title: SIRT7-KO-c9+S7WT

status: Public on Mar 30 2026

type: SRA

city: Piscataway

first: Joshua

middle: K

last: Thackray

state: NEW JERSEY

address: 145 Bevier Road

department: Human Genetics Institute of New Jersey

country: USA

institute: Rutgers University

description: Library name: SIRT7-KO-c9+S7WT

library_source: transcriptomic

data_processing:
Raw read quality was first assessed with FastQC (version 0.11.3), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm10) reference genome with HISAT2 (version 2.1.0, option --dta) and converted to BAM format with SAMtools (version 0.1.19).
SNPsplit (version 0.3.4) was used to sort aligned reads into three categories based on informative SNPs using the command `SNPsplit`: A) reads from mus musculus [genome1]; B) reads from mus Castaneus [genome2]; or C) unassignable reads [unassigned]. The resulting BAM files were then sorted by position and indexed using samtools (version 0.1.19).
StringTie (version 1.3.3) was used to estimate transcript abundance using the Ensembl GRCm38 reference GTF file (obtained from the Illumina iGenomes).
Differential expression was analyzed with DESeq2 (version 1.32.0)
Assembly: mm10
Supplementary files format and content: txt files contain count matricies estimated by StringTie.
Supplementary files format and content: BigWig files contain Counts Per Million RNA-seq read signal

molecule: polyA RNA

organism: Mus musculus

source_name: TTF

extract_protocol:
RNA was extracted with TRIZOL reagent (Thermo Fisher, #15596026) following the manufacturer instructions.
Purified RNA was sent to BGI, which perfomed polyA selection, library construction and sequencing.

tag: Sex

value: Female

tag: cell type

value: TTF

tag: strain

value: C57BL6/CAST hybrid

tag: genotype

value: SIRT7-KO + SIRT7-WT


title: SIRT7-HY-c5

description: Library name: SIRT7-HY-c5


title: SIRT7-HY-c4

description: Library name: SIRT7-HY-c4


title: SIRT7-HY-c7

description: Library name: SIRT7-HY-c7


title: INPUT_S7KO-c9+S7WT

description: Library name: INPUT_S7KO-c9+S7WT

library_source: genomic

data_processing:
Raw read quality was first assessed with FastQC (version 0.11.3), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm10) reference genome with Bowtie2 (version 2.2.9) with options --n 2 --k 10 and converted to BAM format with SAMtools (version 0.1.19).
SNPsplit (version 0.3.4) was used to sort aligned reads into three categories based on informative SNPs using the command `SNPsplit`: A) reads from mus musculus [genome1]; B) reads from mus Castaneus [genome2]; or C) unassignable reads [unassigned]. The resulting BAM files were then sorted by position and indexed using samtools (version 0.1.19).
BigWig ChIP signal files were generated from BAM data using deepTools (version 2.4.2) using a bin size of 50 bp, scaled with SES, and normalized by INPUT.
Peak calling was performed using MACS (version 2.2.7.1) by providing ChIP as --treatment and matched Input as --control. Peak calling was performed in --broad mode with --broad-cutoff 0.1 --qvalue 0.1 --scale-to small.
Assembly: mm10
Supplementary files format and content: BigWig signal files contain INPUT normalized ChIP-seq read counts using a bin size of 50bp and scaled with SES.
Supplementary files format and content: BroadPeak files contain broad peaks as called by MACS.

molecule: genomic DNA

extract_protocol:
cells were crosslinked with 1% formaldehyde for 10 min at room temperature and then quenched with 0.2 M glycine for 5 min and washed once with cold PBS. Nuclei were resuspended in 300 μl Lysis buffer 2 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0, and cOmplete protease inhibitors) and incubated on ice for 30 min. Chromatin was sonicated to an average fragment size range of 300-500bp and subsequently centrifugated at 12,000 x g at 4°C for 15 min. Supernatants were diluted with Dilution Buffer (1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl, and cOmplete protease inhibitors). SNAP-ChIP Spike-ins controls for K-AcylStat and K-MetStat (EpiCypher, #19-1001, #19-3001) were added for quantitative normalization and antibody validation purposes by following the manufacturer's instructions.  ChIP-grade protein A/G magnetic beads (Pierce, 26162) were conjugated for at least 3 hours in 1X PBS and 0.05% NP-40 with anti-H3K36ac (EpiCypher, #13-0035, Cell Signaling, #27683). Chromatin samples and antibody-conjugated magnetic beads were incubated overnight at 4°C on a rotator. Magnetic beads were then washed 3 times with ice-cold RIPA buffer (1% NP-40, 0.7% Na-deoxycholate, 50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 M LiCl2, and complete protease inhibitors) and once with Buffer TE (0.1 mM EDTA, 10 mM Tris-HCl pH 8.0). Magnetic beads and input samples (1% of total chromatin) were resuspended in freshly prepared RC buffer (0.1 M NaHCO3 and 1% SDS) in the presence of proteinase K for 5 hours at 60°C on a thermomixer with 900 rpm. DNA was purified using a Binding Buffer NTB and Nucleospin PCR Clean-up Kit from Macherey-Nagel.
library preparation was performed using NEBNext® Ultra II DNA Library Prep Kit for Illumina® (NEB) according to manufacturer instructions.

tag: chip antibody


title: ChIP-H3K36Ac_S7KO-c9+S7WT

description: Library name: ChIP-H3K36Ac_S7KO-c9+S7WT


title: ChIP-H3K36Ac_S7HY-c5

description: Library name: ChIP-H3K36Ac_S7HY-c5


title: Input_S7WT_TTF_Rep2

value: WT


title: Input_S7KO_TTF_Rep2


title: ChIP_H3K36ac_S7WT_TTF_Rep1


title: ChIP_H3K36ac_S7WT_TTF_Rep2


title: ChIP_H3K36ac_S7KO_TTF_Rep2


title: ChIP_H3K36ac_S7KO_TTF_Rep1


title: Input_S7KO_TTF_Rep2

description:
ChIP_H3K27me3_S7KO_pooled.50bp_ses_ratio_input.bw
ChIP_H3K27me3_S7KO_pooled.genome1.50bp_ses_ratio_input.bw
ChIP_H3K27me3_S7KO_pooled.genome2.50bp_ses_ratio_input.bw
ChIP_H3K27me3_S7KO_pooled.unassigned.50bp_ses_ratio_input.bw

data_processing:
Raw read quality was first assessed with FastQC (version 0.11.3), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm10) reference genome with Bowtie2 (version 2.2.9) with options --n 2 --k 10 and converted to BAM format with SAMtools (version 0.1.19).
SNPsplit (version 0.3.4) was used to sort aligned reads into three categories based on informative SNPs using the command `SNPsplit`: A) reads from mus musculus [genome1]; B) reads from mus Castaneus [genome2]; or C) unassignable reads [unassigned]. The resulting BAM files were then sorted by position and indexed using samtools (version 0.1.19).
BigWig ChIP signal files were generated from BAM data using deepTools (version 2.4.2) using a bin size of 50 bp, scaled with SES, and normalized by INPUT.
Peak calling was performed using MACS (version 2.2.7.1) by providing ChIP as --treatment and matched Input as --control. Peak calling was performed in --broad mode with --broad-cutoff 0.1 --qvalue 0.1 --scale-to small.
Assembly: mm10
Supplementary files format and content: BigWig signal files contain INPUT normalized ChIP-seq read counts using a bin size of 50bp and scaled with SES.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and then quenched with 0.2 M glycine for 5 min and washed once with cold PBS. Nuclei were resuspended in 300 μl Lysis buffer 2 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0, and cOmplete protease inhibitors) and incubated on ice for 30 min. Chromatin was sonicated to an average fragment size range of 300-500bp and subsequently centrifugated at 12,000 x g at 4°C for 15 min. Supernatants were diluted with Dilution Buffer (1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl, and cOmplete protease inhibitors). SNAP-ChIP Spike-ins controls for K-AcylStat and K-MetStat (EpiCypher, #19-1001, #19-3001) were added for quantitative normalization and antibody validation purposes by following the manufacturer's instructions.  ChIP-grade protein A/G magnetic beads (Pierce, 26162) were conjugated for at least 3 hours in 1X PBS and 0.05% NP-40 with anti-H3K27me3 (Cell Signaling, #9733). Chromatin samples and antibody-conjugated magnetic beads were incubated overnight at 4°C on a rotator. Magnetic beads were then washed 3 times with ice-cold RIPA buffer (1% NP-40, 0.7% Na-deoxycholate, 50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 M LiCl2, and complete protease inhibitors) and once with Buffer TE (0.1 mM EDTA, 10 mM Tris-HCl pH 8.0). Magnetic beads and input samples (1% of total chromatin) were resuspended in freshly prepared RC buffer (0.1 M NaHCO3 and 1% SDS) in the presence of proteinase K for 5 hours at 60°C on a thermomixer with 900 rpm. DNA was purified using a Binding Buffer NTB and Nucleospin PCR Clean-up Kit from Macherey-Nagel.
library preparation was performed using NEBNext® Ultra II DNA Library Prep Kit for Illumina® (NEB) according to manufacturer instructions.


