title: mouse, HDAC1-cKO, early-non-TexProg, IgG, biol rep1

description:
Library name: HDAC1-cKO early-non-TexProg IgG biol rep1
CnR-20241114-CD8--Tim3--T-HDAC1-KO-IgG.merged.sorted.rpkm.BigWig


title: mouse, WT, early-TexProg, H3K27ac, biol rep2

status: Public on May 22 2025

type: SRA

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgasse 19

country: Austria

institute: Medical University of Vienna

description:
Library name: WT early-TexProg H3K27ac biol rep2
CnR-20241114-CD8--Ly108--T-WT-H3K27ac.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Ly108--T-WT-H3K27ac.merged.stringent.bed

library_source: genomic

data_processing:
Alignment of raw reads to mm10 genome was done with bowtie2 (version 2.5.0).
Blacklisted regions were removed via bedtools intersect (v2.29.1).
Duplicates were marked and for controls removed with Picard tools MarkDuplicates (version: 3.3.0-5-g46d23b4e4-SNAPSHOT).
Reads which mapped to mm10 as proper pairs were merged to one BAM file per sample using samtools merge (version 1.21).
RPKM normalized coverage files in BigWig format were generated with deeptools bamCoverage (version 3.5.6).
Peaks were called with SEACR (version 1.3) for H3K27ac and H3K27me3 samples against IgG background, and with MACS3 (version 3.0.3) for HDAC1 against KO background and RUNX3 against IgG background samples.
Assembly: mm10
Supplementary files format and content: BigWig files for merged replicates
Supplementary files format and content: BED (from SEACR) or narrowPeak (from MACS3) files for merged replicates, except for controls
Library strategy: CUT&Run

molecule: genomic DNA

organism: Mus musculus

source_name: spleen

extract_protocol:
10 spleens per genotype were pooled, single-cell suspensions were prepared, then enriched for CD8+ T cells using the Miltenyi REAlease CD8a Microbead Kit for mouse. Cells were sorted for viability, TCRb, CD8, CD44, PD1 and then either Ly108 (early-TexProg) or PD-1 (early-non-TexProg). Nuclei were isolated, incubated with antibodies (HDAC1, H3K27ac, Runx3, H3K27me3, or IgG) and fragmented with MNase, DNA was isolated with NEB Monarch PCR and DNA clean up.
CUT&RUN Libraries were prepared from 2 ng using NEBNext Ultra II DNA Library Prep Kit, cleaned up using 0.9x volume of SPRI beads and subjected to PE150 sequencing.

tag: tissue

value: spleen

tag: genotype

value: WT


title: mouse, HDAC1-cKO, early-non-TexProg, H3K27me3, biol rep1

description:
Library name: HDAC1-cKO early-non-TexProg H3K27me3 biol rep1
CnR-20241114-CD8--Tim3--T-HDAC1-KO-H3K27me3.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Tim3--T-HDAC1-KO-H3K27me3.merged.stringent.bed


title: mouse, WT, early-non-TexProg, Runx3, biol rep1

description:
Library name: WT early-non-TexProg Runx3 biol rep1
CnR-20241114-CD8--Tim3--T-WT-RUNX3.merged.sorted.rpkm.BigWig
Tim3--T-WT-RUNX3-keepdup-maxgap-minlen_peaks.narrowPeak


title: mouse, WT, early-non-TexProg, H3K27me3, biol rep1

description:
Library name: WT early-non-TexProg H3K27me3 biol rep1
CnR-20241114-CD8--Tim3--T-WT-H3K27me3.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Tim3--T-WT-H3K27me3.merged.stringent.bed


title: mouse, WT, early-non-TexProg, IgG, biol rep1

description:
Library name: WT early-non-TexProg IgG biol rep1
CnR-20241114-CD8--Tim3--T-WT-IgG.merged.sorted.rpkm.BigWig


title: mouse, HDAC1-cKO, early-non-TexProg, Runx3, biol rep1

description:
Library name: HDAC1-cKO early-non-TexProg Runx3 biol rep1
CnR-20241114-CD8--Tim3--T-HDAC1-KO-RUNX3.merged.sorted.rpkm.BigWig
Tim3--T-HDAC1-KO-RUNX3-keepdup-maxgap-minlen_peaks.narrowPeak


title: mouse, WT, early-non-TexProg, HDAC1, biol rep1

description:
Library name: WT early-non-TexProg HDAC1 biol rep1
CnR-20241114-CD8--Tim3--T-WT-HDAC1.merged.sorted.rpkm.BigWig
Tim3--T-WT-HDAC1-keepdup-maxgap-minlen-dedupKOctrl_peaks.narrowPeak


title: mouse, HDAC1-cKO, early-TexProg, IgG, biol rep1

description:
Library name: HDAC1-cKO early-TexProg IgG biol rep1
CnR-20241114-CD8--Ly108--T-HDAC1-KO-IgG.merged.sorted.rpkm.BigWig


title: mouse, WT, early-TexProg, HDAC1, biol rep2

description:
Library name: WT early-TexProg HDAC1 biol rep2
CnR-20241114-CD8--Ly108--T-WT-HDAC1.merged.sorted.rpkm.BigWig
Ly108--T-WT-HDAC1-keepdup-maxgap-minlen-dedupKOctrl_peaks.narrowPeak


title: mouse, HDAC1-cKO, early-non-TexProg, HDAC1, biol rep1

description:
Library name: HDAC1-cKO early-non-TexProg HDAC1 biol rep1
CnR-20241114-CD8--Tim3--T-HDAC1-KO-HDAC1.merged.sorted.rpkm.BigWig


title: mouse, HDAC1-cKO, early-TexProg, H3K27me3, biol rep1

description:
Library name: HDAC1-cKO early-TexProg H3K27me3 biol rep1
CnR-20241114-CD8--Ly108--T-HDAC1-KO-H3K27me3.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Ly108--T-HDAC1-KO-H3K27me3.merged.stringent.bed


title: mouse, HDAC1-cKO, early-TexProg, Runx3, biol rep1

description:
Library name: HDAC1-cKO early-TexProg Runx3 biol rep1
CnR-20241114-CD8--Ly108--T-HDAC1-KO-RUNX3.merged.sorted.rpkm.BigWig
Ly108--T-HDAC1-KO-RUNX3-keepdup-maxgap-minlen_peaks.narrowPeak


title: mouse, HDAC1-cKO, early-TexProg, H3K27ac, biol rep1

description:
Library name: HDAC1-cKO early-TexProg H3K27ac biol rep1
CnR-20241114-CD8--Ly108--T-HDAC1-KO-H3K27ac.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Ly108--T-HDAC1-KO-H3K27ac.merged.stringent.bed


title: mouse, HDAC1-cKO, early-TexProg, HDAC1, biol rep1

description:
Library name: HDAC1-cKO early-TexProg HDAC1 biol rep1
CnR-20241114-CD8--Ly108--T-HDAC1-KO-HDAC1.merged.sorted.rpkm.BigWig


title: mouse, WT, early-non-TexProg, H3K27ac, biol rep1

description:
Library name: WT early-non-TexProg H3K27ac biol rep1
CnR-20241114-CD8--Tim3--T-WT-H3K27ac.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Tim3--T-WT-H3K27ac.merged.stringent.bed


title: mouse, HDAC1-cKO, early-TexProg, H3K27ac, biol rep2

description:
Library name: HDAC1-cKO early-TexProg H3K27ac biol rep2
CnR-20241114-CD8--Ly108--T-HDAC1-KO-H3K27ac.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Ly108--T-HDAC1-KO-H3K27ac.merged.stringent.bed


title: mouse, WT, early-TexProg, IgG, biol rep1

description:
Library name: WT early-TexProg IgG biol rep1
CnR-20241114-CD8--Ly108--T-WT-IgG.merged.sorted.rpkm.BigWig


title: mouse, WT, early-TexProg, H3K27ac, biol rep1

description:
Library name: WT early-TexProg H3K27ac biol rep1
CnR-20241114-CD8--Ly108--T-WT-H3K27ac.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Ly108--T-WT-H3K27ac.merged.stringent.bed


title: mouse, WT, early-TexProg, Runx3, biol rep1

description:
Library name: WT early-TexProg Runx3 biol rep1
CnR-20241114-CD8--Ly108--T-WT-RUNX3.merged.sorted.rpkm.BigWig
Ly108--T-WT-RUNX3-keepdup-maxgap-minlen_peaks.narrowPeak


title: mouse, WT, early-TexProg, H3K27me3, biol rep1

description:
Library name: WT early-TexProg H3K27me3 biol rep1
CnR-20241114-CD8--Ly108--T-WT-H3K27me3.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Ly108--T-WT-H3K27me3.merged.stringent.bed


title: mouse, HDAC1-cKO, early-non-TexProg, H3K27ac, biol rep1

description:
Library name: HDAC1-cKO early-non-TexProg H3K27ac biol rep1
CnR-20241114-CD8--Tim3--T-HDAC1-KO-H3K27ac.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Tim3--T-HDAC1-KO-H3K27ac.merged.stringent.bed


title: mouse, WT, early-TexProg, HDAC1, biol rep1

description:
Library name: WT early-TexProg HDAC1 biol rep1
CnR-20241114-CD8--Ly108--T-WT-HDAC1.merged.sorted.rpkm.BigWig
Ly108--T-WT-HDAC1-keepdup-maxgap-minlen-dedupKOctrl_peaks.narrowPeak


title: cervical lymph node, CPLI RIPO, IT RIPO, biological rep3

city: Durham

first: Matthias

last: Gromeier

state: NC

address: 203 Research Dr

department: Neurosurgery

country: USA

institute: Duke University

description: Library name: LR-TR-4

library_source: transcriptomic

data_processing:
trim using Trimmomatic v0.39 using arguments ILLUMINACLIP:adapters/TruSeq2-PC.fa:1:25:8, SLIDINGWINDOW:4:30, and MINLEN:30
Aligned using STAR/2.7.5c
Raw counts generated from STAR processed into normalized counts using DESeq2_1.44.0 with batch effects removed using limma_3.60.6
Assembly: mouse reference genome GRCm39, Sabin reference genome GCF_008766755.1 (identical coding sequence to PVSRIPO), BSD (blasticidin resistance in CT2A cell line) from pLenti6.2 V5-DEST, luciferase from pHIV-Luciferase (in CT2A cell line), and human PVR variant 1NM_006505 indexed using STAR/2.7.5c
Supplementary files format and content: tab delineated file per sample containing header information and per gene count generated with STAR
Supplementary files format and content: comma delineated file containing normalized counts from DESeq2 with batch correction from limma, column names are sample names and row names are gene names

molecule: polyA RNA

source_name: Cervical lymph node

extract_protocol:
From snap frozen tissue in liquid nitrogen, TRIzol RNA extraction according to manufacturers protocol
Genewiz standard RNA seq library preparation

treatment_protocol: CT2A glioma bearing mice treated IT (7 and 10 dpi) and CPLI (10 and 13 dpi) with Mock/RIPO lymph nodes harvested 2 days post final treatment

value: Cervical lymph node

tag: treatment

value: CPLI RIPO IT RIPO

tag: batch


title: cervical lymph node, CPLI RIPO, IT RIPO, biological rep1

description: Library name: LR-TR-1


title: cervical lymph node, CPLI RIPO, IT mock, biological rep3

description: Library name: LR-TM-3

value: CPLI RIPO IT mock


title: CD45 cells, treatmen 1

city: Beijing

first: Xuhao

last: Zhang

state: 北京

address: 30 Shuangqing Road, Haidian District

country: China

institute: Tsinghua University

description:
Library name: TIM7
10x Genomics

library_source: transcriptomic single cell

data_processing:
Fastq files of gene expression were aligned to the reference genome using Cellranger counting (Cell Ranger v.7.1.0), performing simultaneous filtering, barcode counting, and UMI counting.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
MC38 cells (5×105) were subcutaneously injected into the right flank of mice. The tumor volume was measured twice a week and calculated by length × width × height/2. After the tumors were established, mice received intraperitoneal injections of PBS, TIM3-ProIL2V2, respectively, every 3 days for a total of two injections unless otherwise indicated. We used the Chromium Next GEM Single Cell 3’ Kit (10x Genomics) to generate scRNA-seq libraries according to the manufacturer’s protocol. FACS sorting of cells from three biological replicates labeled with CD45 Antibody (BioLegend). The sorted cells were loaded onto a Chromium single-cell chip to generate barcoded nucleic acid fragments.
The amplified cDNA was used to generate gene expression libraries. These libraries were sequenced on an Illumina NovaSeq 6000.

