title: RNA_ESC_2

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the mouse genome (mm10) using HISAT2 (v2.2.1) with the default parameter settings.
Gene expression based on GENCODE vM25 annotations was determined using stringtie (v2.0) with the default parameter settings.
Fragments per Kilobase per Million (FPKM) were calculated for representing the expression of each gene.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene FPKM for every gene and every sample

source_name: Mouse blastocyst

growth_protocol: R1 mESCs and riPSCs were seeded on Feeder and maintained in mESC medium. mESC medium contains 47% DMEM/F12, 47% Neural basal medium, 1 x N2 supplement, 1 x B27 supplement, 1% Glutamax, 1% nonessential amino acids (NEAA), 0.055 mM 2-mercaptoethanol (β-ME), 1% P/S, 1000 units/mL mLIF, 3 μM CHIR99021 and 0.2 μM PD0325901. MEFs were cultured in MEF medium, containing DMEM Basic, 10% fetal bovine serum (FBS), 1% penicillin and streptomycin (P/S).                                                                                OG2 MEFs of passages 1-3 were seeded into 6-well plates at density of 2.5 x 10^4 cells/plate. On the next day, medium was changed to reprogramming medium. Medium was changed every 2 days. For reprogramming day 4 to 8, the medium was renewed every day.

extract_protocol:
RNA was isolated using FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme) according to the manufacture’s instruction.
RNA-seq library preparation and sequencing were performed by Novogene. The RNA-seq libraries were sequenced on the Illumina NovaSeq 6000 with read length of 150 bp.

value: R1 mESC


title: RRBS_D0_2

status: Public on May 03 2023

type: SRA

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

country: China

institute: Zhejiang University

library_source: genomic

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the mouse genome (GRCm39) using Bismark (v0.23.0) bowtie2 aligner with options: -N 1 -l 20 --non_directional.
Mapping was done independently for the two ends of each pair. Read pairs that were mapped uniquely to two different fragments or showing more than one unconverted non-CpG cytosine, which occurred at very low frequency were filtered out.
Methylation levels of CpGs in the promoters were performed with R package methylKit from the bioconductor project, CpGs covered by at least 5 distinct reads were retained to calculate the average methylation levels.
Genome_build: GRCm39
Supplementary_files_format_and_content: CpG methylation values txt files

molecule: genomic DNA

organism: Mus musculus

source_name: MEF

growth_protocol: riPSCs were seeded on Feeder and maintained in mESC medium. mESC medium contains 47% DMEM/F12, 47% Neural basal medium, 1 x N2 supplement, 1 x B27 supplement, 1% Glutamax, 1% nonessential amino acids (NEAA), 0.055 mM 2-mercaptoethanol (β-ME), 1% P/S, 1000 units/mL mLIF, 3 μM CHIR99021 and 0.2 μM PD0325901. MEFs were cultured in MEF medium, containing DMEM Basic, 10% fetal bovine serum (FBS), 1% penicillin and streptomycin (P/S).                                                                                OG2 MEFs of passages 1-3 were seeded into 6-well plates at density of 2.5 x 10^4 cells/plate. On the next day, medium was changed to reprogramming medium. Medium was changed every 2 days. For reprogramming day 4 to 8, the medium was renewed every day.

extract_protocol:
Genome DNA was extracted using Quick-DNA Miniprep (ZYMO) according to the manufacture’s instruction.
RRBS was carried out similar as described (Legault et al., 2019). 500 ng DNA was digested by 20 U MspI (NEB) overnight. Then, DNA fragments were added with Gap filling and A-tailing mix (5 U Klenow enzyme, 1 μl dNTP mixture (10 mM dATP, 1 mM dCTP, 1 mM dGTP)) followed by incubating for 20 min at 30 °C and 20 min at 37 °C. 64 μl VAHTS DNA Clean Beads were used to purify DNA fragments. Subsequently, adapter ligation mix (14 μl purified DNA fragments, 25 μl Quick ligase buffer (2×), 10 μl Methylated adapters (15 μM) and 1 μl Quick ligase) was prepared and incubated for 10 min at 25 °C. Then, with 3 μl of USER enzyme added to each sample, samples were incubated for 15 min at 37 °C. After that, 55 μl VAHTS DNA Clean Beads were used for purification. Bisulfite conversion were then conducted using EZ DNA Methylation-Gol Kit according to the manufacture’s instruction. The converted DNA was PCR amplified using NEBNext Multiplex Oligos (NEB) for 15 cycle numbers. Libraries were purified using 50 μl VAHTS DNA Clean Beads. The RRBS libraries were sequenced on the Illumina NovaSeq 6000 with read length of 150 bp.

treatment_protocol: Cells were cultured in indicated medium

tag: strain

value: 129XOG2 E13.5 embryo

tag: cell type

value: MEF


title: RRBS_D0_1


title: RRBS_D2_1

value: Reprogramming intermediate


title: ASH1_d2_100_2

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
Library strategy: ChEC-seq
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
paired end alignment to S288C_R64 with bowtie2 (-p8 --local --very-sensitive --trim-to 30 --dovetail)
genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria)

organism: Saccharomyces cerevisiae

source_name: budding yeast culture at OD=4

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD4 in SC medium with glucose

extract_protocol:
Phenol chlorofrom extraction
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. 2015

tag: genetic information

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ASH1 Δ2 100 SV40 NLS MNase

tag: tagged tf

tag: variant-type

value: Truncation


title: ASH1_d2_100_4


title: ADR1_nonDBD_5

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ADR1 Δ79 161 MNase

value: nonDBD


title: RNA_iPSC_2

library_source: transcriptomic

molecule: total RNA

value: iPSC


title: ASH1_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ASH1 MNase

value: TF


title: U2423; blood; CD19+ B cells; 36 weeks

city: Erlangen

first: Simon

last: Schaefer

state: Bavaria

address: Glueckstr. 6

department: Genetics

country: Germany

institute: FAU Erlangen

data_processing:
Immcantation 4.3.0
pResto; Quality control, Read assembly
Change-O, V(D)J reference alignment
Supplementary files format and content:
fasta formated files after merging and UMI filtering
igblast output text files including filtered and annotated immune repertoires (i.e. quantified annotated data about antibody receptor sequences mapped to germline genes)

source_name: blood

extract_protocol:
RNA was isolated using the Rneasy Micro Plus kit from Qiagen; RNA was collected in 14 µl Rnase-free water and 11 µl were used for cDNA generation
Library was prepared according to "Werner, A., et al., Determining immunoglobulin-specific B cell receptor repertoire of murine splenocytes by next-generation sequencing. STAR Protocols, 2022. 3(2): p. 101277"

tag: tissue

value: blood

value: CD19+ B cells

tag: genotype

tag: time

value: 36 weeks


title: U1513; blood; CD19+ B cells; 48 weeks

value: Siglecg-R26ki/ki mb1cre

value: 48 weeks


title: U1515; blood; CD19+ B cells; 48 weeks

value: TCL1 x Siglecg-R26ki/ki


title: U2517; blood; CD19+ B cells; 36 weeks


title: ADR1_nonDBD_4


title: U2422; blood; CD19+ B cells; 36 weeks


title: U2421; blood; CD19+ B cells; 36 weeks

value: TCL1 x Siglecg-R26ki/ki mb1cre


title: RNA_D12_2

value: 129XOG2 E13.5 embryo


title: U2313; blood; CD19+ B cells; 36 weeks


title: Control replicate 1-4

city: Nagoya

first: Yuji

last: Nakamura

address: Kawasumi 1, Mizuho-cho, Mizuho-ku

department: Department of Pediatrics and Neonatology

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

data_processing:
The barcodes and unique-molecular-identifiers in the reads were extracted using UMI-tools (version 1.0.0) with the command: umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern=NNNNNNCCCCCC --read2-stdout.
The reads were mapped by the aligning software HISAT2 (version 2.1.0) to the reference genome (GRCm38 or GRCh38).
Read counts per gene was performed with featureCounts (version 1.6.4) and UMI-tools with the command: umi_tools count --method=directional --per-gene --per-cell --gene-tag=XT.
The duplicates in unique molecular identifiers were discarded.
Using the resulting counts, differentially expressed genes (those with adjusted p-values < 0.1) were extracted by the R library DESeq2 (version 1.20.0).
Assembly: GRCh38
Supplementary files format and content: count matrix:CSV

molecule: polyA RNA

organism: Homo sapiens

source_name: Cerebral organoids

extract_protocol:
Lysis solution(0.1% Tween and 400 ug/ml of ProteinaseK in PBS) were loaded onto the specimens and incubated for 30 min at 55°C cDNA;mRNA hybrids were purified with QIAGEN Mini Elute PCR Purification Kit.
The eluted aRNAs (5 µl) was combined with RT primer mix [1 µl of 250 ng/µl randomhexRT primer and 0.5 µl of 10mM dNTPs], incubated for 5 min at 65 °C and then quickly cooled to 4 °C. RT reaction mix was then added [2 µl of 5 × First-Strand Buffer, 1 µl of 0.1M DTT, 0.5 µl of 40 U/µl RNase Out and 0.5 µl of 200 U/µl Superscript II Reverse Transcriptase (all from Invitrogen)], incubated for 10 min at 25 °C and further incubated for 1 h at 42 °C. The RT products (9 µl) were combined with PCR mix [1.8 µl each of 10 µM RNA PCR primers 1, 2, and 22.5 µl of Phusion High- Fidelity PCR Master Mix and 9.9 µl of water], and amplifed by PCR (98 °C for 30 s, followed by 11 cycles of 98 °C for 10 s, 60 °C for 30 s and 72 °C for 30 s, with a final extension at 72 °C for 10 min). Fragments of 250–500 bp were then purified and size-selected with AMpure XP beads.

value: Cerebral organoids

tag: cell line

value: iPS cell line derived from control individual

value: apical radial glial cells

value: WT

tag: treatment


title: pooled_endMT_3 [Lane 5 - RNA]

city: Tucson

first: Casey

last: Romanoski

state: AZ

address: 1230 N Cherry Ave

country: USA

institute: U. Arizona

description:
10x Genomics
Lane 5 - RNA

library_source: transcriptomic single cell

data_processing:
library strategy: multi-modal snRNA-seq and snATAC-seq
Alignement, filtering, barcode counting, peak calling, and counting of both ATAC and GEX molecules were made using the Cell Ranger ARC v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
BAM files (output from Cell Ranger ARC) for ATAC and gene expression were concatenated, sorted and indexed for demuxlet input BAM file using samtools (https://github.com/samtools/samtools)
Sample identity and identification of multiplets was performed for all samples and corresponding vcf and proccessed .bam files using demuxlet with --field set to "GT" (https://github.com/statgen/demuxlet)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Ascending aorta

extract_protocol:
Nuclei from primary ECs were isolated according to 10x Genomics Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing Demonstrated Protocol (CG000365, Rev C).
Library was performed according to 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide (CG000338, v1).

