title: ChIPseq CHD4 in Zfp131KO ES cells (iZfp131-HA Zfp131KO) replicate 2

description:
ES(iZfp131-HA Zfp131KO)_ChIPseq_CHD4_rep2
CHD4_2iMINUS_Zfp131KO.events.gz
CHD4_Zfp131_deseq.txt.gz

value: anti-CHD4 (Abcam ab70469)

value: Embryonic stem cells


title: ChIPseq NELF in Zfp131KO ES cells (iZfp131-HA Zfp131KO) replicate 1

status: Public on Jan 07 2022

type: SRA

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

country: USA

institute: Penn State University

description:
ES(iZfp131-HA Zfp131KO)_ChIPseq_NELF_rep1
NELF_2iMINUS_Zfp131KO.events.gz
NELF_Zfp131_deseq.txt.gz

library_source: genomic

data_processing:
Fastq files were aligned to the mouse genome (mm10) using Bowtie (v1.0.1) with options “-q–best–strata -m 1–chunkmbs 1024”.
MultiGPS (v.0.74) was used to call peaks after alignment on all transcription factors. A q-value cutoff of <0.01 was used to identify significant binding events. Histone modification and ATAC-seq peaks were called using the DomainFinder module in SeqCode (https://github.com/seqcode/seqcode-core/blob/master/src/org/seqcode/projects/seed/DomainFinder.java). Contiguous 50-bp genomic bins with significantly higher read enrichment compared with normalized input were identified (binomial test, p <0.05).
Differential binding and modification analyses were done using DESeq2 (v1.28.1) with an adjusted p-value cutoff of <0.05 and all default options. To create the count matrix for DESeq2, peaks were first called independently in the wildtype and knockout ChIP-seq datasets. Overlapping peak regions were merged between the wt and KO. Peak regions found exclusively in either file were also included. The final count matrix was created using Bedtools coverage with the “-counts” option separating each replicate into its own count column. Before running DESeq2 on the matrix, counts were normalized by the length of the corresponding region for histone modifications (domains have differing lengths).
Genome_build: mm10
Supplementary_files_format_and_content: MultiGPS: MultiGPS output files
Supplementary_files_format_and_content: BED: Conversion of MultiGPS output files to BED format, centered on the MultiGPS binding event location

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: ESCs were cultured on 0.1% gelatin (Milipore) coated dishes at 37 °C, 8% CO2 in ESC medium (Advanced DMEM/F12: Neurobasal (1:1) Medium (Gibco), supplemented with 2.5% mESC-grade fetal bovine serum (Corning), 1x N2 (Gibco), 1x B27 (Gibco), 2 mM L-glutamine (Gibco), 0.1 mM ß-mercaptoethanol (Gibco)) supplemented with LIF (leukemia inhibitory factor, 1,000 U ml–1  (Millipore)) and 2-inhibitor cocktail (3 mM CHIR (BioVision) and 1 mM PD0325901 (Sigma)) unless stated otherwise.

extract_protocol:
Wildtype and mutant cells were collected after being grown for 3d in +2i or -2i conditions in the presence or absence of 3 ng/uL doxycycline. 1 mM DSG (ProteoChem) was used for crosslinking at RT for 15min. 1% Formaldehyde (vol/vol) was added for an additional 15min until quenched with glycine (Sigma). Cells were separated into aliquots of 25x106 and centrifuged to freeze pellets at -80°C. Thawed cells were lysed in 5mL of 50 mM HEPES-KOH pH 7.5 (Gibco), 140 mM NaCl (Thermo Fisher), 1 mM EDTA pH 8.0, 10% glycerol (vol/vol) (Thermo Fisher), 0.5% Igepal (vol/vol) (Sigma), 0.25% Triton X-100 (vol/vol) with 1×protease inhibitors (Roche) for 10min at 4°C. Cells were centrifuged for 5min at 1100 rpm and resuspended in 5mL of 10 mM Tris-HCl pH 8.0 (Boston BioProducts), 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0 (Boston BioProducts) with 1×protease inhibitors, and incubated for an additional 10 min at 4°C on a rotating platform. Cells were centrifuged for 5min at 1100 rpm and resuspended in 2mL of Sonication Buffer (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 1% Triton X-100 (vol/vol), 0.1% sodium deoxycholate (wt/vol), 0.1% SDS (vol/vol) with 1×protease inhibitors). Sonication was performed in two Bioruptor tubes per sample with 0.45 g sonication beads. Bioruptor Pico (Diagenode) was used for 18 cycles of 30 sec on and 30 sec off to sonicate to an average size of approximately 200 bp. To immunoprecipitate, Dynabeads protein-G (Thermo Fisher) and antibodies (HA, H3K4me3, H3K27me3, H3K27ac, SIN3A, CHD4) were incubated with sonicated chromatin for 16h at 4°C on a rotating platform. After the immunoprecipitation, the sample was washed with sonication buffer, high salt sonication buffer (500 mM NaCl, LiCl wash buffer (20 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl (Sigma), 0.5% Igepal (vol/vol), 0.5% sodium deoxycholate (wt/vol)), and TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8). The sample was eluted in elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS (vol/vol)) by incubating for 45min at 65°C. Crosslinks were reversed by incubating the sample for 16h at 65°C. RNA was removed by 0.2 mg/mL RNAse A (Sigma) in 200 μL of TE for 2h at 37°C. To remove protein, 0.2 mg/mL Proteinase K (Invitrogen) and CaCl2 (Sigma) were added and the sample incubated at 55°C for 30min. DNA was first purified with phenol:chloroform:isoamyl alcohol (25:24:1; vol/vol) (Invitrogen) and then by performing salt-ethanol precipitation. DNA pellets were resuspended in 50 uL H2O.
Illumina DNA sequencing libraries were prepared with half of the ChIP sample and a 1:100 dilution of the input sample in H2O. Library preparation was performed with end repair, A-tailing and ligating multiplexed adapters (Illumina-compatible Bioo Scientific). Agencourt AmpureXP beads (Beckman Coulter) were used to remove unligated adapters. Libraries were then amplified by PCR with TruSeq primers (Sigma) and Phusion polymerase (New England Biolabs). Libraries with sizes ranging between 250-550bp were gel purified (Qiagen). KAPA library amplification kit was used on Roche Lightcycler 480 to quantify the library prior to sequencing. Libraries were sequenced on Illumina NextSeq 500 using V2.5 chemistry (75 cycles, single-end 75bp) at the Genomics Core Facility at NYU.

treatment_protocol: Wildtype, iZbtb10-HA Zbtb10KO, iZbtb11-HA Zbtb11KO and iZfp131-HA Zfp131KO cells were grown in the absence of doxycycline in +2i+LIF or -2i +LIF media for 3 days.

tag: genotype

value: Ainv15(iZfp131-HA Zfp131KO)

tag: chip target

value: NELF

tag: chip antibody

value: anti-NELF (Sigma HPA007187)

tag: treatment

value: 3d without doxycycline in -2i+LIF

tag: cell type


title: Gan_2

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

description: mRNA expression in human frontal cortical brain cells

library_source: transcriptomic

data_processing:
Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
Seurat v3.0 (Butler et al., 2018) R package used for analysis.
Genome_build: hg38 genome
Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)

molecule: total RNA

organism: Homo sapiens

source_name: single nuclei from frozen postmortem human tissue

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2020
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

tag: age

tag: r47h genotype

value: WT

tag: Sex

value: M

tag: diagnosis

value: AD

value: frontal cortical brain cells


title: ChIPseq NELF in Zbtb11KO ES cells (iZbtb11-HA Zbtb11KO) replicate 2

description:
ES(iZbtb11-HA Zbtb11KO)_ChIPseq_NELF_rep2
NELF_2iMINUS_Zbtb11KO.events.gz
NELF_Zbtb11_deseq.txt.gz

value: Ainv15(iZbtb11-HA Zbtb11KO)


title: 6mA_DIP-seq_AvL1

city: Woods Hole

first: Irina

last: Arkhipova

state: MA

address: 7 MBL St

department: Josephine Bay Paul Center

institute: Marine Biological Laboratory

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence (cutadapt v1.9.2), and masked for short sequences (<15nt) or low-quality scores (<20), then mapped to reference genome using Bowtie, with default parameters and -n 1 -l 30
Aligned sequence reads processed with MACS using nomodel nolambda parameters
BigWig files were generated with deepTools2 using bamCoverage function
Supplementary_files_format_and_content: bed files with peak, BigWig files

organism: Adineta vaga

source_name: whole animal

extract_protocol:
Genomic DNA extraction with Dneasy Tissue Kit (Qiagen). Sonication (Covaris S220) to obtain 200-400 bp range.
DNA library construction with NuGen Ovation Ultra Low System v2

tag: strain

tag: tissue

value: whole animal

tag: medip antibody

value: N6-methyl-A (NEB)


title: blood_149 [SampleGSM4820694]

type: genomic

city: Davis

first: Anita

last: Oberbauer

state: CA

address: One Shields Ave.

department: Animal Science Department

institute: University of California, Davis

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)

hyb_protocol: Hybridization was performed according to the Infinium HD Super Assay documentation using the automated protocol.

scan_protocol: Scanning was performed according to the Infinium HD Super Assay documentation using the automated protocol.

data_processing:
The Illumina GenomeStudio Genotyping Module was used to determine genotypes from the intensity data files (IDAT files) outputted from scanning the BeadChip.
The Illumina GenomeStudio Genotyping Module called genotypes and generated SNP statistics.

label: C-Bio, G-Bio, A-DNP, T-DNP

organism: Bos taurus

source_name: blood from coccygeal vein in the tail

label_protocol: According to the Infinium HD Super Assay documentation (https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/infinium_assays/infinium-hd-super-assay/infinium-hd-super-assay-reference-guide-11322427-03.pdf), labels were added during allele-specific base extension.

extract_protocol: Whole blood sampled from the coccygueal vein of the tail were centrifuged, and the resulting buffy coat layer was stored at 4C until DNA extraction. Genomic DNA was extracted from buffy coat using the QIAGEN QIAamp DNA Blood Mini Kit according to the manufacturer's instructions.

tag: mastitis

tag: metritis

tag: milk fever

tag: farm

value: B

value: female


title: Gan_1

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: ChIPseq CHD4 in Zfp131KO ES cells (iZfp131-HA Zfp131KO) replicate 1

description:
ES(iZfp131-HA Zfp131KO)_ChIPseq_CHD4_rep1
CHD4_2iMINUS_Zfp131KO.events.gz
CHD4_Zfp131_deseq.txt.gz


title: Gan_7

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2025
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: F


title: 4mC_DIP-seq_AvL1

value: N4-methyl-C (NEB)


title: ChIPseq SIN3A in Zbtb11KO ES cells (iZbtb11-HA Zbtb11KO) replicate 1

description:
ES(iZbtb11-HA Zbtb11KO)_ChIPseq_SIN3A_rep1
SIN3A_2iMINUS_Zbtb11KO.events.gz
SIN3A_Zbtb11_deseq.txt.gz

value: anti-SIN3A (Abcam ab3479)


title: ChIPseq CHD4 in Zbtb11KO ES cells (iZbtb11-HA Zbtb11KO) replicate 2

description:
ES(iZbtb11-HA Zbtb11KO)_ChIPseq_CHD4_rep2
CHD4_2iMINUS_Zbtb11KO.events.gz
CHD4_Zbtb11_deseq.txt.gz

value: anti-CHD4 (Abcam ab70469)

value: Embryonic stem cells


title: ChIPseq CHD4 in Zbtb11KO ES cells (iZbtb11-HA Zbtb11KO) replicate 1

description:
ES(iZbtb11-HA Zbtb11KO)_ChIPseq_CHD4_rep1
CHD4_2iMINUS_Zbtb11KO.events.gz
CHD4_Zbtb11_deseq.txt.gz


title: GBC_TNF, scATAC-seq

city: Shanghai

first: Wenbin

last: Liu

address: 800 Xiangyin Rd..