treatment_protocol: MC38 cells were subcutaneously injected into mice

value: tumor

tag: cell line

tag: cell type

value: CD45+ cells


title: CD45 cells, control 1

description:
Library name: PBS1
10x Genomics

value: PBS


title: CD45 cells, control 2

description:
Library name: PBS2
10x Genomics


title: CD45 cells, control 3

description:
Library name: PBS3
10x Genomics


title: CD45 cells, treatmen 2

description:
Library name: TIM8
10x Genomics


title: cervical lymph node, CPLI RIPO, IT mock, biological rep2

description: Library name: LR-TM-2


title: cervical lymph node, CPLI RIPO, IT mock, biological rep4

description: Library name: LR-TM-6


title: cervical lymph node, CPLI RIPO, IT RIPO, biological rep2

description: Library name: LR-TR-2


title: cervical lymph node, CPLI mock, IT RIPO, biological rep6

description: Library name: LM-TR-6

value: CPLI mock IT RIPO


title: CD45 cells, treatmen 3

description:
Library name: TIM9
10x Genomics


title: cervical lymph node, CPLI RIPO, IT RIPO, biological rep4

description: Library name: LR-TR-6


title: cervical lymph node, CPLI mock, IT RIPO, biological rep5

description: Library name: LM-TR-5


title: cervical lymph node, CPLI mock, IT RIPO, biological rep4

description: Library name: LM-TR-4


title: cervical lymph node, CPLI mock, IT RIPO, biological rep3

description: Library name: LM-TR-3


title: cervical lymph node, CPLI mock, IT RIPO, biological rep2

description: Library name: LM-TR-2


title: cervical lymph node, CPLI mock, IT RIPO, biological rep1

description: Library name: LM-TR-1


title: cervical lymph node, CPLI mock, IT mock, biological rep3

description: Library name: LM-TM-4

value: CPLI mock IT mock


title: cervical lymph node, CPLI mock, IT mock, biological rep1

description: Library name: LM-TM-2


title: cervical lymph node, CPLI mock, IT mock, biological rep2

description: Library name: LM-TM-3


title: mES, AID_KAT6B, IAA1d, H3, rep2

city: Shanghai

first: Daixuan

last: ZHANG

address: No. 131, Dongan Road, Xuhui District

institute: The Institutes of Biomedical Sciences

description: Library name: mES_AID_KAT6B_IAA1d_H3_rep2

data_processing:
Raw reads were filtered by Trim Galore (v0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the mm10 genome using Bowtie2 (v2.5.1).
PCR duplicates were removed using samtools (v1.11) rmdup.
Genome coverage bigwig files were generated by deeptools (v2.5.7) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
H3K14Ac bigWig files were normalized using HEK293T spike-ins, which were mapped to hg38 reference genome using Bowtie2 (v2.5.1).
Assembly: Genome_build: mm10
Supplementary files format and content: Genome coverage bigwig files

growth_protocol: E14Tg2a murine embryonic stem cells (mES) were cultured in Dulbecco’ s Modified Eagle’ s Medium (DMEM) supplemented with 10% fetal bovine serum (FBSGibco #16000-044), 1% MEM non-essential amino acid (Gibco #11140), 55 mM β-Mercaptoethanol (Gibco#21985-023), 100 U/mL Penicillin/Streptomycin (Hyclone #SV30010), 1000 units/mL LIF (Millipore #ESG1107,) and MEK inhibitor PD0325901 (1μM) and GSK3β inhibitor CH99021 (3μM) at 37℃ with 5% CO2.

extract_protocol:
Chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

value: Embryonic stem cells

value: dTAG_SPT6, AID_KAT6B

value: 24 hours with 500 uM IAA

tag: spike-in

value: HEK293T spike-in chromatin

tag: chip antibody


title: mES, AID_KAT6B, IAA1d, H3, rep1

description: Library name: mES_AID_KAT6B_IAA1d_H3_rep1


title: mES, AID_KAT6B, DMSO, H3, rep2

description: Library name: mES_AID_KAT6B_DMSO_H3_rep2


title: cervical lymph node, CPLI RIPO, IT mock, biological rep1

description: Library name: LR-TM-1


title: mES, AID_KAT6B, DMSO, H3, rep1

description: Library name: mES_AID_KAT6B_DMSO_H3_rep1


title: mES, AID_KAT6A, IAA1d, H3, rep2

description: Library name: mES_AID_KAT6A_IAA1d_H3_rep2

value: dTAG_SPT6, AID_KAT6A


title: mES, AID_KAT6A, IAA1d, H3, rep1

description: Library name: mES_AID_KAT6A_IAA1d_H3_rep1


title: mES, AID_KAT6A, DMSO, H3, rep2

description: Library name: mES_AID_KAT6A_DMSO_H3_rep2


title: cervical lymph node, CPLI mock, IT mock, biological rep4

description: Library name: LM-TM-5


title: mES, dTAG_SPT6, KAT6AB-dKO, H3, Rep1

description: Library name: mES_dTAG_SPT6_KAT6AB-dKO_H3_Rep1

value: dTAG_SPT6, KAT6AKO, KAT6BKO


title: mES, dTAG_SPT6, KAT6AB-dKO, dTAG3h, H3, Rep1

description: Library name: mES_dTAG_SPT6_KAT6AB-dKO_dTAG3h_H3_Rep1

value: 3 hours with 100 nM dTAG-13


title: mES, dTAG_SPT6, KAT6AB-dKO, dTAG3h, KAT7i, H3, Rep1

description: Library name: mES_dTAG_SPT6_KAT6AB-dKO_dTAG3h_KAT7i_H3_Rep1

value: 3 hours with 100 nM dTAG-13, 6 hours with 50 uM WM-3835


title: mES, dTAG_SPT6, KAT6AB-dKO, H3, Rep2

description: Library name: mES_dTAG_SPT6_KAT6AB-dKO_H3_Rep2


title: mES, dTAG_SPT6, KAT6AB-dKO, dTAG3h, H3, Rep2

description: Library name: mES_dTAG_SPT6_KAT6AB-dKO_dTAG3h_H3_Rep2


title: mES, dTAG_SPT6, KAT7i, H3, Rep1

description: Library name: mES_dTAG_SPT6_KAT7i_H3_Rep1

value: 6 hours with 50 uM WM-3835


title: mES, dTAG_SPT6, KAT6AB-dKO, dTAG3h, KAT7i, H3, Rep2

description: Library name: mES_dTAG_SPT6_KAT6AB-dKO_dTAG3h_KAT7i_H3_Rep2


title: mES, dTAG_SPT6, dTAG3h, H3, Rep1

description: Library name: mES_dTAG_SPT6_dTAG3h_H3_Rep1


title: mES, dTAG_SPT6, dTAG3h, H3, Rep2

description: Library name: mES_dTAG_SPT6_dTAG3h_H3_Rep2


title: mES, dTAG_SPT6, DMSO, H3, Rep2

description: Library name: mES_dTAG_SPT6_DMSO_H3_Rep2


title: mES, dTAG_SPT6, dTAG3h, KAT7i, H3, Rep2

description: Library name: mES_dTAG_SPT6_dTAG3h_KAT7i_H3_Rep2


title: mES, dTAG_SPT6, KAT6AB-dKO, KAT7i, H3, Rep2

description: Library name: mES_dTAG_SPT6_KAT6AB-dKO_KAT7i_H3_Rep2


title: mES, dTAG_SPT6, dTAG3h, KAT7i, H3, Rep1

description: Library name: mES_dTAG_SPT6_dTAG3h_KAT7i_H3_Rep1


title: mES, dTAG_SPT6, DMSO, H3, Rep1

description: Library name: mES_dTAG_SPT6_DMSO_H3_Rep1


title: mES, dTAG_SPT6, KAT7i, H3, Rep2

description: Library name: mES_dTAG_SPT6_KAT7i_H3_Rep2


title: cervical lymph node, CPLI mock, IT mock, biological rep5

description: Library name: LM-TM-6

value: Cervical lymph node


title: mES, dTAG_SPT6, KAT6ABdKO, H3, rep2

description: Library name: mES_dTAG_SPT6_KAT6ABdKO_H3_rep2


title: mES, dTAG_SPT6, KAT6ABdKO, H3, rep1

description: Library name: mES_dTAG_SPT6_KAT6ABdKO_H3_rep1


title: mES, dTAG-SPT6, KAT7i, H3, rep2

description: Library name: mES_dTAG-SPT6_KAT7i_H3_rep2


title: mES, dTAG-SPT6, KAT7i, H3, rep1

description: Library name: mES_dTAG-SPT6_KAT7i_H3_rep1


title: mES, dTAG-SPT6, DMSO, H3, rep2

description: Library name: mES_dTAG-SPT6_DMSO_H3_rep2


title: mES, dTAG_SPT6, KAT6AB-WT, H3, rep2

description: Library name: mES_dTAG_SPT6_KAT6AB-WT_H3_rep2


title: mES, dTAG-SPT6, DMSO, H3, rep1

description: Library name: mES_dTAG-SPT6_DMSO_H3_rep1


title: mES, AID_KAT6A, DMSO, H3, rep1

description: Library name: mES_AID_KAT6A_DMSO_H3_rep1


title: ERCC1 flox gloms, 9w, Rep6

city: Cologne

first: Björn

last: Schumacher

address: Joseph-Stelzmann-Str. 26

country: Germany

institute: CECAD Research Center

description:
Library name: 305078
AFG_1455

data_processing:
Reads were quantified with Salmon v1.9.0 with a decoy-aware transcriptome and the parameter setting –validateMappings –gcBias –seqBias.
The raw transcript abundance files were imported and summarized to the gene-level with tximport(1.14.2). Differential gene analysis was done with edgeR(3.28.1)
Assembly: GRCm39
Supplementary files format and content: The output of the Salmon quantification. For each sample a tab-delimited .sf file with transcript name, TPM and raw read counts.

molecule: total RNA

source_name: kidney glomeruli

extract_protocol:
Glomeruli were isolated from 9 week old control or podocyte-specific deletion of ERCC1 mice using magnetic bead perfusion. Glomeruli were lysed in Trizol and total RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo) according to manufacturer's instruction.
Library preparation and sequencing were performed by the Cologne Centre of Genomics (CCG).

value: kidney glomeruli

value: Ercc1 fl/fl ; TgPod:Cre tg/wt


title: mES, dTAG_SPT6, KAT6AB-dKO, KAT7i, H3, Rep1

description: Library name: mES_dTAG_SPT6_KAT6AB-dKO_KAT7i_H3_Rep1


title: ERCC1 flox gloms, 9w, Rep5

description:
Library name: 305077
AFG_1439


title: ERCC1 flox gloms, 9w, Rep4

description:
Library name: 305076
AFG_1436


title: ERCC1 flox gloms, 9w, Rep2

description:
Library name: 305074
AFG_1410


title: control gloms, 9w, Rep2

description:
Library name: 305070
AEN_1295

value: TgPod:Cre tg/wt


title: ERCC1 flox gloms, 9w, Rep1

description:
Library name: 305073
AFG_1399


title: control gloms, 9w, Rep4

description:
Library name: 305072
AEN_1299


title: mES, dTAG_SPT6, dTAG3h, H3, rep2

description: Library name: mES_dTAG_SPT6_dTAG3h_H3_rep2

data_processing:
Raw reads were filtered by Trim Galore (v0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the mm10 genome using Bowtie2 (v2.5.1).
PCR duplicates were removed using samtools (v1.11) rmdup.
Genome coverage bigwig files were generated by deeptools (v2.5.7) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
H3K14Ac and H3 bigWig files were normalized using HEK293T spike-ins, which were mapped to hg38 reference genome using Bowtie2 (v2.5.1).
Assembly: Genome_build: mm10
Supplementary files format and content: Genome coverage bigwig files


title: mES, dTAG_SPT6, dTAG3h, H3, rep1

description: Library name: mES_dTAG_SPT6_dTAG3h_H3_rep1


title: mES, dTAG_SPT6, DMSO, H3, rep1

description: Library name: mES_dTAG_SPT6_DMSO_H3_rep1

value: DMSO


title: mES, dTAG_SPT6, DMSO, H3, rep2

description: Library name: mES_dTAG_SPT6_DMSO_H3_rep2


title: mES, WT, siSpt6, H3, rep2

description: Library name: mES_WT_siSpt6_H3_rep2

value: WT

value: transfected with SPT6 siRNAs


title: control gloms, 9w, Rep1

description:
Library name: 305069
AEN_1292


title: mES, WT, siSpt6, H3K14Ac, rep2

description: Library name: mES_WT_siSpt6_H3K14Ac_rep2


title: mES, WT, siScramble, H3, rep1

description: Library name: mES_WT_siScramble_H3_rep1

value: siScramble


title: mES, WT, siSpt6, H3, rep1

description: Library name: mES_WT_siSpt6_H3_rep1

value: Embryonic stem cells


title: mES, WT, siScramble, H3K14Ac, rep2

description: Library name: mES_WT_siScramble_H3K14Ac_rep2


title: mES, WT, siScramble, H3K14Ac, rep1

description: Library name: mES_WT_siScramble_H3K14Ac_rep1


title: mES, WT, siSpt6, H3K14Ac, rep1

description: Library name: mES_WT_siSpt6_H3K14Ac_rep1


title: mES, dTAG_SPT6, KAT6AB-WT, H3, rep1

description: Library name: mES_dTAG_SPT6_KAT6AB-WT_H3_rep1


title: D2-IA, biol rep pool 1, scRNAseq

city: Dublin

first: Marina

last: Ainciburu

state: Dublin

address: Foster Avenue

department: Bioinformatics

country: Ireland

institute: NIBRT

description:
Library name: KO1
Column names for metadata.txt.gz are Cell, Sample, Cluster, UMAP1, UMAP2

data_processing:
BCL files processed with bcl2fastq v2.20
Expression matrix generated with CellRanger Count v7.1.0 ), adding the expected number of cells as input: 6,000 for SPF (D2-C) samples and 9,000 each for GF and KO (D2-IA) samples
Downstream analysis done with Seurat v4.3.0.1
Assembly: mm10 (Ensembl 98)
Supplementary files format and content: filtered_feature_bc_matrix.h5 files contain the raw counts expression matrix (gene x cell) generated by CellRanger Count for the indicated sample. Metadata.txt.gz contains the cell barcodes, cluster and UMAP coordinates for the cells used in the downstream analysis.