title: SIRT7-KO-c22+S7WT

description: Library name: SIRT7-KO-c22+S7WT


title: SIRT7-KO-c9

description: Library name: SIRT7-KO-c9


title: ChIP_H3K27me3_S7WT_TTF_Rep1

description:
ChIP_H3K27me3_WT_pooled.50bp_ses_ratio_input.bw
ChIP_H3K27me3_WT_pooled.genome1.50bp_ses_ratio_input.bw
ChIP_H3K27me3_WT_pooled.genome2.50bp_ses_ratio_input.bw
ChIP_H3K27me3_WT_pooled.unassigned.50bp_ses_ratio_input.bw


title: SIRT7-KO-c22

description: Library name: SIRT7-KO-c22


title: SIRT7-KO-c2+S7WT

description: Library name: SIRT7-KO-c2+S7WT


title: INPUT_H3K27me3_S7WT_ES_d7_Rep1

source_name: ES cells

extract_protocol:
cells were crosslinked with 1% formaldehyde for 10 min at room temperature and then quenched with 0.2 M glycine for 5 min and washed once with cold PBS. Nuclei were resuspended in 300 μl Lysis buffer 2 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0, and cOmplete protease inhibitors) and incubated on ice for 30 min. Chromatin was sonicated to an average fragment size range of 300-500bp and subsequently centrifugated at 12,000 x g at 4°C for 15 min. Supernatants were diluted with Dilution Buffer (1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl, and cOmplete protease inhibitors). SNAP-ChIP Spike-ins controls for K-AcylStat and K-MetStat (EpiCypher, #19-1001, #19-3001) were added for quantitative normalization and antibody validation purposes by following the manufacturer's instructions.  ChIP-grade protein A/G magnetic beads (Pierce, 26162) were conjugated for at least 3 hours in 1X PBS and 0.05% NP-40 with anti-H3K27me3 (Cell Signaling, #9733). Chromatin samples and antibody-conjugated magnetic beads were incubated overnight at 4°C on a rotator. Magnetic beads were then washed 3 times with ice-cold RIPA buffer (1% NP-40, 0.7% Na-deoxycholate, 50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 M LiCl2, and complete protease inhibitors) and once with Buffer TE (0.1 mM EDTA, 10 mM Tris-HCl pH 8.0). Magnetic beads and input samples (1% of total chromatin) were resuspended in freshly prepared RC buffer (0.1 M NaHCO3 and 1% SDS) in the presence of proteinase K for 5 hours at 60°C on a thermomixer with 900 rpm. DNA was purified using a Binding Buffer NTB and Nucleospin PCR Clean-up Kit from Macherey-Nagel.
library preparation was performed using NEBNext® Ultra II DNA Library Prep Kit for Illumina® (NEB) according to manufacturer instructions.

treatment_protocol: mouse ES cells were treated with LIF through day 0, after which LIF was withdrawn.

value: ES cells

tag: treatment

tag: timepoint

value: day 7


title: INPUT_S7KO-c22

description: Library name: INPUT_S7KO-c22


title: INPUT_S7KO-c22+S7WT

description: Library name: INPUT_S7KO-c22+S7WT


title: SIRT7-KO-c2

description: Library name: SIRT7-KO-c2


title: INPUT_S7HY-c5

description: Library name: INPUT_S7HY-c5


title: INPUT_S7KO-c9

description: Library name: INPUT_S7KO-c9


title: INPUT_H3K27me3_S7KO_ES_d7_Rep1


title: ChIP-H3K36Ac_S7KO-c22+S7WT

description: Library name: ChIP-H3K36Ac_S7KO-c22+S7WT


title: ChIP-H3K36Ac_S7KO-c22

description: Library name: ChIP-H3K36Ac_S7KO-c22


title: INPUT_S7HY-c7

description: Library name: INPUT_S7HY-c7


title: Input_S7WT_TTF_Rep1


title: ChIP-H3K36Ac_S7KO-c9

description: Library name: ChIP-H3K36Ac_S7KO-c9


title: ChIP_H3K27me3_S7WT_ES_d0_Rep1

value: LIF

value: day 0


title: ChIP-H3K36Ac_S7HY-c7

description: Library name: ChIP-H3K36Ac_S7HY-c7


title: Input_S7KO_TTF_Rep1


title: AC16 TPEN replicate 1

city: Hefei

first: Zhaoyuan

last: Wu

state: Anhui

address: Luyang District

department: Central Laboratory

country: China

institute: Wanbei Coal Electricity Group General Hospital

description: Library name: AC16_TPEN_1

data_processing:
Raw sequencing reads were quality filtered to remove adapter sequences and low-quality reads, then aligned to the human reference genome (GRCh38).
Assembly: GRCh38
Supplementary files format and content: Processed data files include gene-level expression matrices and differential expression analysis results. Specifically, a gene count matrix (XLS format) was generated for all samples and used for downstream analysis. Differentially expressed genes between Control and TPEN-treated groups were identified using DESeq2, and the corresponding annotated results are provided as Excel files. In addition, principal component analysis (PCA) and sample correlation matrices are included to illustrate global transcriptomic variation and sample-level relationships. All processed files are provided in XLS format.

molecule: total RNA

organism: Homo sapiens

growth_protocol: AC16 human cardiomyocytes were cultured in DMEM/F-12 medium supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin at 37 °C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. RNA quality was assessed by NanoDrop spectrophotometry, and samples with acceptable purity and integrity were used for library preparation.
RNA-seq libraries were prepared using a standard poly(A) enrichment protocol and sequenced on the BGISEQ-500 platform.

treatment_protocol: Cells were treated with the zinc chelator TPEN (6.25 μM) or vehicle control for 24 h prior to RNA extraction.

tag: cell line

value: cardiomyocyte


title: ChIP_H3K27me3_S7KO_ES_d0_Rep1


title: Input_S7WT_TTF_Rep2


title: AC16 TPEN replicate 3

description: Library name: AC16_TPEN_3


title: Input_S7KO_TTF_Rep1


title: ChIP_H3K27me3_S7WT_TTF_Rep2


title: ChIP_H3K27me3_S7KO_TTF_Rep2


title: ChIP_H3K27me3_S7KO_TTF_Rep1


title: adult zebrafish heart, injured, 1dpci #6

city: Berlin

first: Janita

last: Mintcheva

address: Robert-Rössle-Str. 10

country: Germany

institute: Max-Delbrück Center for Molecular Medicine

description:
Library name: Hr58
10X Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing and mapping was performed using CellRanger v4.0.0
Assembly: Danio rerio genome GRCz11, release 92 with RFP gene added
Supplementary files format and content: tab separates values filex and matrix files

organism: Danio rerio

source_name: heart

extract_protocol:
Zebrafish hearts were dissociated in HBSS supplemented with Pluronic-F68 and liberase (Roche). A detailed protocol can be found in the source publication.
Libraries were constructed following manufacturers instructions of the 10X Genomics 3' GEX NextGEM v3.1 protocol.

