cas9 homo; Rosa-rtTA homo

value: AAV-Tbx3 gRNA and WD

tag: time

value: 3 months of WD (Western Diet)


title: SK244, DMSO control

value: AA


title: Glomeruli aged rep3

data_processing:
Processed with gsnap based NGS workflow that runs the BCB endorsed RNASeq workflows
Data were analyzed and visualized using Partek®Flow® (https://www.partek.com/partek-flow/).
Assembly: GRCm38
Supplementary files format and content: Tab-separated files with gene counts

extract_protocol:
Mice were perfused transcardially with 10 ml of RPMI with 200 ul of M-450 Dynabeads (Thermo Fisher Scientific, 14013). Kidneys were immediately extracted and minced using a razor blade, then transferred to 5 ml digestion buffer with LiberaseTM (1.5 U/ml; 5401127001, Millipore Sigma) and DNaseI (100 U/ml; D4527, Millipore Sigma) in RPMI-1640, and incubated for enzymatic digestion (37⁰C, 800 rpm, 20 min). Following digestion, samples were sieved via a 100 μm and a 70 μm MACS® SmartStrainers (130-098-463, 130-098-462, Miltenyi Biotec), and 30 ml ice-cold 10% FBS in RPMI-1640 were added to stop digestion. Samples were washed twice with 30 ml ice-cold RPMI-1640 and glomeruli were isolated using a magnetic separator (DynaMag-2, Thermo Fisher Scientific, 12321D). Glomeruli were dissociated in 1 ml digestion buffer with Trypsin (0.5% wt/vol; Thermo Fisher Scientific, 15090046), Dispase II (2 U/ml; Roche, 04942078001), Collagenase D (2 U/ml; Roche, 11088866001), and DNAse I (10 U/ml; D4527, Millipore Sigma), in RPMI-1640, and incubated for enzymatic digestion (37⁰C, 800 rpm, 40-60 min). Samples were kept on ice until further processing. Cell counts and viability were determined before further analyses and viability was determined at >95% viable cells. For bulk RNA sequencing, glomeruli were placed directly into RNeasy Lysis Buffer (Qiagen). RNA was extracted and isolated from samples using RNeasy Mini Kit (74104, Qiagen) according to manufacturer instructions. Regular input RNA-Seq was performed as follows. Total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on 4200 TapeStation (Agilent Technologies).
For sequencinglibrary generation, the Truseq Stranded mRNA kit (Illumina) was used with an input of 100 nanograms of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on 4200 TapeStation (Agilent Technologies).Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 millions single-end 50-base pairreads for each sample.

value: Kidney

value: aged

value: whole tissue


title: FNE1 cells overexpressed with E6E7_rep1

value: non-ciliated human fallopian tube epithelial cells immortalized by telomerase component hTERT

value: FNE1 cells overexpressed with E6E7_rep1

value: transfected with retrovirus


title: Glomeruli aged rep2


title: SK244, ASA treatment

value: F

value: ASA


title: FNE1 cells overexpressed with YapS127A_rep3


title: Tbx3 KO liver #6


title: Glomeruli young rep3

value: young


title: Tbx3 KO liver #5


title: FNE1 cells overexpressed with YapS127A_rep2


title: Aged glomeruli rep1 [scRNA-seq]


title: SK242, ASA treatment

value: EA


title: Tbx3 KO liver #4


title: Tbx3 KO liver #3


title: FNE1 cells overexpressed with YapS127A_rep1


title: Glomeruli young rep2


title: Glomeruli young rep1


title: SK238, DMSO control

value: colonic organoid

value: M

value: DMSO


title: SK238, ASA treatment


title: Tbx3 KO liver #2

value: liver

value: C57BL/6; TetO-Cas9 homo; Rosa-rtTA homo


title: CA10_S5

city: Beijing

first: wanjun

last: Peng

address: No.5, Panjiayuan Nanli,Chaoyang District, Beijing

institute: Institute of Laboratory Animal Science

data_processing:
lllumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Reasearch, 2009.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: spleen