source_name: colon

extract_protocol:
Colon tissue was collected from mice 48 hours post-TNBS-induced colitis, cut into 1-2 cm pieces, and incubated at 37°C for 15 minutes in epithelial removal solution (HBSS -/-, 10 mM HEPES, 5 mM EDTA, and Penicillin-Streptomycin). Tissues were then enzymatically digested for 20 minutes at 37°C in a digestion buffer (HBSS –/–, 1 mM sodium pyruvate, 10 mM HEPES, 5% FBS, 50 U/ml Penicillin-Streptomycin, 1X non-essential amino acids, 250 g/ml collagenase D, 12.5 U/ml dispase, 37.5 g/ml Liberase TM, and 200 g/ml DNase I). The cell suspension was washed with and resuspended in FACS buffer and stained for CD11b and Ly6G. DRAQ7 was used to exclude dead cells. Live neutrophils were sorted on a BD FACS Aria IIIu into ice-cold HBSS -/- (10 mM HEPES, 0.04 % BSA). Four colons were pooled per sorting sample, with two pooled samples (four mice each) per group. Sorted neutrophils were centrifuged (300 g, 5 min, 4°C), washed with HBSS -/- (containing 0.04% BSA), and resuspended at 800-1000 cells/ml with 1 l RNase inhibitor.
Library were prepared with a Chromium Next GEM Single Cell 3’ Gel Bead kit v3.1 and library construction kit (10X Genomics) as per manufacturer’s protocol. Briefly, Briefly, cells were loaded on Chromium Comptroller Instrument (10X Genomics) to obtain GEMs. GEM-RT reaction was performed in a SimpliAmp thermal cycler (53oC for 45 min, 85oC for 5 min, held at 4oC). DynaBeads MyOne Silane Beads were used to purify Single strand cDNAs. Quality and concentration of the cDNAs were assessed with High Sensitivity D5000 DNA Tape on a 4200 Tape Station. cDNAs were amplified as follows: 98oC for 45 sec; 13 cycles of 98oC for 20 sec, 54oC for 30 sec, 72oC for 20 sec; 72oC for 1 min; held at 4oC. Libraries were pooled together after diluting to the same molarity and sequenced on a NovaSeq6000 (Illumina) sequencer. Sequencing lengths were 28 bp for read 1, 10 bp for the i7 index, 10 bp for i5 index, and 90 bp for read 2.

value: colon

value: Neutrophils

value: Duoxa1a2 fl/fl LysmCre +/+

value: TNBS colitis


title: GF, biol rep pool 1, scRNAseq

description:
Library name: GF1
Column names for metadata.txt.gz are Cell, Sample, Cluster, UMAP1, UMAP2


title: GF, biol rep pool 2 scRNAseq

description:
Library name: GF2
Column names for metadata.txt.gz are Cell, Sample, Cluster, UMAP1, UMAP2


title: D2-IA, biol rep pool 2, scRNAseq

description:
Library name: KO2
Column names for metadata.txt.gz are Cell, Sample, Cluster, UMAP1, UMAP2


title: SPF(D2-C), biol rep pool 2, scRNAseq

description:
Library name: SPF2
Column names for metadata.txt.gz are Cell, Sample, Cluster, UMAP1, UMAP2

value: Duoxa1a2 fl/fl


title: SPF(D2-C), biol rep pool 1, scRNAseq

description:
Library name: SPF1
Column names for metadata.txt.gz are Cell, Sample, Cluster, UMAP1, UMAP2


title: ERCC1 flox gloms, 9w, Rep3

description:
Library name: 305075
AFG_1415


title: 4T1 cells, CMTR1 KO, replicate 2

city: Detroit

first: Zeng-Quan

last: Yang

state: MI

address: 4100 John R Street

institute: Wayne State University

description: Library name: CMTR1_KO2

data_processing:
HISAT2 to map reads to the mouse genome (mm10).
Differentially expressed mRNAs were identified using the R package edgeR.
Assembly: mm10
Supplementary files format and content: xlsx files that include fpkm and counts for each sample

source_name: breast

extract_protocol:
RNA was extracted from 4T1 cells using a RNeasy Plus Mini Kit (QIAGEN).
For RNA-seq of 4T1 WT and CMTR1-KO cells, poly(A) RNA sequencing libraries were prepared following Illumina's TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with an Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. Quality control analysis and quantification of the sequencing libraries were performed using an Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-end sequencing was performed on Illumina's NovaSeq 6000 sequencing system.

value: breast

value: tumor cell line

value: CMTR1 KO


title: 4T1 cells, control, replicate 2

description: Library name: WT2


title: control gloms, 9w, Rep3

description:
Library name: 305071
AEN_1298


title: 4T1 cells, CMTR1 KO, replicate 1

description: Library name: CMTR1_KO1


title: 4T1 cells, control, replicate 1

description: Library name: WT1


title: mES, WT, siScramble, H3, rep2

description: Library name: mES_WT_siScramble_H3_rep2

value: HEK293T spike-in chromatin


title: snRNAseq_AregFlox_Foxp3Cre

city: Saint Louis

first: Daniel

last: Kreisel

state: MO

address: 425 S Euclid Ave

department: Department of Surgery

institute: Washington University School of Medicine

description: Library name: snRNAseq_AregFlox_Foxp3Cre

data_processing:
Alignment with Cell Ranger V6
QC and Filtering with Seurat V4
Unsupervised Clustering with Seurat V4
Assembly: mm10
Supplementary files format and content: .rds objects

molecule: nuclear RNA

source_name: lung

extract_protocol: Chromium Single Cell 5ʹ Reagent v1.1 kit from 10X Genomics and Chromium Single Cell 3ʹ Reagent v1.1 kit from 10X Genomics

value: lung

tag: strain

value: re-transplant


title: snRNAseq_AregFlox

description: Library name: snRNAseq_AregFlox


title: TCR_spleen_VDJ

description: Library name: TCR_spleen_VDJ

library_source: other

molecule: other


title: TCR_donor_VDJ

description: Library name: TCR_donor_VDJ


title: TCR_recipient_VDJ

description: Library name: TCR_recipient_VDJ


title: TCR_spleen_RNA

description: Library name: TCR_spleen_RNA


title: TCR_recipient_RNA

description: Library name: TCR_recipient_RNA


title: 21days_recipient

description: Library name: 21days_recipient


title: 7days_recipient

description: Library name: 7days_recipient


title: WT_treatment9

city: Lausanne

first: Antoine

last: Jalil

address: EPFL station 15

country: Switzerland

institute: Ecole Polytechnique federale de Lausanne

description:
Library name: Colon 830
BRB-seq

data_processing:
All libraries were sequenced on an Illumina Novaseq 6000
Assembly: Read trimming, alignment, and quantification steps were performed by Alithea Genomics using STARsolo. R2 reads were trimmed (“--clipAdapterType CellRanger4”) and aligned to the GRCm38 genome
Supplementary files format and content: To generate both raw and UMI-deduplicated counts, the following parameter was used: “--soloUMIdedup NoDedup 1MM_Directional”. UMI-deduplicated count matrices were used for downstream analyses

source_name: Colon

extract_protocol:
RNA was extracted from biobanked liver and terminal ileum using Direct-zol-96 RNA kit (Zymo research)
The generation of bulk RNA Barcoding and sequencing (BRB-seq) libraries was performed using the MERCURIUSTM BRB-seq library preparation kit for Illumina and following the manufacturer’s manual

value: Colon

value: C. scindens


title: WT_treatment7

description:
Library name: 8828_colon
BRB-seq

value: WT


title: KO_treatment10

description:
Library name: 8698_colon
BRB-seq

value: KO


title: KO_treatment9

description:
Library name: Colon 697
BRB-seq


title: KO_treatment8

description:
Library name: 8696_colon
BRB-seq


title: KO_control9

description:
Library name: 8695_colon
BRB-seq

value: vehicle


title: KO_control8

description:
Library name: 8694_colon
BRB-seq


title: KO_control7

description:
Library name: 8693_colon
BRB-seq


title: KO_control6

description:
Library name: 8692_colon
BRB-seq


title: KO_control5

description:
Library name: 8688_colon
BRB-seq


title: KO_control3

description:
Library name: 8678_colon
BRB-seq


title: KO_control4

description:
Library name: 8679_colon
BRB-seq


title: KO_control1

description:
Library name: 8676_colon
BRB-seq


title: KO2

city: Hangzhou

first: Jiajia

last: Wang

address: 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Mouse BMDCs

growth_protocol: Mouse bone marrow-derived dendritic cells (BMDCs) from 8-week-old wild type or OPTN knockout mice were culture by GM-CSF (50 ng/mL) and IL-4 (20 ng/mL) for 6 days.

extract_protocol:
RNA from CII-stimulated wild type or OPTN knockout BMDCs were extracted using TRIZOL (Life Technologies) followed by purification using an RNeasy Mini Kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Wild type or OPTN knockout BMDCs were treated with type II collagen (CII, 100 μg/mL) for 24 h.

tag: tag

value: OPTN knockout BMDCs + CII

tag: age


title: KO1


title: KO3


title: TCR_donor_RNA

description: Library name: TCR_donor_RNA


title: WT_treatment6

description:
Library name: 8666_colon
BRB-seq


title: 7days_donor

description: Library name: 7days_donor


title: WT_treatment8

description:
Library name: 8829_colon
BRB-seq


title: WT_control11

description:
Library name: 8653_colon
BRB-seq


title: WT2

value: wild type BMDCs + CII


title: WT_treatment5

description:
Library name: 8664_colon
BRB-seq


title: WT_treatment4

description:
Library name: 8651_colon
BRB-seq


title: WT1


title: WT_treatment2

description:
Library name: 8648_colon
BRB-seq


title: WT_treatment1

description:
Library name: Colon 647
BRB-seq


title: WT_treatment3

description:
Library name: 8649_colon
BRB-seq


title: KO_treatment7

description:
Library name: 8639_colon
BRB-seq


title: KO_treatment6

description:
Library name: 8638_colon
BRB-seq


title: NMIBC24

city: Bangalore

first: Hari

middle: P

last: S

state: Karnataka

address: 1st Cross, Shankara Matt Premises, Shankarapuram, Basavanagudi

country: India

institute: Sri Shankara Cancer Hospital and Research Centre

description: Library name: 21-S-495

data_processing:
Quality check of raw Fastq files were performed using FastQC. Trimmomatic was used to remove bad quality reads. The processed fastq files then were mapped to GRCh38. HISAT2  was used for alignment and the read counts of each gene were obtained using Feature Counts . The counts were normalised using DESeq2
Assembly: GRCh38
Supplementary files format and content: log2 normalised counts

organism: Homo sapiens

source_name: Urinary Bladder

extract_protocol:
Tumor RNA extraction from FFPE blocks was performed using the All Prep FFPE DNA/RNA Kit (Cat. No. 80234, Qiagen, Valencia, CA, USA). RNA samples passing quality control (QC) were further processed for library construction, involving fragmentation, adapter ligation, and amplification
The Agilent RNA Prep with Enrichment Kit (Cat. No. 5191-6874)  was used for RNA-Seq library preparation.