country: China

institute: Second Military Medical University

description: GBC cell line with stimulation of TNF-a for 8h

data_processing:
The Cell Ranger ATAC software pipeline (version 1.2.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the BWA-MEM aligner.
the unique molecular identifier (UMI) count matrix using the R package Seurat(version 3.1.5)
Library size normalization was performed with NormalizeData function in Seurat.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with peaks for every peak and every cell

extract_protocol:
This is achieved by transposing nuclei in a bulk solution; then using a microfluidic chip, the nuclei are partitioned into nanoliter-scale Gel Beadsin-emulsion (GEMs).
A pool of ~750,000 10x Barcodes is sampled to separately and uniquely index the transposed DNA of each individual nucleus. Libraries are generated and sequenced, and 10x Barcodes are used to associate individual reads back to the individual partitions, and thereby, to each individual nucleus.

tag: cell line

value: GBC

value: TNF-a


title: GBC0, scATAC-seq

description: normal cell line

value: control


title: ChIPseq NELF in wildtype ES cells (iCre) replicate 2

description:
ES(iCre)_ChIPseq_NELF_rep2
NELF_2iMINUS_WT.events.gz

tag: genotype

value: NELF

value: anti-NELF (Sigma HPA007187)

value: 3d without doxycycline in -2i+LIF


title: Viral genomic RNA sequencing of a B.1.617.2/Delta isolate, resequenced

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

description: Viral genomic RNA sequencing of a B.1.617.2/Delta isolate (EPI_ISL_2378732), resequenced

data_processing:
Sequencing reads were trimmed using fastp (ver. 0.21.0).
Sequencing reads were mapped to the viral genome sequence of SARS-CoV-2 Wuhan-Hu-1 (NC_045512.2) using BWA-MEM (ver. 0.7.17).
Variant calling and filtering were performed using BCFtools (ver. 1.9).
Variant annotation was performed using snpEff (ver. 5.0e).
Genome_build: SARS-CoV-2 Wuhan-Hu-1 (NC_045512.2)
Supplementary_files_format_and_content: Variant information  (tsv)

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Viral genomic RNA of a B.1.617.2/Delta isolate (EPI_ISL_2378732)

extract_protocol:
QIAamp viral RNA mini kit (Qiagen)
NEB Next Ultra RNA Library Prep Kit for Illumina (New England Biolabs)

tag: isolate

value: B.1.617.2/Delta isolate


title: RBE_TNF, scATAC-seq

description: RBE cell line with stimulation of TNF-a for 8h

value: RBE


title: Viral genomic RNA sequencing of a D614G-bearing B.1.1 isolate, resequenced

description: Viral genomic RNA sequencing of a D614G-bearing B.1.1 isolate (EPI_ISL_479681), resequenced

source_name: Viral genomic RNA of a D614G-bearing B.1.1 isolate (EPI_ISL_479681)

value: D614G-bearing B.1.1 isolate


title: ChIPseq NELF in wildtype ES cells (iCre) replicate 1

description:
ES(iCre)_ChIPseq_NELF_rep1
NELF_2iMINUS_WT.events.gz

tag: chip target

tag: chip antibody


title: ChIPseq SETD1A in wildtype ES cells (iCre) replicate 2

description:
ES(iCre)_ChIPseq_SETD1A_rep2
SETD1A_2iMINUS_WT.events.gz

value: anti-SETD1A (Abcam ab70378)

tag: treatment

tag: cell type


title: Viral genomic RNA sequencing of a B.1.1.529/Omicron isolate, resequenced

description: Viral genomic RNA sequencing of a B.1.1.529/Omicron isolate (EPI_ISL_6913953), resequenced

source_name: Viral genomic RNA of a B.1.1.529/Omicron isolate (EPI_ISL_6913953)

value: B.1.1.529/Omicron isolate


title: ChIPseq CHD4 in wildtype ES cells (iCre) replicate 2

description:
ES(iCre)_ChIPseq_CHD4_rep2
CHD4_2iMINUS_WT.events.gz


title: RBE0, scATAC-seq

description: normal cell line


title: ChIPseq CHD4 in wildtype ES cells (iCre) replicate 1

description:
ES(iCre)_ChIPseq_CHD4_rep1
CHD4_2iMINUS_WT.events.gz


title: ChIPseq SETD1A in wildtype ES cells (iCre) replicate 1

description:
ES(iCre)_ChIPseq_SETD1A_rep1
SETD1A_2iMINUS_WT.events.gz


title: RNA_Rpd3_S2_se

status: Public on Jan 06 2022

city: Dallas

first: Wen-Chuan

last: Hsieh

state: Texas

address: 5323 Harry Hines Blvd

department: Biochemistry

institute: UTSouthwestern Medical Center

data_processing:
Reads with phred quality scores less than 20 and less than 35 bp after trimming were removed from further analysis using trimgalore version 0.4.1. Quality-filtered reads were then aligned to the yeast reference genome (S288C) using the HISAT (v 2.0.1) (Pertea et al., 2016) aligner using default settings and marked duplicates using Sambamba version 0.6.6 (Tarasov et al., 2015). Aligned reads were quantified using ‘featurecount’ (v1.4.6) (Liao et al., 2014) per ID against reference annotations (R64-2-1) . Log fold changes were used to calculate KEGG pathway enrichment using clusterProfiler (Chiang et al., 2021).
Genome_build: S288C
Supplementary_files_format_and_content: tab-delimited gene count files

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: Strains of interest were grown in SD medium overnight. Cells from overnight cultures were inoculated into fresh SD to 0.2 optical density (OD)/ml and grown at least two generations to log phase (OD600 ~1).

extract_protocol:
Cells were first quenched in TCA (10% final) and washed with acetone. Cell lysis was performed by bead-beating in urea buffer containing 6 M urea, 1% SDS, 50 mM Tris-HCl pH 7.5, 50 mM NaF, 5 mM EDTA, 1 mM PMSF, and protease inhibitor cocktail (Roche). Supernatants of the lysates were collected after heating for 10 min at 75°C.
RNA isolation of one OD600 unit of cells was performed using MasterPure yeast RNA purification kit (Epicenter) following the manufacturer’s protocol. RNA concentration was determined by A260. 1 mg RNA was reverse transcribed to cDNA using Superscript III Reverse Transcriptase from Invitrogen. Real-time PCR was performed in triplicate with SYBR GreenSuper mix from BioRad.

treatment_protocol: To perform glucose starvation, we quickly replaced the media by spinning down the cells, washing the pellets with pre-warmed S media, and then resuspending cells in the same volume of warmed S media. Samples were collected at indicated times. Glucose replenishment was carried out at a final concentration of 2% glucose. All centrifugations were performed at 3000 rpm, 2 min at room temperature.

tag: condition

value: glucose starvation

tag: cell source

value: CEN.PK  cells


title: RNA_Gcn5_S2_pe


title: RNA_WT_S1_pe

value: WT


title: RNA_WT_S2_pe


title: RNA_Gcn5_D2_pe


title: RNA_Gcn5_D1_pe


title: RNA_Gcn5_S1_pe


title: RNA_Rpd3_D2_se


title: ChIPseq NELF in Zbtb11KO ES cells (iZbtb11-HA Zbtb11KO) replicate 1

description:
ES(iZbtb11-HA Zbtb11KO)_ChIPseq_NELF_rep1
NELF_2iMINUS_Zbtb11KO.events.gz
NELF_Zbtb11_deseq.txt.gz

value: Ainv15(iZbtb11-HA Zbtb11KO)


title: RNA_Rpd3_S1_se


title: RNA_Rpd3_D1_se


title: RNA_WT_S2_se


title: RNA_WT_D1_pe


title: RNA_WT_D2_pe


title: RNA_WT_S1_se


title: RNA_WT_D2_se


title: Inp_Gcn5HA_30

data_processing:
We use the BICF ChIP-seq analysis Workflow version 1.1.3 (Barnes et al., 2020). The workflow used trimgalore version 0.4.1 (Martin et al., 2011) on the raw reads to remove adapter sequences and to remove reads shorter than 35bp or with phred quality scores less than 20. Trimmed reads were then aligned to the yeast reference genome (S288C) using default parameters in BWA version 0.7.12 (Li and Durbin, 2009). The aligned reads were subsequently filtered for quality and uniquely mappable reads were retained for further analysis using Samtools version 1.3 (Li and Durbin, 2009) and Sambamba version 0.6.6 (Tarasov et al., 2015). Library complexity was measured using BEDTools version 2.26.0 (Quinlan and Hall, 2010) and meets ENCODE data quality standards (Landt et al., 2012). We determined ChIP enrichment compared to background using ‘plotFingerprint’ in deepTools version 2.5.0 (Ramirez et al., 2016).  Relaxed peaks were called using MACS version 2.1.0 (Feng et al., 2012) with a p-value of 1x10-2 for each replicate, pooled replicates’ reads and pseudoreplicates. Peak calls from the pooled replicates that are either observed in all replicates, or in both pseudoreplicates were kept. Reads were counted at promoter regions using subread ‘featurecount’ (v1.4.6) (Liao et al., 2014) per gene ID against the same genome as above and used for subsequent analysis. Reads overlapping multiple genes were not discarded. Small-RNAs and genes with logcpm of < 10 were filtered out.
Genome_build: S288C
Supplementary_files_format_and_content: bigwig files

extract_protocol:
ChIP was performed as described previously (Cai et al., 2011). Briefly, 100 OD600 units of cells were fixed in 1% formaldehyde for 15 min and then quenched in 125 mM glycine for 10 min. Cell pellets were washed twice with a buffer containing 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM PMSF, and 1 mM benzamide-HCl, and snap-frozen in liquid nitrogen. Frozen pellets were lysed in 0.45 mL ChIP lysis buffer (50 mM HEPES-KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.1% SDS,1 mM PMSF, 10 µM leupeptin, 5 µM pepstatin A, and Roche protease inhibitor cocktail) and lysed by bead-beating. Lysates were split to two tubes and sonicated for 16 cycles (30 sec on, 1 min off, high output) using the Bioruptor (Diagenode). The lysates were then cleared by two consecutive spins at 15,000 rpm for 10 min. For HA ChIP, lysate was incubated overnight with 10 µg antibody. For histone ChIP, lysate was diluted at 1:10 and incubated overnight with 2 µg antibody. 25 µl magnetic beads were added and incubated for an additional 1.5 h. Beads were then washed twice with ChIP lysis buffer, once with deoxycholate buffer (10 mM Tris-HCl, 0.25 M LiCl, 0.5% deoxycholate, 1 mM EDTA), and once with TE buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA). Elution was performed using TES buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, and 1% SDS). Reverse crosslinking was performed at 65°C. An equal volume of TE containing 1.25 mg/mL proteinase K and RNase A was then added and incubated for 2 h at 37°C. DNA was then purified using the Qiagen PCR purification kit.
ChIP samples were prepared as described above in two biological replicates. We constructed sequencing libraries using KAPA Hyper Prep Kit from Kapa Biosystems. The quality and quantity of constructed libraries were determined using Agilent D1000 ScreenTape System and Invitrogen Qubit Fluorometer. The sequencing was performed by the UTSW Next Generation Sequencing Core Facility using the Illumina NextSeq 500 System.

tag: protein

value: HA


title: HA_Gcn5HA_30_2


title: HA_Gcn5HA_30_1


title: RNA_WT_D1_se


title: HA_Gcn5HA_0_1


title: s4_H3_WT_30


title: HA_Gcn5HA_0_2


title: s16_H3K9_WT_30


title: s10_H3K9_WT_30


title: s13_H3K9_WT_0


title: s1_H3_WT_0


title: s17_H3K9_gcn5_30


title: s5_H3_gcn5_30


title: s8_H3K9_gcn5_0


title: WT_30_H3K9_2


title: s2_H3_gcn5_0


title: WT_30_H3


title: WT_30_H3K9_1


title: WT_0_H3K9_2


title: s14_H3K9_gcn5_0


title: WT_0_H3K9_1


title: s7_H3K9_WT_0


title: DMAH96: MNase_rep2_140_min

city: Durham

first: Yulong

last: Li

state: NC

address: 208 Research Dr

institute: Duke University

description: MNase chromatin at T=140 after release from α-factor

data_processing:
All reads were aligned to the sacCer3/R64 version of the S. cerevisiae genome using Bowtie 0.12.7. MNase-seq reads were mapped in paired-end mode and RNA-seq reads were mapped in single-read mode, using Bowtie parameters: -n 2 -l 20 --phred33-quals -m 1 --best --strata -y.
RNA replicates were merged for each time point.
Chromatin replicates were merged for each time point and randomly sampled to retain equal number of fragments per fragment size across all time points.
Per base-pair nucleosome scores were computed through cross correlating a bivariate Gaussian distribution against MNase reads at ChrIV nucleosomes identified by Broggard et al. 2012 and normalized by local DNA copy number. Gene-body nucleosome score was defined as the average nucleosome score of 500 bp window downstream of each ORF’s TSS. A Shannon entropy was computed also for this window as the gene-body nucleosome entropy.
Per base-pair subnucleosome score was computed using a bivariate Gaussian distribution against MNase reads at Abf1p binding sites identified by MacIsaac et al. 2006 and normalized by local DNA copy number. The average subnucleosome score of the window 250 bp upstream of TSS was defined as the promoter subnucleosome score.
RNA reads were counted inside ORF boundaries (from TSS to PAS sites identifed by Park et al. 2014) and normalized by TPM.
Genome_build: Saccharomyces cerevisiae S288C reference genome R64-1-1 (sacCer3)

source_name: yeast cells

growth_protocol: Cells were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) at 30°C.