value: Ascending aorta

value: Primary human aortic endothelial cells

value: Endothelial cells

value: 7d ctrl, 4d siSCR, 7d TGFB2 (10ng/mL), 7d IL1B (10ng/mL)


title: pooled_endMT_5 [Lane 7 - RNA]

description:
10x Genomics
Lane 7 - RNA

value: 7d TGFB2 (10ng/mL), 7d IL1B (10ng/mL)


title: ADR1_nonDBD_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ADR1 Δ79 161 MNase

value: nonDBD


title: Patient replicate 1-4

value: iPS cell line derived from affected individual


title: RNA_D12_1

value: Reprogramming intermediate


title: RNA_ESC_1

value: R1 mESC


title: U1863; blood; CD19+ B cells; 36 weeks

value: blood

value: CD19+ B cells

value: TCL1 x Siglecg-R26ki/ki

value: 36 weeks


title: pooled_endMT_4 [Lane 6 - RNA]

description:
10x Genomics
Lane 6 - RNA


title: ADR1_d923_1323_8

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ADR1 Δ923 1323 SV40 NLS MNase

value: Truncation


title: U1861; blood; CD19+ B cells; 36 weeks

value: TCL1 x Siglecg-R26ki/ki mb1cre


title: ASH1_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ASH1 MNase

value: TF


title: pooled_endMT_2 [Lane 4 - RNA]

description:
10x Genomics
Lane 4 - RNA

value: Ascending aorta

value: Primary human aortic endothelial cells

value: Endothelial cells

value: 7d siRNA, 7d TGFB2 (10ng/mL), 4d TGFB2 (10ng/mL)


title: ADR1_d923_1323_7


title: RNA_D10_2

value: 129XOG2 E13.5 embryo


title: RNA_iPSC_1

value: iPSC


title: RNA_D10_1

value: Reprogramming intermediate


title: ADR1_d923_1323_4


title: RNA_D8_2


title: ADR1_d923_1323_3


title: U1719; blood; CD19+ B cells; 36 weeks


title: U1666; blood; CD19+ B cells; 36 weeks


title: U1664; blood; CD19+ B cells; 36 weeks


title: ADR1_d723_1323_8

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ADR1 Δ723 1323 SV40 NLS MNase


title: il1b6h [Lane 2 - RNA]

description:
10x Genomics
Lane 2 - RNA

value: 6h IL1B (1ng/mL)


title: RNA_D6_2


title: U1663; blood; CD19+ B cells; 36 weeks

value: blood

value: CD19+ B cells


title: U1662; blood; CD19+ B cells; 36 weeks

value: TCL1 x Siglecg-R26ki/ki

value: 36 weeks


title: RNA_D6_1


title: ADR1_d723_1323_7

value: Truncation


title: ctrl6h [Lane 1 - RNA]

description:
10x Genomics
Lane 1 - RNA

value: 6h control media


title: RNA_D4_2


title: U1610; blood; CD19+ B cells; 36 weeks


title: ADR1_d723_1323_5


title: U1607; blood; CD19+ B cells; 36 weeks

value: TCL1 x Siglecg-R26ki/ki mb1cre


title: ADR1_d723_1323_6


title: Sample_42-Hip

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

description: 10x Genomics

data_processing:
The alignment, processing, and peak calling conducted using the Cell Ranger software
Assembly: Hg38
Supplementary files format and content: Output files from CellRanger-atac

source_name: skin

extract_protocol:
4mm skin biopsies were obtained from the palm/hip of a healthy individual. Biopsies were then incubated in 0.4% dispase overnight to separate the epidermis and dermis. After the separation, the epidermis was transferred to 0.25% Trypsin-EDTA + 10 units/mL DNase mixture and incubated at 37°C for 1hr. The Epidermis mixture was then quenched with FBS and precipitated by centrifugation. Cell pellets were then resuspended in PBS + 0.04% BSA. Cell numbers were counted at this step for future dilution calculation. The nuclei isolation protocol was carried out as described by 10x Genomics. Of note, cells obtained from the epidermis were incubated in lysis buffer on ice for 7 min to achieve the best lysis efficacy. The cell lysis efficacy was determined by Countess II FL Automated Cell Counter.
The single-cell ATACseq library was prepared by Advanced Genomics Core at the University of Michigan. 10,000 nuclei/sample and 25,000 reads/nuclei were targeted, and the libraries were sequenced using NovaSeq SP 100 cycle flow cell.

value: skin

value: keratinocytes


title: pooled_endMT_1 [Lane 3 - RNA]

description:
10x Genomics
Lane 3 - RNA

value: Ascending aorta

value: Primary human aortic endothelial cells

value: 7d ctrl, 7d siSCR


title: Sample_42-Palm

description: 10x Genomics


title: RNA_D2_2

value: 129XOG2 E13.5 embryo


title: KARPAS-422, DMSO, Input, replica 2

city: Stanford

first: Sai

last: Gourisankar

state: CA

address: 240 Pasteur Dr, Rm 4700

department: Chemical Systems Biology

institute: Stanford

data_processing:
The data quality was checked using fastqc.
The raw reads were trimmed from adapters with 560trim_galore (parameters: --paired –illumina).
reads were aligned to hg38 human genome 561assembly using bowtie2 (parameters: --local )
Low quality paired reads (at least one read in a pair has a quality score <10), duplicated reads and reads with multiple alignments were removed using samtools and Picard
genome coverage was generated using bedtools (bedtools genomecov -bga).
Peaks were called uing MACS v2.1.0 with the significance cut-off p-value <=0.01
Assembly: hg38
Supplementary files format and content: BigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 12 minutes. After quenching with 125 M glycine and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
The sequencing libraries were prepared using NEBNext Ultra II DNA kit (#E7645S)

value: Diffuse large B-cell lymphoma germinal center B-cell type

tag: chip antibody

value: DMSO

tag: spike-in

value: Drosophila chromatin spike-in normalized


title: RNA_D8_1

value: Reprogramming intermediate


title: ADR1_d723_1323_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ADR1 Δ723 1323 SV40 NLS MNase


title: ADR1_d723_1323_4


title: U1556; blood; CD19+ B cells; 36 weeks

value: blood

value: CD19+ B cells

value: Siglecg-R26ki/ki mb1cre


title: RNA_D2_1


title: U1518; blood; CD19+ B cells; 36 weeks

value: 36 weeks


title: ADR1_d723_1323_1

value: Truncation


title: U1515; blood; CD19+ B cells; 36 weeks

value: TCL1 x Siglecg-R26ki/ki


title: RNA_D0_2

value: MEF


title: ADR1_d523_1323_6

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ADR1 Δ523 1323 SV40 NLS MNase


title: KARPAS-422, 4hr 10 nM TCIP1, POLIISER5P, replica 2

value: POLIISER5P (ActiveMotif 3E8)

value: 4hr 10 nM TCIP1


title: KARPAS-422, DMSO, Input, replica 1


title: RNA_D0_1


title: ADR1_d523_1323_5


title: KARPAS-422, 4hr 10 nM TCIP1, POLIISER5P, replica 1


title: H3K27me3_iPSC_2

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the mouse genome (mm10) using Bowtie2 (v2.2.5) with options: --no-unal --no-mixed –nodiscordant --local --very-sensitive-local --phred33 -I 10 -X 700.
For peak calling, parameters used were macs2 (v2.1.2) callpeak: -p 1e-5 -f BAMPE --keep-dup all -g mm.
The bigwig files were generated with bamCoverage function in deepTools (v3.4.3) with default parameter settings.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files
Supplementary_files_format_and_content: peak text files

extract_protocol:
CUT&Tag assay was carried out similar as described (Kaya-Okur et al., 2019). 1 x 105 cells were collected, washed once with 500 μl Wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1× Protease inhibitor) and centrifuged for 4 min at 600 g. After aspirating the liquid supernatant, the cells were resuspended in 90 μl Wash Buffer. 10 μl ConA beads (CST) were prepared and added to each sample. Then, tubes were rotated at room temperature for 10 min. After short centrifugation, the tubes were placed on a magnetic stand until clear. Liquid supernatant was aspirated and beads were resuspended in 50 μl primary antibody (Primary antibody was 1:100 diluted in antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1× Protease inhibitor cocktail, 0.05% Digitonin, 2 mM EDTA, 0.01% BSA)). After overnight rotation at 4 ℃, primary antibody was removed, beads were resuspended in 50 μl secondary antibody (Secondary antibody was 1:100 diluted in Dig-wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1× Protease inhibitor cocktail, 0.05% Digitonin)), following by rotation at RT for 1h. Then, the beads were washed for 3 times with 800 μl Dig-wash Buffer, 5 min each time. After that, beads were incubated in TTE Mix (Vazyme, TTE Mix was 1:100 diluted in Dig-med Buffer (0.05% Digitonin, 20mM HEPES, pH 7.5, 300mM NaCl, 0.5mM Spermidine, 1× Protease inhibitor cocktail)) and rotated at room temperature for 1h. Then, the beads were washed for 3 times with 800 μl Dig-med Buffer, 2 min each time. After that, the beads were resuspended with 300 μl Tagmentation Buffer (10mM MgCl2 in Dig-med Buffer) and incubated at 37℃ for 1h. Stop tagmentation mix (10 μl of 0.5 M EDTA, 3 μl of 10% SDS and 2.5 μl of 20 mg/mL Proteinase K) was added directly to each sample to stop fragmentation by incubating at 50 ℃ for 1h. To extract DNA, 300 μl PCI (Phenol: Chloroform: isoamylol= 25:24:1) was added, mixed, followed by centrifugation at 16,000 g for 5 min. The water phase was transferred to a new tube, added with 300 μl Chloroform and centrifuged at 16,000 g for 3 min. Afterwards, the water phase was transferred to a new tube, added with 750 μl cold 100% ethanol and centrifuged at 16,000 g for 15 min at 4℃. Then, supernatant was aspirated and 1 ml 100% ethanol was added to resuspend, followed by centrifugation at 16,000 g for 1 min at 4℃. Then, all the ethanol was aspirated, airdried, and DNA was resuspended with H2O.
DNA was PCR amplificated using a TruePrep Index Kit V2 (Vazyme) and purified by 60 μl DNA clean beads. For H3K3me3, H3K9me3, H3K27me3 and H3K27ac, the PCR cycle number was 12. For H3K18la, the PCR cycle number was 14. The CUT&Tag libraries were sequenced on the Illumina NovaSeq 6000 with read length of 150 bp.
CUT&Tag

value: iPSC


title: RNA_D4_1

value: 129XOG2 E13.5 embryo


title: KARPAS-422, 2hr 10 nM TCIP1, POLIISER5P, replica 2

value: Diffuse large B-cell lymphoma germinal center B-cell type

value: 2hr 10 nM TCIP1


title: H3K27me3_iPSC_1


title: ADR1_d523_1323_4


title: U2423; blood; CD19+ B cells; 28 weeks

value: 28 weeks


title: U2517; blood; CD19+ B cells; 28 weeks


title: ADR1_d523_1323_3


title: U2422; blood; CD19+ B cells; 28 weeks


title: KARPAS-422, 2hr 10 nM TCIP1, POLIISER5P, replica 1

value: Drosophila chromatin spike-in normalized


title: H3K27me3_D12_2

value: Reprogramming intermediate


title: ADR1_d523_1323_2


title: ADR1_d523_1323_1


title: H3K27me3_D12_1


title: KARPAS-422, 1hr 10 nM TCIP1, POLIISER5P, replica 2

value: 1hr 10 nM TCIP1


title: U1863; blood; CD19+ B cells; 28 weeks

value: blood

value: CD19+ B cells


title: H3K27me3_D10_2


title: KARPAS-422, 1hr 10 nM TCIP1, POLIISER5P, replica 1


title: U1513; blood; CD19+ B cells; 36 weeks

value: Siglecg-R26ki/ki mb1cre

value: 36 weeks


title: U2421; blood; CD19+ B cells; 28 weeks

value: TCL1 x Siglecg-R26ki/ki mb1cre


title: H3K27me3_D10_1


title: ADR1_d423_1323_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ADR1 Δ423 1323 SV40 NLS MNase

value: Truncation


title: KARPAS-422, DMSO, POLIISER5P, replica 2

value: POLIISER5P (ActiveMotif 3E8)

value: DMSO


title: U1719; blood; CD19+ B cells; 28 weeks


title: ADR1_d373_1323_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ADR1 Δ373 1323 SV40 NLS MNase


title: H3K27me3_D8_1

value: 129XOG2 E13.5 embryo


title: H3K27me3_D8_2


title: U1666; blood; CD19+ B cells; 28 weeks


title: ADR1_d323_1323_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ADR1 Δ323 1323 SV40 NLS MNase

value: DBD


title: KARPAS-422, DMSO, POLIISER5P, replica 1

value: Diffuse large B-cell lymphoma germinal center B-cell type

value: POLIISER2P (Abcam ab5095)