value: Urinary Bladder

tag: gender

value: M

tag: t stage

tag: grade

value: BCG

tag: eortc group

value: Intermediate

tag: aua group

value: High

tag: focality

value: Unifocal

tag: recurrence status

value: Recurrent


title: NMIBC21

description: Library name: 21-S-1013

tag: tissue

value: F

value: TA

value: mitomycin

value: Low

value: Non-recurrent


title: NMIBC23

description: Library name: 21-S-31

tag: treatment


title: NMIBC22

description: Library name: 21-S-1096B

value: Multifocal


title: NMIBC25

description: Library name: 21-S-514


title: KO_treatment5

description:
Library name: 8637_colon
BRB-seq

value: Colon

tag: genotype

value: KO

value: C. scindens


title: KO_control2

description:
Library name: Colon 677
BRB-seq

value: vehicle


title: NMIBC20

description: Library name: 20-S-3357

value: Urinary Bladder


title: WT_treatment

description:
Library name: 8665_colon
BRB-seq

value: WT


title: KO_treatment4

description:
Library name: 8636_colon
BRB-seq


title: NMIBC19

description: Library name: 20-S-3353

value: BCG


title: KO_treatment3

description:
Library name: 8629_colon
BRB-seq


title: WT_control10

description:
Library name: 8652_colon
BRB-seq


title: KO_treatment2

description:
Library name: 8627_colon
BRB-seq


title: WT3

value: wild type BMDCs + CII


title: NMIBC17

description: Library name: 20-S-3056

value: M

value: High


title: NMIBC16

description: Library name: 20-S-2974

value: Unifocal


title: WT_control9

description:
Library name: 8625_colon
BRB-seq


title: KO_treatment1

description:
Library name: 8626_colon
BRB-seq


title: NMIBC15

description: Library name: 20-S-2612J

value: Recurrent


title: WT_control7

description:
Library name: 8623_colon
BRB-seq


title: NMIBC13

description: Library name: 20-S-163

value: TA

value: Intermediate

value: multifocal


title: WT_control6

description:
Library name: 8622_colon
BRB-seq


title: NMIBC12

description: Library name: 20-S-1187

value: Non-recurrent


title: WT_control8

description:
Library name: 8624_colon
BRB-seq


title: NMIBC11

description: Library name: 20-S-1040AB

value: Multifocal


title: WT_control1

description:
Library name: 8613_colon
BRB-seq

value: Colon


title: NMIBC9

description: Library name: 19-S-3966A

value: F


title: NMIBC10

description: Library name: 19-S-4219


title: WT_control3

description:
Library name: 8615_colon
BRB-seq


title: WT_control2

description:
Library name: 8614_colon
BRB-seq


title: NMIBC7

description: Library name: 19-S-3221B


title: NMIBC8

description: Library name: 19-S-3503

value: mitomycin

value: Low


title: NMIBC6

description: Library name: 19-S-2056D

value: Urinary Bladder


title: Cd11c-Cre/Fbxl5F/F (FBXL5ΔDC) mice 6 h-2

city: Kumamoto

first: Toshiro

last: Moroishi

address: 1-1-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

description: Library name: 6hKO2

data_processing:
Raw reads were trimmed to remove adapter sequence by Trim Galore (v0.6.6)
HISAT2 (v2.2.1) was used to align to the mm10 mouse reference genome.
Assembly: mm10
Supplementary files format and content: comma-separated values file includes raw counts for all sample

source_name: Liver

growth_protocol: All animal experiments were conducted using male mice aged 7 to 10 weeks, housed under specific pathogen-free (SPF) conditions.

extract_protocol:
Total RNA was extracted from liver tissues of Fbxl5F/F mice and CD11c-Cre/Fbxl5F/F mice with or without acetaminophen treatment using ISOGEN (Nippon Gene, 319-90211).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice were fasted for 16 hours prior to receiving an intraperitoneal (i.p.) injection of 300 mg/kg or 500mg/kg APAP (Nacalai tesque, M1R4379) diluted in PBS to 20 mg/ml. Food was provided immediately after the injection.

value: Liver

value: Acetaminophen


title: Cd11c-Cre/Fbxl5F/F (FBXL5ΔDC) mice 6 h-3

description: Library name: 6hKO3


title: NMIBC18

description: Library name: 20-S-3148

value: BCG


title: Cd11c-Cre/Fbxl5F/F (FBXL5ΔDC) mice 6 h-1

description: Library name: 6hKO1


title: NMIBC5

description: Library name: 19-S-2045

value: M


title: NMIBC14

description: Library name: 20-S-1991B


title: NMIBC4

description: Library name: 19-S-1708


title: NMIBC3

description: Library name: 18-S-787A

value: High


title: FBXL5F/F (control) mice 6 h-2

description: Library name: 6hFF2


title: FBXL5F/F (control) mice 6 h-3

description: Library name: 6hFF3


title: Cd11c-Cre/Fbxl5F/F (FBXL5ΔDC) mice 0 h-3

description: Library name: 0hKO3

value: No treatment


title: FBXL5F/F (control) mice 6 h-1

description: Library name: 6hFF1


title: NMIBC1

description: Library name: 18-S-3501


title: NMIBC2

description: Library name: 18-S-3926


title: WT_control5

description:
Library name: 8617_colon
BRB-seq

value: WT

value: vehicle


title: HEK293T, siKAT7, H3, rep2

description: Library name: HEK293T_siKAT7_H3_rep2

data_processing:
Raw reads were filtered by Trim Galore (v0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the hg38 genome using Bowtie2 (v2.5.1).
PCR duplicates were removed using samtools (v1.11) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Assembly: Genome_build: hg38
Supplementary files format and content: Genome coverage bigwig files

growth_protocol: HEK293T cells were cultured in Dulbecco’ s Modified Eagle’ s Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS, Gibco #16000-044), 1% MEM Non-essential Amino Acid (Gibco #11140),  100 U/mL Penicillin/Streptomycin (Hyclone #SV30010) at 37℃ with 5% CO2.

treatment_protocol: HEK293T Cells were transfected with control and KAT7/6A/6B siRNAs with RNAiMAX according to manufacturer's protocol.

tag: cell line

value: Human Embryonic Kidney

value: transfected with KAT7 siRNA


title: Cd11c-Cre/Fbxl5F/F (FBXL5ΔDC) mice 0 h-2

description: Library name: 0hKO2


title: Cd11c-Cre/Fbxl5F/F (FBXL5ΔDC) mice 0 h-1

description: Library name: 0hKO1


title: HEK293T, siScramble, H3, rep2, for_siKAT7

description: Library name: HEK293T_siScramble_H3_rep2_for_siKAT7

tag: cell type


title: WT_control4

description:
Library name: 8616_colon
BRB-seq


title: HEK293T, siKAT7, H3, rep1

description: Library name: HEK293T_siKAT7_H3_rep1


title: FBXL5F/F (control) mice 0 h-2

description: Library name: 0hFF2


title: HEK293T, siScramble, H3, rep1, for_siKAT7

description: Library name: HEK293T_siScramble_H3_rep1_for_siKAT7


title: HEK293T, siKAT6AB, H3, rep1

description: Library name: HEK293T_siKAT6AB_H3_rep1

value: transfected with KAT6A and KAT6B siRNAs


title: FBXL5F/F (control) mice 0 h-1

description: Library name: 0hFF1


title: 4T1,  LATS1/2 double-knockout, biol rep 3

description: Library name: Sample6

data_processing:
Fastp (v0.23.0) was used for quality control and adapter trimming
The sequenced reads were mapped to mus musculus genome assembly GRCm38 (mm10) from Genome Reference Consortium using HISAT2 (v2.2.1)
The count matrix was obtained using StringTie (v2.2.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: Spheroids generated from WT or LATS1/2 dKO 4T1 cell lines were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified incubator with 5% CO2 at 37℃

extract_protocol:
Spheroids were collected and RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: triple-negative breast cancer

value: LATS1/2 double-knockout

tag: culture condition

value: spheroid


title: HEK293T, siKAT6B, H3, rep2

description: Library name: HEK293T_siKAT6B_H3_rep2

value: transfected with KAT6B siRNA

tag: chip antibody


title: 4T1,  LATS1/2 double-knockout, biol rep 2

description: Library name: Sample5


title: HEK293T, siKAT6B, H3, rep1

description: Library name: HEK293T_siKAT6B_H3_rep1


title: HEK293T, siKAT6AB, H3, rep2

description: Library name: HEK293T_siKAT6AB_H3_rep2


title: 4T1,  LATS1/2 double-knockout, biol rep 1

description: Library name: Sample4


title: 4T1,  WT, biol rep 3

description: Library name: Sample3


title: HEK293T, siScramble, H3, rep2, for_siKAT6AB

description: Library name: HEK293T_siScramble_H3_rep2_for_siKAT6AB


title: 4T1,  WT, biol rep 2

description: Library name: Sample2


title: HEK293T, siKAT6A, H3, rep2

description: Library name: HEK293T_siKAT6A_H3_rep2

value: transfected with KAT6A siRNA


title: 4T1,  WT, biol rep 1

description: Library name: Sample1


title: mES, dTAG_SPT6, dTAG3h, rep2, PRO-seq

data_processing:
Raw reads were filtered by Trim Galore (v0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with “-q 25”, remaining reads were mapped to mouse rDNA database using Bowtie2  (v2.5.1) with parameter “--very-sensitive-local” to remove rRNA contamination.
Unmapped reads were aligned to mm10 genome and hg38 genome respectively, using Bowtie2 (v2.5.1) with default parameter.
Samtools (v1.11) was used to filter and deduplicate SAM files.
Genome coverage bigwig files were normalized using HEK293T spike-ins, which were mapped to hg38 reference genome using Bowtie2 (v2.5.1).
Assembly: Genome_build: mm10
Supplementary files format and content: Supplementary_files_format_and_content: Genome coverage bigwig files
Library strategy: PRO-Seq

extract_protocol:
Nascent RNA was extracted using a Total RNA Puriﬁcation Kit following the manufacturer’s instructions (ZOME). The total RNA is subjected to three biotin-Streptavidin enrichment to select nascent RNA away from other RNA. We isolated nascent RNAs with magnetic beads coated with streptavidin, followed by 3’ adapter ligation. After another round of biotin-streptavidin affinity purification, we removed the mRNA cap and ligated the 5’ adapter. Following the third biotin-streptavidin affinity purification, we generated cDNA by reverse transcription and prepared PRO-seq libraries for sequencing using Illumina TruSeq small-RNA adaptors with twelve cycles of PCR.
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

treatment_protocol: mESCs treated with DMSO or 100 nM dTAG-13 for 3 hours. PRO-seq run-on reactions for mESCs were carried out as follows: 106 permeabilized cells were added to the same volume of 2x Nuclear Run-On reaction mixture (10 mM Tris-HCl pH 8.0, 300 mM KCl, 1%Sarkosyl, 5 mM MgCl2, 1 mM DTT, 200 mM biotin-11-A/C/G/UTP (Perkin-Elmer), 0.8 u/mL SUPERaseIN inhibitor [Ambion]) and incubated for 5 min at 37ºC and the reaction were stopped by Trizol.

value: Embryonic stem cells

value: 3 hours with 100 nM dTAG-13

tag: fraction

value: Nascent RNA


title: HEK293T, siScramble, H3, rep1, for_siKAT6AB

description: Library name: HEK293T_siScramble_H3_rep1_for_siKAT6AB


title: mES, dTAG_SPT6, dTAG3h, rep1, PRO-seq


title: mES, dTAG_SPT6, DMSO, rep2, PRO-seq


title: Breast cancer tumor tissue, patient 99

city: Turku

first: Maija

last: Hollmén

address: Tykistökatu 6A 4th floor

country: Finland

institute: University of Turku

description: Library name: Tumor_99

data_processing:
Data post-processing including demultiplexing, read alignment and quality control were performed using Cell Ranger package (v3.1, 10X Genomics).
Assembly: GRCh38
Supplementary files format and content: Filtered feature barcode matrices from Cell Ranger, tsv and matrix files

source_name: Breast cancer tumor

extract_protocol:
Untreated, fresh tumor or adjacent tissue was cut into small pieces on ice using scalpel. Tissue pieces were digested in 0.2 mg/ml collagenase P (Sigma), 0.8 mg/ml dispase and 0.1 mg/ml DNase for 1h at +37°C. Cells were re-suspended in freshly-prepared 0,04% ultrapure BSA-PBS (ThermoFisher, cat. AM2616) for single-cell partitioning.
Single-cell partitioning was done with Chromium Controller and scRNA-seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v2 and Chromium Chip A Single Cell Kit (10X Genomics, cat. PN-120237, cat. PN-120236) according to manufacturer’s instructions. Full-length cDNA amplified by PCR (Veriti, Applied Biosystems) and cleaned using SPRIselect Reagent Kit (Beckman Coulter, cat. B23318). Amplified cDNA was fragmented, end-repaired and A-tailed prior to sample index PCR. Library quality and quantity were analyzed using Bioanalyzer (Agilent).