extract_protocol:
Total RNA was extracted using the hot phenol method. MNase digestions were performed as previously described by Henikoff et al. 2011 and Belsky et al. 2015.
RNA-seq libraries were prepared using TruSeq Stranded Total RNA-seq Kit (Illumina) and ribosomal RNA was removed with Ribo-Zero Gold Kit (Human-Mouse-Rat, Illumina). MNase-seq libraries were prepared using 2 µg of DNA as previously described by Henikoff et al. 2011, with the following modifications: NEBNext multiplex oligos for Illumina Kit (New England Biolabs) was used in adapter ligation and PCR steps. PCR reactions were performed with 12 cycles and the reactions were cleaned using Agencourt AMPure XP beads (Beckman).

treatment_protocol: Cells were grown to an OD600 of ~0.3 and arrested in G1 phase with α-factor at a final concentration of 50 ng/mL for 2 h. Samples were taken right before release as the “α-factor” timepoint. Cells were then washed twice in sterile water, resuspended in fresh YPD medium, and samples were collected every 10 min until 150 min post release.

tag: strain

value: released from α-factor

tag: time

value: 140 min


title: WT_0_H3


title: rpd3_0_H3K9_1


title: rpd3_30_H3K9_2


title: DMAH95: MNase_rep2_130_min

description: MNase chromatin at T=130 after release from α-factor

value: 130 min


title: rpd3_0_H3K9_2

value: control


title: rpd3_30_H3


title: s11_H3K9_gcn5_30


title: DMAH93: MNase_rep2_110_min

description: MNase chromatin at T=110 after release from α-factor

value: 110 min


title: rpd3_30_H3K9_1


title: rpd3_0_H3


title: DMAH92: MNase_rep2_100_min

description: MNase chromatin at T=100 after release from α-factor

value: 100 min


title: DMAH91: MNase_rep2_90_min

description: MNase chromatin at T=90 after release from α-factor

value: 90 min


title: DMAH90: MNase_rep2_80_min

description: MNase chromatin at T=80 after release from α-factor

value: 80 min


title: DMAH89: MNase_rep2_70_min

description: MNase chromatin at T=70 after release from α-factor

value: 70 min


title: DMAH88: MNase_rep2_60_min

description: MNase chromatin at T=60 after release from α-factor

value: 60 min


title: DMAH94: MNase_rep2_120_min

description: MNase chromatin at T=120 after release from α-factor

value: 120 min


title: DMAH87: MNase_rep2_50_min

description: MNase chromatin at T=50 after release from α-factor

value: 50 min


title: DMAH85: MNase_rep2_30_min

description: MNase chromatin at T=30 after release from α-factor

value: 30 min


title: DMAH84: MNase_rep2_20_min

description: MNase chromatin at T=20 after release from α-factor

value: 20 min


title: DMAH86: MNase_rep2_40_min

description: MNase chromatin at T=40 after release from α-factor

value: 40 min


title: DMAH83: MNase_rep2_10_min

description: MNase chromatin at T=10 prior to α-factor release

value: 10 min


title: DMAH82: MNase_rep2_0_min

description: MNase chromatin at T=0 prior to α-factor release

value: 50 ng/mL α-factor

value: 0 min


title: DMAH79: MNase_rep1_150_min

description: MNase chromatin at T=150 after release from α-factor

value: released from α-factor

value: 150 min


title: DMAH78: MNase_rep1_140_min

value: 140 min


title: DMAH77: MNase_rep1_130_min

value: 130 min


title: DMAH76: MNase_rep1_120_min


title: DMAH75: MNase_rep1_110_min

value: 110 min


title: DMAH74: MNase_rep1_100_min

value: 100 min


title: Inp_Gcn5HA_0

value: HA

value: control

value: CEN.PK  cells


title: DMAH73: MNase_rep1_90_min

value: 90 min


title: DMAH67: MNase_rep1_30_min


title: DMAH72: MNase_rep1_80_min

value: 80 min


title: DMAH69: MNase_rep1_50_min

value: 50 min


title: DMAH68: MNase_rep1_40_min


title: DMAH70: MNase_rep1_60_min

value: 60 min


title: DMAH66: MNase_rep1_20_min

value: 20 min


title: DMAH114: RNA_rep2_140_min

description: RNA at T=140 after release from α-factor


title: DMAH64: MNase_rep1_0_min


title: DMAH112: RNA_rep2_120_min

description: RNA at T=120 after release from α-factor

value: 120 min


title: DMAH113: RNA_rep2_130_min

description: RNA at T=130 after release from α-factor


title: DMAH110: RNA_rep2_100_min

description: RNA at T=100 after release from α-factor


title: DMAH107: RNA_rep2_70_min

description: RNA at T=70 after release from α-factor

value: 70 min


title: DMAH109: RNA_rep2_90_min

description: RNA at T=90 after release from α-factor


title: DMAH105: RNA_rep2_50_min

description: RNA at T=50 after release from α-factor


title: DMAH104: RNA_rep2_40_min

description: RNA at T=40 after release from α-factor

value: 40 min


title: DMAH102: RNA_rep2_20_min

description: RNA at T=20 after release from α-factor

value: released from α-factor


title: DMAH100: RNA_rep2_0_min

description: RNA at T=0 prior to α-factor release

value: 50 ng/mL α-factor

value: 0 min


title: Pt3_Tum2006002

city: Paris

first: Julie

last: HELFT

state: Ile-de-France

address: 26 Rue d'Ulm

department: U932 - Immunity and Cancer

country: France

institute: Institut Curie

description:
Single Cell RNAseq
Raw_Counts_Human_SC_RNAseq_Fig1_and_2.csv

data_processing:
The initial files were demultiplexed using BCL2FASTQ
Human and mouse raw sequencing data were respectively aligned using 10X software CellRanger (Version 3.0.2) with default parameters. And STAR aligner (v2.5.3a) for Bulk RNAseq.
Bulk expression data was normalized using DESeq2 algorithm / For the Single Cell RNAseq, data was normalized by total counts following the Seurat 3 R pipeline
Differentially expressed genes were identified using DESeq2 R package in Bulk RNAseq / For the Single Cell RNAseq, Differential gene expression analysis applied using the Seurat function FindAllMarkers()
Genome_build: GRCh38/84 and GRCm38/84 (mm10). And hg19 for Bulk RNAseq
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample and Single Cell metada (clusters…)

source_name: Myeloid cells

extract_protocol:
Myeloid cells were FACS-sorted according to the phenotype of interest and processed using either 10x Genomics protocol for scRNA-seq or single-cell RNA purification kit (Norgen, Cat#51800) for bulk RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols (NovaSeq 6000)

tag: tissue

value: Tumor


title: Pt3_Tum2006013


title: Pt3_Tum2005820


title: DMAH101: RNA_rep2_10_min

description: RNA at T=10 after release from α-factor

value: 10 min


title: Pt3_LN2006013

value: Invaded Lymph Node


title: DMAH71: MNase_rep1_70_min


title: DMAH35: RNA_rep1_140_min

value: 140 min


title: Pt3_LN2005820


title: DMAH36: RNA_rep1_150_min

description: RNA at T=150 after release from α-factor

value: 150 min


title: Pt3_Blood2006013

value: Blood


title: DMAH108: RNA_rep2_80_min

description: RNA at T=80 after release from α-factor


title: Pt7_LN


title: DMAH106: RNA_rep2_60_min

description: RNA at T=60 after release from α-factor


title: Pt3_Blood2006002


title: Pt6_Tum


title: Pt3_Blood2005820


title: DMAH34: RNA_rep1_130_min

value: 130 min


title: DMAH33: RNA_rep1_120_min


title: DMAH31: RNA_rep1_100_min

value: 100 min


title: DMAH32: RNA_rep1_110_min

description: RNA at T=110 after release from α-factor

value: 110 min


title: DMAH9: RNA_rep1_80_min

description: RNA at T=80 after release from α-factor

value: 80 min


title: DMAH10: RNA_rep1_90_min

description: RNA at T=90 after release from α-factor

value: 90 min


title: DMAH8: RNA_rep1_70_min

description: RNA at T=70 after release from α-factor


title: Pt3_LN2006002


title: DMAH7: RNA_rep1_60_min

description: RNA at T=60 after release from α-factor

value: 60 min


title: DMAH4: RNA_rep1_30_min

description: RNA at T=30 after release from α-factor

value: 30 min


title: DMAH103: RNA_rep2_30_min

description: RNA at T=30 after release from α-factor


title: DMAH6: RNA_rep1_50_min

description: RNA at T=50 after release from α-factor

value: 50 min


title: Pt6_LN


title: DMAH1: RNA_rep1_0_min

description: RNA at T=0 prior to α-factor release


title: P1_LN_1_FOLR2

description:
Bulk RNAseq
Raw_Counts_Human_Bulk_RNAseq_Fig2.csv

source_name: Macrophages FOLR2 pos


title: Pt2_Tum


title: LN_AG3861_TAMsFOLR2pos


title: P1_LN_2_FOLR2


title: Pt5_Tum


title: LN_AG4637_TAMsFOLR2pos


title: LN_AH1126_TAMsFOLR2pos


title: P1_FOLR2


title: T_AG7577_TAMsFOLR2pos


title: T_AG7536_TAMsFOLR2pos


title: P2_FOLR2


title: Raji cells treated w/ bryostatin - IgG rep3

city: Seattle

first: Rimas

last: Orentas

state: Washington

address: 1100 Olive Way NE

department: BTCCCR

institute: Seattle Children's Research Institute

data_processing:
Library strategy: Cut&Tag
sequenced on a HiSeq instrument (Novogene, Sacramento, CA), paired-end 150, with read depth of 17M per sample, basecallling bcl2fastq
Sequencing adaptors identified and trimmed by TrimGalore (Trim Galore (RRID:SCR_011847)).
Sequencing reads were aligned to the UCSC Hg38 using the Bowtie2 package
Alignment results were normalized by the RPKM (Reads Per Kilobase of transcript, per Million mapped reads) method by DeepTools2
Peak calling analysis was done by SEACR
Differential peak analysis was done by DESeq2 and peaks were annotated by GSCA (Ji Z and Ji H (2014), GSCA: Gene Set Context Analysis. R package version 1.4.0.).
Genome_build: Hg38
Supplementary_files_format_and_content: Peak text files
Supplementary_files_format_and_content: BigWig generated by Deeptools2

source_name: Burkitt's lymphoma cell line

growth_protocol: Cell lines were cultured in RPMI 1640 supplemented with 2 mM l-glutamine, 10 mM HEPES (Invitrogen), and 10% heat-inactivated FBS (VWR).