title: H3K27me3_D6_2

value: Reprogramming intermediate


title: KARPAS-422, 4hr 10 nM TCIP1, POLIISER2P, replica 2

value: 4hr 10 nM TCIP1

value: Drosophila chromatin spike-in normalized


title: H3K27me3_D6_1


title: KARPAS-422, 4hr 10 nM TCIP1, POLIISER2P, replica 1


title: U1664; blood; CD19+ B cells; 28 weeks

value: blood

value: CD19+ B cells

value: 28 weeks


title: U1663; blood; CD19+ B cells; 28 weeks


title: ADR1_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ADR1 MNase

value: TF


title: KARPAS-422, 15min 10 nM TCIP1, POLIISER5P, replica 2

value: 15min 10 nM TCIP1


title: U1861; blood; CD19+ B cells; 28 weeks

value: TCL1 x Siglecg-R26ki/ki mb1cre


title: ADR1_d373_1323_2

value: Truncation


title: U1662; blood; CD19+ B cells; 28 weeks

value: TCL1 x Siglecg-R26ki/ki


title: KARPAS-422, 15min 10 nM TCIP1, POLIISER5P, replica 1

value: POLIISER5P (ActiveMotif 3E8)


title: ADR1_1


title: H3K27me3_D4_1

value: 129XOG2 E13.5 embryo


title: U1610; blood; CD19+ B cells; 28 weeks


title: ACE2_nonDBD_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ACE2 Δ603 657 MNase::kanMX

value: nonDBD


title: H3K27me3_D2_2


title: KARPAS-422, 1hr 10 nM TCIP1, POLIISER2P, replica 2

value: Diffuse large B-cell lymphoma germinal center B-cell type

value: POLIISER2P (Abcam ab5095)

value: 1hr 10 nM TCIP1


title: U1607; blood; CD19+ B cells; 28 weeks


title: ACE2_nonDBD_3


title: H3K27me3_D2_1

value: Reprogramming intermediate


title: KARPAS-422, 2hr 10 nM TCIP1, POLIISER2P, replica 1

value: 2hr 10 nM TCIP1

value: Drosophila chromatin spike-in normalized


title: H3K27me3_D4_2


title: U1556; blood; CD19+ B cells; 28 weeks

value: blood

value: CD19+ B cells

value: Siglecg-R26ki/ki mb1cre

value: 28 weeks


title: KARPAS-422, 1hr 10 nM TCIP1, POLIISER2P, replica 1


title: ACE2_nonDBD_2


title: ADR1_d323_1323_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ADR1 Δ323 1323 SV40 NLS MNase

value: DBD


title: H3K27me3_D0_2

value: MEF


title: U1518; blood; CD19+ B cells; 28 weeks

value: TCL1 x Siglecg-R26ki/ki mb1cre


title: KARPAS-422, 15min 10 nM TCIP1, POLIISER2P, replica 2

value: 15min 10 nM TCIP1


title: KARPAS-422, 2hr 10 nM TCIP1, POLIISER2P, replica 2


title: H3K27me3_D0_1

value: 129XOG2 E13.5 embryo


title: U1515; blood; CD19+ B cells; 28 weeks

value: TCL1 x Siglecg-R26ki/ki


title: KARPAS-422, 15min 10 nM TCIP1, POLIISER2P, replica 1

value: Diffuse large B-cell lymphoma germinal center B-cell type


title: ACE2_nonDBD_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ACE2 Δ603 657 MNase::kanMX

value: nonDBD


title: ACE2_d2_550_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ACE2 Δ2 550 SV40 NLS MNase::kanMX


title: KARPAS-422, DMSO, POLIISER2P, replica 2

value: POLIISER2P (Abcam ab5095)

value: DMSO


title: H3K27ac_iPSC_1

value: iPSC


title: H3K27ac_iPSC_2


title: U1513; blood; CD19+ B cells; 28 weeks

value: blood

value: CD19+ B cells


title: T7551; blood; CD19+ B cells; 48 weeks

value: 48 weeks


title: ACE2_d2_550_3


title: KARPAS-422, DMSO, POLIISER2P, replica 1

value: Drosophila chromatin spike-in normalized


title: ACE2_d2_50_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ACE2 Δ2 50 SV40 NLS MNase::kanMX

value: Truncation


title: H3K27ac_D12_2

value: Reprogramming intermediate


title: ACE2_d2_50_3


title: T7548; blood; CD19+ B cells; 48 weeks

value: Balb/c WT


title: T7549; blood; CD19+ B cells; 48 weeks


title: ACE2_d2_500_8

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ACE2 Δ2 500 SV40 NLS MNase::kanMX


title: KARPAS-422, 4hr 10 nM TCIP1, H3K27AC, replica 1

value: H3K27AC (Abcam ab4729)

value: 4hr 10 nM TCIP1


title: H3K27ac_D10_2

value: 129XOG2 E13.5 embryo


title: KARPAS-422, 2hr 10 nM TCIP1, H3K27AC, replica 2

value: Diffuse large B-cell lymphoma germinal center B-cell type

value: 2hr 10 nM TCIP1


title: ACE2_d2_500_7


title: KARPAS-422, 2hr 10 nM TCIP1, H3K27AC, replica 1


title: H3K27ac_D10_1


title: T6020; blood; CD19+ B cells; 48 weeks

value: Siglecg-/-


title: ACE2_d2_500_4


title: H3K27ac_D8_2


title: T6015; blood; CD19+ B cells; 48 weeks


title: KARPAS-422, 1hr 10 nM TCIP1, H3K27AC, replica 2

value: 1hr 10 nM TCIP1


title: ACE2_d2_500_3


title: H3K27ac_D8_1


title: H3K27ac_D6_2


title: T6012; blood; CD19+ B cells; 48 weeks

value: TCL1 x Siglecg-/-


title: T6007; blood; CD19+ B cells; 48 weeks

value: blood


title: KARPAS-422, 15min 10 nM TCIP1, H3K27AC, replica 2

value: 15min 10 nM TCIP1


title: ACE2_d2_500_2


title: ACE2_d2_500_1


title: KARPAS-422, 1hr 10 nM TCIP1, H3K27AC, replica 1


title: H3K27ac_D12_1


title: H3K27ac_D6_1


title: KARPAS-422, 4hr 10 nM TCIP1, H3K27AC, replica 2


title: T6022; blood; CD19+ B cells; 48 weeks

value: CD19+ B cells

value: 48 weeks


title: T6006; blood; CD19+ B cells; 48 weeks


title: KARPAS-422, 15min 10 nM TCIP1, H3K27AC, replica 1

value: Drosophila chromatin spike-in normalized


title: ACE2_d2_450_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ACE2 Δ2 450 SV40 NLS MNase::kanMX

value: Truncation


title: H3K27ac_D4_2

value: Reprogramming intermediate


title: KARPAS-422, DMSO, H3K27AC, replica 2

value: DMSO


title: T5966; blood; CD19+ B cells; 48 weeks

value: Balb/c WT


title: H3K27ac_D4_1


title: KARPAS-422, DMSO, H3K27AC, replica 1

value: H3K27AC (Abcam ab4729)


title: H3K27ac_D2_2

value: 129XOG2 E13.5 embryo


title: T5965; blood; CD19+ B cells; 48 weeks


title: ACE2_d2_400_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ACE2 Δ2 400 SV40 NLS MNase::kanMX


title: H3K27ac_D2_1


title: T7620; blood; CD19+ B cells; 36 weeks

value: 36 weeks


title: PPBC3_3

city: Bangalore

first: Jyothi

middle: S

last: Prabhu

state: Karnataka

address: Koramangala, 4th Block

department: Division of Molecular Medicine

country: India

institute: St. John's Research Institute

data_processing:
The quality control of the raw data was performed using FastQC
Adaptor contaminants and low-quality reads with a Phred Score of < 20 were removed using TrimGalore
High quality reads were aligned to the GRCh38 reference genome using STAR v2.7
Mapped reads were counted by FeatureCounts v2.0.3
The genes that had zero counts were removed from the analysis and the differential expression analysis was performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: breast cancer

extract_protocol:
Total RNA was extracted from 10 fresh frozen tissue samples stored in liquid nitrogen using Tri reagent (Sigma Aldrich, cat no. T9424). 2-3 sections of 20 µm thickness were used per tumor.
Total RNA (100 ng) was used for RNA-Seq library preparation, using NebNext Ultra II RNA library prep kit for Illumina (E7770L) according to manufacturer’s protocols.

treatment_protocol:
NA
NA

tag: age diagnosis

tag: age

value: Postpartum duration till diagnosis-21yrs

value: breast cancer

tag: ihc er_status

value: Negative

tag: ihc pr_status

tag: ihc her2_status

tag: t size

tag: grade

value: III

value: Appropriate treatment received


title: PPBC3_4

value: Postpartum duration till diagnosis-13yrs

value: Positive

tag: LumB

value: II


title: T7618; blood; CD19+ B cells; 36 weeks

value: blood

tag: cell type

value: CD19+ B cells

value: Siglecg-/-


title: ACE2_d2_400_3

tag: genetic information

tag: tagged tf

tag: variant-type

value: Truncation


title: T7616; blood; CD19+ B cells; 36 weeks

tag: tissue

tag: genotype

value: TCL1 x Siglecg-/-

tag: time


title: PPBC3_2

value: Postpartum duration till diagnosis-19yrs

tag: Basal

tag: treatment


title: ACE2_d2_350_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ACE2 Δ2 350 SV40 NLS MNase::kanMX


title: H3K27ac_D0_1

tag: strain

value: 129XOG2 E13.5 embryo

value: MEF


title: ACE2_d2_350_2


title: H3K27ac_D0_2


title: T7552; blood; CD19+ B cells; 36 weeks

value: 36 weeks


title: H3K18la_iPSC_2

value: iPSC


title: ACE2_d2_450_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ACE2 Δ2 450 SV40 NLS MNase::kanMX


title: T7551; blood; CD19+ B cells; 36 weeks


title: ACE2_d2_200_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ACE2 Δ2 200 SV40 NLS MNase::kanMX


title: H3K18la_iPSC_1


title: H3K18la_D12_2

value: Reprogramming intermediate


title: PPBC3_1

tag: age diagnosis

tag: age

value: Postpartum duration till diagnosis-11yrs

value: breast cancer

value: Negative

tag: Normal

value: Appropriate treatment received


title: ACE2_d2_300_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ACE2 Δ2 300 SV40 NLS MNase::kanMX


title: T7549; blood; CD19+ B cells; 36 weeks

value: blood

value: CD19+ B cells


title: ACE2_d2_300_1

value: Truncation


title: H3K18la_D12_1


title: ACE2_d2_200_3


title: PPBC2_2

value: Postpartum duration till diagnosis-7yrs

tag: ihc er_status

value: Positive

tag: ihc pr_status

tag: ihc her2_status

tag: LumA

value: II


title: T7548; blood; CD19+ B cells; 36 weeks

tag: cell type

value: Balb/c WT


title: T7547; blood; CD19+ B cells; 36 weeks

value: 36 weeks


title: PPBC1_3

value: Postpartum duration till diagnosis-1yr

tag: t size

tag: grade

value: III


title: H3K18la_D10_2

value: 129XOG2 E13.5 embryo


title: ACE2_d2_150_4

tag: genetic information

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ACE2 Δ2 150 SV40 NLS MNase::kanMX

tag: tagged tf

tag: variant-type


title: PPBC1_2

value: Postpartum duration till diagnosis- 5yrs

tag: tissue

value: I


title: ACE2_d2_150_1


title: T6022; blood; CD19+ B cells; 36 weeks

tag: genotype

value: TCL1 x Siglecg-/-

tag: time


title: ACE2_d2_100_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ACE2 Δ2 100 SV40 NLS MNase::kanMX


title: PPBC1_1

value: Postpartum duration till diagnosis-2 yrs

value: breast cancer

value: Negative

tag: treatment

value: Appropriate treatment received


title: H3K18la_D10_1

tag: strain

value: Reprogramming intermediate


title: PPBC2_3

tag: age diagnosis

tag: age

value: Postpartum duration till diagnosis-7yrs

value: Positive


title: T6015; blood; CD19+ B cells; 36 weeks

value: blood

value: CD19+ B cells

value: Siglecg-/-


title: T6020; blood; CD19+ B cells; 36 weeks

value: 36 weeks


title: H3K18la_D8_2

value: 129XOG2 E13.5 embryo


title: H3K18la_D8_1


title: K562Rlma_3

city: xi'an

first: Liangliang

last: Shen

address: West changle road 169

institute: The fourth military medical university

data_processing:
2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
Bioinformatics analysis of RNA-seq fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions)    exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCh38
Supplementary files format and content: The data related to gene counts and FPKM values were listed in the folder "1_genes_fpkm_expression.txt "