extract_protocol:
Tissues were removed, flsah frozen on dry ice, and RNA was harvested using Trizol reagent. Lllumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction
RNA libraries were prepared for sequencing using standard lllumina protocols

value: spleen

value: WT

value: CA10 infection


title: FNE1 cells transfected with MXIV backbones_rep2


title: SK236, DMSO control

value: AA


title: FNE1 cells overexpressed with E6E7 and YapS127A_rep1


title: Tbx3 KO liver #1

value: AAV-Tbx3 gRNA and WD

value: 3 months of WD (Western Diet)


title: FNE1 cells transfected with MXIV backbones_rep3

value: non-ciliated human fallopian tube epithelial cells immortalized by telomerase component hTERT


title: SK242, DMSO control


title: Srebf1 KO liver #5

value: AAV-Srebf1 gRNA and WD


title: CA10_S4


title: SK236, ASA treatment

value: F


title: pd-1 ko lungs, M.tb-infected, 7days

description: 10x Genomics

value: lung

value: PD-1 knockout

value: bacterium infection


title: Glomeruli aged rep1

value: Kidney

value: aged

value: whole tissue


title: CA10_S3


title: Endometrial stromal cells from ESC_59

city: Herston

first: Sally

last: Mortlock

state: QLD

address: School of Public Health

department: School of Public Health

country: Australia

institute: University of Queensland

data_processing:
Low quality sequencing reads and contaminating HiSeq Illumina adaptor sequences were trimmed using Trimmomatic v0.36
Trimmed reads were aligned to the human reference genome (Ensembl Homosapiens GRCh38 relesse 84) using with HISAT2 v2.05
Assembled into transcripts and counted using StringTie v1.3.1 and the EnsemblHomo sapiensGRCh38 release 91 reference assembly
Lowly expressed genes with counts per million (CPM) <0.22 (~10 counts) and expressed in <90% of the samples, were removed
Counts were normalized using the Trimmed Mean of M (TMM) method, converted to CPM and log2 transformed (log2-CPM) using the edgeR R package v3.22.3
Assembly: hg38
Supplementary files format and content: csv file containing raw counts for each sample
Supplementary files format and content: csv file containing counts normalized using the Trimmed Mean of M (TMM) method, converted to CPM and log2 transformed (log2-CPM)

source_name: endometrial stromal cells

growth_protocol: Endometrial stromal cells were maintained in IMEM with 10% fetal calf serum and 1% antibiotics in a humidified atmosphere and 5% C02

extract_protocol:
Total RNA was isolated via the AllprepDNA/RNA Mini kit. RNA was treated with Turbo DNA-free kit.
Stranded RNA-seq libraries were prepared using the Illumina Tru-seq Strandard Total RNA Gold protocol, including ribosomal depletion (Illumina, USA)

treatment_protocol: No treatment was performed

value: endometrial stromal cells

tag: menstrual cycle_phase

value: Peri-ovulatory

tag: passage

tag: flowcell

tag: lane


title: SK234, DMSO control

value: colonic organoid

tag: cell line

tag: Sex

value: M

tag: age

tag: ethnicity

value: DMSO


title: CA10_S2

value: spleen

value: WT

value: CA10 infection


title: Endometrial stromal cells from ESC_58

value: Proliferative


title: Srebf1 KO liver #4

value: liver

value: C57BL/6; TetO-Cas9 homo; Rosa-rtTA homo

value: AAV-Srebf1 gRNA and WD

value: 3 months of WD (Western Diet)


title: SK234, ASA treatment

value: AA

value: ASA


title: Srebf1 KO liver #3


title: CA10_S1


title: Endometrial stromal cells from ESC_57

value: Amenorrheic


title: Endometrial stromal cells from ESC_56


title: SK230, DMSO control

value: EA


title: Srebf1 KO liver #2


title: CA10_T5

source_name: thymus

value: thymus


title: Srebf1 KO liver #1


title: CA10_T4


title: FNE1 cells transfected with MXIV backbones_rep1

value: non-ciliated human fallopian tube epithelial cells immortalized by telomerase component hTERT