extract_protocol:
Fresh cells (2x105 to 5x105 per treatment) were harvested and washed twice in 1.5 Ml wash buffer (20mM HEPES pH 7.5; 150mM NaCl; 0.5mM Spermidine (Sigma S2501); 1× Protease inhibitor cocktail, Roche), and Cut&Tag libraries generated, following the protocol “Bench top CUT&Tag V.2” (Hatice S Kaya-Okur, Steven Henikoff 2019. Bench top CUT&Tag. protocols.io, dx.doi.org/10.17504/protocols.io.bcuhiwt6)
Cut&Tag libraries generated, following the protocol “Bench top CUT&Tag V.2” (Hatice S Kaya-Okur, Steven Henikoff 2019. Bench top CUT&Tag. protocols.io, dx.doi.org/10.17504/protocols.io.bcuhiwt6)

treatment_protocol: treated with 1nM Bryostatin at 37°C overnight

value: Raji

value: treated with 1nM Bryostatin

tag: cut&tag antibodies

value: IgG


title: Raji cells treated w/ bryostatin - IgG rep1


title: Raji cells treated w/ bryostatin - H3K27me3 rep3


title: Pt5_LN


title: Raji cells treated w/ bryostatin - IgG rep2


title: Raji cells treated w/ bryostatin - H3K27me3 rep1


title: DMAH5: RNA_rep1_40_min

description: RNA at T=40 after release from α-factor

value: released from α-factor

value: 40 min


title: P3_CADM1

source_name: Macrophages CADM1 pos

value: Tumor


title: T_AG7643_TAMsFOLR2pos


title: Pt1_LN

value: Invaded Lymph Node


title: Raji cells treated w/ bryostatin - H3K4me3 rep2


title: Raji cells treated w/ bryostatin - H3K4me3 rep1


title: P4_CADM1


title: DMAH3: RNA_rep1_20_min

description: RNA at T=20 after release from α-factor

value: 20 min


title: P5_CADM1


title: Raji cells treated w/ bryostatin - H3K27me3 rep2


title: Raji cells treated w/ bryostatin- H3K4me2 rep3


title: P6_CADM1


title: P7_CADM1


title: Raji cells treated w/ bryostatin - H3K4me2 rep2


title: P7_Mono

source_name: Monocytes CCR2 pos


title: P6_Mono


title: Raji cells treated w/ bryostatin - H3K4me2 rep1


title: Raji cells treated w/ bryostatin - H3K4me3 rep3


title: Raji cells - IgG rep1

value: no treatment


title: Raji cells - IgG rep3


title: Raji cells - H3K27me3 rep3


title: P2_Mono


title: Raji cells - IgG rep2


title: P1_Mono


title: P4_Mono


title: P1_LN_2_Mono


title: Raji cells - H3K27me3 rep1


title: P3_Mono


title: Raji cells - H3K27me3 rep2


title: P1_LN_1_Mono


title: T_AG7577_MonoCCR2pos


title: Raji cells - H3K4me3 rep2


title: Raji cells - H3K4me3 rep3


title: T_AG7643_MonoCCR2pos


title: Raji cells - H3K4me2 rep3


title: Raji cells - H3K4me2 rep2


title: Raji cells - H3K4me3 rep1


title: parabiosis-facs

city: Stanford

first: Robert

last: Palovics

address: 290 Jane Stanford Way

department: Neurology

institute: Stanford University

description: SmartSeq2 single-cell raw counts

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.20.
Reads were aligned with Gencode v.M19 annotations using STAR version 2.5.2b with parameters TK.
Gene counts were produced using HTSEQ version 0.6.1p1 with default parameters, except ‘stranded’ was set to ‘false’, and ‘mode’ was set to ‘intersection-nonempty’.
Genome_build: Gencode v.M19
Supplementary_files_format_and_content: Processed data is available as h5ad.

source_name: 20 organs of male parabionts

extract_protocol: RNAeasy (mini and micro) Qiagen RNA isolation from homogenized tissue. 10X genomics and Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT. Nextera tagmentation according to the standard protocol for single cell RNA-seq.

tag: Sex

value: male


title: Raji cells - H3K4me2 rep1


title: LN_AG4637_MonoCCR2pos


title: REH cells treated w/ bryostatin - IgG rep3

source_name: Acute lymphocytic leukemia cell line

value: REH


title: TAMsCADM1_Medium_Tumor_2

description:
Bulk RNAseq
Raw_Counts_Bulk_Mouse_TAMs_Fig7.csv

source_name: Macrophages

value: PyMT +/-

tag: tumor size (mg)

tag: age

value: 22 weeks old


title: REH cells treated w/ bryostatin - IgG rep2

tag: cell line


title: LN_AG3861_MonoCCR2pos


title: REH cells treated w/ bryostatin - IgG rep1


title: LN_AH1126_MonoCCR2pos


title: T_AG7536_MonoCCR2pos


title: REH cells treated w/ bryostatin - H3K27me3 rep3


title: REH cells treated w/ bryostatin - H3K27me3 rep2


title: REH cells treated w/ bryostatin - H3K4me3 rep3


title: TAMsCADM1_Small_Tumor_1

tag: genotype


title: HMLE XIST KO ML rep2

first: Laia

last: Richart

address: 13 Rue Pierre et Marie Curie

department: Developmental Biology

data_processing:
The human reference genome hg19 was masked with a list of informative heterozygous SNPs on the X chromosome using BEDtools maskfasta (v2.2.2).
Fastq files were aligned to the human reference genome hg19, using the gene annotation from GENCODE and the aligner STAR (v2.7.0a) with the following parameters: --outFilterMultimapNmax 1 --outSAMattributes NH HI NM MD --alignEndsType EndToEnd.
For gene expression analyses, reads overlapping exons or genes (GENCODE annotation) were counted using FeatureCounts (Subread v1.5.1) with the following parameters: -t exon -g gene_name -p -B -C.
For allele-specific analyses, PCR duplicates were removed from mapped reads using Picard tools (v1.97) with the following parameters: REMOVE_DUPLICATES=true ASSUME_SORTED=true.
Remaining reads were then split by allele using SNPsplit (v0.3.2) (options: --paired) and reads overlapping informative SNPs were quantified using SAMtools (v1.9) mpileup.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file "FeatureCounts.raw.txt" contains raw counts overlapping exons and genes for HMLE samples.

source_name: HMLE

growth_protocol: HMLE cells were cultured in DMEM:F-12/GlutaMAX supplemented with 10% FBS, 1% MEM Non-Essential Amino Acids, 1% Pen/Strep, 10 µg/ml insulin, 1 µg/mL hydrocortisone, and 10 ng/mL human epidermal growth factor (EGF).

extract_protocol:
RNA was isolated with Trizol-Chloroform followed by isopropanol precipitation.
RNA-Seq libraries were prepared using the Swift RNA Library Kit (Swift Biosciences, ref. R1024 and R1096) according to manufacturer’s instructions and sequenced on an Illumina NovaSeq 6000 (PE100).

treatment_protocol: Cells were tripsinized, resuspended in FACS buffer (PBS 1X, 1% BSA, 5mM EDTA), and stained with FACS-grade primary antibodies against ESA or a combination of CD44 and CD24. HMLE were FACS-sorted into two populations according to their ESA positivity. In the case of HMLER, only CD44+/CD24- cells (corresponding to CSCs) were selected for subsequent analyses.

value: Immortalized human mammary epithelial cells

value: XIST-KO

tag: cell compartment

value: ML (ESA+)


title: HMLE XIST KO ML rep3


title: REH cells treated w/ bryostatin - H3K4me3 rep2


title: TAMsCADM1_Medium_Tumor_1


title: REH cells treated w/ bryostatin - H3K27me3 rep1


title: REH cells treated w/ bryostatin - H3K4me3 rep1


title: HMLE XIST KO ML rep1


title: REH cells treated w/ bryostatin - H3K4me2 rep2


title: TAMsFOLR2_Small_Tumor_2


title: REH cells treated w/ bryostatin- H3K4me2 rep3


title: HMLE XIST KO MaSC rep3

value: MaSC (ESA-)


title: TAMsFOLR2_Medium_Tumor_1


title: REH cells treated w/ bryostatin - H3K4me2 rep1


title: REH cells - IgG rep2


title: REH cells - IgG rep3


title: TAMsCADM1_Small_Tumor_2


title: REH cells - IgG rep1


title: TAMsFOLR2_Small_Tumor_1


title: HMLE XIST KO MaSC rep2


title: HMLE XIST KO MaSC rep1


title: REH cells - H3K27me3 rep2


title: MacFOLR2_NoTumor_3

value: Mammary Gland

value: PyMT -/-


title: REH cells - H3K27me3 rep3


title: TAMsFOLR2_Medium_Tumor_2


title: REH cells - H3K27me3 rep1


title: HMLE Wildtype ML rep3

value: WT


title: REH cells - H3K4me3 rep2


title: MacFOLR2_NoTumor_2


title: MacFOLR2_NoTumor_1


title: REH cells - H3K4me3 rep3


title: HMLE Wildtype MaSC rep3


title: REH cells - H3K4me2 rep3


title: PyMT_Ms1

description:
Single Cell RNAseq
Raw_Counts_SC_Mouse_Fcgr1pos_FigS3.csv


title: HMLE Wildtype ML rep1


title: NALM6 cells treated w/ bryostatin - IgG rep2

value: treated with 1nM Bryostatin

value: IgG


title: PyMT_Ms2

value: Tumor


title: HMLE Wildtype ML rep2


title: NALM6 cells treated w/ bryostatin - IgG rep3


title: REH cells - H3K4me2 rep2


title: NALM6 cells treated w/ bryostatin - IgG rep1


title: REH cells - H3K4me3 rep1


title: HMLE Wildtype MaSC rep2


title: REH cells - H3K4me2 rep1


title: HMLE Wildtype MaSC rep1


title: NALM6 cells treated w/ bryostatin - H3K27me3 rep3


title: NALM6 cells treated w/ bryostatin - H3K27me3 rep1


title: NALM6 cells treated w/ bryostatin - H3K27me3 rep2


title: HMLE KO MaSC ChIP IgG

data_processing:
Trimmed fastq files were aligned to the human reference genome hg19 using the Bowtie2 aligner (v2.2.5) with default parameters.
PCR duplicates were discarded using Picard tools (v1.97) with the option REMOVE_DUPLICATES=true.
bigWig files were created using deepTools bamCoverage (v3.0.2) with the following parameters: --normalizeUsingRPKM --ignoreForNormalization chrX chrY --samFlagInclude 64 --binSize 50 --extendReads. Reads overlapping problematic, blacklisted regions from the Encode Consortium (wgEncodeDacMapabilityConsensusExcludable.bed) were excluded from the computation of coverage with the option ----blackListFileName.
bigWig files from biological replicates were merged with the UCSC tools (v2017.05.03) bigWigMerge and bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: bigWigs result from the merging of 2 biological replicates.

extract_protocol:
ChIP-Seq for MED1 was performed as previously described (Holoch et al., 2021) with minor modifications. Briefly, WT and KO MaSC HMLE were FACS-sorted and expanded in culture for 72 h before being cross-linked in the culture dishes by incubation at RT in pre-warmed (37˚C) cross-linking medium (DMEM supplemented with 15 mM HEPES-NaOH pH 7.9, 15 mM NaCl, 0.15 mM EDTA, 0.075 mM EGTA and 1% formaldehyde).
After 10 min, the cross-linking reaction was stopped by addition of 0.125 M glycine at RT for 5 min. Cells were then rinsed with cold PBS, scraped from the dishes, and transferred to 50-mL conical tubes, pelleted, and washed again in PBS. Next, cells were lysed by incubation at 4°C for 10 min in 1 mL buffer 1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100 supplemented with protease inhibitors).
Nuclei were pelleted, resuspended in 1 mL of buffer 2 (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA plus protease inhibitors) and rocked at RT for 10 min. Nuclei were pelleted again, resuspended in 1.3 mL of buffer 3 (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 0.5% N-lauroyl-sarcosine supplemented with protease inhibitors) and sonicated using a pre-cooled Diagenode Bioruptor for 30 min (30 s ON/30 s OFF). Solubilized chromatin was recovered by centrifuging at 20,000xg and saving the supernatant. To determine chromatin concentration, 20 μL of chromatin extract were de-crosslinked o/n at 65˚C in 180 μL of T50E10S1 (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS) and were purified the next day by phenol:chloroform extraction and ethanol precipitation.
10 μg of chromatin per sample were used to immunoprecipitate MED1. Sample volumes were equalized using buffer 3. For each sample, 50 µL of Protein A Dynabeads slurry were washed in 500 µL 0.5% BSA in PBS (3X) and then rocked at 4˚C for several hours in 200 µL 0.5% BSA in PBS and 10 µg of MED1 antibody. Just prior to the IP, 0.5 volume buffer 4 (15 mM EDTA, 3% Triton X-100, 0.3% sodium deoxycholate with protease inhibitors) was added to each chromatin sample, and 1/10th of the resulting volume was set aside as input.
For each sample, Dynabeads were washed in 500 µL 0.5% BSA in PBS (3X), resuspended in 50 µL of a 2:1 mixture of buffers 3 and 4, and added to the chromatin extract. After an o/n IP at 4˚C (on a rotating wheel), beads were washed 6X in 0.4 mL ice-cold buffer 5 (50 mM HEPES-KOH pH 7.5, 0.5 M LiCl, 10 mM EDTA, 0.7% sodium deoxycholate, 1% NP-40 with protease inhibitors), with 2 min RT rotation per wash, and 1X in 0.4 mL 10 mM Tris-HCl pH 8, 50 mM NaCl, 1 mM EDTA. Precipitated chromatin was then eluted by incubating beads in 200 µL T50E10S1 at 65°C for 30 min (with vigorous shaking). The IP chromatin samples and the input were incubated o/n at 65°C to reverse cross-links, and then treated with 80 μg of Rnase A at 37°C for 1 h and 40 μg of proteinase K at 55°C for 1 h. DNA was extracted with phenol:chloroform and precipitated in ethanol.
ChIP-Seq libraries were prepared using the Accel-NGS 2S Plus DNA library kit and sequenced on an Illumina Novaseq 6000 (PE100) at the Institut Curie Next Generation Sequencing Core Facility.