source_name: K562 cells, imatinib resistant

extract_protocol:
RNA was harvested usingTRIzol reagent (Invitrogen, Carlsbad, CA, USA) . 1 ug of total RNA was used for the construction of sequencing libraries.
The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

tag: cell line

value: chronic myelogenous leukemia

value: IM resistance


title: K562Rlma_2


title: T6012; blood; CD19+ B cells; 36 weeks


title: ACE2_d2_100_3

value: Truncation


title: T6007; blood; CD19+ B cells; 36 weeks


title: ACE2_d2_100_1


title: PPBC2_1

value: Postpartum duration till diagnosis-8yrs

tag: ihc er_status

tag: ihc pr_status

tag: Normal

value: I


title: K562Rlma_1

tag: cell type


title: H3K18la_D6_1


title: H3K18la_D6_2


title: K562shTXNIP_3

source_name: K562cells, shTXNIP

value: TXNIP knockdown


title: T6006; blood; CD19+ B cells; 36 weeks

value: TCL1 x Siglecg-/-


title: H3K18la_D4_2


title: Control - Fresh - FR-5

city: Merelbeke

first: Katrien

last: Smits

address: Salisburylaan 133

department: Internal Medicine, Reproduction and Population Medicine

country: Belgium

institute: Ghent University

data_processing:
Quality trimming and adapter removal, trim_galore --stringency 3 --length 25 -a AGATCGGAAGAGC  -a AAAAAAAAAA "   --output_dir <out_dir> <in.fastq.gz>
Mapping reads with STAR, STAR --genomeDir <genome_dir> --readFilesIn <trimmed.fastq.gz> --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM Unsorted --outReadsUnmapped Fastx --outFileNamePrefix star/<sample_name> --quantMode TranscriptomeSAM
Samtools sort, samtools sort -o <out_sorted.bam> <star.bam>
Deduplication of the UMIs, umi_tools dedup -I <bam>
Samtools sort on name, samtools sort-n -o <out.bam> <in.bam>
Quantify with rsem, rsem-calculate-expression --forward-prob 1 --no-bam-output --bam <in.bam> <index_rsem>
Assembly: Equus_caballus.EquCab3.0 release 108 Ensembl
Supplementary files format and content: normalized_counts_deseq2.csv: comma-delimited text file (csv) contains normalized gene expression counts with DESeq2's standard method

organism: Equus caballus

source_name: Equine oocytes

growth_protocol: Routine in vitro maturation was used for equine embryo production, as described previously by (Papas et al, Animals (Basel). 2021 Jul; 11(7)). During in vitro maturation, an average of 20 cumulus oocyte complexes were cultured in 500-µL of maturation medium (Medium 199 with Earl’s salts (Gibco) containing 10% (v/v) FBS (Gibco), 9.4 μg/mL folli-cle-stimulating hormone, and 1.88 μg/mL luteinizing hormone (Stimufol, Reprobiol, Ouffet, Belgium) and 50-µL gentamacyn )  covered with Paraffin oil (SAGE oil for tissue culture, ART-4008-5P, Cooper Surgical Company), at 38.5 °C in 5% CO2 in air .

extract_protocol:
Three groups of equine oocytes in matured stage were collected (equine oocytes after vitrification – warming – and in vitro maturation (VGV), in vitro maturation – vitrification – warming (VMAT), and fresh in vitro matured oocytes (FR). For each group, total RNA was isolated from 5 replicates of average 23 oocytes using the RNeasy Micro kit (Qiagen) according to the manufacturer's protocol. The quality and concentration of the RNA samples were examined using an RNA 6000 Pico Chip (Agilent Technologies) and a Quant-iT RiboGreen RNA Assay kit (Life Technologies), respectively.
Transcriptome library preparation was done by Qiaseq UPX 3' transcriptome kit (Qiagen)

treatment_protocol: Vitrification was performed on immatured oocytes surrounded by corona radiata, warmed and in vitro matured, then denuded, polar body evaluated and frozen for RNA extraction (VGV group), this was compared with oocytes in vitro matured, denuded, polar body visualized, vitrified and warmed and frozen for transcriptomics (VMAT group) and compared with fresh oocytes, in vitro matured, denuded and polar body evaluated before being frozen for RNA extraction.

value: Equine oocytes

value: FR


title: Control - Fresh - FR-4


title: T5967; blood; CD19+ B cells; 36 weeks


title: Control - Fresh - FR-1


title: K562shTXNIPC_3

source_name: K562 cells

value: Control


title: K562shTXNIP_2


title: Control - Fresh - FR-2


title: T5964; blood; CD19+ B cells; 36 weeks


title: H3K18la_D2_1

value: Reprogramming intermediate


title: K562shTXNIPC_2


title: T7620; blood; CD19+ B cells; 24 weeks

value: 24 weeks


title: K562shTXNIPC_1


title: H3K18la_D0_2

value: MEF


title: Vitrified in Metaphase II - VMAT-2

value: VMAT


title: Vitrified in Metaphase II - VMAT-3


title: H3K18la_D0_1


title: Vitrified in Metaphase II - VMAT-1


title: H3K18la_D4_1


title: T7618; blood; CD19+ B cells; 24 weeks

value: blood

value: CD19+ B cells

value: Siglecg-/-


title: K562shTXNIP_1

value: chronic myelogenous leukemia


title: T7552; blood; CD19+ B cells; 24 weeks


title: T5966; blood; CD19+ B cells; 36 weeks

value: Balb/c WT

value: 36 weeks


title: KARPAS-422, 100 nM TCIP1, BRD4, replica 2

value: Diffuse large B-cell lymphoma germinal center B-cell type

tag: chip antibody

value: Brd4 (E2A7X) Rabbit mAb #13440

value: 100 nM TCIP1


title: KARPAS-422, 100 nM TCIP1, BRD4, replica 1


title: Control - Fresh - FR-3


title: H3K9me3_iPSC_1

value: 129XOG2 E13.5 embryo

value: iPSC


title: T7616; blood; CD19+ B cells; 24 weeks

value: TCL1 x Siglecg-/-


title: H3K9me3_iPSC_2


title: Vitrified in germinal vesicle-VGV-4

value: Equine oocytes

value: VGV


title: T5965; blood; CD19+ B cells; 36 weeks


title: KARPAS-422, DMSO, BRD4, replica 2

value: DMSO


title: H3K18la_D2_2

value: Reprogramming intermediate


title: Vitrified in germinal vesicle-VGV-2


title: Vitrified in germinal vesicle-VGV-3


title: T7551; blood; CD19+ B cells; 24 weeks

value: 24 weeks


title: H3K9me3_D12_2


title: H3K9me3_D12_1


title: KARPAS-422, input

value: none (input)


title: KARPAS-422, DMSO, BRD4, replica 1


title: Vitrified in germinal vesicle-VGV-1


title: T7549; blood; CD19+ B cells; 24 weeks

value: blood

value: CD19+ B cells


title: H3K9me3_D10_2


title: human muscle stem cells-2_differentiated ATAC-seq

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

data_processing:
cellranger-atac v2.0 (http://support.10xgenomics.com/) was utilized to process the raw sequence data generated.
Signac (v1.7) and Seurat (v4 were used to analyze the filtered barcode-peak matrices and fragment file generated from running cellragner-arc.
The gene expression and chromatin accessiblity data were process separately, WNN (weighted nearest neighbor) was used for cell clustering and visulization.
Assembly: GRCh38 (from 10X: refdata-cellranger-arc-GRCh38-2020-A-2.0.0)
Supplementary files format and content: 10x Genomics cellranger-arc output files (the files needed for further analysis): filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi, per_barcode_metrics.csv

source_name: Skeletal muscle

growth_protocol: Human stem cells were cultured 6 passages in a 60 mm petri dish with primary cell media composed of F12-DMEM (low glucose) at 3:1 ratio, 5% FBS, 1% penicillin-streptomycin, 0.4 µg/ml hydrocortisone, 5 µg/ml insulin, 20 ng/ml EGF, 24 µg/ml adenine, 5 µM Rock inhibitor (Y-27632), 1 µM BMP inhibitor DMH-1, 1 µM TGFβ pathway inhibitor A-83-01, and p38 kinase inhibitor losmapimod 2 µM/ml. Plates used were pre-coated with laminin-rich conditioned media from 804G cell line overnight. Next, ( for myotubbe generation) human muscle stem cells were cultured in a differentiation assay media (5% FBS in primary cell culture medium was replaced by 2% horse serum) for 7 day myogenesis until long elongated myotube-like fibers were observed.

extract_protocol: Paired ATAC and gene expression libraries from the same single nuclei were generated from the isolated nuclei following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide CG000338 RevA (10X Genomics, Inc).

value: Skeletal muscle

value: skeletal myotubes

value: myotubes

value: in culture


title: T7548; blood; CD19+ B cells; 24 weeks

value: Balb/c WT


title: H3K9me3_D10_1


title: human muscle stem cells-2_differentiated RNA-seq


title: T7547; blood; CD19+ B cells; 24 weeks


title: T6022; blood; CD19+ B cells; 24 weeks


title: M53 Organoid DMSO control

city: New York

first: Julia

middle: Nanyi

last: Zhao

state: NY

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Quality of the raw fastqc files was evaluated using fastqc v0.11.8, and Trim Galore! v0.6.5 was applied to raw reads then to remove adaptor and low-quality reads with a quality threshold of 20.
Trimmed reads were aligned to mouse genome reference GRCm38.p6 (GENCODE release M25) using Bowtie2 v2.2.8. Aligned sam files were converted to bam files and were filtered to remove mitochondrial reads using samtools v.1.11.
PCR duplication were removed using Picard v2.2.4 (Picard Toolkit 2019).
RPKM normalized Bigwig files were generated from the post-filtering bam files using bamcoverage function from Deeptools v3.2.1 (Ramírez et al. 2016).
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: Cut and Run

source_name: HCC organoid

extract_protocol:
Tumor organoids were grown in 24 well plates, and after drug treatment for 24 hours, were collected in Cell Recovery Solution (Corning). Tumor organoids were left to rotate at 4° for one hour in order to dissolve the Matrigel. Tumor organoids were spun down at 300 g at 4° for 5 minutes. 100,000 cells per condition were counted and washed with PBS. Nuclei were prepared using Epicypher’s CUTANA kit and slowly frozen in nuclear extraction buffer.
Epicypher CUTANA kit

value: HCC organoid

value: HCC organoid cells

tag: time point

value: Day 7

value: H3K27me3, Active Motif, 39155


title: M53 Organoid WNTinb 1 day

value: Wntinib

value: Day 1


title: H3K9me3_D6_2

value: 129XOG2 E13.5 embryo


title: H3K9me3_D8_2

value: Reprogramming intermediate


title: H3K9me3_D8_1


title: human muscle stem cells -2  ATAC-seq

value: skeltal muscle stem cells

value: stem cells


title: M53 Organoid WNTinb 7 day


title: T6020; blood; CD19+ B cells; 24 weeks

value: blood

value: Siglecg-/-

value: 24 weeks


title: Organoid Input control


title: MCB Organoid WNTinb 7 day


title: H3K9me3_D6_1


title: human muscle stem cells -2 RNA-seq

value: Skeletal muscle


title: T6015; blood; CD19+ B cells; 24 weeks

value: CD19+ B cells


title: T6012; blood; CD19+ B cells; 24 weeks

value: TCL1 x Siglecg-/-


title: human muscle stem cells-1_differentiated RNA-seq

value: skeletal myotubes

value: myotubes

value: in culture


title: MCB Organoid WNTinb 1 day

value: HCC organoid

value: HCC organoid cells


title: human muscle stem cells-1_differentiated ATAC-seq


title: H3K9me3_D4_2


title: T6007; blood; CD19+ B cells; 24 weeks


title: human muscle stem cells -1 ATAC-seq


title: MCB Organoid DMSO control

value: DMSO

value: Day 7

value: H3K27me3, Active Motif, 39155


title: H3K9me3_D4_1

value: 129XOG2 E13.5 embryo

value: Reprogramming intermediate


title: human muscle stem cells -1 RNA-seq

value: skeltal muscle stem cells

value: stem cells


title: T6006; blood; CD19+ B cells; 24 weeks

value: blood


title: H3K9me3_D2_2


title: H3K9me3_D2_1


title: T5966; blood; CD19+ B cells; 24 weeks

value: Balb/c WT

value: 24 weeks


title: H3K9me3_D0_2

value: MEF


title: Human myotubes-SKBR-3 CM-2

description: BR-3 CM-2

data_processing:
FASTQ files were aligned with STAR v.2.5.2b using parameter “--outSAMmapqUnique 60”
Aligned reads in BAM files were counted with featureCounts from the subread package v.1.5.1 with parameters “-s 2 –p –Q 10”
Assembly: GRCh38
Supplementary files format and content: tab-separated text file containing log2FPKM and raw counts