tag: tissue

value: heart

value: AB

value: cryoinjury


title: adult zebrafish heart, injured, 6hpci #5

description:
Library name: Hr54
10X Genomics


title: adult zebrafish heart, injured, 1dpci #4

description:
Library name: Hr56
10X Genomics


title: INPUT_H3K27me3_S7WT_ES_d0_Rep1


title: HSapiens_exp1_chip1_CRISPR

city: Planegg

first: Ines

last: Hellmann

address: Großhaderner Straße 2

institute: Ludwig-Maximilians-Universität München

description: Library name: HSapiens_exp1_chip1_CRISPR_lib

library_source: other

data_processing:
Per batch and library type, the experimental workflow yielded up to 128 FASTQ files due to the different combinations of 10x and flow cell lanes as well as the paired-end setup. All FASTQ data were processed using Cell Ranger (10x Genomics, v7.0.0). Reads of the GEX libraries were aligned to the hg38 and macFas6 reference genomes extended by the sequence of the dCas9 insert, while reads of the CRISPR libraries were aligned to a custom reference containig the gRNA protospacer sequences.
We demultiplexed the reads by species using cellsnp-lite (v1.2.2) and vireo (v0.2.3), based on a list of single nucleotide polymorphisms (SNPs) derived from bulk RNA-seq data of the wild-type cell lines.
We assigned perturbations to the cells based on the gRNA calls.  We only kept cells that contained a single dominant gRNA (i.e., all other detected gRNAs in the cell contributed <10% of gRNA UMIs and <1000 UMIs combined) and with >10 UMIs supporting the dominant gRNA. To generate the subset of data presented in this repository, we filtered the FASTQ files, count matrices, and gRNA calls to include only POU5F1-perturbed and control cells.
Assembly: GRCh38/hg38 GENCODE release 32 and Macaca fascicularis 6.0/macFas6 ENSEMBL release 105, both extended by the sequence of the dCas9 insert
Supplementary files format and content: Hierarchical data format 5 (h5)  files - filtered count matrices output by Cell Ranger
Supplementary files format and content: Comma-separated values (csv) files - gRNA calls per cell output by Cell Ranger

molecule: other

growth_protocol: For standard maintenance, iPSCs were grown in geltrex-coated 12-wells in StemFit Basic03. Medium was changed every other day.

extract_protocol:
To quantify mRNA and gRNAs of the cells, cells were dissociated to single cells using Accumax, washed and stored in PBS +0.04 % Bsa. Human and cynomolgus cells were pooled to equal cell numbers per cell line, then the single cell suspension was loaded on a 10x Genomics Chromium Controller for GEM generation. RT and cDNA amplification were conducted according to the manufacturer’s instructions (Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) with Feature Barcode technology for CRISPR Screening; USER GUIDE: CG000510 Rev B).
We performed three CRISPRi screens in total, using one 10x chip in the first two and three 10x chips in the third experiment (5 batches in total). Per 10x chip and lane, two libraries were generated: a gene expression library and a CRISPR library (identified as GEX and CRISPR lib in the sample names). For details see the manufacturer’s protocol.

treatment_protocol: To conduct single-cell CRISPRi screens, iPSCs were seeded as single-cells in geltrex-coated wells. Cells were transduced with lentiviral gRNA libraries (MOI 0.1). Transduced cells were selected with puromycin, then they were expanded for 5 days, while also inducing KRAB-dCas9 expression by adding doxycycline to the SF03 medium.

value: induced pluripotent stem cell

value: KRAB-dCas9-HA-P2A-mCherry insertion at AAVS1 locus

tag: library type

value: 10x Genomics 5' CRISPR Guide Capture


title: EE-RM2

city: Saitama

first: Shinji

last: Tsukahara

address: 255 Shimo-Okubo, Sakura-ku

department: Graduate School of Science and Engineering

country: Japan

institute: Saitama University

data_processing:
Data were processed by Cutadapt (V1.9.1) to remove technical sequences.
Hisat2 (v2.0.1) was used to index the reference genome sequence of Japanese quail (Coturnix japonica 2.1, GCF_001577835.2) and align clean data to the reference genome.
FPKM was calculated based on read counts from the HT-seq (v0.6.1).
Differential gene expression analysis was performed using DESeq2 (V1.6.3).
GOSeq (v1.34.1) and TopGO (v2.18.0) were used for GO enrichment analysis and drawing directed acyclic graphs, respectively.
Assembly: GCF_001577835.2
Supplementary files format and content: all.fpkm_anno.xlsx

organism: Coturnix japonica

source_name: Müllerian duct

extract_protocol:
Total RNA was extracted and purified from the Müllerian ducts using an RNeasy Plus Micro Kit (Qiagen) or an RNeasy Plus Mini Kit (Qiagen).
Poly(A) mRNA was isolated from the total RNA samples using oligo(dT) beads.

treatment_protocol: Embryos were cultured in a surrogate eggshell culture systme and treated with sesame oil (Oil) or ethynylestradiol (EE)-containing sesame oil during embryonic days 3–12.

value: Müllerian duct

tag: side

value: Right side

value: Ethynylestradiol (EE)


title: EE-RM1

value: Female


title: Input_S7WT_TTF_Rep1

value: TTF

value: C57BL6/CAST hybrid


title: INPUT_H3K27me3_S7KO_ES_d0_Rep1

value: ES cells


title: ChIP_H3K27me3_S7WT_ES_d7_Rep1

value: WT

value: day 7


title: OIL-RM2

value: Sesame oil (Oil)


title: AC16 Control replicate 3

description: Library name: AC16_Control_3

value: cardiomyocyte

value: control


title: AC16 TPEN replicate 2

description: Library name: AC16_TPEN_2


title: AC16 Control replicate 2

description: Library name: AC16_Control_2


title: ChIP_H3K27me3_S7KO_ES_d7_Rep1


title: AC16 Control replicate 1

description: Library name: AC16_Control_1


title: Ctehor, scRNAseq

city: Basel

first: Antoine

last: Fages

address: Vesalgasse 1

country: Switzerland

institute: University of Basel

data_processing:
Cell Ranger v5.0 software (10X Genomics)
Assembly: Oreochromis niloticus GCA_001858045.3, RefSeq assembly GCF_001858045.2
Supplementary files format and content: Tab-separated values and matrix files

organism: Shuja horei

source_name: intestine

extract_protocol:
Intestinal samples were flushed, chopped and dissociated at 25ºC for 20 minutes in pre-warmed DMEM/F-12 medium 1X (Fisher Scientific) supplemented with 1 mg / mL of dispase II (Sigma). Suspensions were centrifuged at 500 rcf for 7 minutes at 4ºC, resuspended in 10% Fetal Bovine Serum (FBS) in DMEM/F-12, filtered with a 20 µm cell strainer (CellTrics), centrifuged again with the same conditions, resuspended in 10% FBS in DMEM/F-12, and centrifuged one last time at low speed (200-250 rcf) for 5 minutes at 4ºC.
Following instructions from 10X Genomics Chromium Next GEM  Gene Expression 3' v3.1

value: intestine


title: Simdia, scRNAseq

organism: Simochromis diagramma


title: Batfer, scRNAseq

organism: Bathybates ferox


title: EE-LM3

value: Left side


title: EE-LM2


title: adult zebrafish heart, injured, 6hpci #6

description:
Library name: Hr55
10X Genomics

value: heart

value: AB

value: cryoinjury


title: Tromoo, scRNAseq

organism: Tropheus moorii


title: adult zebrafish heart, injured, 6hpci #4

description:
Library name: Hr53
10X Genomics


title: adult zebrafish heart, injured, 1dpci #5

description:
Library name: Hr57
10X Genomics


title: Benhor, scRNAseq

organism: Benthochromis horii


title: Lepelo, scRNAseq

organism: Lepidiolamprologus elongatus


title: EE-LM1

value: Müllerian duct


title: OIL-RM3

value: Right side


title: EE-RM3

value: Ethynylestradiol (EE)