treatment_protocol: Cells were tripsinized, resuspended in FACS buffer (PBS 1X, 1% BSA, 5mM EDTA), and stained with the FACS-grade primary antibody against ESA. HMLE were FACS-sorted according to their ESA positivity. MaSC cells were expanded in culture for 48-72h and then processed for ChIP-Seq.


title: NALM6 cells treated w/ bryostatin - H3K4me3 rep2


title: HMLE KO MaSC ChIP MED1 rep2


title: NALM6 cells treated w/ bryostatin - H3K4me3 rep1


title: NALM6 cells treated w/ bryostatin - H3K4me2 rep1


title: HMLE WT MaSC ChIP MED1 rep2


title: HMLE KO MaSC ChIP MED1 rep1


title: NALM6 cells treated w/ bryostatin - H3K4me2 rep2


title: Spleen_3 [miRNA-Seq]

city: ningbo

first: huilin

last: Ou

address: xinning road

institute: lihuili hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts.Then, chose a certain range of length from clean reads to do all the downstream analyses. The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNAs. miRBase20.0 was used as the reference, and the modified software mirdeep2 and sRNA-tools-cli were used to obtain the potential miRNA and draw the secondary structures. The software miREvo and mirdeep2 were integrated to predict novel miRNAs.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010):Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
For the samples with biological replicates:Differential expression analysis of two conditions/groups was performed using the DESeq R package (3.0.3). The P-values was adjusted using the Benjamini& Hochberg method. Corrected P-value of 0.05 was set as the threshold for significantly differential expression by default.
Gene Ontology (GO) enrichment analysis was used on the target gene candidates of differentially expressed miRNAs.We used KOBAS (Maoet al., 2005) software to test the statistical enrichment of the target gene candidates in KEGG pathways.
Genome_build: mus_musculus_Ensembl_97
Supplementary_files_format_and_content: TPM

source_name: spleen

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for  Illumina®(NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute  sequences to each sample.

value: BALB/c

value: spleen

value: untreated


title: PD_1_Spleen_1  [miRNA-Seq]

value: treated with pd-1 antibody


title: NALM6 cells - IgG rep2

value: no treatment


title: NALM6 cells - IgG rep3


title: NALM6 cells treated w/ bryostatin- H3K4me2 rep3


title: Spleen_2 [miRNA-Seq]


title: PD_1_Spleen_3  [miRNA-Seq]


title: NALM6 cells - H3K27me3 rep3


title: NALM6 cells - H3K27me3 rep2


title: HMLE WT MaSC ChIP MED1 rep1


title: PD_1_Lung_3 [miRNA-Seq]

source_name: lung

value: lung


title: NALM6 cells treated w/ bryostatin - H3K4me3 rep3


title: PD_1_Lung_2 [miRNA-Seq]


title: HEK293T-KD

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

data_processing:
For both the RNA samples (CT and KD), the library were sequencd using MinKNOW v20.10.3 with real-time basecalling using Guppy v4.2.2.
Sequencing adapters were trimmed using Porechop v0.2.4 from quality filtered reads and the reads were mapped against hg38 draft genome using Hisat2 with parameters: (-5 35 -3 35 --sensitive -f --ignore-quals --sensitive; including trimming the ends for 35 bases).
Mapped fragments were segregated into plus and minus strands. Regions CT in KD and KD in CT were obtained using bedtools intersect with CT encompaased in KD (CT in KD) and KD encompassed in CT (KD in CT) for plus and minus strands respectively.
Genome_build: hg38 (UCSC; unmasked)

source_name: HEK293T (stable cell line; CGGBP1-targetting shRNA)

growth_protocol: HEK293T CT and KD [lentivirally transduced shRNA system as described in PMID 31547883] were cultured in DMEM supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic solution.

extract_protocol:
HEK293T CT and KD cells were harvested from two 10cm dishes for each sample. RNA extraction was carried ou following the manufacturer's protocol using TRIzol reagent followed by elution in DEPC water.
Libraries were synthesized as per the PCR-cDNA Sequencing Kit SQK-PCS109
Oxford Nanopore Long-read sequencing for CT and KD

treatment_protocol: HEK293T cells were transduced with following shRNA lentiviruses: non-targeting (CT), CGGBP1-silencing (KD) [Origene Lentiviral system TL313955V]. For stable transduction, control and CGGBP1 shmiR transduced cells were selected with 10 ug/ml puromycin.

tag: genotype/variation

value: CGGBP1-targetting shRNA


title: NALM6 cells - H3K4me3 rep3


title: PD_1_Lung_1 [miRNA-Seq]


title: Control 021_ND1

city: Cincinnati

first: Brian

middle: Michael

last: Varisco

state: OH

address: 3333 Burnet Avenue, MLC 7006

department: Critical Care Medicine

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Novaseq 6000
Bismark Alignment to GRCh38
methylkit
ToppGene
Genome_build: GRCh38
Supplementary_files_format_and_content: cov

source_name: Nasal

extract_protocol:
Specimens stored in RNAProtect. 1:100 beta-mercaptoethanol added during thawing, cells extracted and DNA collected using QIAShredder and AllPrep columns.
DNA was sheared to ~250 bp using a Covaris defice and enzymatic methyl-seq and barcoding performed using NEB Enzymatic Methyl-Seq Kit
Specimens were sequenced, demultiplexed and each  aligned and counted using Bismark

tag: group

value: Control

tag: methyl subgroup

tag: study day


title: PD_1_Spleen_2  [miRNA-Seq]

tag: treatment


title: Control 022_ND1


title: Lung_3 [miRNA-Seq]


title: HEK293T-CT

source_name: HEK293T (stable cell line; non-targetting shRNA)

value: non-targetting shRNA


title: Spleen_1 [miRNA-Seq]


title: Control 020_ND1


title: NALM6 cells - IgG rep1


title: Control 019_ND1


title: Lung_1 [miRNA-Seq]


title: Control 012_ND1


title: NALM6 cells - H3K4me2 rep3


title: NALM6 cells - H3K4me2 rep2


title: shASIrs2_3

city: Tokyo

first: Motoharu

last: Awazawa

address: 1-21-1 Toyama, Shinjuku

institute: National Institute for Global Health and Medicine

data_processing:
FASTQ files were imported to CLC Genomics Workbench (Ver.10.1.1, Qiagen).
Reads were mapped to mouse reference genome (mm10) and quantified for 49585 genes.
Total counts were normalized by quantile method.
Differentially expressed genes were identified using Empirical Analysis of DGE tool in CLC Genomics Workbench.
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft Excel file format, containing gene name, raw read counts and normalized read counts.

source_name: Liver

extract_protocol:
Livers were removed, flash frozen in liquid nitrgen, and RNA was harvested using Trizol reagent.
500 ng of total RNA was converted to sequencing library with NEBNext rRNA-depletion Kit (New England Biolabs, E6310) and Directional RNA Library Prep Kit (E7420).

value: Liver

value: 12 weeks

value: wild type


title: Control 013_ND1


title: shASIrs2_2


title: Control 009_ND1


title: PD_1_Spleen_3.

data_processing:
clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data
Index of the reference genome was built using hisat2-2.0.4 and  paired-end clean reads were mapped to the reference genome.
Stringtie-1.3.3b ）was used to count the read numbers mapped to each gene. And then  FPKM was calculated.It normalizes for both  sequencing depth and genome size.
(For samples with biological replicates, edgeR_3.24.3 (lncRNA), DESeq2_1.24.0(circRNA)) Differential expression analysis of two conditions/groups  (at least two biological replicates per condition/group) was performed using the edgeR.The  resulting P-values were adjusted using the Benjamini and Hochberg’s approach for  controlling the false discovery rate . Genes with an adjusted P-value <0.05 were  assigned as differentially expressed ones.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P-value less than 0.05 were considered as significantly enriched GO functions of gene set. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecularlevel information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used KOBAS to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: mus_musculus_Ensembl_97
Supplementary_files_format_and_content: readcount, FPKM

extract_protocol:
RNA was harvested using Trizol reagent.
A total of 1 µg total RNA per sample was used as input material for the lncRNA  library preparation. Strand-specific libraries were generated using NEBNext® UltraTM  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations and index codes were added to attribute sequences to each sample


title: Lung_2 [miRNA-Seq]


title: NALM6 cells - H3K27me3 rep1


title: shASIrs2_1


title: NALM6 cells - H3K4me3 rep1


title: Control 011_ND1


title: control4


title: PD_1_Spleen_1.


title: NALM6 cells - H3K4me3 rep2


title: ARDS 008_ND1

value: ARDS


title: control3


title: Spleen_3


title: RXR_Day7_ML792_rep1

city: Oslo

first: Pierre

last: Chymkowitch

address: Blindernveien 31

department: Biosciences

country: Norway

institute: University of Oslo

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie v1.1.2 with the following parameters --no-unal -m 1 --seedlen 40 --best --strata --chunkmbs 1024 --sam --tryhard.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated using the tool makeUCSCfile from HOMER with the following parameters -norm 11258036 -fragLength 200.

source_name: 3T3L1 cells

growth_protocol: 3T3-L1 preadipocytes were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% bovin calf serum and 1 % Penicillin/Streptavidin at 37 °C in a humidified incubator in a 5 % CO2 in air atmosphere

extract_protocol:
Chromatin extraction was adapted from Baik et al, Cancer Res., 2018.
ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + 5 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.

treatment_protocol: Differentiation of 3T3-L1 cells was induced with DMEM supplemented with 10 % fetal bovine serum, 1mM dexamethasone, 0.5 mM 3-isobutyl-1-methylxanthine, 10 µg/mL insulin and 1 % P/S). At day 3 post adipogenic induction, the differentiation medium was replaced with the adipocyte maintenance medium (DMEM supplemented with 10 % FBS, 10 µg/mL of insulin and 1 % P/S). Adipocyte maintenance medium was then refreshed every second day. SUMOylation was inhibited by supplementing the culture medium with 0.5 µM of ML-792.

value: 3T3L1 cells

tag: antibody

value: RXR antibody (433900,Thermo Fisher Scientific)

value: Day 7 after adipogenic induction


title: RXR_Day7_ML792_rep2


title: shASIrs2_4


title: control2


title: ARDS 002_TD7

source_name: Bronchial


title: control1


title: ARDS 024_ND1


title: Control 003_ND1


title: RXR_Day2_rep2

value: Day 2 after adipogenic induction


title: PD_1_Lung_3

value: BALB/c


title: PD_1_Lung_2


title: PD_1_Spleen_2.