value: Breast cancer tumor

tag: patient


title: Adjacent breast tissue, patient 98

description: Library name: Adjacent_98

source_name: Adjacent breast tissue

value: Adjacent breast tissue


title: FBXL5F/F (control) mice 0 h-3

description: Library name: 0hFF3

value: Liver


title: mES, dTAG_SPT6, dTAG3h, rep2, RNA-seq

data_processing:
Raw reads were filtered by Trim Galore (v0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped to mouse rDNA database using Bowtie2 (v2.5.1) with parameter “--very-sensitive-local” to remove rRNA contamination.
Unmapped reads were aligned to the mm10 genome using STAR (v2.7.5c) with parameters "-outFilterMultimapNmax 1”.
Genome coverage bigwig files were generated by deeptools (v2.5.7) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Assembly: Genome_build: mm10
Supplementary files format and content: Supplementary_files_format_and_content: Genome coverage bigwig files

extract_protocol:
Total RNAs were isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instruction. Strand specific total RNA library preparation was performed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420S).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

treatment_protocol: 3 hours with DMSO or 100 nM dTAG-13


title: Adjacent breast tissue, patient 95

description: Library name: Adjacent_95


title: mES, dTAG_SPT6, dTAG3h, rep1, RNA-seq


title: mES, dTAG_SPT6, DMSO, rep2, RNA-seq


title: mES, dTAG_SPT6, DMSO, rep1, RNA-seq


title: Adjacent breast tissue, patient 92

description: Library name: Adjacent_92


title: Breast cancer tumor tissue, patient 92

description: Library name: Tumor_92


title: Breast cancer tumor tissue, patient 95

description: Library name: Tumor_95


title: HEK293T, siKAT6A, H3, rep1

description: Library name: HEK293T_siKAT6A_H3_rep1


title: mES, AID_KAT6B, IAA1d, H3K14Ac, rep1

value: dTAG_SPT6, AID_KAT6B

value: 24 hours with 500 uM IAA

tag: spike-in

value: HEK293T spike-in chromatin


title: mES, AID_KAT6B, IAA1d, H3K14Ac, rep2


title: Breast cancer PDEC, IgG4, patient 163

description: Library name: T_163_IG

data_processing:
fastp (v2019/9/27 from https://github.com/novogene-europe/fastp) was used to filter out reads with adapter contamination, high proportion of uncertain nucleotides (>10%), length lower than 150 bp or low Phred score (≤5 in more than 50% of bases).
Reads were mapped using STAR (v2.6.1.d) with 2 mismatches allowed.
Paired-end reads were quantified with featureCounts (subread v1.6.3).
Assembly: GRCh38
Supplementary files format and content: Raw readcounts from each sample in .xlsx file

source_name: Breast cancer

growth_protocol: Fresh breast cancer tumor and adjacent cancer-free tissues were cut into 9 replicate tissue pieces representing different areas. From each selected tissue area, 1 – 2 mm^3 pieces were cut and divided across treatment conditions.

extract_protocol:
Tissue pieces dissociated in 1 ml TRIsure (Bioline, cat. BIO-38032) using gentleMACS M tubes and by running program RNA.01_01 on gentleMACS Dissociator (both Miltenyi Biotec, cat. 130-093-235 and 130-093-236). Total RNA was extracted following Bioline’s TRIsure protocol.
mRNA purification with poly-T oligo-attached beads, reverse transcription using random hexamer primers, non-directional library preparation and sequencing were performed by Novogene (Cambridge, United Kingdom) using their standard protocols.

treatment_protocol: Ex vivo culture (48h) was performed on a 96-well ultra-low attachment plate (Corning, cat. 7007) with 200 μl RPMI-1640 (Sigma, cat. 5886) + 10% FBS + 1% GlutaMAX + 12.8 U/ml penicillin-streptomycin + 20 μg/ml bexmarilimab (FP-1305, Abzena) or IgG4 isotype control (human IgG4 [S241P/L248E], Abzena) and 3 replicate tissue pieces per well.

value: Breast cancer

tag: cancer type

value: IDC, Luminal B


title: Breast cancer tumor tissue, patient 85

description: Library name: Tumor_85


title: Adjacent breast tissue, patient 99

description: Library name: Adjacent_99


title: mES, AID_KAT6B, dTAG3h, HA, rep2

value: HA (Cell Signaling,#3724)


title: mES, AID_KAT6B, DMSO, H3K14Ac, rep1


title: Breast cancer PDEC, IgG4, patient 162

description: Library name: T_162_IG

value: IDC, HER2


title: mES, AID_KAT6B, dTAG3h, HA, rep1


title: Breast cancer tumor tissue, patient 98

description: Library name: Tumor_98


title: Breast cancer PDEC, IgG4, patient 161

description: Library name: T_161_IG


title: mES, dTAG_SPT6, DMSO, rep1, PRO-seq


title: mES, AID_KAT6A, IAA1d, H3K14Ac, rep2

value: dTAG_SPT6, AID_KAT6A


title: Breast cancer PDEC, bexmarilimab, patient 162

description: Library name: T_162_BEX

value: bexmarilimab


title: Breast cancer PDEC, bexmarilimab, patient 161

description: Library name: T_161_BEX


title: mES, AID_KAT6B, DMSO, HA, rep1


title: Breast cancer PDEC, bexmarilimab, patient 160

description: Library name: T_160_BEX

value: ILC, Luminal A


title: Breast cancer PDEC, IgG4, patient 160

description: Library name: T_160_IG


title: Breast cancer PDEC, bexmarilimab, patient 163

description: Library name: T_163_BEX


title: mES, AID_KAT6A, DMSO, H3K14Ac, rep2


title: mES, AID_KAT6A, IAA1d, H3K14Ac, rep1


title: Adjacent breast tissue, patient 85

description: Library name: Adjacent_85


title: mES, AID_KAT6B, DMSO, HA, rep2


title: Breast cancer PDEC, bexmarilimab, patient 157

description: Library name: T_157_BEX


title: mES, AID_KAT6A, DMSO, H3K14Ac, rep1


title: Breast cancer PDEC, IgG4, patient 157

description: Library name: T_157_IG


title: mES, AID_KAT6B, DMSO, H3K14Ac, rep2


title: mES, AID_KAT6A, dTAG3h, HA, rep2


title: mES, AID_KAT6A, dTAG3h, HA, rep1


title: Breast cancer PDEC, bexmarilimab, patient 156

description: Library name: T_156_BEX


title: mES, AID_KAT6A, DMSO, HA, rep2


title: Breast cancer PDEC, IgG4, patient 155

description: Library name: T_155_IG


title: mES, AID_KAT6A, DMSO, HA, rep1


title: Breast cancer PDEC, bexmarilimab, patient 155

description: Library name: T_155_BEX


title: mES, dTAG_SPT6, KAT6AB-dKO, dTAG3h, KAT7i, H3K14Ac, rep1

value: dTAG_SPT6, KAT6AKO, KAT6BKO

value: 3 hours with 100 nM dTAG-13, 6 hours with 50 uM WM-3835


title: mES, dTAG_SPT6, KAT6AB-dKO, dTAG3h, KAT7i, H3K14Ac, rep2

value: Embryonic stem cells


title: Breast cancer PDEC, bexmarilimab, patient 134

description: Library name: T_134_BEX


title: mES, dTAG_SPT6, KAT6AB-dKO, KAT7i, H3K14Ac, rep2

value: 6 hours with 50 uM WM-3835


title: Breast cancer PDEC, IgG4, patient 133

description: Library name: T_133_IG


title: Breast cancer PDEC, bexmarilimab, patient 133

description: Library name: T_133_BEX


title: mES, dTAG_SPT6, KAT6AB-dKO, dTAG3h, H3K14Ac, rep2

value: 3 hours with 100 nM dTAG-13


title: Breast cancer PDEC, IgG4, patient 132

description: Library name: T_132_IG


title: Breast cancer PDEC, IgG4, patient 131

description: Library name: T_131_IG

value: ILC, Luminal B


title: mES, dTAG_SPT6, KAT6AB-dKO, dTAG3h, H3K14Ac, rep1


title: mES, dTAG_SPT6, KAT6AB-dKO, H3K14Ac, rep2


title: Breast cancer PDEC, IgG4, patient 156

description: Library name: T_156_IG


title: Breast cancer PDEC, IgG4, patient 134

description: Library name: T_134_IG


title: Breast cancer PDEC, IgG4, patient 128

description: Library name: T_128_IG


title: Breast cancer PDEC, IgG4, patient 121

description: Library name: T_121_IG


title: Breast cancer PDEC, bexmarilimab, patient 128

description: Library name: T_128_BEX


title: mES, dTAG_SPT6, KAT7i, H3K14Ac, rep2


title: Breast cancer PDEC, bexmarilimab, patient 131

description: Library name: T_131_BEX


title: Breast cancer PDEC, bexmarilimab, patient 121

description: Library name: T_121_BEX


title: mES, dTAG_SPT6, KAT6AB-dKO, KAT7i, H3K14Ac, rep1


title: Adjacent breast tissue PDEC, IgG4, patient 163

description: Library name: A_163_IG

value: Adjacent breast tissue


title: mES, dTAG_SPT6, dTAG3h, H3K14Ac, rep1


title: mES, dTAG_SPT6, dTAG3h, KAT7i, H3K14Ac, rep2


title: Adjacent breast tissue PDEC, bexmarilimab, patient 163

description: Library name: A_163_BEX


title: mES, dTAG_SPT6, dTAG3h, H3K14Ac, rep2


title: mES, dTAG_SPT6, dTAG3h, KAT7i, H3K14Ac, rep1


title: mES, dTAG_SPT6, DMSO, H3K14Ac, rep2


title: Adjacent breast tissue PDEC, bexmarilimab, patient 162

description: Library name: A_162_BEX


title: mES, dTAG_SPT6, dTAG3h, KAT7, rep2

value: KAT7 (Abcam, #ab70183)


title: Adjacent breast tissue PDEC, IgG4, patient 162

description: Library name: A_162_IG


title: mES, dTAG_SPT6, KAT6AB-dKO, H3K14Ac, rep1


title: mES, dTAG_SPT6, DMSO, H3K14Ac, rep1


title: Adjacent breast tissue PDEC, IgG4, patient 161

description: Library name: A_161_IG


title: Breast cancer PDEC, bexmarilimab, patient 132

description: Library name: T_132_BEX


title: mES, dTAG_SPT6, dTAG3h, KAT7, rep1


title: Adjacent breast tissue PDEC, IgG4, patient 160

description: Library name: A_160_IG


title: Adjacent breast tissue PDEC, bexmarilimab, patient 160

description: Library name: A_160_BEX


title: mES, dTAG_SPT6, DMSO, KAT7, rep1


title: mES, dTAG_SPT6, DMSO, KAT7, rep2


title: mES, dTAG_SPT6, KAT7i, H3K14Ac, rep1


title: Adjacent breast tissue PDEC, bexmarilimab, patient 161

description: Library name: A_161_BEX


title: mES, dTAG_SPT6, KAT6ABdKO, H3K14Ac, rep2


title: Adjacent breast tissue PDEC, IgG4, patient 157

description: Library name: A_157_IG


title: Adjacent breast tissue PDEC, bexmarilimab, patient 157

description: Library name: A_157_BEX


title: Adjacent breast tissue PDEC, IgG4, patient 156

description: Library name: A_156_IG


title: mES, dTAG_SPT6, KAT6AB-WT, H3K14Ac, rep1


title: Adjacent breast tissue PDEC, bexmarilimab, patient 156

description: Library name: A_156_BEX


title: mES, dTAG-SPT6, KAT7i, H3K14Ac, rep2


title: mES, dTAG_SPT6, KAT6ABdKO, H3K14Ac, rep1


title: Adjacent breast tissue PDEC, IgG4, patient 155

description: Library name: A_155_IG


title: mES, dTAG-SPT6, KAT7i, H3K14Ac, rep1


title: Adjacent breast tissue PDEC, bexmarilimab, patient 155

description: Library name: A_155_BEX


title: Adjacent breast tissue PDEC, IgG4, patient 134

description: Library name: A_134_IG


title: mES, dTAG-SPT6, dTAG3h, H3K14Ac, rep2


title: Adjacent breast tissue PDEC, bexmarilimab, patient 134

description: Library name: A_134_BEX


title: Adjacent breast tissue PDEC, IgG4, patient 133

description: Library name: A_133_IG


title: mES, dTAG-SPT6, DMSO, H3K14Ac, rep2


title: mES, dTAG_SPT6, H3K14Ac, rep1


title: mES, dTAG_SPT6, H3K14Ac, rep2


title: Adjacent breast tissue PDEC, bexmarilimab, patient 133

description: Library name: A_133_BEX


title: Adjacent breast tissue PDEC, IgG4, patient 132

description: Library name: A_132_IG


title: Adjacent breast tissue PDEC, bexmarilimab, patient 132

description: Library name: A_132_BEX


title: mES, dTAG_SPT6, dTAG3h, FLAG, rep2

value: DYKDDDDK (Flag) (Smart-lifesciences, #SLAB01)