title: OIL-RM1

value: Female


title: OIL-LM3


title: OIL-LM2


title: HSapiens_exp1_chip1_GEX

description: Library name: HSapiens_exp1_chip1_GEX_lib

value: induced pluripotent stem cell

value: KRAB-dCas9-HA-P2A-mCherry insertion at AAVS1 locus

value: 10x Genomics 5' Gene Expression


title: RNA_CP_dHPC_2

city: St. Louis

first: Gabor

last: Egervari

email: gabor@wustl.edu, egervarilab@gmail.com

state: MO

address: 4515 McKinley Ave, Couch Building

department: Genetics, Biochemistry and Molecular Biophysics

institute: Washington University School of Medicine

description: Library name: CP_dHPC_2

data_processing:
Base calling and demultiplexing: Base calls and demultiplexing were performed using Element Biosciences' bases2fastq software (CTX, dHPC; DSIL@CGSSB) or using Illumina's bcl2fastq software and a custom python demultiplexing program (vHPC, DS, VS; GTAC@MGI) allowing 1 mismatch in the indexing read.
Trimming: Adapters were trimmed from sequencing reads using Cutadapt 5.0 with parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -m 15
Alignment: Trimmed reads were aligned to the Mus musculus GRCm39 reference genome assembly using STAR v2.7.10a with parameters --runMode alignReads --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --quantMode TranscriptomeSAM GeneCounts
Quantification: Counts were generated using featureCounts v2.0.6 and Mus_musculus.GRCm39.113.gtf. Gene counts were quantified with parameters -t exon -g gene_id -s 2 -p -B -C -O -M ; Transcript isoform counts were quantified with parameters -t exon -g transcript_id -s 2 -p -B -C -O -M
Assembly: GRCm39 (NCBI RefSeq GCF_000001635.27)
Supplementary files format and content: gene_counts.csv contains gene counts ; transcript_counts.csv contains transcript isoform counts

source_name: dorsal hippocampus

growth_protocol: C57BL/6J male mice 8-10 weeks of age were housed on a 12h/12h light/dark cycle with food and water provided ad libitum.

extract_protocol:
Total RNA was extracted using TRIzol-chloroform and the RNeasy Mini Kit (Qiagen 74104) with on-column RNase-free DNase (Qiagen 79254) treatment according to manufacturer protocols. Total RNA quality was assessed using the High Sensitivity RNA ScreenTape Assay on a TapeStation 4200 system (Agilent 5067-5579, 5067-5580).
mRNA was isolated from total RNA using the NEBNext PolyA mRNA Magnetic Isolation Module (NEB E7490). Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB E7770) [CTX, dHPC] or the NEBNext Ultra II Directional RNA Library Prep Kit (NEB E7760) [vHPC, DS, VS] in coordination with compatible NEBNext Multiplex Oligos (NEB E7335, E7500, E7710 [CTX, dHPC]; NEB E6440 [vHPC, DS, VS]) and HighPrep PCR beads (MagBio AC-60050). Library quality was assessed using the DNA ScreenTape Assay on a TapeStation 4200 System (Agilent 5067-5602, 5067-5582). Libraries were quantified using the NEBNext Library Quant Kit (NEB E7630) on an Applied Biosystems QuantStudio 5 Real-Time PCR system, and the concentration of amplifiable templates in each library was calculated using the NEBioCalculator qPCR Library Quantification Web Tool. Libraries were then pooled in equal concentrations and submitted for sequencing.

treatment_protocol: Each mouse was administered a daily dose of 2 g/kg ethanol (20% ethanol in saline solution) or equivalent volume saline (vehicle control) via i.p. injection for 1 day (acute) or 10 days (chronic). Mice were sacrificed 4 hours after the final injection.

value: dorsal hippocampus

tag: paradigm

value: chronic

value: saline

tag: condition

value: chronic saline

tag: group

tag: mouse

value: male

tag: batch


title: OIL-LM1

value: Sesame oil (Oil)


title: Calple, scRNAseq

organism: Callochromis pleurospilus

value: intestine


title: Neobri, scRNAseq

organism: Neolamprologus brichardi


title: Cypcol, scRNAseq

organism: Cyprichromis coloratus


title: FLASH-seq Plate 2, 384 single cells

city: Lausanne

first: Felix

last: Naef

address: EPFL SV IBI

institute: EPFL

description:
Library name: Plate2
384 single-cell FLASH-seq libraries sorted by FACS (4 Nr1d1-Venus bins x 2 H2B-iRFP bins). See Metadata_all_samples.csv for per-cell annotations.

data_processing:
Raw paired-end reads were aligned per cell to a custom mouse reference genome (GRCm39, GENCODE vM38) augmented with YFP and iRFP reporter sequences using STAR v2.7.11a. BAM files were sorted by coordinate and indexed with SAMtools.
A combined exon/intron GTF annotation was constructed by extracting exonic intervals from GENCODE vM38 and deriving intronic intervals by subtracting exonic from gene body coordinates using BEDTools subtractBed.
Per-cell exon counts were quantified using htseq-count with -t exon -m intersection-strict
Assembly: GRCm39 (mm39)
Supplementary files format and content: Tab-separated count matrices with genes as rows and cells as columns.

growth_protocol: NIH3T3-Rev-VNP1-H2B-iRFP fibroblasts were cultured in DMEM high glucose with sodium pyruvate (Gibco, 41966-029) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37C, 5% CO2. Cells were grown to 95% confluency (approximately 5 days post-seeding) without synchronization.

extract_protocol:
Cells were trypsinized, washed with PBS, resuspended in FACS buffer (PBS, 0.5% BSA, 2-5 mM EDTA) at 1e6 cells/mL, and filtered through a 40 um mesh. DAPI was added to exclude dead cells. Single cells were sorted on a FACS S8 Discovery system into 384-well plates containing lysis buffer using a binned strategy (4 bins on Nr1d1-Venus, 2 bins on H2B-iRFP). RNA was denatured at 72C prior to reverse transcription.
Full-length scRNA-seq libraries were generated using Mercurius FLASH-seq kits (Alithea Genomics). cDNA was amplified by PCR (21 cycles), quantified using PicoGreen dsDNA Assay (Thermo Fisher), diluted to 200 pg/uL, and tagmented. Sequencing adapters were added via secondary PCR (8 cycles). Libraries were sequenced on an Element AVITI system (Element Biosciences, CloudBreak) with paired-end 75 bp reads.

tag: plate


title: RNA_CP_CTX_6

description: Library name: CP_CTX_6

source_name: cortex

value: cortex

tag: Sex


title: FLASH-seq Plate 1, 384 single cells

description:
Library name: Plate1
384 single-cell FLASH-seq libraries sorted by FACS (4 Nr1d1-Venus bins x 2 H2B-iRFP bins). See Metadata_all_samples.csv for per-cell annotations.

tag: cell type


title: RNA_CE_dHPC_1

description: Library name: CE_dHPC_1

value: ethanol

value: chronic ethanol

tag: strain


title: RNA_CE_dHPC_6

description: Library name: CE_dHPC_6


title: RNA_CP_dHPC_5

description: Library name: CP_dHPC_5


title: RNA_CE_dHPC_4

description: Library name: CE_dHPC_4


title: RNA_CP_dHPC_6

description: Library name: CP_dHPC_6


title: RNA_AE_dHPC_3

description: Library name: AE_dHPC_3

value: acute

value: acute ethanol


title: RNA_AE_dHPC_2

description: Library name: AE_dHPC_2


title: RNA_AP_CTX_6

description: Library name: AP_CTX_6

value: acute saline


title: RNA_AP_CTX_2

description: Library name: AP_CTX_2


title: Dectin1_9mo_NeuN_Olig2_sorted_2

city: Saint Louis

first: Khai

last: Nguyen

address: 425 South Euclid Ave, 8107, 8th floor BJCIH,

department: Pathology & Immunology

institute: Washington University in St. Louis

description: Library name: Sample18

data_processing:
Raw sequencing data was processed using CellRanger v8 or v9
Assembly: GRChm39 with Clec7a recombinant sequence added
Supplementary files format and content: cell x gene matrix, h5ad file

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Brains from perfused mice were harvested and flash frozen. Nuclei were isolated from 4-5 randomly selected brains. NeuN- or NeuN- Olig2- nuclei were isolated by FACS.
Library was prepared using 10X Chromium Single-Cell 3' v3 and v4 kit (NeuN- samples) or 10X Chromium Single-Cell 5' v2 kit (NeuN- Olig2- samples) according to manufacturer instructions.