value: spleen


title: RXR_Day7_rep2


title: db4

description: NCGM_005_m_db_totalcount_qunatile_normalized.xlsx

extract_protocol:
Livers were removed, flash frozen in liquid nitrgen, and RNA was purified using Trizol reagent according to the standard protocol.
500 ng of total RNA was converted to sequencing library with NEBNext rRNA-depletion Kit (New England Biolabs, E6310) and Directional RNA Library Prep Kit (E7420).  RRNA-depletion, directional RNA-sequencing library

value: db/db

value: 10 weeks


title: RXR_Day2_rep1


title: PD_1_Lung_1

value: treated with pd-1 antibody


title: db3


title: ARDS 020_ND1


title: NALM6 cells - H3K4me2 rep1

value: no treatment


title: db2


title: ARDS 002_TD4


title: ARDS 006_ND1


title: Input Day2


title: Input Day7


title: db1


title: Lung_3

value: lung

value: untreated


title: Lung_2


title: misty4

value: misty/misty

value: misty/misty (lean control)


title: Spleen_1


title: RXR_Day7_rep1


title: ARDS 002_TD1


title: Spleen_2


title: Lung_1


title: misty3

value: Liver


title: AdipoqCre_PU.1_flox_3114

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Transcriptomic index was prepared using the Salmon indexer on Mus_musculus.GRCm38.95. Raw reads were 1) QC using FastQC, 2) quantified with Salmon, and 3) Summed to a gene-level using tximport.
Genome_build: Mus_musculus.GRCm38.95
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Epididymal adipocytes

growth_protocol: Mice were fed on a standard chow diet (Lab Diet 5053; Purina Mills). All procedures used in animal experiments were approved by the Institution of Animal Care and Use Committee at Baylor College of Medicine. Mice were maintained under conditions of controlled temperature (~75°F) and illumination (12-hour light/12-hour dark cycle, 6am to 6pm) with free access to water.

extract_protocol: Epididymal adipocytes RNA were extracted using the RNeasy Lipid Tissue Mini Kit ( QIAGEN). The cells were homogenized in 1 ml QIAzol lysis reagent andcentrifuged at 12,000 g for 10 min at 4°C. The lysates under the lipid layer were transferred to a fresh tube and extracted with 200 μl chloroform, centrifuged at 12,000 g for 15 min at 4°C. The upper aqueous phase was transferred out and mixed with 1 volume of 70% ethanol. The samples were then applied to RNeasy Mini spin column and centrifuged at room temperature for 15 s at 8,000 g. The columns were washed once with 700 μl Buffer RW1, and twice with 500 μl Buffer RPE. The RNA samples were eluded with 30–50 μl RNase-free water.

treatment_protocol: Epididymal fat pads from mice were minced in Krebs-Ringer phosphate buffer and digested with 1 mg/ml collagenase type I (Worthington Biochemical) at 37°C for 1 h. Digested tissue was filtered through a nylon mesh and centrifuged at 500 rpm for 10 min. The top layer (adipocyte fraction) was collected.

value: 10-11 months

tag: gender

value: male

value: AdipoqCre_PU.1 fl/fl


title: AdipoqCre_PU.1_flox_3118

tag: strain


title: misty2


title: Control 002_TD3-Red

value: Control


title: MEF

city: Schwerzenbach

first: Ori

last: Bar-Nur

state: Zurich

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

description: single cell

data_processing:
CellRanger v4.0 used for demultiplexing + read mapping + barcode assignment + UMI counting
Seurat v3.2.3 used for quality control + normalization + dimensionality reduction + clustering
PanglaoDB and Mouse Cell Atlas used for cell type annotation
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: List of 10x barcodes
Supplementary_files_format_and_content: List of features
Supplementary_files_format_and_content: Raw count matrix

source_name: Mouse Embryonic Fibroblasts

extract_protocol:
Cultured cells were trypsinized, resuspended with PBS in single cell level, and used for 10X GEM generation.
Single cell 3’ GEM kit v3 (10xGenomics, Pleasanton, CA) were used for 10x library construction following the manufacturer’s protocol. Briefly, cells were re-suspended in PBS as a concentration of 1000 cells/µl. Resuspended cells were loaded in chromium chip B as a recovery yield of ~10,000 with gel beads and oil. Generated GEM was used for cDNA amplification by PCR. Amplified cDNA then was fragmented, end repaired, and A-tailed. Adaptors was ligated, followed by index PCR and double sized selection. As a final step, the library was diluted in 10nM and used for sequencing. The sequencing was performed using Novaseq 6000 (Illumina, Inc, California, USA) with full SP flowcell. About 560 million reads were obtained for around 10,000 cells (over 40,000 reads per cells).
10x scRNA-Seq

treatment_protocol: Cultured in F/R/C containing media, generated by means of MyoD+F/R/C treatment

tag: cell type

value: Fibroblasts

value: cultured in MEF media


title: AdipoqCre_PU.1_flox_3102


title: PU.1_flox_3120

value: PU.1 fl/fl


title: PU.1_flox_3112


title: Control 002_TD1


title: ARDS 011_ND1

value: ARDS


title: Control 004_ND1


title: misty1

tag: tissue


title: Induced myogenic progenitors cells (iMPCs)

description: single cell

extract_protocol:
Cultured cells were trypsinized, resuspended with PBS in single cell level, and used for 10X GEM generation.
Single cell 3’ GEM kit v3 (10xGenomics, Pleasanton, CA) were used for 10x library construction following the manufacturer’s protocol. Briefly, cells were re-suspended in PBS as a concentration of 1000 cells/µl. Resuspended cells were loaded in chromium chip B as a recovery yield of ~10,000 with gel beads and oil. Generated GEM was used for cDNA amplification by PCR. Amplified cDNA then was fragmented, end repaired, and A-tailed. Adaptors was ligated, followed by index PCR and double sized selection. As a final step, the library was diluted in 10nM and used for sequencing. The sequencing was performed using Novaseq 6000 (Illumina, Inc, California, USA) with full SP flowcell. About 560 million reads were obtained for around 10,000 cells (over 40,000 reads per cells).

value: Induced myogenic progenitor cells

value: Cultured in F/R/C containing media, generated by means of MyoD+F/R/C treatment


title: HFD4

description: NCGM_005_NCD_HFD_totalcount_qunatile_normalized.xlsx

value: 24 weeks

value: wild type


title: HFD3


title: iMPC_2

data_processing:
bcl2fastq v2.19 software used for demultiplexing + basecalling
Trimmomatic v0.36 used for trimming adapter sequences and low quality reads
Kallisto v0.44 used for mapping reads and quantifying gene expression
edgeR v3.28 used for differential gene expression analysis
WebGestalt used for pathway enrichment analysis
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab delimited raw counts

source_name: Embryo

extract_protocol:
Cultured cells were harvested using trypsin and total RNA was extracted using RNeasy mini kit (Qiagen, 74104). FACS-purified cells were directly sorted into cell lysis buffer and processed for total RNA extraction using the same kit.
The RNA quality was measured with a Fragment Analyzer (Agilent, Santa Clara, California, USA) and only those samples with a 28S/18S ratio over 1.9 were used for library construction according to the TruSeq Stranded mRNA protocol (Illumina, Inc., California, USA). Briefly, 100-1000 ng of ploy A-enriched total RNA was reverse-transcribed into double-stranded cDNA. The cDNA was fragmented, end-repaired and adenylated. Then, TruSeq adapters containing unique dual indices (UDI) were ligated to processed cDNA for multiplexing. Using PCR, fragments containing TruSeq adapters on both ends were selectively enriched and the quality and quantity of the enriched libraries were determined using a Fragment Analyzer, which showed an average fragment size of approximately 360 bp. As a final step, the libraries were diluted in a concentration of 10 nM in Tris-Cl buffer (10 mM, pH8.5) with 0.1% Tween 20 and used for sequencing. The sequencing was carried out on Novaseq 6000 (Illumina, Inc., California, USA) with 100bp single end reads according to standard protocol.

value: Cultured in F/R/C containing media 13 days of Dox+F/R/C treatment


title: ARDS 015_ND1


title: iMPC_3


title: PU.1_flox_3101


title: iMPC_1


title: ARDS 019_ND1


title: HFD2


title: CML 7

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
mm10 mouse genome assembly and Refseq 3’UTR coordinates were downloaded from UCSC (4 August 2020) using Table Browser.
Sequencing reads were mapped and filtered with SlamDunk pipeline v0.4.3
Mapped reads were counted and merged using SlamDunk - Alleyoop, Reads with ≥ 1 T>C conversions were considered as labeled reads.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated table merged tcount information based upon total expression(Quant-seq, alleyoop_merge_ReadCount.txt), only labeled reads(SLAM-seq, alleyoop_merge_TcReadCount.txt).

source_name: 3T3-L1 cells

extract_protocol:
Cells were lysed, homogenized and collected using 1 ml of RNAzol®RT before adding 0.4 ml of water per 1 ml of homogenate. The mixture was vortexed for 5 min and centrifuged at 12,000 g for 15 min. Following centrifugation, DNA, proteins and polysaccharides form a semisolid pellet at the bottom of the tube. The RNA remains soluble in the supernatant. The supernatant was transferred to a new tube and 1 volume of 70% ethanol was added. The mixture was homogenized by pipetting. Samples were then applied to a RNeasy spin column and RNAs were purified according to Qiagen’s instructions. Base conversion was performed using the Quant-seq 3’ mRNA-Seq library preparation kit.
mRNA-Seq libraries were generated according to manufacturer's instructions from 500 ng of total RNA using the QuantSeq 3′mRNA‐Seq Library Prep Kit for Illumina (FWD) (# 015, Lexogen GmbH, Vienna, Austria). Reverse transcription was initiated by oligo dT priming. After first strand cDNA synthesis the RNA was removed and second strand synthesis was initiated by random priming. Oligo dT primer and random primers contain Illumina-compatible adapter sequences. The resulting double-stranded cDNA was then purified and PCR amplified (30 sec at 98oC; [10 sec at 98oC, 20 sec at 65oC, 30 sec at 72oC] x 11 cycles; 1 min at 72oC), introducing i7 indexes. Surplus PCR primers were further removed by purification using SPRI-select beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using capillary electrophoresis. The libraries were sequenced on Illumina Hiseq 4000 sequencer as Single-Read 50 base reads following Illumina’s instructions.

treatment_protocol: Differentiation of 3T3-L1 cells was induced with DMEM supplemented with 10 % fetal bovine serum, 1mM dexamethasone, 0.5 mM 3-isobutyl-1-methylxanthine, 10 µg/mL insulin and 1 % P/S). At day 3 post adipogenic induction, the differentiation medium was replaced with the adipocyte maintenance medium (DMEM supplemented with 10 % FBS, 10 µg/mL of insulin and 1 % P/S). Adipocyte maintenance medium was then refreshed every second day. SUMOylation was inhibited by supplementing the culture medium with 0.5 µM of ML-792. RNAs were labelled with 100 µM of 4-thiouridine during 45 min.

value: Mouse embryonic fibroblast chemically inducible to differentiate into adipocytes

tag: cell line source


title: ARDS 005_ND1


title: CML 3


title: HFD1


title: Pax7-GFP+ myoblast 3

source_name: Skeletal muscle

value: FACS-purified Pax7+ myoblasts

value: FACS-purified


title: CML 1


title: Control 002_ND1


title: Control 005_ND1


title: NCD4

value: Liver


title: Pax7-GFP+ myoblast 1


title: CML_ 2


title: Pax7-GFP+ myoblast 2


title: Control 006_ND1


title: CDMSO 7


title: ARDS 008_TD1


title: CDMSO 3


title: NCD3


title: Primary myoblast_2

value: Primary myoblasts- bulk

value: Untreated


title: NCD2


title: Control 001_TD1


title: Primary myoblast_1


title: ARDS 018_ND1


title: CDMSO_ 2


title: CDMSO 1


title: NCD1


title: ARDS 010_ND14


title: BML 7


title: SKOV6_EpCAMlow_2

city: Rotterdam

first: Mathijs

last: Verhagen

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

data_processing:
IIllumina paired-end reads of 76 bases were trimmed by removing the TrueSeq adapter sequences using Trimmomatic (v.0.33)
Subsequently, the reads were mapped in a two-pass procedure to the human reference genome build hg38 with the RNA-seq aligner STAR (v2.4.2a) and the Homo sapiens GENCODE v23 annotation.
Raw counts were summed with the summarize overlaps function with union mode from the Bioconductor Genomic Alignments package (v1.14.0).
Supplementary_files_format_and_content: tab-delimited text files include Ensemble Gene Id, hgnc symbols and CPM

source_name: ovarian cancer cell line

growth_protocol: Cell populations were sorted from established ovarian cancer cell lines grown in standard culture medium. Sorted cells were put in culture for 4 days before RNA was extracted.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA-Seq was performed at the Erasmus MC Center for Biomics (Rotterdam, The Netherlands) according to manufacturer’s instructions (Illumina) and using the TruSeq RNA sample prep kit v2. Briefly, polyA containing mRNA molecules were purified using poly-T oligo attached magnetic beads. Following purification, the mRNA was fragmented into ~200 bp fragments using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand synthesis using DNA polymerase I and RNaseH treatment. These cDNA fragments were end repaired, a single A base was added and Illumina adapters were ligated. The products were purified and size selected on gel and enriched by PCR. The PCR products were purified by Qiaquick PCR purification and used for cluster generation according to the Illumina cluster generation protocols (www.illumina.com).