source_name: human muscle stem cells (hMuSC)

growth_protocol: Human stem cells were cultured 6 passages in a 60 mm petri dish with primary cell media composed of F12-DMEM (low glucose) at 3:1 ratio, 5% FBS, 1% penicillin-streptomycin, 0.4 µg/ml hydrocortisone, 5 µg/ml insulin, 20 ng/ml EGF, 24 µg/ml adenine, 5 µM Rock inhibitor (Y-27632), 1 µM BMP inhibitor DMH-1, 1 µM TGFβ pathway inhibitor A-83-01, and p38 kinase inhibitor losmapimod 2 µM/ml. Plates used were pre-coated with laminin-rich conditioned media from 804G cell line overnight. Next, human muscle stem cells were cultured in a differentiation assay media (5% FBS in primary cell culture medium was replaced by 2% horse serum) for 7 day myogenesis until long elongated myotube-like fibers were observed.

extract_protocol:
Cultured myotubes were harvested and total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using KAPA mRNA Hyperprep Kit (KK8581).

treatment_protocol: Myotubes were treated with vehicle (control group) or CMs from MCF-7, MD-468 or SKBR-3 for 36 hours

value: skeletal muscles

value: myotubes derived from hMuSC

tag: passages

value: anterior tibialis

value: conditioned medium (CM) treatment 36 hours


title: Human myotubes-SKBR-3 CM-3

description: BR-3 CM-3


title: Human myotubes-MD-468 CM-3

description: MD468 CM-3


title: T5965; blood; CD19+ B cells; 24 weeks

value: CD19+ B cells


title: T5964; blood; CD19+ B cells; 24 weeks


title: H3K9me3_D0_1


title: Human myotubes-MD-468 CM-2

description: MD468 CM-2


title: H3K4me3_iPSC_1

value: iPSC


title: Human myotubes-MD-468 CM-1

description: MD468 CM-1


title: H3K4me3_D12_2


title: H3K4me3_D12_1


title: Human myotubes-MCF-7 CM-2

description: MCF7 CM-2


title: Human myotubes-MCF-7 CM-3

description: MCF7 CM-3


title: Human myotubes-MCF-7 CM-1

description: MCF7 CM-1


title: H3K4me3_D10_2


title: T7551; blood; CD19+ B cells; 12 weeks

value: 12 weeks


title: Human myotubes-control-3

value: vehicle treatment 36 hours


title: T7552; blood; CD19+ B cells; 12 weeks


title: Human myotubes-SKBR-3 CM-1

description: BR-3 CM-1


title: parental_3D_microtissues_ex6A-KO

city: Padova

first: Milena

last: Bellin

state: PD

address: Via Ugo Bassi 58/B

department: Department of Biology

country: Italy

institute: University of Padova

data_processing:
Residual Illumina adapters were trimmed from the RNA sequences using cutadapt with parameter -m 20
Reads were aligned to the human genome (build 38, Ensembl version 96) using STAR
Exon counts were retrieved using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: hiPSCs

extract_protocol:
Total RNA was isolated either from hiPSC-CMs on day 21 of differentiation using Nucleospin kit (Machery and Nagel) andd from MTs on day 21 of culture using RNeasy Micro Kit (Qiagen), according the manufacturers’ instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: scn5a genotype

value: 3D microtissues


title: H3K4me3_D10_1

value: 129XOG2 E13.5 embryo


title: T7620; blood; CD19+ B cells; 12 weeks

value: TCL1 x Siglecg-/-


title: T5967; blood; CD19+ B cells; 24 weeks


title: T7549; blood; CD19+ B cells; 12 weeks


title: T7548; blood; CD19+ B cells; 12 weeks


title: Human myotubes-control-2


title: T7618; blood; CD19+ B cells; 12 weeks

value: Siglecg-/-


title: Human myotubes-control-1


title: 2517-RP-60

city: Frederick

first: Himanshu

last: Goel

state: MD

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute (BHSAI)

description: Control

data_processing:
RNA-seq data were analyzed using the Kallisto tool (version 0.42.4) for read alignment and quantification.
We calculate uncertainties of transcript abundance estimates by repeating the analyses 100 times after resampling with replacement. We pseudo-aligned the reads to the Cavia porcellus  (Cavpor3.0) transcriptome downloaded from the Ensembl website
Kallisto input: kallisto quant -i $REF_KAL2 -b 100 -o rat_Edik/"$sample"  $DATA_DIR/3744-"$sample"_R1_001.fastq.gz $DATA_DIR/3744-"$sample"_R2_001.fastq.gz -t 10
Assembly: Cavia porcellus transcriptome  (Cavpor3.0)
Supplementary files format and content: tab-delimited text files, including abundance measurements

organism: Cavia porcellus

source_name: Kidney

extract_protocol:
Frozen whole kidney samples were powdered in liquid nitrogen, since these organs are histologically heterogeneous. Total RNA was isolated from powdered kidney, using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA MiniPrep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing
At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (Roche, Indianapolis, IN). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (Roche). Pooled libraries were subjected to 75-bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq6000, San Diego, CA). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

tag: breed

value: Hartley

value: Kidney

tag: Sex

value: male

value: 9 h

tag: agent

value: Vehicle (1 ml/kg saline)


title: T7616; blood; CD19+ B cells; 12 weeks

tag: tissue

value: blood

tag: genotype

tag: time


title: 2517-RP-58

description: Control


title: H3K4me3_D8_1

tag: strain

value: Reprogramming intermediate


title: H3K4me3_D8_2


title: H3K4me3_iPSC_2


title: EVs from CPC LNP-treated rep3

city: Skövde

first: Jane

last: Synnergren

address: Högskolevägen 1

country: Sweden

institute: University of Skövde

data_processing:
Clustering was done by 'cBot' and samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.7.5/RTA v3.4.4) a 151nt (Read1)-10nt(Index1)-10nt(Index2)- 151nt(Read2) setup using 'NovaSeqXp' workflow in 'S4' mode flowcell.
The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite.
The quality scale used was Sanger / phred33 / Illumina 1.8+.
Sequenced reads were quality controlled with the FastQC software and pre-processed with Trim Galore.
Processed reads were aligned to the Homo sapiens reference genome (build GRCh38) with the STAR aligner. Read counts for genes were generated using the featureCounts library.
Raw gene counts were generated by Salmon and the normalized TPM values were calculated with StringTie.
Assembly: GRCh38
Supplementary files format and content: tab-separated text file with raw gene counts for every gene and every sample
Supplementary files format and content: tab-separated text file with transcript-per-million (TPM) values for every gene and every sample

source_name: Extracellular vesicles from CPC

extract_protocol:
EVs were isolated from cell culture medium by ultracentrifugation. To removed cell debris, the cell culture medium were centrifuged at 3000 x g for 15 min at 4°C, ultracentrifuged at 60,000 x g for 35 min at 4°C, followed by filtration through 0.2μm filters at 60,000 x g for 30 minutes at 4 °C. The EV pellet were collected and resuspended in PBS after a second round of ultracentrifugation at 120,000 x g for 70 minutes at 4°C.
Library construction was performed using Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit, which is specifically designed for very low input total RNA samples.

treatment_protocol: Cells were treated with 50 uL of MC3-LNPs containing 5000ng of VEGF-A mRNA per flask. Supernatants, and cell lysates were harvested after 24h of LNP treatment. Untreated cells were used as negative controls.

value: Lung epithelial

tag: treatment

value: LNP-treated

tag: seeding density

tag: culturing flask

value: 6-well multiwall plate


title: H3K4me3_D6_2

source_name: MEF


title: 2517-RP-57

description: Treatment

value: High (1.50 mg/kg HgCl2)


title: H3K4me3_D6_1


title: T6020; blood; CD19+ B cells; 12 weeks

value: CD19+ B cells

value: 12 weeks


title: EVs from CPC LNP-treated rep2


title: T6022; blood; CD19+ B cells; 12 weeks


title: T6015; blood; CD19+ B cells; 12 weeks


title: 2517-RP-56

description: Treatment


title: EVs from CPC LNP-treated rep1


title: 2517-RP-55

description: Treatment


title: T6012; blood; CD19+ B cells; 12 weeks


title: H3K4me3_D4_1


title: 2517-RP-59

description: Control


title: EVs from CPC Untreated rep3

value: Untreated


title: EVs from CPC Untreated rep2


title: T7547; blood; CD19+ B cells; 12 weeks

value: Balb/c WT


title: 2517-RP-54

description: Treatment


title: 2517-RP-53

description: Treatment


title: H3K4me3_D2_1

value: 129XOG2 E13.5 embryo


title: EVs from CPC Untreated rep1


title: H3K4me3_D2_2


title: T5967; blood; CD19+ B cells; 12 weeks


title: 2517-RP-51

description: Treatment

value: Low (1.00 mg/kg HgCl2)


title: T6006; blood; CD19+ B cells; 12 weeks

value: TCL1 x Siglecg-/-


title: EVs from HUVEC LNP-treated rep4

source_name: Extracellular vesicles from HUVEC

value: T75 flask


title: H3K4me3_D0_2

value: MEF


title: 2517-RP-52

description: Treatment

value: Hartley

value: Kidney

value: male


title: EVs from HUVEC LNP-treated rep3


title: ATAC_iPSC_2

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the mouse genome (mm10) using Bowtie2 (v2.2.5) with options: --no-unal --no-mixed --no-discordant -X 2000 --local.
The null, not unmapped, and duplicated reads were removed by view and markdup functions in sambamba (v0.7.1) with default parameter settings and mitochondrial reads were removed by samtools.
For peak calling, parameters used were macs2 (v2.1.2) callpeak: -p 1e-5 --nomodel -f BAMPE --keep-dup all -g mm.
The bigwig files were generated with bamCoverage function in deepTools (v3.4.3) with default parameter settings.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files
Supplementary_files_format_and_content: peak text files

extract_protocol:
1 x 10^5 cells were collected, washed once with cold DPBS. Then, cell nuclei were collected by lysis buffer (10 mM Tris-HCl at pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) treating for 10 min on ice and centrifugation at 800 g at 4 ℃.
Fragmentation mix (10 μl 5X TTBL, 5 μl TTE Mix V50 and 35 μl ddH2O) was used for resuspending the cell nuclei followed by incubating at 37℃ for 30 min. Then, DNA fragments were purified by 100 μl VAHTS DNA Clean Beads (Vazyme). Purified DNA fragments were amplified by PCR for 15 cycles using the TruePrep Index Kit V2 (Vazyme). Finally, PCR products were purified by 60 μl VAHTS DNA Clean Beads. The ATAC-seq libraries were sequenced on the Illumina NovaSeq 6000 with read length of 150 bp.