value: Brain

value: NeuN- Olig2- sorted nuclei

tag: genotype

tag: age


title: RNA_CE_CTX_6

description: Library name: CE_CTX_6

tag: treatment


title: Dectin1_9mo_NeuN_Olig2_sorted_1

description: Library name: Sample17


title: RNA_CE_CTX_5

description: Library name: CE_CTX_5


title: Megf10_9mo_NeuN_Olig2_sorted_2

description: Library name: Sample16


title: RNA_CE_CTX_1

description: Library name: CE_CTX_1


title: Megf10_9mo_NeuN_Olig2_sorted_1

description: Library name: Sample15


title: RNA_CP_CTX_3

description: Library name: CP_CTX_3


title: RNA_CP_CTX_5

description: Library name: CP_CTX_5


title: GFP_9mo_NeuN_Olig2_sorted_2

description: Library name: Sample14


title: Dectin1_5mo_NeuN_Olig2_sorted_2

description: Library name: Sample12


title: RNA_AP_CTX_4

description: Library name: AP_CTX_4


title: GFP_5mo_NeuN_Olig2_sorted_2

description: Library name: Sample8


title: GFP_9mo_NeuN_Olig2_sorted_1

description: Library name: Sample13


title: GFP_5mo_NeuN_Olig2_sorted_1

description: Library name: Sample7


title: RNA_AE_dHPC_4

description: Library name: AE_dHPC_4


title: Sorted mCAT MdMs CD45.2 CCR2creERT2/+ mcat lsl/wt donor_6

city: Zürich

first: Juan

last: Villar Vesga

address: Winterthurerstrasse 190

institute: University of Zurich

description:
Library name: sample12
C2_2_B_S3

data_processing:
Raw sequencing reads were quality controlled using FastQC.
Adapter sequences and low-quality bases were trimmed using fastp.
Trimmed reads were pseudo-aligned to the mouse reference transcriptome (GRCm39, Ensembl release 111) using Salmon with selective alignment and decoy-aware indexing.
Transcript-level abundances were imported into R for downstream analysis.
Assembly: GRCm39 (Mouse reference genome, Ensembl release 111)
Supplementary files format and content: CSV file with gene-level expression matrix. Rows correspond to genes (Ensembl_ID and Gene_Symbol), and columns correspond to individual samples. Expression values are normalized and log-transformed counts derived from RNA-seq analysis.

source_name: CNS

growth_protocol: Bone marrow (BM) mixed chimeras were generated by lethally irradiating host mice with a split dose (2 × 5.5 Gy, 24 h interval), followed by intravenous injection of 5 × 10^6 donor BM cells via tail vein. For 50:50 mixed chimeras, 2.5 × 10^6 BM cells from each genotype (wt CD45.1 and mCAT CD45.2) were used.

extract_protocol:
Total RNA was extracted from sorted wt (CD45.1) and mCAT (CD45.2) MdMs using the Qiagen RNeasy Micro Kit according to the manufacturer’s instructions.
RNA-seq libraries were prepared using the Smart-seq2 protocol.
Sequencing was performed as paired-end 150 bp reads on an Illumina NovaSeq X Plus platform, generating approximately 500 million reads per data package

treatment_protocol: No in vitro treatment was applied. Monocyte-derived macrophages (MdMs) were obtained from BM mixed chimeras and sorted based on genotype (wt CD45.1 and mCAT CD45.2) for downstream transcriptomic analysis.

value: CNS

value: MdMs

value: Tamoxifen


title: Sorted wt MdMs CD45.1 donor_6

description:
Library name: sample11
C2_2_A_S7


title: Sorted mCAT MdMs CD45.2 CCR2creERT2/+ mcat lsl/wt donor_5

description:
Library name: sample10
C2_1_B_S10


title: Sorted wt MdMs CD45.1 donor_4

description:
Library name: sample7
C1_5_A_S13


title: Sorted mCAT MdMs CD45.2 CCR2creERT2/+ mcat lsl/wt donor_4

description:
Library name: sample8
C1_5_B_S14


title: Dectin1_5mo_NeuN_Olig2_sorted_1

description: Library name: Sample11


title: ChIP, TBP, SSRP1-FKBP-E14, DMSO

city: Oxford

first: Catherine

last: Chahrour

address: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Library name: chip-e14-ssrp1-fkbp-dmso_tbp
bigWig file

data_processing:
Data was processed using SeqNado (https://github.com/alsmith151/SeqNado). In short, reads where trimmed using trim_galore with Cutadapt (v0.6.10), mapped with Bowtie2 (v2.5.1), PCR duplicates were removed with picard MarkDuplicates (v3.0.0), problematic genomic regions in the ENCODE Blacklist were discarded, bigWig files were generated with deepTools (v3.5.1) and scaled according to spike-in reads.
Assembly: mm39
Supplementary files format and content: bigWigs

source_name: Embryo

growth_protocol: Mouse embryonic stem cells (E14 Tg2a IV) were maintained in 0.1% gelatin (Sigma G1890) coated flasks in Glasgow MEM x1 media (Gibco 21710-025) complemented with 10% FCS (Gibco 10270-106), 1x GlutaMAX (Gibco 35050-061), 1 mM sodium pyruvate (Gibco 11360-039), 1x non-essential amino acids (Gibco 11140-035), mercaptoethanol (Gibco 31350-010) and LIF (Cambridge Bioscience Ltd GFM200). The cells were grown in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
2.5M cells were fixed with 1% FA and 2mM DSG for 1h. Fixed cells were lysed with an SDS lysis buffer (1% SDS, 10 mM Tris-HCl pH 8.0, 1 mM EDTA) and via passage through a 27G needle. Samples were sonicated (Covaris ME220) aiming for 200–300 bp fragments. Sonicated chromatin from Drosphila (S2 fixed cells) was spiked in a ratio of 4:1 (mouse:dros) To reduce non-specific binding, samples were pre-cleared with Protein A and G-coupled dynabeads (1:1). Five percent of the sample was separated as an input, and the rest was incubated with the corresponding antibody overnight. Antibody-chromatin complexes were isolated with Protein A- and G-coupled dynabeads, washed with RIPA (3 washes), Tris-EDTA (1 wash) and eluted with SDS lysis buffer. Samples were treated with RNase, Proteinase K and kept at 65C overnight to reverse crosslinks. DNA was then purified with the Monarch PCR & DNA Cleanup Kit (T1030)
The protoocol for NEBNext Ultra II library prep kit (E7645) was followed as indicated by the manufacturer.

value: Embryo

value: E14 Tg2a IV

tag: spike-in cell_line

value: S2 sg4

value: mouse embryonic stem cells

value: DMSO

tag: antibody

value: TBP


title: RNA_AE_CTX_2

description: Library name: AE_CTX_2

tag: tissue

value: cortex

value: male


title: Sorted wt MdMs CD45.1 donor_2

description:
Library name: sample2
C1_2_A_S5


title: RNA_AP_dHPC_2

description: Library name: AP_dHPC_2

value: dorsal hippocampus

value: saline


title: ChIP, input, SSRP1-FKBP-E14, dTAG-13 3h

description:
Library name: chip-e14-ssrp1-fkbp-dtag3h_Input
bigWig file

tag: cell line


title: RNA_AE_CTX_4

description: Library name: AE_CTX_4

value: acute

value: ethanol

value: acute ethanol


title: ChIP, TBP, SSRP1-FKBP-E14, dTAG-13 3h

description:
Library name: chip-e14-ssrp1-fkbp-dtag3h_tbp
bigWig file


title: RNA_AP_dHPC_5

description: Library name: AP_dHPC_5

value: acute saline


title: RNA_AE_CTX_5

description: Library name: AE_CTX_5


title: RNA_AP_dHPC_4

description: Library name: AP_dHPC_4


title: Sorted wt MdMs CD45.1 donor

description:
Library name: sample1
C1_1_A_S9

value: CNS


title: RNA_AE_dHPC_5

description: Library name: AE_dHPC_5


title: ChIP-H2AX_S7KO-c9

description: Library name: ChIP-H2AX_S7KO-c9

data_processing:
Raw read quality was first assessed with FastQC (version 0.11.3), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm10) reference genome with Bowtie2 (version 2.2.9) with options --n 2 --k 10 and converted to BAM format with SAMtools (version 0.1.19).
SNPsplit (version 0.3.4) was used to sort aligned reads into three categories based on informative SNPs using the command `SNPsplit`: A) reads from mus musculus [genome1]; B) reads from mus Castaneus [genome2]; or C) unassignable reads [unassigned]. The resulting BAM files were then sorted by position and indexed using samtools (version 0.1.19).
BigWig ChIP signal files were generated from BAM data using deepTools (version 2.4.2) using a bin size of 50 bp, scaled with SES, and normalized by INPUT.
Peak calling was performed using MACS (version 2.2.7.1) by providing ChIP as --treatment and matched Input as --control. Peak calling was performed in --broad mode with --broad-cutoff 0.1 --qvalue 0.1 --scale-to small.
Assembly: mm10
Supplementary files format and content: broadPeak files contain peaks as called by macs