treatment_protocol: no treatment was applied

tag: cancer type

value: ovarian


title: Pax7-GFP+ iMPC_3

source_name: Induced myogenic progenitor cells

value: FACS-purified Pax7+Induced myogenic progenitor cells


title: Pax7-GFP+ iMPC_2


title: SKOV6_EpCAMhigh_2


title: ARDS 001_TD1


title: BML 3


title: BML 1


title: D10_MyoD_FRC_3

source_name: Mouse embryonic fibroblasts expressing MyoD and F/R/C

value: Muscle fibers and progenitor cells

value: Treated with Dox+F/R/C for 10 days


title: SKOV6_bulk_2


title: BML_ 2


title: ARDS 001_TD7


title: D10_MyoD_FRC_2


title: SKOV6_bulk_1


title: SKOV6_EpCAMhigh_1


title: Primary myoblast_3


title: CAOV3_EpCAMlow_2


title: D10_MyoD_FRC_1


title: BDMSO 7


title: BDMSO 3


title: D10_MyoD_3

source_name: Mouse embryonic fibroblasts expressing MyoD

value: Myotubes

value: Treated with Dox for 10 days


title: CAOV3_EpCAMlow_1


title: ARDS 004_ND1

value: ARDS


title: ARDS 013_ND1


title: CAOV3_bulk_2


title: ARDS 001_TD4


title: D10_MyoD_2


title: BDMSO_2


title: CAOV3_bulk_1


title: D10_MyoD_1


title: ARDS 025_ND1


title: Pax7-GFP+ iMPC_1


title: AML 7


title: ARDS 010_ND1


title: OV90_EpCAMlow_3


title: AML 3


title: ARDS 007_ND1


title: SKOV6_EpCAMlow_1


title: OV90_EpCAMlow_2


title: AML 1


title: ARDS 001_ND7


title: D8_MyoD_FRC_2

value: Treated with Dox+F/R/C for 8 days


title: D8_MyoD_FRC_1


title: ARDS 009_ND7


title: OV90_EpCAMlow_1


title: AML_ 2


title: D8_MyoD_3

value: Treated with Dox for 8 days


title: ARDS 017_ND1


title: OV90_EpCAMhigh_3


title: ARDS 021_ND1


title: ADMSO 7


title: OV90_EpCAMhigh_2


title: D8_MyoD_2


title: D8_MyoD_1


title: ARDS 009_ND1


title: OV90_EpCAMhigh_1


title: ADMSO 1


title: ARDS 003_ND1


title: ADMSO_2


title: D6_MyoD_FRC_3

value: Treated with Dox+F/R/C for 6 days


title: OV90_bulk_3


title: ARDS 001_ND1


title: Sumo2-3_Day7_rep2

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

extract_protocol:
Cells were lysed, homogenized and collected using 1 ml of RNAzol®RT before adding 0.4 ml of water per 1 ml of homogenate. The mixture was vortexed for 5 min and centrifuged at 12,000 g for 15 min. Following centrifugation, DNA, proteins and polysaccharides form a semisolid pellet at the bottom of the tube. The RNA remains soluble in the supernatant. The supernatant was transferred to a new tube and 1 volume of 70% ethanol was added. The mixture was homogenized by pipetting. Samples were then applied to a RNeasy spin column and RNAs were purified according to Qiagen’s instructions. Base conversion was performed using the Quant-seq 3’ mRNA-Seq library preparation kit.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

tag: chip antibody

value: SUMO-2/3 antibody (ab3742)

tag: time

value: Day 7 after adipogenic induction


title: D8_MyoD_FRC_3


title: OV90_bulk_1

tag: cell line


title: Sumo2-3_Day1_rep2

value: Day 1 after adipogenic induction


title: iETV2-EC day21, rep2

city: Leuven

first: Yoke Chin

last: Chai

state: Leuven

address: Herestraat 49, ON5

department: Development & Regeneration

country: Belgium

institute: KU Leuven

description:
gene_count_matrix_day21
84_S84

data_processing:
All reads were trimmed by removing poor quality base pair (bp), poly N tails, ribosomal RNA and adaptors. Quality controls were performed before and after trimming using AfterQC and FastQC followed by mapping every read to the reference human genome GRCH38 (release 81.2) using STAR. Assembly of all mapped reads was performed using python package StringTie generating raw gene counts for further downstream analysis.
Genome_build: GRCH38 (release 81.2)
Supplementary_files_format_and_content: gene_count_matrix

source_name: Sigma hiPSC

growth_protocol: hiPSC colonies were cultured in E8flex medium till confluent. Medium was changed to neuro maintenance medium and 5ug/ml of doxycycline was added into the culture to induce endothelial differentiation. bFGF, 2% FBS and endothelial cell growth supplement were added at different time points and the cells were harvested on day 8, 14 and 21 days for total RNA extraction.

extract_protocol:
Endothelial cells were harvested using Trizol reagent and total RNA was extracted and sequenced single-end on NovaSeq SP 100x6bp resulting on an average of 10 million reads per sample.
NovaSeq SP 100x6bp
QuantiSeq

value: hiPSC-derived EC

value: neuro maintenance medium and doxycycline


title: D6_MyoD_2

tag: genotype

value: Treated with Dox for 6 days


title: Sumo2-3_Day-2_rep2

value: Day -2 before adipogenic induction


title: D6_MyoD_1


title: BDMSO 1

value: Mouse embryonic fibroblast chemically inducible to differentiate into adipocytes


title: Sumo2-3_Day3_rep2

value: Day 3 after adipogenic induction


title: iETV2-EC day14, rep3

description:
gene_count_matrix_day14
79_S79


title: D6_MyoD_3


title: D4_MyoD_FRC_3

value: Muscle fibers and progenitor cells

value: Treated with Dox+F/R/C for 4 days


title: ADMSO 3


title: iETV2-EC day14, rep2

description:
gene_count_matrix_day14
78_S78


title: Sumo2-3_Day7_rep1


title: ArjKOLT4

city: Bangalore

first: Maneesha

middle: S

last: Inamdar

state: Karnataka

address: JNCASR, Jakkur, Bangalore.

department: Molecular Biology and Genetics Unit (MBGU)

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

data_processing:
Quality of reads was assessed using FastQC
Raw reads were trimmed using Trim Galore to remove Illumina adaptor sequence and low quality reads and then aligned to the GRCm38/mm10 reference transcripts using Bowtie 2
All downstream analyses including principal component analysis, differential expression analysis and statistical tests were performed using custom R scripts
Transcripts with absolute log2 fold change > 1.5 and adjusted p-value < 0.05 were considered differentially expressed
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Long-term HSCs

extract_protocol:
Long-term HSCs were sorted and immediately processed for RNA isolation using RNeasy Mini Kit (Qiagen); 100 ng of total RNA was used to generate RNA-Seq libraries using NEBNext Ultra RNA Library Prep Kit for Illumina
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

tag: age

value: 6 months

value: asrij KO

value: hematopoietic stem cells


title: OV90_bulk_2

value: ovarian


title: D6_MyoD_FRC_2

value: Treated with Dox+F/R/C for 6 days


title: ARDS 012_ND1

value: ARDS


title: D6_MyoD_FRC_1


title: iETV2-EC day21, rep3

description:
gene_count_matrix_day21
85_S85


title: ArjKOLT2


title: D4_MyoD_FRC_2


title: Wt-LLT5

value: asrij floxed


title: ArjKOLT5


title: iETV2-EC day14, rep1

description:
gene_count_matrix_day14
77_S77


title: Sumo2-3_Day1_rep1

value: SUMO-2/3 antibody (ab3742)

value: Day 1 after adipogenic induction


title: D4_MyoD_FRC_1


title: Wt-LLT4


title: Sumo2-3_Day-2_rep1


title: iETV2-EC day8, rep3

description:
gene_count_matrix_day8
73_S73

value: hiPSC-derived EC

value: neuro maintenance medium and doxycycline


title: D4_MyoD_3

value: Myotubes

value: Treated with Dox for 4 days


title: iETV2-EC day21, rep1

description:
gene_count_matrix_day21
83_S83


title: ArjKOLT3


title: Wt-LLT3


title: iETV2-EC day8, rep2

description:
gene_count_matrix_day8
72_S72


title: Wt-LLT1


title: D4_MyoD_2


title: iETV2-EC day8, rep1

description:
gene_count_matrix_day8
71_S71


title: D4_MyoD_1


title: Input_Day3

value: Day 3 after adipogenic induction


title: Input_Day1


title: D2_MyoD_FRC_3

value: Muscle fibers and progenitor cells

value: Treated with Dox+F/R/C for 2 days


title: Sumo2-3_Day3_rep1


title: iMPCs_2 (Omni-ATAC-Seq)

data_processing:
bcl2fastq v2.19 software used for demultiplexing + basecalling
Bowtie2 v2.4.1 used for read mapping
Picard used for de-duplication of mapped reads
MACS2 used for peak calling
ChIPseeker used for peak annotation
chromVAR used for peak quantification
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab delimited called peak regions

extract_protocol:
Cultured cells were lysed on ice by cold lysis buffer containing 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, 10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 3 mM MgCl2 in Nuclease-free water. Nuclei were collected by centrifugation and subjected then to transposition reaction in 1x Tagment DNA buffer containing 5% Tn5 Transposase (Illumina, 20034197), 0.1% Tween-20, 0.01% Digitonin at 37°C for 30 mins on thermomixer, followed by DNA purification using MinElute PCR purification kit (Qiagen, 28004)
Index PCR amplification was performed by mixing 10 µL of transposed DNA with 10 µL nuclease-free water, 25 µL NEBNext High-Fidelity 2X PCR Master Mix, 2.5uL of each 25 µM Ad.1 and Ad.2, as previously published. Total PCR cycle was determined according to the amplification graph after the first 12 cycles. To remove primer dimers and larger fragment, double-sided bead purification was carried out using AMPure XP.
Omni-ATAC-Seq

treatment_protocol: For reprogramming, MEFs were treated by Dox (MyoD condition) and Dox in concert with 3 small molcules; Forskolin (F), RepSox (R) and CHIRF99021 (C) (abbreviated henceforth as F/R/C) (MyoD+F/R/C condition).