value: transfected with retrovirus


title: Smyd2 KO liver #6

value: AAV-Smyd2 gRNA and WD


title: CA10_T3


title: SK230, ASA treatment

value: colonic organoid

value: M


title: Endometrial stromal cells from ESC_54

value: endometrial stromal cells

value: Secretory


title: Endometrial stromal cells from ESC_55

value: Proliferative


title: SK222, DMSO control

value: DMSO


title: SK214, DMSO control


title: CA10_T2

value: WT

value: CA10 infection


title: Endometrial stromal cells from ESC_53


title: CA10_T1


title: Smyd2 KO liver #4

value: liver

value: C57BL/6; TetO-Cas9 homo; Rosa-rtTA homo

value: 3 months of WD (Western Diet)


title: SK222, ASA treatment

value: ASA


title: Smyd2 KO liver #5


title: Smyd2 KO liver #2


title: Smyd2 KO liver #3


title: Endometrial stromal cells from ESC_51


title: CA10_M4

source_name: muscle

value: muscle


title: Endometrial stromal cells from ESC_52


title: SK214, ASA treatment

value: AA


title: SK248, DMSO control


title: Endometrial stromal cells from ESC_50


title: SK248, ASA treatment


title: CA10_M5


title: Endometrial stromal cells from ESC_49


title: CA10_M3


title: sgLacZ control liver #2

value: AAV-LacZ gRNA and WD


title: Smyd2 KO liver #1


title: SK228, ASA treatment

value: F


title: CA10_M2


title: Endometrial stromal cells from ESC_48


title: sgLacZ control liver #1


title: TJY-D

city: Nanjing

first: Peizhao

state: Jiangsu

address: Zhongshan East Road 305#

institute: Jingling Hospital, Medical School of Nanjing University

description: Singleron

data_processing:
Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.  Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.5.2 pipeline.  Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 to trim poly-A tail and adapter sequences.  Cell barcode and UMI were extracted.  UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 software, and used to generate expression matrix files for subsequent analysis.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Colon

extract_protocol:
The fresh colon tissues were stored in the sCelLiveTM Tissue Preservation Solution (Singleron) on ice after the surgery within 30 min. After digesting with sCelLiveTM Tissue Dissociation Solution (Singleron) and incubating with GEXSCOPE red blood cell lysis buﬀer (RCLB, Singleron), the samples were stained with Trypan Blue and the cell viability was evaluated microscopically.
Single-cell suspensions (2×10^5 cells/ mL) were loaded onto microwell chip using the Singleron Matrix Single Cell Processing System.  Barcoding Beads were subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification.  The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE Single Cell RNA Library Kits (Singleron).

value: Colon

tag: subject status

value: CD patient

value: Surgery


title: SK228, DMSO control

value: colonic organoid


title: Irs1 KO liver #4

value: AAV-Irs1 gRNA and WD


title: Endometrial stromal cells from ESC_46

value: endometrial stromal cells

value: Proliferative


title: TJY-C

description: Singleron


title: CA10_B5

source_name: blood

value: blood

value: WT


title: Endometrial stromal cells from ESC_47


title: CA10_B4

value: CA10 infection


title: Endometrial stromal cells from ESC_45


title: CA10_M1


title: Irs1 KO liver #3

value: liver

value: C57BL/6; TetO-Cas9 homo; Rosa-rtTA homo


title: CA10_B3


title: Endometrial stromal cells from ESC_44

value: Secretory


title: LWF-D

description: Singleron


title: LWF-C

description: Singleron


title: CA10_B2


title: DTJ-D

description: Singleron


title: CA10_B1


title: Endometrial stromal cells from ESC_43


title: CA16_S10

value: spleen

value: CA16 infection


title: sgGFP control liver #4

value: AAV-GFP gRNA and WD

value: 3 months of WD (Western Diet)


title: Endometrial stromal cells from ESC_42


title: Irs1 KO liver #5


title: Endometrial stromal cells from ESC_41


title: sgGFP control liver #3


title: scAAA5_center

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

institute: Kobe University Graduate School of Medicine

description: 10x Genomics

data_processing:
Cell Ranger Single Cell Software (v 6.1.2) by 10X Genomics against the GRCh38 human reference genome with default parameter
Assembly: GRCh38 human reference genome