extract_protocol:
cells were crosslinked with 1% formaldehyde for 10 min at room temperature and then quenched with 0.2 M glycine for 5 min and washed once with cold PBS. Nuclei were resuspended in 300 μl Lysis buffer 2 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0, and cOmplete protease inhibitors) and incubated on ice for 30 min. Chromatin was sonicated to an average fragment size range of 300-500bp and subsequently centrifugated at 12,000 x g at 4°C for 15 min. Supernatants were diluted with Dilution Buffer (1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl, and cOmplete protease inhibitors). ChIP-grade protein A/G magnetic beads (Pierce, 26162) were conjugated for at least 3 hours in 1X PBS and 0.05% NP-40 with anti-H2A.X antibody (ab20669, Abcam), or anti-ɣH2AX (Sigma, 05-636-I). Chromatin samples and antibody-conjugated magnetic beads were incubated overnight at 4°C on a rotator. Magnetic beads were then washed 3 times with ice-cold RIPA buffer (1% NP-40, 0.7% Na-deoxycholate, 50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 M LiCl2, and complete protease inhibitors) and once with Buffer TE (0.1 mM EDTA, 10 mM Tris-HCl pH 8.0). Magnetic beads and input samples (1% of total chromatin) were resuspended in freshly prepared RC buffer (0.1 M NaHCO3 and 1% SDS) in the presence of proteinase K for 5 hours at 60°C on a thermomixer with 900 rpm. DNA was purified using a Binding Buffer NTB and Nucleospin PCR Clean-up Kit from Macherey-Nagel.
library preparation was performed using NEBNext® Ultra II DNA Library Prep Kit for Illumina® (NEB) according to manufacturer instructions.

treatment_protocol: Cells were treated with 5Gy of Xrays and allowed to recover for 30 minutes

tag: chip antibody

value: Female

value: TTF

value: C57BL6/CAST hybrid

value: 5Gy XRAY


title: ChIP-H2AX_S7KO-c22+S7WT

description: Library name: ChIP-H2AX_S7KO-c22+S7WT

value: SIRT7-KO + SIRT7-WT


title: ChIP, input, SSRP1-FKBP-E14, DMSO

description:
Library name: chip-e14-ssrp1-fkbp-dmso_Input
bigWig file

value: Embryo

value: E14 Tg2a IV

value: S2 sg4

value: mouse embryonic stem cells


title: ChIP-H2AX_S7KO-c22

description: Library name: ChIP-H2AX_S7KO-c22


title: Megf10_5mo_NeuN_Olig2_sorted_2

description: Library name: Sample10

value: Brain

value: NeuN- Olig2- sorted nuclei


title: Megf10_5mo_NeuN_Olig2_sorted_1

description: Library name: Sample9


title: Sorted mCAT MdMs CD45.2 CCR2creERT2/+ mcat lsl/wt donor_7

description:
Library name: sample14
C2_4_B_S8

value: MdMs

value: Tamoxifen


title: Sorted wt MdMs CD45.1 donor_7

description:
Library name: sample13
C2_4_A_S4


title: Sorted wt MdMs CD45.1 donor_5

description:
Library name: sample9
C2_1_A_S6


title: Sorted mCAT MdMs CD45.2 CCR2creERT2/+ mcat lsl/wt donor_1

description:
Library name: sample3
C1_2_B_S2


title: Sorted wt MdMs CD45.1 donor_3

description:
Library name: sample4
C1_3_A_S12


title: ChIP-H2AX_S7HY-c5

description: Library name: ChIP-H2AX_S7HY-c5


title: ChIP-gH2AX_S7KO-c22+S7WT

description: Library name: ChIP-gH2AX_S7KO-c22+S7WT


title: Sorted mCAT MdMs CD45.2 CCR2creERT2/+ mcat lsl/wt donor_3

description:
Library name: sample6
C1_4_B_S15


title: ChIP-H2AX_S7KO-c9+S7WT

description: Library name: ChIP-H2AX_S7KO-c9+S7WT


title: ChIP-gH2AX_S7HY-c7

description: Library name: ChIP-gH2AX_S7HY-c7


title: ChIP-gH2AX_S7KO-c9

description: Library name: ChIP-gH2AX_S7KO-c9


title: CAT, SSRP1-FKBP-E14, dTAG3h, TBP, clone13

description: Library name: SSRP1-FKBP-E14-dTAG3h-13_TBP

data_processing:
Data was processed using SeqNado (https://github.com/alsmith151/SeqNado). In short, reads where trimmed using trim_galore with Cutadapt (v0.6.10), mapped with Bowtie2 (v2.5.1), PCR duplicates were removed with picard MarkDuplicates (v3.0.0), problematic genomic regions in the ENCODE Blacklist were discarded, bigWig files were generated with deepTools (v3.5.1) using RPKM for normalization.
Assembly: mm39
Supplementary files format and content: bigWigs
Library strategy: CUT&Tag

extract_protocol:
Nuclei from 20,000M mESC and 6,000 S2 cells were extracted and lighlty fixed wit 0.1% FA. Nuclei were incubated with 5uL of activated ConA beads, 0.5uL primary Ab and 1:100 secondary Ab. Chromatin was then tagemented with 1:20 pAG-Tn5. Nuclei were washed to remove unbound pAG-Tn5  and then lysed with 5 μl SDS-ProK Buffer (1% SDS, 10 mM TAPS pH 8.5, Thermolabile Proteinase K).15uL 6% Triton was used to neutralise SDS.
The tagmented DNA was amplified with NEBNext Ultra II Q5 Master Mix (M0544) and Nextera indexed primers. DNA was cleaned up with AMPure XP beads.