value: Induced myogenic progenitor cells

value: Cultured in F/R/C containing media 13 days of Dox+F/R/C treatment

tag: protocol

value: DNA cut by Tn5 Transposase


title: CAFR3

city: Guangzhou

first: xiang

last: zhang

state: Guangzhou

address: 58 Zhongshan Second Road, Yuexiu District

department: Department of General Surgery

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Raw data was filtered using Cutadapt (https://cutadapt.readthedocs.io/en/stable/, v1.16) and a self-made program for removing adaptor contamination and low quality reads, respectively. rRNA contamination was filtered by Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml, version: bowtie2, v2.3.3.1).
The expression level of mRNA were calculte using RSEM (RNA-Seq by Expectation Maximization) (v1.3.1) by normalized to FPKM (Fragments Per Kilobase Per Million reads). The differentially expressed mRNAs were screened using edgeR package (https://bioconductor.org/packages/release/bioc/html/edgeR.html) in R. |log2Foldchange| ≥ 1and Pvalue < 0.05 was considered siginificant. GO and KEGG enrichment was completed using clusterprofiler package in R, subsequently.
Transcription was assembled using cufflink (http://cole-trapnell-lab.github.io/cufflinks/, v2.2.1) and mapped to reference genome using cuffcompare (v2.2.1) to correct the boundary of 5’ and 3’ UTR regions. Rules in correcting are as follows: overlap between transcription and reference ≥180bp；The boundary of 200bp on both sides overlapped with known genes in the reference genome and the coverage >90%.                    Novel transcript was identified as follows: the distance from the existing annotated gene was more than 200bp; no less than 180bp in length; sequencing depth ≥2.
File of juntion.bed format was obtained by cufflink. Alternative splicing was counted using a self-made program with the flie of juntion.bed.
GSEA_Linux_4.0.3 (https://www.gsea-msigdb.org/gsea/index.jsp) was performed to complete the enrichment analysis of the gene set with default parameters using expression file obtained by RSEM as input.
Genome_build: Genome Reference Consortium Human Build 38 patch release 13 (GRCh38.p13)
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

source_name: pancreatic cancer tissue

extract_protocol:
Total RNA was isolated and purified using TRIzol(Life, cat.265709, CA, USA) following the manufacturer's procedure. After the quality inspection of Agilent 2100 Bioanalyzer (Agilent, cat.G2939AA, CA, USA) and NanoPhotometer ® (Implen, cat.N60, Munich, Germany), mRNA with poly(A) is purified from 1μg total RNA using VAHTS ® mRNA Capture Beads with Oligo (dT) (Vazyme, cat.N401-01, Nanjing, China) through two rounds of purification.
Subsequently, mRNA fragment was interrupted using VAHTS ® Universal V6 RNA-seq Library Prep Kit (Vazyme, cat.NR604, Nanjing, China) under 94℃ 8min and reversed transcription into cDNA which would use to synthesise U-labeled second-stranded DNAs. An A-base was added to the blunt ends of each strand to ligase the indexed adapters which contains a T-base at the tail end. After UDG enzyme treatment of the U-labeled double-strand DNA, size selection was performed with VAHTS ® DNA Clean Beads (Vazyme, cat.N411, Nanjing, China). Then the ligated products are amplified with PCR by the following conditions: initial denaturation at 98℃ for 5 min; 12-17 cycles of denaturation at 98℃ for 10 sec, annealing at 60℃ for 30 sec, and extension at 72℃ for 30 sec; final extension at 72℃ for 5 min. The average insert size of cDNA library was 280±80 bp.

value: pancreatic cancer tissue

tag: phenotype

value: chemoresistant

value: primary CAFs


title: Input_Day-2

value: Day -2 before adipogenic induction


title: CAFR2


title: iMPCs_1 (Omni-ATAC-Seq)


title: D2_MyoD_FRC_2


title: D2_MyoD_FRC_2 (Omni-ATAC-Seq)


title: CAFR1


title: D2_MyoD_FRC_1


title: L3

city: Merelbeke

first: Osvaldo

last: Bogado Pascottini

state: Flanders

address: Salisburylaan 133

institute: Ghent University

description: n = 10 blastocyst per sample

data_processing: First, the reads were trimmed with Trim Galore version 0.6.6. (https://github.com/FelixKrueger/TrimGalore) to remove Illumina adapters, poly-A tails, and low-quality bases. The trimmed reads were mapped against the Bos taurus ARS-UCD1.2 reference genome using STAR software version 2.7.9a. Unique Molecular Identifiers (UMIs) were used during the sequencing to characterize the expression levels more accurately and were processed with UMI-tools version: 1.1.1. Finally, the RSEM software, version 1.3.1, was used to generate the count tables.

source_name: In vitro produced

extract_protocol:
Total RNA was isolated from eight pools (four control and four lycopene in four replicates) of ten blastocysts per pool using the RNeasy Micro kit (Qiagen, Germantown, USA) according to the manufacturer's protocol. The quality and concentration of the RNA samples were examined using an RNA 6000 Pico Chip (Agilent Technologies, Carlsbad, CA, United States) and a Quant-iT RiboGreen RNA assay kit (Life Technologies, Carlsbad, CA, United States), respectively.
Transcriptome library preparation was done by Qiaseq UPX 3' transcriptome kit (Qiagen) according to the manufacturer's instructions with 10 PCR cycles. Quality of the library preparation was checked with a high sensitivity DNA chip (Agilent technologies) and library quantification was performed by qPCR according to the Illumina qPCR quantification protocol (NXTGNT sequencing facility, Ghent, Belgium), followed by equimolar pooling of libraries based on qPCR. Sequencing was performed on a high throughput Illumina NextSeq 500 flow cell with 20% PhiX spiked in (Read 1: 57 cycles; read 2: 27 cycles and index 6 cycles).

value: Day 8 blastocysts

value: Supplemented with lycopene during oocyte maturation


title: CAFS3

value: chemosensitive


title: L4

description: n = 10 blastocyst per sample


title: D2_MyoD_3

value: Treated with Dox for 2 days


title: D2_MyoD_FRC_1 (Omni-ATAC-Seq)


title: CAFS2


title: L2

description: n = 10 blastocyst per sample


title: D2_MyoD_2


title: Input_Day7

value: Day 7 after adipogenic induction


title: CAFS1


title: D2_MyoD_1 (Omni-ATAC-Seq)

value: Myotubes


title: MEFs_2 (Omni-ATAC-Seq)

source_name: Mouse embryonic fibroblasts

value: Mouse embryonic fibroblasts

value: Untreated


title: SPMS [S8]

city: La Jolla

first: Yasuyuki

last: Kihara

state: California

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Raw FASTQ files were input into the cellranger count pipeline (Cell Ranger V3.0.2, 10x Genomics) for barcode correction, alignment to the GRCh38 genome, and UMI collapsing.
gene-UMI count matrices from individual samples were normalized, clustered, and integrated in Seurat V3.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: We provide the error-corrected gene-UMI count matrices that were directly ouput by Cellranger. We also provide a cell-level metadata file that contains only quality-filtered cells as well as the corresponding cell type annotations that are included in our final analysis.

source_name: Post-mortem prefrontal cortices (BA10)_SPMS

extract_protocol:
Post-mortem prefrontal cortices (BA10) from donors who suffered from RRMS or SPMS were cryo-sectioned at 300 µm. The buffers used in this procedure were made in autoclaved diethyl pyrocarbonate (DEPC; MilliporeSigma, Cat# D5758)-treated water. All the steps from here on were performed at 4 ºC with additional equilibration time at each step. The samples were initially placed in 0.5 mL of nuclear extraction buffer (NEB; 0.32 M Sucrose, 5 mM CaCl2.2H20, 3 mM (CH3COO)2Mg.4H2O, 0.1 mM EDTA, 10 mM Tris/HCl (pH 8.0), 0.1% Triton X-100 with cOmpleteTM mini protease inhibitor cocktail tablet (MilliporeSigma, Cat# 11836153001) and fresh 0.2% RNase inhibitor (Takara, Cat# 2313A)) for 15 minutes. After adding another 0.5 mL NEB, the samples were homogenized thoroughly with a Dounce homogenizer. Upon transferring this homogenate to a new tube, the Dounce homogenizer was rinsed with 1 mL of NEB. Homogenates were then passed through a CellTrics® 50 µm filer (Sysmex, Cat# 04-004-2324). After washing the filter with NEB once, the filtrates were centrifuged at 1600 x g for 5 mins. The resulting pellets were resuspended with 1 mL of PBSE (1X PBS, 2 mM EGTA and fresh 0.2% RNase inhibitor), transferred into a new tube, diluted with PBSE, and centrifuged again at 1600 x g for 5 mins. Meanwhile, density gradients of OptiPrepTM (MilliporeSigma, Cat# D1556) were made in FACS tubes with 0.4 mL 35% OptiPrepTM on bottom and 2 mL 10% OptiPrepTM on top. Solutions used for density gradients were as follows: OptiPrepTM, solution B (6X concentrations: 120 mM Tricine/NaOH pH 7.8, 150 mM KCl and 30 mM MgCl2.6H2O) and solution D (0.25 M Sucrose in 1X solution B with freshly added 0.2% RNase inhibitor). The OptiPrepTM solutions were diluted with solution D to make the final concentrations to 35% and 10%. Nuclear pellets were resuspended with 0.2 mL solution D, followed by addition of 0.2 mL of 10% OptiPrepTM solutions, which were layered onto the 10% OptiPrepTM solution, and centrifuged at 3250 x g for 10 mins. The nuclei that settled at the boundary of 35% and 10% were collected, washed twice with PBSE containing 1% fatty acid-free bovine serum albumin (BSA; Gemini Bio, Cat# 700-107P), passed through CellTrics® 50 µm filter, washed again with PBSE + BSA, and labeled with DAPI (1:100,000, 4',6-diamidino-2-phenylindole; MilliporeSigma, Cat# D9542). About 3 x 105 nuclei were sorted using a BD FACSAria™ II (BD Biosciences) into a precoated collection tube filled with 1 mL of PBSE + BSA. The nuclei were washed once and resuspended in PBSE + BSA to obtain around 1500 cells/µL, and the counts were confirmed using a CountessTM II (Thermo Fisher Scientific). Single-nucleus capture (target capture of 5,000 nuclei per sample) and library preparation was conducted using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3 (10x Genomics, Cat# PN-1000075) and Chromium Single Cell B Chip Kit (10X Genomics, Cat# PN-1000074) according to the manufacturer's instruction.
Single-nucleus libraries were prepared using standard Illumina protocols and were sequenced on the Illumina NovaSeq 6000 machine at GENEWIZ, Inc.

tag: subject status

value: suffered from SPMS

tag: post-mortem interval

tag: age at death

tag: Sex

value: M

value: Post-mortem prefrontal cortices (BA10)

tag: edss

tag: rin


title: C4

description: n = 10 blastocyst per sample

tag: cell type

tag: treatment

value: No supplementation during oocyte maturation


title: D0_MEF_3


title: C3

description: n = 10 blastocyst per sample


title: SPMS [S7]

value: F

tag: tissue


title: MEFs_1 (Omni-ATAC-Seq)

value: DNA cut by Tn5 Transposase


title: D0_MEF_2


title: RRMS [S5]

source_name: Post-mortem prefrontal cortices (BA10)_RRMS

value: suffered from RRMS


title: D0_MEF_1


title: SPMS [S4]


title: D2_MyoD_2 (Omni-ATAC-Seq)


title: wild type [YTa32-6]

city: Boston

first: Lai Ping

last: Wong

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Transcriptome mapping was performed with STAR aligner by using the NCBI37 assembly gene
Read counts for individual genes were produced using the unstranded count feature in HTSeq program
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files of read count for each sample

source_name: RGLs Ribosomal profiling

extract_protocol:
We used Gli1CreERT2:Rpl22HAf/+:Klf9f/f or +/+ mice which enables expression of haemagglutinin (HA)-tagged ribosomal protein RPL22 (RPL22–HA) following Cre recombination in Gli1+ Klf9f/f or +/+ RGLs. RiboTag immunoprecipitation and RNA extraction were performed 4 days after last TAM injection following the original protocol with minor modifications (Sanz et al., 2009). 6 dentate gyri from 3 mice were pooled per sample and homogenized with a dounce homogenizer in 900 ul cycloheximide-supplemented homogenization buffer. Homogenates were centrifuged and the supernatant incubated on a rotator at 4°C for 4 hours with 9ul anti-HA antibody (CST Rb anti-HA #3724, 1:100) to bind the HA- tagged ribosomes. Magnetic IgG beads (Thermo Scientific Pierce #88847) were conjugated to the antibody-ribosome complex via overnight incubation on a rotator at 4°C. RNA was isolated by RNeasy Plus Micro kit (Qiagen 74034) following the manufacturer’s protocol. Eluted RNA was stored at -80°C. For enrichment analysis, 45ul of homogenate (pre- anti-HA immunoprecipitation) was set aside after centrifugation, kept at -20°C overnight, and purified via RNeasy Micro kit as an ‘input’ sample, and used to determine NSC enrichment. RNA quantity and quality were measured with a Tape Station (Agilent) and Qubit fluorimeter (Thermo Fisher Scientific). Sequencing libraries were prepared using Ultra Low Input RNA Kit (Clontech).
See above

treatment_protocol: TAM

tag: genotype/variation

value: GliCreERT2 Klf9 +/+ Ribotag


title: knock down [YTa32-5]

value: GliCreERT2 Klf9 f/f Ribotag


title: C2

description: n = 10 blastocyst per sample

value: Day 8 blastocysts


title: C1

description: n = 10 blastocyst per sample


title: L1

description: n = 10 blastocyst per sample

value: Supplemented with lycopene during oocyte maturation