source_name: Aorta

extract_protocol:
Each sample was washed, cut into small pieces, and digested in enzymatic digestion buffer with 3 mg/ml collagenase type II (LS004176, Worthington), 0.15 mg/ml collagenase type XI (H3506, Sigma), 0.25 mg/ml soybean trypsin inhibitor (LS003571, Worthington), 0.1875 mg/ml elastase lyophilized (LS002292, Worthington), 0.24 mg/ml hyaluronidase type I (H3506, Sigma), and 2.38 mg/ml 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES, H4034, Sigma) in PBS with Ca2+ and Mg2+ at 37 °C for 60 minutes while shaking.
Single cell RNA libraries for RNA-seq were prepared using 10X following manufacturer's protocols.

value: Aorta

tag: tissue source

value: center


title: CA16_S9

tag: tissue


title: Endometrial stromal cells from ESC_40

tag: cell type

value: Peri-ovulatory


title: sgGFP control liver #2

last: Zhu

tag: genotype


title: sgGFP control liver #1

tag: treatment


title: scAAA4_center

description: 10x Genomics


title: Endometrial stromal cells from ESC_39


title: CA16_S7


title: CA16_S8


title: Endometrial stromal cells from ESC_38


title: Irs1 KO liver #2


title: scAAA3_proximal

description: 10x Genomics

value: proximal


title: scAAA3_center

description: 10x Genomics


title: Bcl6 KO liver #5

value: AAV-Bcl6 gRNA and WD


title: Irs1 KO liver #1

value: AAV-Irs1 gRNA and WD


title: Endometrial stromal cells from ESC_37

value: endometrial stromal cells


title: scAAA2_proximal

description: 10x Genomics


title: Endometrial stromal cells from ESC_36


title: Bcl6 KO liver #4


title: CA16_T10

value: thymus


title: scAAA2_center

description: 10x Genomics


title: Bcl6 KO liver #3


title: DTJ-C

description: Singleron

value: Colon

value: CD patient

value: Surgery


title: CA16_T9

value: WT


title: Endometrial stromal cells from ESC_35

value: Proliferative


title: Bcl6 KO liver #2

value: liver

value: C57BL/6; TetO-Cas9 homo; Rosa-rtTA homo


title: scAAA1_proximal

description: 10x Genomics


title: Endometrial stromal cells from ESC_34

value: Secretory


title: Bcl6 KO liver #1

value: 3 months of WD (Western Diet)


title: scAAA1_center

description: 10x Genomics

value: Aorta


title: CA16_T7

value: CA16 infection


title: Endometrial stromal cells from ESC_33


title: 5480-miR-196b-/-Dnmt3a+/-Flt3ITD AML

city: Philadelphia

first: Sara

middle: E

last: Meyer

state: PA

department: Cancer Biology

institute: Thomas Jefferson University

description: miR196b-/- Dnmt3a/Flt3-mutant leukemia, mouse 5480

data_processing:
FASTQ sequence files were aligned to the mouse genome version 10 using Kallisto with de novo junction discovery in AltAnalyze. Dnmt3a+/-Flt3ITD AML (or FD AML) RNA-seq data published previously in Meyer et al., 2016, GEO accession GSE77846 were used as comparator. All FASTQ files were processed together.
The fastq files were aligned to mouse genome Mm10 Kallisto and gene level FPKM (Fragments Per Kilobase of transcript per Million mapped reads) were obtained using AltAnalyze 2.1.1 (Emig et al., 2010; Salomonis et al., 2009; Salomonis et al., 2010). To identify differentially expressed genes using default parameters moderated t-test with Benjamini-Hochberg multiple testing correction, adjusted p-value cut-off of 0.05, and an expression cut-off of 2-fold.
For all RNAseq experiments pathways and ontology enrichment analyses were performed with ToppGene (Chen et al., 2009) and GO-Elite (Zambon et al., 2012). All heatmaps from AltAnalyze were created using the HOPACH package via a connection to R (Salomonis et al., 2005).
Genome_build: mouse genome mm10
Supplementary_files_format_and_content: tab-delimited text files

growth_protocol: miR-196b-/-,Dnmt3afl/fl,Flt3ITD/ITD,Mx1Cre (miR196b-/-Dnmt3a+/-Flt3ITD AML, or BKO AML) leukemic splenocytes were isolated from moribund mice (n=3 mice) and enriched for c-Kit+ cells.