value: dTAG-13 3h


title: CAT, SSRP1-FKBP-E14, dTAG3h, noprimary, clone36

description: Library name: SSRP1-FKBP-E14-dTAG3h-36_noprimary


title: ChIP-H2AX_S7HY-c7

description: Library name: ChIP-H2AX_S7HY-c7


title: Sorted mCAT MdMs CD45.2 CCR2creERT2/+ mcat lsl/wt donor_2

description:
Library name: sample5
C1_3_B_S11


title: CAT, SSRP1-FKBP-E14, dTAG3h, KDM2B, clone13

description: Library name: SSRP1-FKBP-E14-dTAG3h-13_KDM2B


title: CAT, SSRP1-FKBP-E14, dTAG3h, CBP, clone13

description: Library name: SSRP1-FKBP-E14-dTAG3h-13_CBP


title: CAT, SSRP1-FKBP-E14, dTAG3h, P300, clone36

description: Library name: SSRP1-FKBP-E14-dTAG3h-36_P300


title: CAT, SSRP1-FKBP-E14, dTAG3h, RING1B, clone1

description: Library name: SSRP1-FKBP-E14-dTAG3h-1_RINGB


title: CAT, SSRP1-FKBP-E14, dTAG3h, KDM2B, clone36

description: Library name: SSRP1-FKBP-E14-dTAG3h-36_KDM2B


title: CAT, SSRP1-FKBP-E14, dTAG3h, noprimary, clone1

description: Library name: SSRP1-FKBP-E14-dTAG3h-1_noprimary


title: CAT, SSRP1-FKBP-E14, dTAG3h, KDM2B, clone1

description: Library name: SSRP1-FKBP-E14-dTAG3h-1_KDM2B


title: CAT, SSRP1-FKBP-E14, dTAG3h, RING1B, clone13

description: Library name: SSRP1-FKBP-E14-dTAG3h-13_RINGB


title: CAT, SSRP1-FKBP-E14, dTAG3h, CBP, clone36

description: Library name: SSRP1-FKBP-E14-dTAG3h-36_CBP


title: CAT, SSRP1-FKBP-E14, dTAG3h, RING1B, clone36

description: Library name: SSRP1-FKBP-E14-dTAG3h-36_RINGB


title: CAT, SSRP1-FKBP-E14, DMSO, RING1B, clone36

description: Library name: SSRP1-FKBP-E14-DMSO-36_RINGB

value: DMSO


title: ChIP-gH2AX_S7HY-c5

description: Library name: ChIP-gH2AX_S7HY-c5


title: CAT, SSRP1-FKBP-E14, DMSO, TBP, clone36

description: Library name: SSRP1-FKBP-E14-DMSO-36_TBP


title: CAT, SSRP1-FKBP-E14, DMSO, noprimary, clone36

description: Library name: SSRP1-FKBP-E14-DMSO-36_noprimary


title: CAT, SSRP1-FKBP-E14, dTAG3h, noprimary, clone13

description: Library name: SSRP1-FKBP-E14-dTAG3h-13_noprimary


title: CAT, SSRP1-FKBP-E14, DMSO, CBP, clone36

description: Library name: SSRP1-FKBP-E14-DMSO-36_CBP


title: CAT, SSRP1-FKBP-E14, dTAG3h, TBP, clone1

description: Library name: SSRP1-FKBP-E14-dTAG3h-1_TBP


title: CAT, SSRP1-FKBP-E14, DMSO, RING1B, clone13

description: Library name: SSRP1-FKBP-E14-DMSO-13_RINGB


title: CAT, SSRP1-FKBP-E14, DMSO, TBP, clone13

description: Library name: SSRP1-FKBP-E14-DMSO-13_TBP


title: CAT, SSRP1-FKBP-E14, DMSO, noprimary, clone13

description: Library name: SSRP1-FKBP-E14-DMSO-13_noprimary


title: CAT, SSRP1-FKBP-E14, DMSO, P300, clone13

description: Library name: SSRP1-FKBP-E14-DMSO-13_P300


title: CAT, SSRP1-FKBP-E14, DMSO, KDM2B, clone13

description: Library name: SSRP1-FKBP-E14-DMSO-13_KDM2B


title: CAT, SSRP1-FKBP-E14, DMSO, TBP, clone1

description: Library name: SSRP1-FKBP-E14-DMSO-1_TBP


title: CAT, SSRP1-FKBP-E14, dTAG3h, CBP, clone1

description: Library name: SSRP1-FKBP-E14-dTAG3h-1_CBP


title: CAT, SSRP1-FKBP-E14, DMSO, CBP, clone13

description: Library name: SSRP1-FKBP-E14-DMSO-13_CBP


title: CAT, SSRP1-FKBP-E14, DMSO, RING1B, clone1

description: Library name: SSRP1-FKBP-E14-DMSO-1_RINGB


title: CAT, SSRP1-FKBP-E14, DMSO, P300, clone1

description: Library name: SSRP1-FKBP-E14-DMSO-1_P300


title: CAT, SSRP1-FKBP-E14, DMSO, KDM2B, clone1

description: Library name: SSRP1-FKBP-E14-DMSO-1_KDM2B


title: CAT, SSRP1-FKBP-E14, DMSO, CBP, clone1

description: Library name: SSRP1-FKBP-E14-DMSO-1_CBP


title: Panel1_CW20047D-2_i

type: RNA

city: Singapore

first: Jinyue

last: Liu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing:
Cell nuclei were segmented using a deep-learning method based on image-style transfer with some modifications. Each RNA spot located within a segmented nucleus was directly assigned to this segmented nucleus. Each RNA spot located within 2.2um of any segmented nucleus was assigned to the nearest segmented nucleus. We used a binary search algorithm to find its nearest segmented nucleus over different radius lengths from 0 to 2.2um.
MERFISH cells in panel 1 were filtered by the following criteria: cells (1) smaller than value at half-peak of area distribution, (2) above 99.9th quantile of area distribution, (3) with 10 counts or less, (4) with blank fraction greater than 0.1, (5) with area-normalized counts above 98%, (6) with fewer than 10 genes and (7) with 70% or more counts from smFISH, were discarded. Genes present in less than 1% of all cells in each diagnosis were discarded.
Counts were normalized using SCTransform using Seurat v4.0
Non-forebrain and necrotic zones were identified BANKSY at lambda = 0.75, k_geometric = 10 and n.neighbors
MERFISH cells in panel 2-4 were filtered by the following criteria: cells (1) smaller than value at half-peak of area distribution, (2) above 99.9th quantile of area distribution, (3) with 3 counts or less, (4) with blank fraction greater than 0.1, (5) with area-normalized counts above 98%.
genome build: hG38
processed data files format and content: csv files containing preprocessed RNA counts for each cell per MERFISH dataset (csv gene-cell matrix), (csv cell location); h5 (raw count)

source_name: 8-week forebrain organoid

growth_protocol: On Day 0, hiPSC colonies were lifted using Collagenase type IV and transferred onto ultra-low attachment six-well plates containing DMEM/F12, 20% KOSR, 1x GlutaMAX, 1x MEM-NEAA, 0.1mM 2-Mercaptoethanol, 1x Penicillin/Streptomycin, 2µM Dorsomorphin, 2µM A-83. On Day 5 and 6, 50% medium was replaced with DMEM/F12, 1x N2 supplement, 1x GlutaMAX, 1x MEM-NEAA, 1x Penicillin/Streptomycin, 1µM CHIR-99021, 1µM SB-431542. On Day 7, organoids were embedded in growth factor reduced (GFR)-Matrigel. On Day 14, organoids were mechanically dissociated from GFR-Matrigel and cultured with shaking in DMEM/F12, 1x N2 supplement, 1x B27 supplement, 1x GlutaMAX, 1x MEM-NEAA, 1x Penicillin/Streptomycin, 0.1mM 2-Mercaptoethanol, 2.5µg/ml Insulin. Medium was supplemented with 0.5% (v/v) GFR-Matrigel from Day 35 onwards.

extract_protocol:
8-week old fresh organoids were OCT-embedded and cryosectioned at 8-10µm thickness onto glass coverslips functionalized with 2% vol/vol (3-aminopropyl) triethoxysilane/acetone. Sections were fixed in 4% PFA/PBS for 15 minutes, permeabilized with 0.1% Triton X-100/PBS and preincubated with hybridization buffer. Sections were then incubated with encoding probe library at 37oC overnight in humidified chambers. Probe concentration was optimized for each MERFISH panel library. The next day, sections were incubated with DAPI (1:1000) and 0.1µm TetraSpeck fluorescent microspheres (1:1000, Invitrogen, T7279), rinsed with 2x SSC and kept cold till imaging.
A Modified Hamming Distance 4 encoding scheme was adopted for MERFISH probe design. 30-nucleotide long target regions were identified using a previously published algorithm, with GRCh38 as reference, a specificity cut-off of 0.5 and isospecificity cut-off of 0.4. Three readout sequences per encoding probe were used; they were either 20-nucleotide long as published in Moffitt et al. , or 30-nucleotide long as published in Chen et al. . smFISH genes were similarly detected, except that all encoding probes for the same gene carried the same readout sequence to allow spot detection in a single hybridization channel. Encoding probe libraries prepared as previously described (34). Encoding probes were synthesized as an oligonucleotide pool (CustomArray) and PCR-amplified (Phusion Hot Start Flex 2x Master Mix M0536L): 98oC, 30secs; 98oC, 5 secs, 72oC, 15secs, 72oC, 18secs for 22 cycles; 98oC, 5mins. PCR products were then purified and concentrated before in vitro transcription (HiScribe T7 Quick High Yield RNA Synthesis Kit E2050) and reverse transcription (Maxima H Minus Reverse Transcriptase EP0752). RNA templates were removed by alkaline hydrolysis with 1M NaOH and 0.5M EDTA at 95oC, 10 minutes. Probes were purified and eluted in nuclease-free water, evaporated in a vacuum concentrator and resuspended in hybridization buffer to 1mM. Readout probes were ordered from IDT.