title: mES, dTAG_SPT6, DMSO, FLAG, rep2


title: mES, dTAG_SPT6, KAT6AB-WT, H3K14Ac, rep2

value: HEK293T spike-in chromatin


title: Adjacent breast tissue PDEC, IgG4, patient 131

description: Library name: A_131_IG


title: Adjacent breast tissue PDEC, IgG4, patient 128

description: Library name: A_128_IG


title: Adjacent breast tissue PDEC, bexmarilimab, patient 131

description: Library name: A_131_BEX


title: mES, dTAG_SPT6, dTAG3h, FLAG, rep1


title: mES, dTAG_SPT6, DMSO, FLAG, rep1


title: mES, WT, SPT6, rep2

value: WT

value: SUPT6H (proteintech, #23073-1-AP)


title: Adjacent breast tissue PDEC, bexmarilimab, patient 121

description: Library name: A_121_BEX


title: Adjacent breast tissue PDEC, IgG4, patient 121

description: Library name: A_121_IG


title: Adjacent breast tissue PDEC, bexmarilimab, patient 128

description: Library name: A_128_BEX


title: WT, NPC, Control treatment, Rep4

city: Reykjavik

first: Kimberley

middle: J

last: Anderson

address: Sturlugata 8

country: Iceland

institute: University of Iceland

data_processing:
Reads were filtered from raw data using the following steps: (1) Remove reads containing adapters. (2) Remove reads containing N > 10% (N represents the base cannot be determined). (3) Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Reads were pseudoaligned to the GRCm39 transcriptome using Kallisto using paired-end mode and 100 bootstraps
Assembly: GRCm39
Supplementary files format and content: Tab delimited text file includes raw abundances for each sample

source_name: E18.5 cortical neuronal progenitor

growth_protocol: NPCs were cultured in neurobasal growth medium containing 1X B27 supplement (Thermo Fisher Scientific, 17504044), 1X Penicillin/Streptomycin (Thermo Fisher Scientific, 15140122), 1X Glutamax (Thermo Fisher Scientific, 35050038), 20 ng/mL FGF-2 (Peprotech, 100-18B), 20 ng/mL EFG (Peprotech, AF-100-15), and 2 μg/mL Heparin (MP Biomedicals, 210193125). NPCs were either sub-cultured or media was replaced every 2 days.

extract_protocol:
RNA was isolated using the Direct-zol RNA isolation kit (Zymo, R2062) according to the manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Cells were treated either with 10 nM dihydrotestosterone (DHT) or DMSO vehicle control for 6h prior to RNA extraction.

value: E18.5 cortical neuronal progenitor

value: DMSO


title: TOP1-AID_WAPL-dTAG_nn -aux -dtag, repl. 1

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

institute: IMP - Research Institute of Molecular Pathology

description:
Library name: 206277
TOP1-AID_WAPL-dTAG_nn.merged-n.ref.hic

data_processing:
Basecalling software: Illumina RTA
Hi-C preprocessing of PE fastq files using hicup version 0.7.4
bowtie2 version 2.2.5 mapping against hg19 reference assembly
truncating, mapping, filtering and deduplicating of Hi-C raw data through hicup process, conversion to input files for HOMER software and juicer tools.
Analyzing Hi-C data with Homer for TAD detection and insulation scores.
juicer tools pre version 1.22.01 to derive .hic files (Aiden Lab) containing Hi-C matrices for usage with Juicebox and juicer tools for further Hi-C processing like loop a.k. corner peak calling using hiccups subroutine.
Assembly: hg19
Supplementary files format and content: hic files: contain Hi-C matrices for usage with Juicebox, made with  juicer tools pre command

source_name: HeLa Kyoto

growth_protocol: HeLa Kyoto (RRID:CVCL_1922) were got from Narumiya S (Kyoto University; Kyoto; Japan)

extract_protocol:
Cells were cross-linked in falcon tube. The DNA was fragmented, biotynilated at both ends, and ligated at newly blunted ends together. Biotinylated DNA was captured and prepared for paired-end Illumina sequencing.
Libraries were prepared for sequencing using standard Illumina protocols.

value: HeLa Kyoto

value: human cervical cancer cells

tag: group

value: nn = -aux -dtag


title: mES, WT, SPT6, rep1

data_processing:
Raw reads were filtered by Trim Galore (v0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the mm10 genome using Bowtie2 (v2.5.1).
PCR duplicates were removed using samtools (v1.11) rmdup.
Genome coverage bigwig files were generated by deeptools (v2.5.7) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
H3K14Ac bigWig files were normalized using HEK293T spike-ins, which were mapped to hg38 reference genome using Bowtie2 (v2.5.1).
Assembly: Genome_build: mm10
Supplementary files format and content: Genome coverage bigwig files


title: WT, NPC, Control treatment, Rep3


title: TOP1-AID_WAPL-dTAG_Yn +aux -dtag, repl.1

description:
Library name: 206279
TOP1-AID_WAPL-dTAG_Yn.merged-n.downS.122mio.hic

value: Yn = +aux -dtag


title: WT, NPC, DHT treatment, Rep4

value: DHT


title: TOP1-AID_WAPL-dTAG_nY -aux +dtag, repl. 1

description:
Library name: 206278
TOP1-AID_WAPL-dTAG_nY.merged-n.downS.122mio.hic

value: nY = -aux +dtag


title: TOP1-AID_WAPL-dTAG_YY +aux +dtag, repl.1

description:
Library name: 206280
TOP1-AID_WAPL-dTAG_YY.merged-n.downS.122mio.hic

value: YY = +aux +dtag


title: WT, NPC, DHT treatment, Rep3


title: Mutant, NPC, Control treatment, Rep4


title: N/P(14) treat rep2

city: Taipei

first: Tsung-Han

last: Hsieh

address: XinYi dist.,WuXing Street, No.250.

country: Taiwan

institute: Taipei Medical University

description: Library name: sample 4

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hg19 whole genome using STAR v2.7.2b
Reads number were calculated using RSEM v1.3.1.
Assembly: Hg19
Supplementary files format and content: Matrix table with raw count for every gene and every sample

extract_protocol:
Total RNA was isolated from cells using Trizol reagent (Life Technologies, Invitrogen, Carlsbad, CA), according to the manufacturer's instructions
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA protocols

tag: medium

value: RPMI1640, supplemented with  10%FBS

tag: time

value: 24 hours

value: Hinokiflavone treatment


title: Mutant, NPC, Control treatment, Rep3


title: N/P(14) treat rep1

description: Library name: sample 3


title: Mutant, NPC, DHT treatment, Rep4


title: N/P(14) untreated rep2

description: Library name: sample 2

value: untreat


title: Mutant, NPC, DHT treatment, Rep3


title: Mutant, NPC, Control treatment, Rep2


title: mES, dTAG-SPT6, dTAG3h, H3K14Ac, rep1

extract_protocol:
Chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

value: Embryonic stem cells

value: 3 hours with 100 nM dTAG-13


title: N/P(14) untreated rep1

description: Library name: sample 1


title: Mutant, NPC, DHT treatment, Rep2


title: HLM_2+UAB116 25µM

city: BOYNTON BEACH

first: Swatika

last: Butey

state: Florida

address: 107 North Monterey Cir

department: Pediatric Surgery

institute: UAB Beierle Lab

description: Library name: 2HLM2116

data_processing:
Basecalls were performed using bclconvert version 4.0.3
Sequence reads were mapped to reference genome using STAR version 2.7.11a using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the STAR alignment BAM files using Cufflinks version 2.2.1 using parameters --library-type fr-firststrand -G -L
Cuffmerge, Cuffquant and Cuffdiff were used with default settings to identify differentially expressed genes
Assembly: Gencode GRCh38.p13.Release43
Supplementary files format and content: tab-delimited Excel file containing gene symbol and FPKM values for each gene in each sample

extract_protocol: Total cellular RNA was extracted using the RNeasy kit (Qiagen Inc., Germantown, MD, USA).

value: UAB116 25µM


title: sh_LRP8-2#-3

city: Zhan Jiang

first: Xiaoyu

last: Li

state: Guangdong

address: 57 People's Avenue

institute: Affiliated Hospital of Guangdong Medical University

description:
Library name: Sample8
sh_ctrl vs sh_LRP8-2#.xlsx

data_processing:
The clean data were mapped to the reference genome using Hisat2 software. Guiding by the Ensembl GTF gene annotation file, featureCounts was used to obtain the gene level FPKM as the expression profiles of mRNA, fold change and p-value were calculated based on FPKM.
Assembly: GRCh38
Supplementary files format and content: excel format. Gene expression values (TPM and Counts)

source_name: breast cancer cell

extract_protocol:
Total RNA was isolated from the cells using TRIZOL reagent (Invitrogen, 15596018CN), 2 ug of total RNA was used for the construction of sequencing libraries.
Eukaryotic mRNA with polyA tail was enriched by magnetic beads with Oligo(dT), and the mRNA was interrupted by buffer solution. Using fragmented mRNA as template and random oligonucleotides as primer, the first cDNA strand was synthesized in M-MuLV reverse transcriptase system, then the RNA strand was degraded by RNaseH, and the second cDNA strand was synthesized in DNA polymerase I system using dNTPs as raw material. The purified double-stranded cDNA was end-repaired, A-tail was added, and sequencing joints were connected. cDNA of about 200bp was screened by AMPure XP beads for PCR amplification, and PCR products were purified by AMPure XP beads again. Finally, A library was obtained. The construction principle of the database is shown below.

value: breast cancer cell

value: LRP8 knockdown


title: HLM_2

description: Library name: 1HLM2Ctrl


title: sh_LRP8-2#-2

description:
Library name: Sample7
sh_ctrl vs sh_LRP8-2#.xlsx


title: WT, NPC, DHT treatment, Rep2

value: E18.5 cortical neuronal progenitor


title: WT, NPC, Control treatment, Rep2

value: DMSO


title: WT, NPC, DHT treatment, Rep1


title: sh_ctrl-3

description:
Library name: Sample5
sh_ctrl vs sh_LRP8-2#.xlsx

value: WT


title: Mutant, NPC, Control treatment, Rep1


title: WT, NPC, Control treatment, Rep1


title: sh_LRP8-2#-1

description:
Library name: Sample6
sh_ctrl vs sh_LRP8-2#.xlsx


title: Mutant, NPC, DHT treatment, Rep1


title: sh_ctrl-1

description:
Library name: Sample3
sh_ctrl vs sh_LRP8-2#.xlsx


title: RNA_Piezo1KO_Yoda1_rep3

city: Xiamen

first: Lanfen

last: Chen

state: Fujian

address: Xiang'an south rd, Xiang'an district

department: Life Science

institute: Xiamen University

data_processing:
Basecalls were performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence and low quality bases using cutadapt(v.2.6)
Clean reads were mapped to mm10 refernece genome using STAR (v.2.7.5a) .
Read counts were obtained by mapping the aligned reads to the transcripts of known genes from UCSC by using GenomicAlignments (v.1.30.0).
Differential expression analysis was performed with methods based on the negative binomial distribution in DESeq2 (v.1.34.0), using default parameters. Benjamini and Hochberg correction were used for significance tests and multiple comparisons.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts and FPKM values for each gene in each sample.

source_name: Piezo1 KO BMDMs

growth_protocol: For BMDMs, the femur and tibia were collected from mice of each genotype, and bone marrow cells were flushed with complete DMEM containing 50 mg ml−1 streptomycin and 10% FBS. Erythrocytes were removed via treatment with red blood cell lysis buffer, and the cell suspensions were filtered through a 40-μm cell strainer for the removal of any cell clumps. The single-cell suspensions were then plated in complete DMEM with recombinant mouse M-CSF (carrier-free, 50 ng ml−1). For full differentiation of BMDMs, the cells were cultured for an additional 8 days with replacement of the medium every day. All cells were CD11b+F4/80+ when analyzed by flow cytometry.