extract_protocol:
Leukemic splenocytes were harvested from three independent miR-196b-/-,Dnmt3afl/fl,Flt3ITD/ITD,Mx1Cre (miR196b-/-Dnmt3a+/-Flt3ITD AML) mice. Red blood cells were lysed, and enriched for c-Kit+ using Miltenyi CD117 magnetic beads. c-Kit+ cells were lysed with Trizol. RNA was extracted according to Meyer et al., 2009. RNA quality and quantity were measured by Agilant 2200 Tape Station. Then samples with a RIN>8.0 were processed by ribosome depletion, stranded True-seq, paired-end 150 base pair (bp), 30 million reads. As a control, Dnmt3a+/-Flt3ITD AML RNA-seq data were published previously in Meyer et al., 2016, GEO accession GSE77846.
RNAs were detected by RNAseq analysis using paired-end 150 nucleotide (nt) sequencing and 30 million reads for all samples. RNA Seq libraries were generated with Illumina TruSeq Stranded mRNA HT kits.

value: leukemic splenocytes

value: acute myeloid leukemia

tag: cdna synthesis

value: TRUseq RNA sample kit  (Illumina)

tag: library prep


title: Endometrial stromal cells from ESC_32


title: CA16_S6

value: spleen


title: CA16_M10

value: muscle


title: AGS-SLC7A9, rep1

city: shanghai

first: Haoran

last: Feng

address: ruijin 2 road. NO.197

institute: shanghai ruijin hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp ).
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCh38.p13
Supplementary files format and content: processed data files.txt   The differentially expressed genes were calculated between AGS/VECTOR and AGS/SLC7A9 cells.

source_name: AGS

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: AGS

value: gastric cancer

tag: transduced with


title: AGS-vector, rep2

value: vector


title: 5348-miR-196b-/-Dnmt3a+/-Flt3ITD AML

description: miR196b-/- Dnmt3a/Flt3-mutant leukemia, mouse 5348


title: CA16_M9


title: Endometrial stromal cells from ESC_31

value: endometrial stromal cells

tag: menstrual cycle_phase


title: AGS-vector, rep1


title: Endometrial stromal cells from ESC_29

tag: passage


title: Endometrial stromal cells from ESC_30

tag: flowcell


title: CA16_M8

value: WT


title: CA16_M7


title: y3-mouse-muscle-KOH

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

institute: University of Gothenburg

data_processing:
Library strategy: HydEn-seq
All reads were trimmed for quality and adaptor sequence with cutadapt 1.2.1 (-m 15 -q 10–match-read-wildcards). Pairs with one or both reads shorter than 15 nt were discarded. Mate 1 of the remaining pairs was aligned to an index containing the sequence of all oligonucleotides used in the preparation of these libraries using Bowtie 0.12.8 (DOI: 10.1186/gb-2009-10-3-r25) and the flags -m1 -v2. All pairs with successful alignments were discarded. Pairs passing this filter were subsequently aligned to the mm10 Mus musculus UCSC reference genome (-m1 -v2 -X10000–best). Single-end alignments were then performed with mate 1 of all unaligned pairs with the flags -m1 -v2.
Genome_build: mm10
Supplementary_files_format_and_content: bed: tab-separated bedgraph file format. Column one holds the chromosome name, column two and three hold the nucleotide position, column four holds the read count.