value: iPSC


title: H3K4me3_D4_2

value: Reprogramming intermediate


title: EVs from HUVEC LNP-treated rep2

value: Lung epithelial

value: LNP-treated


title: H3K4me3_D0_1


title: T5966; blood; CD19+ B cells; 12 weeks

source_name: blood

value: blood


title: 2517-RP-50

description: Treatment


title: T5965; blood; CD19+ B cells; 12 weeks

value: CD19+ B cells


title: 2517-RP-49

description: Treatment


title: T6007; blood; CD19+ B cells; 12 weeks

value: Siglecg-/-

value: 12 weeks


title: ATAC_D12_2


title: 2517-RP-48

description: Treatment


title: EVs from HUVEC LNP-treated rep1


title: ATAC_iPSC_1


title: ATAC_D12_1


title: 2517-RP-47

description: Control

value: Vehicle (1 ml/kg saline)


title: Chow, biol rep 8, isotype, scRNAseq

city: Cambridge

first: Ken

last: Dower

state: MA

address: 1 Portland St.

department: Inflammation and Immunology Research Unit

institute: Pfizer, Inc.

description:
10x Genomics
XC24_11

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were performed using Cell Ranger software (multiple versions) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Demultiplexing of lipid hashtag oligos was performed as described in PMID 31209384 and only cells mapping to a single hashtag oligo were retained for downstream processing.
Spliced and unspliced read counts were generated from Cell Ranger outputs using the run10x wrapper in the velocyto CLI as described in PMID 30089906 and at http://velocyto.org/velocyto.py/tutorial/cli.html#run10x-run-on-10x-chromium-samples.
Demultiplexed gene counts, hashtag counts and spliced/unspliced counts were merged in R. Only cells mapping to a single hashtag oligo were retained for downstream processing.
Additional details of data processing are described in the publication and are available from the authors upon inquiry.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Murine livers were collected in RPMI1640 media on ice, minced and digested in 100 U/mL collagenase (Sigma-Aldrich) at 37°C for 1 hour with shaking. Digested tissue was filtered through 70 μm nylon mesh and hepatocytes removed by spinning at 50xg for 3 minutes. The remaining cells were passed through a 25 % Percoll (GE Life Sciences) cushion and erythrocytes were lysed with ammonium-chloride-potassium buffer. Isolated cells were stained with 30 μg/mL Hoechst 33342 (Miltenyi) and Zombie NIR viability dye (diluted 1:250 in PBS; Biolegend) before FACS sorting (Sony SH800) to obtain live, single cells. These were methanol fixed based on the 10x Genomics recommended fixation protocol and stored at -80°C.
Library was performed according to the manufacter’s instructions for methanol fixed samples (single cell 3’ v2 or v3.1 protocols, 10x Genomics). Briefly, hepatic cells in methanol were pelleted, counted, washed and resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. For samples that were lipid hashed, library construction was performed as described in PMID 31209384 (McGinnis, Gartner et al., 2019).

value: Liver

value: Hepatic cells

value: Male

value: Isotype

tag: disease state

value: Control

tag: mmpsense signal

tag: age

value: 50-52 weeks


title: EVs from HUVEC Untreated rep3

tag: cell type

value: Untreated

value: T75 flask


title: EVs from HUVEC Untreated rep2


title: EVs from HUVEC Untreated rep4


title: 2517-RP-45

description: Control

value: Hartley

value: Kidney

value: male

tag: time point


title: ATAC_D10_1

value: 129XOG2 E13.5 embryo

value: Reprogramming intermediate


title: Chow, biol rep 9, isotype, scRNAseq

description:
10x Genomics
XC24_12


title: Chow, biol rep 7, isotype, scRNAseq

description:
10x Genomics
XC24_10


title: ATAC_D10_2


title: GAN, biol rep 6, anti-TGFβ, scRNAseq

description:
10x Genomics
XC24_6

value: anti-TGFβ

value: Fibrosis


title: EVs from HUVEC Untreated rep1

value: Lung epithelial


title: EVs from HTB LNP-treated rep4

source_name: Extracellular vesicles from HTB-177

value: LNP-treated


title: GAN, biol rep 5, anti-TGFβ, scRNAseq

description:
10x Genomics
XC24_5

value: Liver


title: ATAC_D8_1


title: GAN, biol rep 4, anti-TGFβ, scRNAseq

description:
10x Genomics
XC24_4

value: Hepatic cells


title: 2517-RP-46

description: Control

value: Vehicle (1 ml/kg saline)


title: 2517-RP-44

description: Control


title: T5964; blood; CD19+ B cells; 12 weeks

data_processing:
Immcantation 4.3.0
pResto; Quality control, Read assembly
Change-O, V(D)J reference alignment
Supplementary files format and content:
fasta formated files after merging and UMI filtering
igblast output text files including filtered and annotated immune repertoires (i.e. quantified annotated data about antibody receptor sequences mapped to germline genes)

extract_protocol:
RNA was isolated using the Rneasy Micro Plus kit from Qiagen; RNA was collected in 14 µl Rnase-free water and 11 µl were used for cDNA generation
Library was prepared according to "Werner, A., et al., Determining immunoglobulin-specific B cell receptor repertoire of murine splenocytes by next-generation sequencing. STAR Protocols, 2022. 3(2): p. 101277"

value: blood

value: CD19+ B cells

value: 12 weeks


title: 2517-RP-42

description: Treatment

value: 9 h

value: High (1.50 mg/kg HgCl2)


title: GAN, biol rep 9, isotype, scRNAseq

description:
10x Genomics
XC24_3

value: Male

value: Isotype

value: 50-52 weeks


title: EVs from HTB LNP-treated rep2

value: T75 flask


title: EVs from HTB LNP-treated rep1


title: ATAC_D6_2

value: 129XOG2 E13.5 embryo

value: Reprogramming intermediate


title: GAN, biol rep 8, isotype, scRNAseq

description:
10x Genomics
XC24_2

value: Fibrosis


title: ATAC_D4_2


title: 2517-RP-39

description: Treatment

value: Hartley

value: Kidney

value: male


title: GAN, biol rep 7, isotype, scRNAseq

description:
10x Genomics
XC24_1

value: Liver

value: Hepatic cells


title: ATAC_D8_2


title: 2517-RP-41

description: Treatment


title: EVs from HTB Untreated rep4

value: Lung epithelial

value: Untreated


title: 2517-RP-43

description: Control

value: Vehicle (1 ml/kg saline)


title: EVs from HTB Untreated rep3


title: 2517-RP-38

description: Treatment

value: 9 h


title: EVs from HTB LNP-treated rep3

value: LNP-treated


title: ATAC_D2_2


title: ATAC_D4_1


title: ATAC_D2_1


title: GAN, biol rep 4, scRNAseq

description:
10x Genomics
XC23_6

value: Male


title: EVs from HTB Untreated rep1


title: GAN, biol rep 5, scRNAseq

description:
10x Genomics
XC23_7


title: ATAC_D0_2

value: MEF


title: EVs from HTB Untreated rep2


title: 2517-RP-37

description: Treatment

value: Low (1.00 mg/kg HgCl2)


title: ATAC_D6_1


title: 2517-RP-35

description: Treatment


title: 2517-RP-36

description: Treatment


title: Chow, biol rep 6, scRNAseq

description:
10x Genomics
XC23_5

value: Control

value: 50-52 weeks


title: ATAC_D0_1

value: 129XOG2 E13.5 embryo


title: 2517-RP-40

description: Treatment

value: High (1.50 mg/kg HgCl2)


title: 2517-RP-34

description: Treatment

value: Hartley


title: Chow, biol rep 5, scRNAseq

description:
10x Genomics
XC23_4


title: Sevo-R2h

city: ZhengZhou city

first: Enqiang

last: Chang

state: Henan

address: No.7, Weiwu Road, ZhengZhou city, HeNan province, China

institute: Henan Provincial People’s Hospital

data_processing:
Sequencing depth was normalized by using CellRanger (version v3.0.1).
We used Seurat package (version 3.0)  in R (version 3.5.3) to perform data filtering (both gene and cell), normalization, PCA and t-SNE.
Cells defined as Astrocytes, OPCs, Intemeurons, Excitatory neurons, Microglia;
We constructed single-cell trajectory for all celltypes by using reversed graph embedding method implemented in R Monocle package (version 2.14.0)
GSEA enrichment analysis for all celltypes implemented in R clusterProfiler package (version 3.14.0 )
Genome_build: hsa
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Nerve cells

growth_protocol: Foetal prefrontal cortex tissues were collected and dissected in ice-cold HibernateTM-E medium (Invitrogen, A1247601) with penicillin and streptomycin (Solarbio, P1400). The PFC tissues were chopped into small pieces with a scalpel blade and digested in 0.25% trypsin-EDTA (Solarbio, T1300) at 37°C for 10 min. The cell suspension was further pipetted to be dispersed to single cells, then the cells were passed through 70 μm filter and centrifuged at 1000 rpm for 7 min at 4°C. The supernatant was aspirated, and the cell pellet was resuspended and seeded to 6-well plates, covered with 20 μg/ml paraformaldehyde (PDL) (Sigma, P1524), in Dulbecco’s Modified Eagle Medium (DMEM) (Hyclon, SH30022.01) with 10% foetal bovine serum (FBS) (Gbico, 10099141C). After 4 hrs incubation, the medium was aspirated, and the cells were cultured in Neurobasal medium (Gbico, 21103049) supplemented with 2% B27. Every three days half of the medium was replaced by fresh Neurobasal medium.

extract_protocol:
After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification.
Libraries were constructed using the Single Cell 3’ Library Kit V3 (10× Genomics).

treatment_protocol: The cultured cells were incubated in a 1.5 L airtight temperature-controlled chambers with inlet and outlet valves and an internal electric fan. For sevoflurane (Jiangsu Hengrui Medicine, China) delivery, the chamber inlet was connected to a closed gas delivery system consisting of a calibrated oxygen flow metre and an inline sevoflurane vaporiser (Abbott Laboratories, Maidenhead, UK). The outlet gas was monitored (Datex gas monitor, Helsinki, Finland) to ensure the sevoflurane in chamber reach the target concentration (3.3%, the equivalent of 1.0 minimum alveolar concentration, MAC). Cells were then incubated in the sealed chamber for 6 hrs at 37°C. In the propofol group, the PFC cells were treated with 20 μΜ propofol (AstraZeneca, UK) for 6 hrs (the equivalent of half maximal effective concentration in vitro). An exposure duration of 6 hrs and the anaesthetic concentrations were chosen in accordance with previous studies and reflect the concentration and duration for the longest paediatric anaesthesia. In any groups either during anaesthetic or mock exposure or recovery phase, all cells were treated under identical conditions except with or without anaesthetics and exposed to the identical mixture gases of 20% oxygen, 5% carbon dioxide and balanced with nitrogen at 37°C.

value: prefrontal cortex

value: microglia, excitatory neurons, interneurons, astrocytes and oligodendrocyte progenitor cells

value: Sevoflurane and recovery 2h


title: GAN, biol rep 6, scRNAseq

description:
10x Genomics
XC23_8

value: Liver

value: Hepatic cells

value: Fibrosis


title: CD45-Ter119-  bone marrow niche cells [XZ21487]

city: Houston

first: Xiang

last: Zhang

state: Texas

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
The mm10 genome was used for reads mapping. Raw sequencing files were imported into 10x Genomics Cell Ranger toolkit (v3.1.0) with default settings for quantifications.
Genome_build: mm10
Supplementary_files_format_and_content: *filtered_feature_bc_matrix.tar.gz files contains the filtered_feature_bc_matrix output folder from Cellranger. Each .gz file contains a .mtx file which is the count matrix and two .tsv files that list the feature names and sample annotations.

source_name: CD45-Ter119-  bone marrow niche cells

extract_protocol:
To isolate the BM niche and HSPC cells, the muscle tissue on the tibia and femur were completely removed, then flushed out the BM cells. The remaining bone were cut and crashed into fragments and digest in DMEM containing 1 mg/mL Collagenase 1, 1 mg/mL Collagenase 2 , 4 mg/mL Dispase 2 , 0.1 mg/mL DNase 1 , 1 mg/mL BSA, 1% HEPES and antibiotics for 45 min at 37°C. Flushed BM cells also incubate in the same digest buffer for 15 min at 37°C. After digestion, bone cells and BM cells are filtered through a 70 µm strainer and resuspended in RBC lysis buffer, then combined into one sample (per mouse) for subsequent step analysis. Lin-cKit+ or CD45-Ter119- from the same batch of experiment were sorted into single-cell suspension and immediately submitted to the Single Cell Genomics Core at Baylor College of Medicine.
The single-cell gene expression library was prepared according to the Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics).