extract_protocol:
Total RNA was isolated using RaPure Total RNA Micro Kit (Magen, R4012).
The cDNA libraries were constructed from 1 mg RNA sample using mRNA-seq Lib Prep Kit for illumina (ABclonal, RK20302) following the guidelines of the manufacturers.

treatment_protocol: BMDSs were treated with DMSO or Yoda1.

value: Bone marrow derived macrophages

value: BMDMs

value: Piezo1 KO


title: BM6

description:
Library name: Sample2
BM0 vs BM6.xlsx


title: RNA_Piezo1KO_Yoda1_rep2


title: RNA_Piezo1KO_Yoda1_rep1


title: WT Clone 2, day 35, replicate 2

city: London

first: Mariya

last: Moosajee

address: 11-43 Bath Street

department: Institute of Ophthalmology

country: United Kingdom

institute: UCL

description: Library name: WT2_d35_n2

data_processing:
Paired-end reads were trimmed using TrimGalore
Trimmed sequences were aligned to GRcH38 human genome using Bowtie2 v2.3.4.3
BAM files of technical and biological replicates of the same condition were then merged, indexed and sorted by query names using SAMtools v1.6
Peaks of significantly opened chromatin regions in each condition was called using the name-sorted, merged BAM file by Genrich v0.5
Differential accessibility analysis from the count matrix generated by featureCounts was done using DESeq2 v1.42
Assembly: GRCh38
Supplementary files format and content: featurecounts of merged replicates
Supplementary files format and content: normalised BigWiz

source_name: iPSC derived

growth_protocol: adapted protocol based upon Eintracht et al 2022

extract_protocol:
Organoids were resuspended and dounced in 300 ul of RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water) containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin. Homogenates were transferred to a 1.5 ml microfuge tube and incubated on ice for 10 min. Nuclei were filtered through a 40 μm cell strainer and nuclei were washed with RSB buffer and counted. Fifty thousand nuclei were resuspended in 50 μl of transposition mix38 (2.5 μl transposase (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1000 r.p.m. Reactions were cleaned with Qiagen columns.
standard ATAC-seq library construction

value: iPSC derived

value: Retinal organoids


title: RNA_Piezo1KO_DMSO_rep3


title: WT Clone 2, day 35, replicate 1

description: Library name: WT2_d35_n1


title: RNA_Piezo1KO_DMSO_rep2


title: WT Clone 1, day 35, replicate 2

description: Library name: WT1_d35_n2


title: RNA_Piezo1KO_DMSO_rep1


title: RNA_WT_Yoda1_rep3

source_name: WT BMDMs


title: mES, dTAG-SPT6, DMSO, H3K14Ac, rep1

first: Daixuan

last: ZHANG

address: No. 131, Dongan Road, Xuhui District

institute: The Institutes of Biomedical Sciences

value: HEK293T spike-in chromatin


title: WT Clone 1, day 35, replicate 1

description: Library name: WT1_d35_n1


title: RNA_WT_Yoda1_rep2


title: RNA_WT_DMSO_rep3


title: PX Clone 1, day 35, rep[licate 1

description: Library name: PX1_d35_n1

value: PX


title: RNA_WT_DMSO_rep2


title: RNA_WT_Yoda1_rep1


title: PX Clone 2, day 35, rep[licate 1

description: Library name: PX2_d35_n1


title: RNA_WT_DMSO_rep1


title: AN Clone 2, day 35, replicate 1

description: Library name: AN2_d35_n1

value: AN


title: AN Clone 2, day 35, replicate 2

description: Library name: AN2_d35_n2


title: sh_ctrl-2

description:
Library name: Sample4
sh_ctrl vs sh_LRP8-2#.xlsx


title: 4-months-old skin-treated-rep3

city: Nanjing

first: Yuanyuan

last: Wu

state: Jiangsu

address: 138 Xianlin Avenue

institute: Nanjing University of Chinese Medicine

data_processing:
Filtering of clean reads by Fastp (version 0.18.0)
Alignment with Ribosome RNA (rRNA) with Bowtie2 (version 2.2.8)
Alignment with Reference Genome
Quantification of Gene Abundance
Assembly: GRCm39
Supplementary files format and content: an Excel format including gene expression matrix representing expression levels for all genes across all samples, fpkm values and raw counts

source_name: skin

extract_protocol:
Total RNA from skin tissue  was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer's protocol with 3 replicates per group according to the manufacturer’s instructions.
The library was constructed using the NEB Next Ultra RNA Library Prep Kit for Illumina (neb# 7530, New England Biolabs).

value: skin

tag: age

value: radiofrequency treated


title: BM0

description:
Library name: Sample1
BM0 vs BM6.xlsx


title: 4-months-old skin-treated-rep2


title: 4-months-old skin-treated-rep1


title: AdKLF15-3

city: shanghai

first: jiajia

last: zhao

address: Ruijin 2nd Road 197

institute: Shanghai Institute of Hypertension, Ruijin Hospital

description: Library name: Sample 6

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to GRCh38 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Human Umbilical Vein

growth_protocol: Human Umbilical Vein Endothelial Cells were were cultured in Endothelial Cell Medium (ECM) medium containing 5% fetal bovine serum (FBS) , 50 mg/mL Endothelial Cell Growth Supplement (ECGS), and 100 U/mL penicillin and streptomycin. Cells were cultured in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated from HUVECs infected with AdKLF15 or AdCTL using Trizol reagent.
According to the instructions of the experiment, the purified Total RNA was separated into mRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

value: Human Umbilical Vein

value: HUVECs

value: Human Umbilical Vein Endothelial Cells

value: AdCTL


title: 4-months-old skin-untreated-rep3

value: untreated


title: AdKLF15-1

description: Library name: Sample 4


title: 4-months-old skin-untreated-rep2


title: AdCTL-3

description: Library name: Sample 3


title: 4-months-old skin-untreated-rep1


title: AdCTL-1

description: Library name: Sample 1


title: AdCTL-2

description: Library name: Sample 2


title: 1-year-old skin-treated-rep3


title: 1-year-old skin-treated-rep2


title: 1-year-old skin-treated-rep1


title: PX Clone 1, day 35, rep[licate 2

description: Library name: PX1_d35_n2


title: caMKL1_2

first: Miaomiao

last: Hou

address: No. 12 Jiangwang Temple, Xuanwu District

institute: Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College,

description: Library name: Sample 14

data_processing:
Sequencing reads that passed quality control were aligned with Bowtie2 (version 2.2.8) to remove short reads that mapped with ribosome RNA (rRNA). Clean reads were then mapped to human genome GRCh38 using HISAT2 (version 2.2.4) with default parameters. Mapped reads were assembled with StringTie (version 1.3.1) in a reference-based approach. For each transcript, an FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated with RSEM tool as a quantification of its abundance or expression level. Analysis of differentially expressed genes (DEGs) between two distinct groups was performed by DESeq2, with false discovery rate (FDR) below 0.05 and absolute fold change >= 2 considered statistically significant.
Assembly: human genome GRCh38
Supplementary files format and content: Excel table files containing raw counts, FPKM, Log2 fold change, p value and FDR.

extract_protocol:
RNA was extracted using Trizol reagent, and performed with standard procedures
RNA quality was checked by running RNase-free agarose gel and on an Agilent 2100 Bioanalyzer. mRNA was enriched by Oligo(dT) beads, fragmented, and reverse-transcribed into cDNA using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, E7770).

value: Melanoma

value: caMKL1 overexpression


title: caMKL1_3

description: Library name: Sample 15


title: 1-year-old skin-untreated-rep3


title: MKL1_3

description: Library name: Sample 12

value: MKL1 overexpression


title: caMKL1_1

description: Library name: Sample 13


title: PX Clone 2, day 35, rep[licate 2

description: Library name: PX2_d35_n2


title: PNA2

city: Jinan

first: Shan

last: Han

address: Wenhua West road

institute: Shandong University

data_processing:
these cDNA libraries were then sequenced using an Illumina Novaseq6000 platform
Following sequencing, the obtained reads were subjected to a filtering process to remove any low-quality reads,
and the remaining clean reads were aligned to a reference genome using the HISAT2 software
Differentially expressed genes were identified with the P-value<0.05 and fold change>1.5 between the two groups.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include real count for each Sample

source_name: blastula

extract_protocol:
Total RNAs of blastula from mice subjected to either vehicle or DHT exposure were extracted using single cell lysis from BGI.
The extracted RNAs were used to construct RNA libraries using the MGIEasy Fast RNA Library Prep Kit for Illumina from MGI Tech Co., Ltd.

value: blastula

value: DHT


title: AdKLF15-2

description: Library name: Sample 5


title: MKL1_2

description: Library name: Sample 11


title: Control_3

description: Library name: Sample 9

value: Control


title: 1-year-old skin-untreated-rep1


title: PNA1


title: AN Clone 1, day 35, replicate 2

description: Library name: AN1_d35_n2

value: iPSC derived

value: Retinal organoids


title: Control_2

description: Library name: Sample 8


title: Control_1

description: Library name: Sample 7


title: CON3

value: vehicle


title: PNA4


title: CON2


title: A375_Starve_3

description: Library name: Sample 6


title: A375_Starve_2

description: Library name: Sample 5


title: CON1


title: KO_NCT3

city: Cologne

first: Ulrike

last: Göbel

state: NRW

address: Joseph Stelzmann Strasse, 26

department: Bioinformatics Core Facility

institute: CECAD Research Center

data_processing:
Mapping to the genome and read counting was done with nf-core/rnaseq revision 3.7, by the following call: nextflow run nf-core/rnaseq -bg -c nf.conf -profile singularity -r 3.7 --input samplesheet.csv --outdir ./results --multiqc_title "RNA-Seq - AG Trifunovic (Harshita Kaul) 01/15/2024" --fasta 'http://ftp.ensembl.org/pub/release-105/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz' --gtf 'http://ftp.ensembl.org/pub/release-105/gtf/mus_musculus/Mus_musculus.GRCm39.105.gtf.gz' --gtf_extra_attributes gene_name --gtf_group_features gene_id --gtf_count_type exon --save_reference --seq_center 'Cologne Center For Genomics' –deseq2_vst . The reported quant.sf files are the output of the Salmon aligner (https://salmon.readthedocs.io/en/latest/) invoked during this run.
Assembly: Mus_musculus.GRCm39.dna.primary_assembly.fa.gz (Ensembl version 105)
Supplementary files format and content: The output of the Salmon software is described here: https://salmon.readthedocs.io/en/latest/file_formats.html#fileformats

source_name: primary BAT

growth_protocol: Cells were maintained in growth medium at 37°C and 5% CO2. Cultures were not allowed to become completely confluent for expansionCells were detached using trypsinization and then mBA growth medium was added to them. Suspensions were centrifuged for 5 min at 200 g. Pellets were resuspend in mBA growth medium and mixed with freezing medium at a ratio of 1:1 to achieve a final DMSO concentration of 10%. The optimal cell density is 1 million cells per ml. 1.8 x 105 cells per well of a 6-well plate were seeded in mBA growth medium (day -4). After 48 hours (day -2) the medium was removed and mBA differentiation medium was added. Adipogenic differentiation was induced after additional 48 hours (day 0) by exchanging mBA differentiation medium with mBA induction medium. Care was taken to prepare the medium freshly before use. Cultures need to be confluent when inducing adipogenesis. After a 48 hours induction phase (day 2) the cells were maintained in mBA differentiation medium. Medium was replenished every second day until day 8, when the cells are differentiated into mature brown adipocytes.

extract_protocol:
RNA was extracted from cells using RNA extraction kit from Qiagen.
Illumina TruSeq Stranded mRNA

treatment_protocol: NCT-503 treatment (in DMSO) was done for 72 hours, was added to media at concentration of 20uM, with fresh addition every 24 hours. Octyl 2-HG treatment (in DMSO) was done for 72 hours, waas added to the media at concentration of 500 uM, fresh addition every 24 hours.

value: primary BAT

value: mature adipocytes

value: CLPP knockout

value: treated with PHGDH inhibitor NCT505


title: A375_Starve_1

description: Library name: Sample 4


title: KO_NCT2

value: treated with PHGDH inhibitor NCT504


title: 1-year-old skin-untreated-rep2

value: skin


title: KO_UT3


title: KO_NCT1

value: treated with PHGDH inhibitor NCT503


title: A375_10_2

description: Library name: Sample 2

value: 10% FBS


title: MKL1_1

description: Library name: Sample 10

value: Melanoma


title: A375_10_1

description: Library name: Sample 1


title: CON2

city: China

first: huijing

last: lv

address: Zunyi Medical University

institute: Zunyi Medical University

description: Library name: Samples 5

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations
Data were fltered using the following specifications
peaks were called using PeaksFind version 2.2 with the following setting: RNA threshold (0 .2), Enrichment Fold (2 .5), Rescue Fold (3).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: LX-2 human hepatic stellate cell

extract_protocol:
Total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification.
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.