growth_protocol: All procedures were performed in accordance with the institutional guidelines of the University of Gothenburg and experiments were approved by the Institutional Review Board of the Swedish Board of Agriculture (Ethical approval number 62/14 and 1469/2019). Samples from three 7.5-week-old and three 30-week-old male mice (C57BL6) were used for our experiments. Mice were euthanized by placing them into an induction chamber (Abbott Scandinavia AB) for 10 min with 4% isoflurane (Forene isoflurane, Abbott Scandinavia AB) followed by cervical dislocation. Whole blood was immediately harvested and the heart surgically excised thereafter. 300-600 µL of whole blood were thoroughly mixed with 30 µl 0.1 M EDTA to prevent coagulation, 200 µL aliquots were transferred to 1.5 mL tubes and frozen at -80 °C. Tibia and femur bones (for extraction of bone marrow), brain, heart, kidney, liver, lung, thigh muscle and spleen were removed and small sections were flash frozen with liquid nitrogen, then stored at -80 °C until further processing.

extract_protocol:
DNA was extracted using the MasterPure Complete DNA and RNA purification kit (MC85201, lucigen) preceded by adjusted approaches for homogenization and lysis of tissues. DNA from whole blood was extracted using the kit following manufacturer’s instruction for the extraction from whole blood with RBC lysis. DNA from bone marrow originated from tibia and fibula. Bones were freed from any remaining tissue and broken at the knee joints. Placing this opening downward in a perforated 0.5 mL tube set in a 1.5 mL tube allowed to centrifuge out the bone marrow at 10,000 g for 20 s. 100 µL of RCB lysis buffer were added and mixed and then incubated at RT for 10 min while vortexing every 5 min. Samples were centrifuged at 10,000 g for 25 s and supernatant discarded. 300 µL of tissue and cell lysis buffer including proteinase K were added and incubated at 65 °C for 15 min while shaking at 1,500 rpm. Further extraction steps were performed following the kit’s instructions. 2-70 mg of brain, heart, kidney, liver, lung, muscle or spleen tissue were added to a 1.5 mL tube containing 5-15 stainless steel homogenizing beads (0.9-2 mm, SSB14B, next advanced Inc.) and 100 µL tissue and cell lysis buffer including proteinase K. Samples were vortexed for about 20-30 min until tissue pieces were no longer visible. Beads were pelleted using a magnetic rack (DynaMag-2, Invitrogen) and the supernatant was transferred to a new tube containing 200 µL of tissue and cell lysis buffer including proteinase K. Samples were incubated at 65 °C for 15 min while shaking briefly every 5 min. After cooling the samples on ice for 5 min, further extraction steps were performed as instructed. Final DNA concentrations were determined using the Qubit dsDNA BR Assay Kit (molecular probes life technologies).
1 µg extracted DNA was mixed with 0.3 M KOH and incubated at 55°C for 2 hours. After ethanol precipitation, the pellet was dissolved in 20 µl elution buffer (Qiagen, 1014609). DNA was denatured by 3 min incubation at 85°C. In the phosphorylation step, 5'-OH end generated after KOH hydrolysis at the ribonucleotide site was phosphorylated using a mix of 10 U 3'-phosphatase minus T4 polynucleotide kinase (BioLabs, M0236L), 2.5 µl of 10X reaction buffer (BioLabs, B0201S), and 2.5 µl of 10 mM adenosine 5'-triphosphate (BioLabs, P0756S) in a total volume of 25 µl. After 30 min incubation at 37°C, the reaction was stopped by 20 min incubation at 65°C. The samples were bead-washed using CleanPCR kit (GC biotech, CPCR-0050). In the ligation step, ARC140 adaptor was ligated to the 5'-OP. Denatured DNA was ligated using a mix of 10 U T4 RNA Ligase 1 (ssRNA Ligase) (BioLabs, M0204S), 5 µl of 10X reaction buffer (BioLabs, B0216S), 0.5 µl of 2 mM adenosine 5'-triphosphate (BioLabs, P0756S), 25 µl PEG8000(50%), 5 µl of 10 mM [Co(NH3)6]Cl3, and 0.5 µl of 100 µM oligo ARC140 in a total volume of 50 µl. After overnight incubation at the room temperature, the samples were twice beads-washed and dissolved in 14 µl elution buffer. In second strand synthesis step, denatured DNA was polymerized at the room temperature for 5 min using a mix of 4 U T7 DNA polymerase (unmodified) (BioLabs, M0274L), 2 µl of 10X reaction buffer (BioLabs, B0274A), 2 µl of 2 mM adenosine 5'-triphosphate (BioLabs, P0756S), 0.8 µl of BSA (1 mg/ml) (BioLabs, B9000S), and a heterodimer oligo, ARC76/77 in a total volume of 20 µl. After beads-wash and elution, the libraries were amplified by PCR reactions using KAPA HiFi hotstart readymix (2X) kit (KAPA biosystems, KK2602, 07958935001) with PCR parameters as follows: 95 °C for 45 s, followed by 18 cycles at 95 °C for 15 s, 65 °C for 30 s, and 72 °C for 30 s. The amplified libraries were beads-washed and eluted in 20 µl TE. The library concentration was measured using Qubit® dsDNA HS Assay Kit (Life technologies, molecular probes, Q32854). The library quality was checked by the Agilent 2100 bioanalyzer system (Agilent Technologies). Illumina NextSeq 500 system was used for paired-end sequencing.