value: Bone marrow

value: Bone marrow niche cells

tag: inoculated tumor cell line

value: PyMT-N

tag: sample type

value: Tumor-bearing


title: Prop-R2h

value: Propofol 6h and recovery 2h


title: 2517-RP-32

description: Control

tag: breed

value: Kidney

value: male

value: 9 h

value: Vehicle (1 ml/kg saline)


title: Prop 6h

value: Propofol 6h


title: Chow, biol rep 4, scRNAseq

description:
10x Genomics
XC23_3

tag: Sex

value: Male

value: Control

value: 50-52 weeks


title: CD45-Ter119-  bone marrow niche cells [XZ21486]

value: Tumor-free


title: 15_Ventricular tissue, P09, biol rep 04

city: Helsinki

first: Lotta

last: Pohjolainen

address: Viikinkaari 5 E

country: Finland

institute: University of Helsinki

data_processing:
bcl2fastq2 Conversion Software was used to convert BCL files to FASTQ file format and demultiplex samples.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic.
Trimmed reads were mapped to GRCm38.p6 whole genome using STAR aligner in two-pass mode.
Counts per gene were calculated using featureCounts software. Parameters used: -s 1 -T 12 -t exon -g gene_id -a Mus_musculus.GRCm38.92.gtf
Differential expression analysis using the DESeq2 software in R environment. Procedures included: Normalization of count values between samples using a geometric mean, estimation of sample-wise factors to correct for library size variability (for example), estimation of dispersion (i.e. variance, scatter) of gene-wise values between conditions, negative binomial linear model and Wald test to produce p-values, removal of low-expression outliers (using Cook's distance) results to optimize for p-value adjustment and finally, multiple testing adjustment of p-values with Benjamini-Hochberg procedure.
Assembly: Gencode Mouse Release M17 (GRCm38.p6) and annotations from Ensembl Release 92
Supplementary files format and content: Raw count matrix of sequencing reads (featureCounts meta-feature level) as .xlsx

source_name: Ventricular tissue

growth_protocol: Laboratory mouse male and female pups were allowed to grow in standard laboratory conditions as per recommended guidelines for laboratory animals. Neonatal mouse heart (ventricular) tissues were harvested from pups on day 01 (P01)., Day 04 (P04), Day 09 (P09), and Day 23 (P23). Total RNA was extracted from heart tissue samples for further studies.

extract_protocol:
Heart (ventricular) tissue samples were homogenized in TriZol regaent. Total RNA was extracted using chloroform-isopropanol protocol. Isolated total RNA was purified using DNA-free kit (Ambio) according to manufacturer's instructions. RNA quality and integrity was analyzed using NanoDrop 2000 spectrophotometer and Agilent 4200 Tapestation system.
The smRNA-sequencing libraries were constructed by using SMARTer smRNA-Seq kit for Illumina (Takara Bio) following manufacturer’s recommended standard protocol.

tag: neonatal developmental_stage

tag: organ

value: Heart

value: Ventricular tissue

value: Day 09


title: 16_Ventricular tissue, P23. biol rep 04

tag: tissue

value: Day 23


title: Sevo 6h

value: prefrontal cortex

value: microglia, excitatory neurons, interneurons, astrocytes and oligodendrocyte progenitor cells

value: Sevoflurane 6h


title: NC

value: untreated


title: CD45+Lin-c-Kit+ cell from the bone marrow [XZ20627]

value: Bone marrow

value: Hematopoietic stem cells and progenitor cells

value: PyMT-N

value: Tumor-bearing


title: 2517-RP-33

description: Treatment

value: Hartley

value: Kidney

value: male

value: 9 h

tag: agent

value: Low (1.00 mg/kg HgCl2)


title: CD45+Lin-c-Kit+ cell from the bone marrow [XZ20626]

tag: strain

value: Tumor-free


title: 2517-RP-31

description: Control

value: Vehicle (1 ml/kg saline)


title: 13_Ventricular tissue, P01, biol rep 04

value: Heart

value: Ventricular tissue

value: Day 01


title: Huh7 cells, Si-KDM4C#2-3

city: Wuhan

first: Zhen

last: Zeng

address: Xinhua Road

institute: Huazhong University of Science and Technology

data_processing:
The sequencing quality were assessed with FastQC (v0.11.5) and then low quality data were filtered using NGSQC (v2.3.3).
The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0) with default parameters.The processed reads from each sample were aligned using HISAT2 against the reference genome.
The gene expression analyses were performed with StringTie (v1.3.3b).DESeq(v1.28.0) was used to analyze the DEGs between samples.
Analysis description: Calculate the expression read count using the FeatureCounts and Stringtie software. Then, the gene and transcript FPKM were calculated. In this process we simply filtered the expression:1）Remove genes or transcripts with length less than 100 bp. ;2）If the FPKM of a gene or transcript is less than 0.0001, it is considered to be expressed as 0. Remove genes with a table of 0 in all samples.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: FPKMs

growth_protocol: All the cells were cultured in DMEM medium containing 10% FBS and 100 μg/mL penicillin and streptomycin in 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen)
The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing.

treatment_protocol: Huh7 cells transfected with Scrambled or SiRNAs targeting KDM4C for 48 hours.

value: Human hepatocellular carcinoma cells

tag: cell line

tag: treatment

tag: genotype

value: KDM4C knockdown


title: 14_Ventricular tissue, P04, biol rep 04

value: Day 04


title: Huh7 cells, Si-KDM4C#2-2


title: 2818-RP-36

description: Treatment

growth_protocol: We cultured renal cells for 48 hours before expososure to mercuric chloride or vehicle (Hepatocyte Maintenance Medium).

extract_protocol:
Total RNA was isolated from culture cells using TRIzol Reagent (Thermo Fisher Scientific) and further purifed from the aqueous phase of TRIzol using RNeasy Plus Mini kit (Qiagen) and eliminated genomic DNA by in-column DNase I digestion. Total RNA quality was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, CA).
At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (Roche, Indianapolis, IN). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (Roche). Pooled libraries were subjected to 75-bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq6000, San Diego, CA). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

value: Renal tube epithelial cells

value: High (40 microM HgCl2)


title: 2818-RP-35

description: Treatment


title: 12_Ventricular tissue, P23. biol rep 03

value: Day 23


title: 2818-RP-34

description: Treatment


title: Huh7 cells, Si-KDm4C#2-1


title: Huh7 cells, Si-KDM4C#1-3


title: 2818-RP-33

description: Treatment


title: 2818-RP-31

description: Treatment


title: Huh7 cells, Si-KDM4C#1-1


title: Patient 81

type: RNA

city: Singapore

first: Jason

middle: Yongsheng

last: Chan

address: 30 Hospital Blvd

country: Singapore

institute: National Cancer Centre Singapore

hyb_protocol: Hybridation was performed as per manufacturer's protocol

scan_protocol: Analysed in the nCounter Digital Analyser at 555 FOV

data_processing: Normalization was performed using the nSolver 4.0 Advanced Analysis software using default parameters

label: biotin

source_name: Angiosarcoma tissue

label_protocol: 100 ng total RNA was used as input into the hybridisation step and carried out according to the manufacturer's protocol

extract_protocol: Total RNA was extracted using FFPE RNA/DNA Purification Plus Kit (Norgen) from five 10 μm tissue sections with adequate tumor available and analyzed using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). After excluding samples with suboptimal RNA integrity and content, the remaining samples were included in the nCounter analysis.

value: Female

tag: Stage

value: Non-metastatic


title: Huh7 cells, Scramble-3

value: Scramble

value: control


title: Huh7 cells, Scramble-2


title: Patient 80

value: Male


title: Patient 76

value: Metastatic


title: Patient 75


title: Huh7 cells, Scramble-1


title: A8

type: genomic

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Samples were normalized using the Bioconductor Package wateRmelon

label: Cy3, Cy5

source_name: cell line

label_protocol: methylation was analyzed using the Infinium MethylationEPIC array

growth_protocol: Cells were cultured in high glucose, no glutamine, no methionine, no cystine DMEM (ThermoFisher Scientific, Waltham MA) supplemented with 5% dialyzed serum (BioTechne, Minneapolis, MN), 100 IU penicillin and streptomycin (ThermoFisher), 4 mM L-glutamine (ThermoFisher) and 1 mM sodium pyruvate (ThermoFisher). L-cystine (Millipore-Sigma, Burlington, MA) was resuspended in PBS with NaOH added until complete solubilization, and added to the cell media at a final concentration of 150 µM. For control medium, L-methionine (Millipore-Sigma) was resuspended in PBS and added to the cell media at a final concentration of 200 µM. For methionine-free, homocysteine containing media, L-homocysteine (Chem-impex, Wood Dale, IL) was resuspended in 1M HCl in PBS and added to the cell media at a final concentration of 200 µM.

extract_protocol: DNA was extracted using the AllPrep kit following the manufacturer’s instructions (Qiagen, Germantown, MD).

value: melanoma

value: methionine dependence


title: 11_Ventricular tissue, P09, biol rep 03

value: Heart

value: Day 09


title: Huh7 cells, Si-KDM4C#1-2


title: Patient 85


title: Patient 82


title: 2818-RP-29

description: Treatment

value: Hartley

value: Low (30 microM HgCl2)


title: 2818-RP-25

description: Treatment


title: 2818-RP-27

description: Treatment


title: 8_Ventricular tissue, P23. biol rep 02

value: Ventricular tissue


title: Patient 84


title: 5_Ventricular tissue, P01, biol rep 02

value: Day 01


title: 6_Ventricular tissue, P04, biol rep 02

value: Day 04


title: 7_Ventricular tissue, P09, biol rep 02


title: 9_Ventricular tissue, P01, biol rep 03


title: 4_Ventricular tissue, P23. biol rep 01


title: 2818-RP-26

description: Treatment

value: Renal tube epithelial cells


title: A7


title: 2818-RP-28

description: Treatment


title: 10_Ventricular tissue, P04, biol rep 03


title: 2818-RP-24

description: Control

value: Vehicle


title: A6


title: Patient 72


title: Patient 73


title: Patient 74

value: Unknown


title: 3_Ventricular tissue, P09, biol rep 01


title: 2_Ventricular tissue, P04, biol rep 01


title: Patient 71

value: Female

value: Non-metastatic


title: A5


title: Patient 70


title: 2818-RP-22

description: Control


title: 2818-RP-23

description: Control


title: 1_Ventricular tissue, P01, biol rep 01


title: A4


title: 2818-RP-21

description: Control


title: Patient 69


title: 2818-RP-17

description: Treatment

value: High (40 microM HgCl2)


title: WT7_RM11

city: Rome

first: Lorenzo

last: D'Ambrosio

address: Via Elio Chianesi 53

department: Dept. Of Research, Advanced Diagnostic, and Technological Innovation

institute: Regina Elena National Cancer Institute, IRCCS

data_processing:
All data processing was conducted through RNA-Seq Analysis Pipeline (RAP) webtool  (D’Antonio et al. BMC Genomics, 2015), with default parameters.
Assembly: mm10
Supplementary files format and content: Text (.txt) file with fpkm normalized gene counts

source_name: skin – epidermis

extract_protocol:
Total RNA was extracted using Qiazol (Qiagen, IT), purified from DNA contamination through a DNase I (Qiagen, IT) digestion step and further enriched by Qiagen RNeasy columns for gene expression profiling (Qiagen, IT). Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies, DE) and by Agilent 2100 Bioanalyzer (Agilent Technologies, CA), respectively.
RNA libraries for sequencing were generated using the same amount of RNA for each sample according to the Illumina TruSeq Stranded Total RNA kit with an initial ribosomal depletion step using Ribo Zero Gold (Illumina, CA). The libraries were quantified by qPCR and sequenced in paired-end mode (2x75 bp) with NextSeq 500 (Illumina, CA).