value: LX-2 human hepatic stellate cell

value: Hepatocyte Cells


title: CON3

description: Library name: Samples 6


title: KO_UT2

value: untreated


title: WT_HG3

value: wild type

value: treated with metabolite octyl 2-hydroxyglutarate


title: CON1

description: Library name: Samples 4


title: WT_HG2


title: WT_UT2


title: ALB1

description: Library name: Samples 1


title: ALB3

description: Library name: Samples 3


title: WT_UT3


title: WT_HG1


title: HEK293T, siScramble, H3K14Ac, rep2, for_siKAT7

city: Shanghai

data_processing:
Raw reads were filtered by Trim Galore (v0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the hg38 genome using Bowtie2 (v2.5.1).
PCR duplicates were removed using samtools (v1.11) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Assembly: Genome_build: hg38
Supplementary files format and content: Genome coverage bigwig files

value: Human Embryonic Kidney


title: ALB2

description: Library name: Samples 2


title: BKO4

data_processing:
Mapping to the genome and read counting was done with nf-core/rnaseq revision 3.0, by the following call: nextflow run nf-core/rnaseq --input design.csv --fasta 'ftp://ftp.ensembl.org/pub/release-103/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna. toplevel.fa.gz' --gff 'ftp://ftp.ensembl.org/pub/release-103/gff3/mus_musculus/Mus_musculus.GRCm39.103.gff3.gz' --gtf_count_type exon --gtf_gro up_features gene_id --gtf_extra_attributes Name --skip_biotype_qc --save_reference --aligner star_salmon -profile singularity --outdir ./result s_RNA-seq -c nf-conf.conf -r 3.0 . The reported quant.sf files are the output of the Salmon aligner (https://salmon.readthedocs.io/en/latest/) invoked during this run.
Assembly: Mus_musculus.GRCm39.dna.toplevel.fa.gz (Ensembl version 103)
Supplementary files format and content: The output format of the Salmon software is described here: https://salmon.readthedocs.io/en/latest/file_formats.html

source_name: brown adipose tissue

extract_protocol:
For isolation of total RNA from mouse tissue, the entire adipose tissue was homogenized in 1 mL Trizol (Life Technologies) and ceramic beads (Mobio, Dianova GmbH) with a FastPrep homogenizer (MP Biomedicals) at 5500 rpm for 2.~ 20 sec. After 5 min incubation at RT, 200 μL chloroform were added and mixed for 15 sec, before centrifugation at 12000 g for 15 min at 4 °C was performed. The aqueous upper phase containing the RNA was collected and precipitated with 500 μL isopropanol (10 min incubation at RT, following centrifugation at 12000 g for 10 min, 4°C). RNA pellet was washed with 75% ethanol (5 min centrifugation at 7500 g, 4 °C) and briefly dried. Finally, the RNA pellet was resuspended in 50 μL ultra-pure H2O and incubated at 60°C for 10 min. The RNA concentration and purity was determined with a NanoDrop ND-1000 UV-Vis spectrophotometer (Peqlab). Before cDNA synthesis, 10 μg RNA was digested with DNase I (New England Biolabs). The digestion mix (10 μg RNA, diluted 10X digestion buffer and 1 μL DNase I in a total volume of 20 μL) was incubated 10 min at 37°C. Afterwards, heat inactivation of DNase I was performed at 75°C for 10 min. RNA concentration was redetermined and the samples were stored at −80°C.
Illumina TruSeq Stranded mRNA

value: brown adipose tissue

value: BAT specific CLPP knockout


title: A375_10_3

description: Library name: Sample 3


title: BKO3


title: BKO2


title: BKO1


title: HEK293T, siKAT6AB, H3K14Ac, rep2

value: transfected with KAT6A and KAT6B siRNAs


title: KO_UT1

value: primary BAT

value: mature adipocytes


title: AKO4

value: adipose specific CLPP knockout


title: AKO3


title: HEK293T, siKAT6AB, H3K14Ac, rep1


title: HEK293T, siKAT6B, H3K14Ac, rep2

value: transfected with KAT6B siRNA


title: AKO2


title: AKO1


title: HEK293T, siKAT6A, H3K14Ac, rep2

value: transfected with KAT6A siRNA


title: HEK293T, siKAT6B, H3K14Ac, rep1


title: WT_UT1


title: KO4

value: whole body CLPP knockout


title: HEK293T, siScramble, H3K14Ac, rep2, for_siKAT6AB


title: HEK293T, siKAT7, H3K14Ac, rep1

value: transfected with KAT7 siRNA


title: HEK293T, siKAT7, H3K14Ac, rep2


title: HEK293T, siKAT6A, H3K14Ac, rep1


title: KO3


title: KO2


title: HEK293T, siScramble, H3K14Ac, rep1, for_siKAT6AB


title: KO1


title: SE initiating cells, rep2

city: Guangzhou

first: Jiafeng

last: Liu

address: No.7 Jinsui Road, Tianhe District, Guangzhou

institute: sun yat-sen university

data_processing:
The raw sequenced reads underwent quality testing and were trimmed of adapters using the trimmomatic tool (version 0.39)
The STAR software (version 2.6.1) was utilized to align the trimmed reads to the human hg19 reference genome.
The gene expression levels were quantified and the transcripts per kilobase million (TPM) values were calculated using the RSEM tool (version 1.3.0).
Using DESeq2 (version 1.20.0), differentially expressed genes were identified with a q-value cutoff of ≤ 0.05 and a fold change of ≥ 2.
Assembly: hg19
Supplementary files format and content: excel file includes normalized counts foe each sample

extract_protocol:
Total RNA was extracted using the MolPure Cell/Tissue Total RNA Kit (Yeasen)
The TruSeq Stranded mRNA Library Prep kit (Illumina) was used for the RNA-seq libraries construction

value: human embryonic stem cell

value: WT

value: SE differentiation


title: WT4


title: HEK293T, siScramble, H3K14Ac, rep1, for_siKAT7


title: hESC, rep2


title: SE initiating cells, rep1


title: WT3


title: hESC, rep1


title: WT2


title: WT1


title: SE matutating cells, scramble_SP6, rep2

value: scramble shRNA-treated


title: RNAseq_ESC_NPM1siRNA_rep3

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

institute: University of Zurich

data_processing:
The quality of the 100 bp single end reads generated by the machine was checked by FastQC (Andrews, 2010). The quality of the reads was increased by applying: a) SortMeRNA (Kopylova, 2012) (version 2.1) tool to filter out ribosomal RNA; b) Trimmomatic (Bolger, 2014) (version 0.36) software package to trim the sorted (a) reads. The sorted (a), trimmed (b) reads were mapped against the mouse genome (mm10) using the default parameters of the STAR (Spliced Transcripts Alignment to a Reference, version 2.4.0.1) (Dobin et al., 2013). For each gene, exon coverage was calculated using a custom pipeline and then normalized in reads per kilobase per million (RPKM) (Mortazavi et al., 2008), the method of quantifying gene expression from RNA sequencing data by normalizing for total read length and the number of sequencing reads.
Assembly: mm10 (GRCm38)
Supplementary files format and content: xlsx
Supplementary files format and content: Excel file includes the DESeq2 computed mean of normalized count of all samples based on sequencing depth

growth_protocol: Mouse embryonic stem cells (E14) were cultured in N2B27 medium with LIF/2i

extract_protocol:
Total RNA was purified with TRIzol reagent (Life Technologies).
The quality of the isolated RNA was determined with a Qubit® 4 Fluorometer and 4200 Tape Station system. Only those samples with a 260nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5-2 were further processed. The TruSeq Stranded mRNA (Illumina) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were polyA enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® 4 Fluorometer. The product is a smear with an average fragment size of approximately 260 bp. Libraries were normalized to 10 nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. TheIllumina NovaSeq X Pluswas used for cluster generation and sequencing according to standard protocol. Sequencing was single end at 100 bp.

treatment_protocol: 8x10^4 parental ESCs were seeded into gelatin-coated 6 cm plate. Cells were let to attach for 4 hour and then transfected with 2 μl of 40 μM siRNA stock using Lipofectamine RNAiMAX Transfection Reagent (Invitrogen, 13778150) following the manufacturing instructions

value: Mouse embryonic stem cells (ESCs)

value: NPM1 knockdown

value: ESCs were transfected with siRNA targeting NPM1 and collected 3 days post transfection


title: RNAseq_ESC_NPM1siRNA_rep2


title: SE initiating cells, shSP6, rep2

value: SP6 knockdown


title: SE matutating cells, scramble_SP6, rep1


title: RNAseq_ESC_NPM1siRNA_rep1


title: RNAseq_ESC_ContsiRNA_rep3

value: ESCs were transfected with control siRNA and collected 3 days post transfection


title: SE initiating cells, shSP6, rep1


title: RNAseq_ESC_ContsiRNA_rep2


title: SE initiating cells, scramble_SP6, rep1


title: SE matutating cells, shFOXO4, rep2

value: FOXO4 knockdown


title: H3K9me2_CHIPseq_CHIPsample_NPM1KD_2i

data_processing:
The single-end 100bp ChIPseq reads were aligned to the mouse mm10 reference genome using Bowtie2 (version 2.3.4.3).Read counts were computed and normalized using “bamCoverage” from deepTools (version 3.2.1) using a bin size of 50 bp. To calculate read coverage for 20 kb bin region of H3K9me2 ChIPseq, “multiBamSummary” from deepTools was used.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Integrative Genome Viewer (IGV, version 2.5.2) was used to visualize and extract representative ChIPseq tracks in bigwig file format

extract_protocol:
Briefly, 1% formaldehyde was added to cultured cells to cross-link proteins to DNA. Isolated nuclei were then lysed with lysis buffer [(50 mM Tris-HCl, pH 8.1, 10 mM EDTA, pH 8, 1% SDS, 1X cOmplete™ protease inhibitor EDTA-free cocktail (Roche, 1187358001)]. Nuclei were sonicated using a Bioruptor ultrasonic cell disruptor (Diagenode) to shear genomic DNA to an average fragment size of 200 bp. 20 μg of chromatin for H3K9me2 CHIP  was diluted to a total volume of 500 μl with ChIP buffer (16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100) and pre-cleared with 10 μl packed Protein A Sepharose CL-4B resin (Cytivia, 17078001) for 2 hours at 4°C. Pre-cleared chromatin was incubated overnight with the ChIP-grade antibody against H3K9me2 (abcam, ab1220). The next day, Dynabeads™ Protein G (Invitrogen, 10003D) for H3K9me2 CHIP was added and incubated for 4 hours at 4°C. After washing, bound chromatin was eluted with the elution buffer (1% SDS, 100 mM NaHCO3). Upon proteinase K (ThermoFisher Scientfic, EO0491) digestion at 50 °C for 3 h and reversion of cross-linking (65 °C, overnight), DNA was purified with phenol/chloroform, ethanol precipitated and quantified.
For ChIPseq library preparation, the quantity and quality of the isolated DNA was determined with Qubit® 4 Fluorometer (Life Technologies). Libraries were prepared using the NEBNext®Ultra™II DNA Library Prep for Illumina (New England Biolabs, E7645S and E7645L) following the manufacturer’s protocol. Briefly, ChIP and input samples (10 ng) were first end-repaired and polyadenylated. Then, the ligation of Illumina compatible adapters containing the index for multiplexing was performed. The quality and quantity of the enriched libraries were evaluated using Qubit®4 Fluorometer and 4200 TapeStation System (Agilent). Sequencing was performed on an Illumina NovaSeq6000 machine with single end at 100 bp reads for H3K9me2.

treatment_protocol: For CHIP of H3K9me2, 0.4X106 ES cells were seeded into gelatin coated 10 cm dishes 4 hour prior to siRNA transfection using Lipofectamine® RNAiMAX Transfection Reagent  (Invitrogen, 13778150) in Opti‐MEM® GlutaMAX™ (Gibco, 31985062) reduced‐serum medium Transfection Reagent (Invitrogen 13778150) following the manufacturer’s instructions. The cells were harvested post 72 hours for CHIP.

tag: antibody


title: SE initiating cells, scramble_SP6, rep2


title: SE matutating cells, scramble_FOXO4, rep2


title: H3K9me2_CHIPseq_CHIPsample_WT2i