value: KOH


title: y3-mouse-muscle-KCl

value: KCl


title: CA16_T8

value: thymus


title: ATF2_OE, IP

city: Hefei

first: xiang

middle: yong

last: Li

state: Anhui

address: JiXi Avenue

department: Department of General Surgery

institute: The First Affiliated Hospital of Anhui Medical University

data_processing:
Raw data quality control were performed using FastQC version v0.11.5 for Generate NGS quality control.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.36, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using STAR version 2.5.3a. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off p-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: hg38
Supplementary files format and content: tab-delimited text file for annotated peaks

extract_protocol:
The cell was fixed in 1% formaldehyde for 10 min at room temperature. after which 0.125 M glycine was added and the mixture was sat for 5 min to terminate the crosslinking reaction. The grinded cells was treated with cell lysis buffer and nucleus was collected by centrifuging at 2000g for 5min.Then, nucleus was treated with nucleus lysis buffer and sonicated to fragment chromatin DNA.
ChIP-seq libraries were prepared using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: gastric cancer cell

value: ATF2 overexpression

tag: chip antibody

value: ATF2 (Abcam, #ab32160)


title: Endometrial stromal cells from ESC_28

value: Proliferative

tag: lane


title: CA16_M6

value: CA16 infection


title: CA16_T6


title: y3-mouse-blood-KOH

value: blood


title: shATF2, 3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (version 0.36), ILLUMINACLIP:{adaptor.fa}:2:30:10  -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:0 MINLEN:36 PE
Trimmed sequence reads were mapped to GRCh38 using STAR version 2.5.3a,-outSAMtype BAM SortedByCoordinate
Read count extraction and normalization were performed using featureCounts Version 1.5.1,  -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.

tag: cell line

value: ATF2 knockdown


title: AGS-SLC7A9, rep2


title: Endometrial stromal cells from ESC_27

value: Secretory


title: CA16_B10


title: 5451-miR-196b-/-Dnmt3a+/-Flt3ITD AML

description: miR196b-/- Dnmt3a/Flt3-mutant leukemia, mouse 5451

value: leukemic splenocytes

value: acute myeloid leukemia

value: TRUseq RNA sample kit  (Illumina)


title: y3-mouse-blood-KCl


title: Endometrial stromal cells from ESC_26

value: Peri-ovulatory


title: y2-mouse-muscle-KOH

value: muscle


title: Endometrial stromal cells from ESC_25

value: endometrial stromal cells


title: CA16_B9

value: WT


title: CA16_B8


title: ATF2_OE, Input

value: AGS


title: Control_ATF2, 3


title: shATF2, 2


title: Endometrial stromal cells from ESC_24


title: y2-mouse-muscle-KCl

value: KCl


title: CA16_B7


title: Control_ATF2, 2

value: gastric cancer cell


title: Endometrial stromal cells from ESC_23


title: y2-mouse-blood-KOH

value: KOH


title: y2-mouse-blood-KCl


title: CA16_B6


title: Endometrial stromal cells from ESC_22


title: y1-mouse-muscle-KOH


title: Control_ATF2, 1


title: Endometrial stromal cells from ESC_21


title: EV71_S5

value: spleen

value: EV71 infection


title: EV71_S4