treatment_protocol: Skin from newborn mice was isolated from either wild type or ZFP750 knock-out mice and incubated dermis side-down in Trypsin-EDTA 0.25% overnight at 4°C. Then, epidermis was peeled from dermis, washed in PBS and snap-frozen.

value: skin - epidermis

value: WT


title: A1

value: melanoma


title: A2

value: methionine dependence


title: M7

value: MeWo

value: methionine independent


title: M8


title: Patient 68

value: Male


title: Patient 65


title: Patient 66


title: KO4_RM44

value: KO


title: Patient 64


title: 2818-RP-18

description: Treatment

value: Hartley


title: WT5_RM14


title: 2818-RP-15

description: Treatment


title: WT1_RM44


title: M6


title: KO3_RM44


title: 2818-RP-14

description: Treatment


title: Patient 63


title: A3


title: 2818-RP-13

description: Treatment


title: Patient 62

value: Metastatic


title: 2818-RP-19

description: Control


title: WT2_RM44


title: KO1_RM14


title: 2818-RP-11

description: Treatment

value: Low (30 microM HgCl2)


title: KO1_RM11


title: M5


title: 2818-RP-10

description: Treatment

value: Renal tube epithelial cells


title: iPSC, scRNAseq

city: Hangzhou

first: Yunkun

last: Lu

address: 3 Qingchun East Rd.

institute: Zhejiang University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: iPSC

extract_protocol:
RNA extraction was performed at LC bio.
Libraries were constructed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics) at LC bio.

value: iPSC

value: iPSCs were seeded on Feeder and maintained in mESC medium. mESC medium contains 47% DMEM/F12, 47% Neural basal medium, 1 x N2 supplement, 1 x B27 supplement, 1% Glutamax, 1% nonessential amino acids (NEAA), 0.055 mM 2-mercaptoethanol (β-ME), 1% P/S, 1000 units/mL mLIF, 3 μM CHIR99021 and 0.2 μM PD0325901. MEFs were cultured in MEF medium, containing DMEM Basic, 10% fetal bovine serum (FBS), 1% penicillin and streptomycin (P/S).                                                                                OG2 MEFs of passages 1-3 were seeded into 6-well plates at density of 2.5 x 10^4 cells/plate. On the next day, medium was changed to reprogramming medium. Medium was changed every 2 days. For reprogramming day 4 to 8, the medium was renewed every day.


title: 2818-RP-9

description: Treatment


title: Patient 61


title: M2


title: M3


title: D12, scRNAseq

description: 10x Genomics

source_name: Reprogramming intermediate

growth_protocol: iPSCs were seeded on Feeder and maintained in mESC medium. mESC medium contains 47% DMEM/F12, 47% Neural basal medium, 1 x N2 supplement, 1 x B27 supplement, 1% Glutamax, 1% nonessential amino acids (NEAA), 0.055 mM 2-mercaptoethanol (β-ME), 1% P/S, 1000 units/mL mLIF, 3 μM CHIR99021 and 0.2 μM PD0325901. MEFs were cultured in MEF medium, containing DMEM Basic, 10% fetal bovine serum (FBS), 1% penicillin and streptomycin (P/S).

treatment_protocol: OG2 MEFs of passages 1-3 were seeded into 6-well plates at density of 2.5 x 10^4 cells/plate. On the next day, medium was changed to reprogramming medium. Medium was changed every 2 days. For reprogramming day 4 to 8, the medium was renewed every day.

value: Reprogramming intermediate


title: M1


title: Patient 59

value: Non-metastatic


title: D8, scRNAseq

description: 10x Genomics


title: D4, scRNAseq

description: 10x Genomics


title: 2818-RP-8

description: Treatment


title: 2818-RP-7

description: Treatment


title: D0, scRNAseq

description: 10x Genomics

value: MEF


title: MT-1 Comb

city: saga

first: yuki

last: kurahashi

state: saga

address: nabeshima 5-1-1

institute: saga university

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: Genome Studio software (V2011.1 Methylation module 1.9.0) and MethylationEPIC_v-1-0_B4 was used. Beta values were obtained after background correction and normalization to internal controls.

label: Cy5 and Cy3

source_name: Adult T cell Leukemia (ATL)

label_protocol: Standard Illumina Protocol

growth_protocol: MT-1 cells were cultured in RPMI-1640 (Sigma-Aldrich) containing 10% fetal bovine serum (FBS).

extract_protocol: Genomic DNA samples were isolated using QIAamp DNA Kit (Qiagen)

treatment_protocol: MT-1 cells were treated with 500nM OR21 and/or 2500nM EPZ for 96h. Each compound was added immediately and 48h after seeding.

value: 500nM OR21 and 2500nM EPZ treated


title: 2818-RP-5

description: Control

value: Vehicle


title: Patient 53

value: Female


title: Patient 56


title: Patient 57


title: Patient 52


title: Patient 58


title: M4

value: melanoma


title: ChIP Control T Day3

city: Berlin

first: Pavel

last: Tsaytler

address: Ihnestrasse  63-73

institute: MPI Molecular Genetics

data_processing:
For ChIP-Seq, reads were trimmed to 50 bp length. The trimmed reads were aligned to the reference genome using bowtie2 (version 2.2.4) (Langmead, 2012) with the following arguments: -3 5 -I 100 -X 500 --no-discordant --no-mixed. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. For visualization, the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing CPM --extendReads 200 --smoothLength 9 -bs 3 -ignore chrM.
Assembly: mm10
Supplementary files format and content: bigWig files representing density for ChIP-Seq

source_name: ES cells

growth_protocol: ES cells were deprived of feeder cells and cultured for 24 hours. Cells were then dissociated, and 40,000 cell/ml cell suspension was plated onto tissue culture plates in 5 µl droplets. Plates were then inverted and incubated for 24 hours. Drops containing mES cell aggregates (corresponding to differentiation day 0, or ES) were then pooled and resuspended in differentiation medium: 48% (v/v) DMEM/F12 (ThermoFisher; 11320033), 48% (v/v) Neurobasal medium (ThermoFisher; 21103049), 1% (v/v) 200 mM L-glutamine (Lonza; BE17-605E), 1% (v/v) penicillin and streptomycin, 1% (v/v) B27 (Gibco; 17504044), 0.5% (v/v) N2 (Gibco; 17502048), 0,5% (v/v) 7.5% BSA fraction V (Gibco; 15260037), 0.1 mM thioglycerol (Sigma-Aldrich; M1753) supplemented with 20 ng/ml mouse recombinant Bmp4 (R&D Systems; 5020-BP-010). To start differentiation, mESC aggregates resuspended in differentiation medium containing Bmp4 were immediately plated on plates pre-coated with fibronectin (Calbiochem; 341631). Differentiation medium supplemented with Bmp4 was refreshed every 24 hours.

extract_protocol:
For sonication, complete protease inhibitors without EDTA (Roche) at 1x final concentration was added to all lysis buffers (LB) prior to use. Each pellet was resuspended in 2.5 ml LB1 (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.75% NP-40, 0.25% triton X-100) and rotated at 4°C for 20 minutes. The cell suspension was homogenized using a douncer. The chromatin was pelleted by centrifugation at 1400g and 4°C for 5 minutes and resuspended in 2.5 ml LB2 (10 mM Tris pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). After 10 minutes rotation at 4°C, the centrifugation step was repeated and each pellet was resuspended in 1.5 ml LB3 (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine), transferred to 15 ml Falcon tubes and sonicated using a W-450D Digital Sonifier (Branson) sonicator for 14 cycles of 10s on/50s off in a 4°C cold room with tubes chilled in ice water. After sonication, 150 μl of Triton X-100 was added per tube, transferred to two 1.5 ml Eppendorf tubes and debris was pelleted by centrifugation at 20,000g and 4°C for 10 minutes. The solubilized chromatin was then pooled and mixed thoroughly. After taking 50 μl as an input control, the chromatin was distributed into 1.5 ml aliquots, snap frozen and stored at -80°C until use.  The input was reverse-crosslinked with the addition of 50 μl 2x elution buffer (100 mM Tris pH 8, 20 mM EDTA pH 8, 2% SDS) and 13-15 hour incubation at 65°C. 100μl of TE buffer were added, and RNA was digested using 0.2 μg/ml RNase A at 37°C for 2 hours. Proteins were digested with the addition of 0.2 μg/ml proteinase K and incubation at 55°C for 2 hours. The DNA was purified with two subsequent phenol:chloroform:isoamyl alcohol (25:24:1, pH 8) extractions and a subsequent MinElute (Qiagen) purification. The input DNA was quantified using a NanoPhotometer (Implen).    For ChIP, 100 μl protein G-coated Dynal beads (Life Technologies) were washed 3x with 1 ml of blocking buffer (PBS, 0.5% BSA), resuspended in 500 μl of blocking solution containing 5 μg primary ChIP antibody (listed in the Key resources table) and rotated overnight at 4°C. Beads were then washed 3x with 1 ml of blocking buffer and resuspended in 100 μl blocking buffer. Chromatin equivalent to 5x107 cells was added and rotated overnight at 4°C. The following day, 6 washing steps (9 for T) with 1 ml RIPA buffer (50 mM Hepes pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and one washing step with 1 ml of TEN (10 mM Tris pH 8, 1 mM EDTA, 50 mM NaCl) were performed. The elution was performed in two subsequent steps using 100 μl of 1x elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) and incubation at 65°C while shaking for 10 minutes each. The eluates were combined and incubated for 13-15 hours at 65°C. 200 μl of TE were added and the ChIP DNA was purified as described for the input above. ChIP DNA was quantified using the Qubit (Life Technologies) DNA HS assay.
The ChIP-seq libraries were generated using the TruSeq ChIP library kit (Illumina) with the previously described modifications (Koch, 2017). After adapter ligation, 0.95x of AMPure XP beads (Beckman Coulter) were used for a single purification and the DNA was eluted using 14 μl of resuspension buffer (RSB, Illumina). After the addition of 1 μl primer mix (25 mM each) and 15 μl 2x Kapa HiFi HotStart Ready Mix (Kapa Biosystems), amplification was performed for 45 seconds at 98°C, 5 cycles of [15 seconds at 98°C, 30 seconds at 63°C and 30 seconds at 72°C] and a final 1 minute incubation at 72°C. The PCR products were purified using 0.95x of beads and eluted using 21 μl of RSB. Ligation products were then separated using a 1.5% agarose gel. Post-run staining was performed using SYBR Gold under agitation for 30 minutes. Gel slices corresponding to 250-400 bp fragment size were cut out. using a Dark Reader Transilluminator.  The gel extraction was performed using 5 gel volumes of QG buffer (Qiagen) with the addition of one gel volume of isopropanol. The MinElute (Qiagen) columns were washed once with QG buffer and twice with PE buffer, air-dried for at least 10 minutes and eluted using 21 μl of EB buffer. 19 μl of the eluate was used in the final amplification, with the addition of 1 μl primer mix and 20 μl 2x Kapa HiFi Hotstart premix. The same protocol as for the pre-amplification was used, with the exception of using 13 amplification cycles. The libraries were quantified using the Qubit DNA HS assay and the library size was validated using DNA HS Bioanalyzer chips.

treatment_protocol: Crosslinking was performed directly on differentiating cells in differentiation medium with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 50mM Hepes pH 7.8) for 10 minutes at room temperature, while shaking. The crosslinking reaction was quenched with the addition of 1/10th volume of 2.5M glycine and 5 minutes incubation. Cells were washed twice with cold PBS, scraped in cold PBS containing 0.05% Triton X-100, pelleted in aliquots of 50 million cells, snap frozen and stored at -80°C until sonication.

value: ES cells

value: T KO

value: in vitro differentiated cardiac mesoderm progenitors


title: Patient 50

value: Male


title: MT-1 OR21

value: 500nM OR21 treated


title: 2818-RP-4

description: Control

source_name: Kidney

value: Hartley


title: ChIP Control P-Smad2 Day2

value: Smad4 KO


title: ChIP Control P-Smad1/5/9 Day2


title: MT-1 control

value: control