tag: gender

value: M

tag: diagnosis

value: control


title: CAT, SSRP1-FKBP-E14, DMSO, KDM2B, clone36

description: Library name: SSRP1-FKBP-E14-DMSO-36_KDM2B


title: CAT, SSRP1-FKBP-E14, DMSO, noprimary, clone1

description: Library name: SSRP1-FKBP-E14-DMSO-1_noprimary


title: CAT, SSRP1-FKBP-E14, dTAG3h, P300, clone1

description: Library name: SSRP1-FKBP-E14-dTAG3h-1_P300


title: ChIP, H3, SSRP1-FKBP-E14, dTAG-13 3h, clone36

description:
Library name: cl-36-dTAG-3h_H3
bigWig file

extract_protocol:
2.5M cells were fixed with 1% FA for 10min. Fixed cells were lysed with an SDS lysis buffer (1% SDS, 10 mM Tris-HCl pH 8.0, 1 mM EDTA) and via passage through a 27G needle. Samples were sonicated (Covaris ME220) aiming for 200–300 bp fragments. Sonicated chromatin from Drosphila (S2 fixed cells) was spiked in a ratio of 4:1 (mouse:dros) To reduce non-specific binding, samples were pre-cleared with Protein A and G-coupled dynabeads (1:1). Five percent of the sample was separated as an input, and the rest was incubated with the corresponding antibody overnight. Antibody-chromatin complexes were isolated with Protein A- and G-coupled dynabeads, washed with RIPA (3 washes), Tris-EDTA (1 wash) and eluted with SDS lysis buffer. Samples were treated with RNase, Proteinase K and kept at 65C overnight to reverse crosslinks. DNA was then purified with the Monarch PCR & DNA Cleanup Kit (T1030)
The protoocol for NEBNext Ultra II library prep kit (E7645) was followed as indicated by the manufacturer.


title: ChIP, input,  SSRP1-FKBP-E14, dTAG-13 3h, clone36

description:
Library name: cl-36-dTAG-3h_input
bigWig file


title: Panel1_CW60171E-2_ii

value: case


title: ChIP, H3, SSRP1-FKBP-E14, DMSO, clone36

description:
Library name: cl-36-dmso_H3
bigWig file


title: Panel1_CW20324C-1_ii

data_processing:
Cell nuclei in panel 1 were segmented using a deep learning segmentation pipeline, Cellpose 2. We dilated our segmented nucleus by 2.2um using Euclidean distance transform method to obtain cell mask. For remaining RNA spots, each RNA spot, located inside a segmented cell, was directly assigned to this segmented cell mask.
MERFISH cells in panel 1 were filtered by the following criteria: cells  (1) smaller than value at half-peak of nuclei area distribution for all datasets combined, (2) above 99.9th quantile of nuclei area distribution for all datasets combined, (3) with 10 counts or less per cell, (4) with blank fraction per cell ( blank counts per cell divided by total spots counts per cell) greater than 0.1, (5) with fewer than 10 genes and (vi) with 70% or more counts from smFISH, were discarded.
Counts were normalized using SCTransform using Seurat v4.0
Non-forebrain and necrotic zones were identified BANKSY at lambda = 0.75, k_geometric = 10 and n.neighbors
Cell nuclei in panel 2-4  were segmented using a deep-learning method based on image-style transfer with some modifications. Each RNA spot located within a segmented nucleus was directly assigned to this segmented nucleus. Each RNA spot located within 2.2um of any segmented nucleus was assigned to the nearest segmented nucleus. We used a binary search algorithm to find its nearest segmented nucleus over different radius lengths from 0 to 2.2um.
MERFISH cells in panel 2-4 were filtered by the following criteria: cells (1) smaller than value at half-peak of nuclei area distribution for all datasets combined, (2) above 99.9th quantile of nuclei area distribution for all datasets combined, (3) with 3 counts or less, (4) with blank fraction per cell ( blank counts per cell divided by total spots counts per cell) greater than 0.1, (5) with area-normalized counts above 98%.
Assembly: hG38
Supplementary files format and content: csv files containing preprocessed RNA counts for each cell per MERFISH dataset


title: Panel1_CW60172A-1_i


title: ChIP, H2B, SSRP1-FKBP-E14, dTAG-13 3h, clone36

description:
Library name: cl-36-dTAG-3h_H2B
bigWig file


title: ChIP, H3K27AC, SSRP1-FKBP-E14, DMSO, clone36

description:
Library name: cl-36-dmso_H3K27ac
bigWig file


title: ChIP, H3K27AC, SSRP1-FKBP-E14, dTAG-13 3h, clone36

description:
Library name: cl-36-dTAG-3h_H3K27ac
bigWig file


title: CAT, SSRP1-FKBP-E14, DMSO, P300, clone36

description: Library name: SSRP1-FKBP-E14-DMSO-36_P300


title: Panel1_CW60109C-2_i


title: ChIP, input,  SSRP1-FKBP-E14, DMSO, clone36

description:
Library name: cl-36-dmso_input
bigWig file


title: Panel1_CW60245L-1_i

value: F


title: ChIP, H2B, SSRP1-FKBP-E14, DMSO, clone36

description:
Library name: cl-36-dmso_H2B
bigWig file


title: Panel1_CW20002A-1_i


title: ChIP, H2A, SSRP1-FKBP-E14, DMSO, clone36

description:
Library name: cl-36-dmso_H2A
bigWig file


title: ChIP, input,  SSRP1-FKBP-E14, dTAG-13 3h, clone13

description:
Library name: cl-13-dTAG-3h_input
bigWig file


title: ChIP, H2A, SSRP1-FKBP-E14, dTAG-13 3h, clone36

description:
Library name: cl-36-dTAG-3h_H2A
bigWig file


title: Panel1_CW20041A-1_i


title: Panel1_CW60171E-2_i


title: Panel1_CW60109C-1_i


title: Panel1_CW60134F-1_i


title: ChIP, H2B, SSRP1-FKBP-E14, dTAG-13 3h, clone13

description:
Library name: cl-13-dTAG-3h_H2B
bigWig file


title: CAT, SSRP1-FKBP-E14, dTAG3h, TBP, clone36

description: Library name: SSRP1-FKBP-E14-dTAG3h-36_TBP


title: ChIP-gH2AX_S7KO-c9+S7WT

description: Library name: ChIP-gH2AX_S7KO-c9+S7WT

value: Female

value: TTF

value: C57BL6/CAST hybrid


title: ChIP-gH2AX_S7KO-c22

description: Library name: ChIP-gH2AX_S7KO-c22

value: 5Gy XRAY


title: Panel1_CW20324C-1_i


title: Panel1_CW60108A-1_i


title: Panel1_CW60171E-1_i


title: Panel1_CW60228D-1_i


title: ChIP, H3K27AC, SSRP1-FKBP-E14, dTAG-13 3h, clone13

description:
Library name: cl-13-dTAG-3h_H3K27ac
bigWig file

value: Embryo

value: E14 Tg2a IV


title: ChIP, input,  SSRP1-FKBP-E14, DMSO, clone13

description:
Library name: cl-13-dmso_input
bigWig file

value: S2 sg4

value: mouse embryonic stem cells


title: Panel1_CW20320C-1_i


title: CAT, SSRP1-FKBP-E14, dTAG3h, P300, clone13

description: Library name: SSRP1-FKBP-E14-dTAG3h-13_P300


title: ChIP, H2B, SSRP1-FKBP-E14, DMSO, clone13

description:
Library name: cl-13-dmso_H2B
bigWig file


title: ChIP, H3, SSRP1-FKBP-E14, dTAG-13 3h, clone1

description:
Library name: cl-1-dTAG-3h_H3
bigWig file


title: Panel1_CW60218E-3_i


title: ChIP, H3K27AC, SSRP1-FKBP-E14, dTAG-13 3h, clone1

description:
Library name: cl-1-dTAG-3h_H3K27ac
bigWig file


title: ChIP, H3, SSRP1-FKBP-E14, dTAG-13 3h, clone13

description:
Library name: cl-13-dTAG-3h_H3
bigWig file


title: ChIP, H2B, SSRP1-FKBP-E14, dTAG-13 3h, clone1

description:
Library name: cl-1-dTAG-3h_H2B
bigWig file


title: ChIP, H2A, SSRP1-FKBP-E14, dTAG-13 3h, clone13

description:
Library name: cl-13-dTAG-3h_H2A
bigWig file


title: Panel1_CW60230E-3_i


title: Panel1_CW20081F-1_i


title: ChIP, H3, SSRP1-FKBP-E14, DMSO, clone13

description:
Library name: cl-13-dmso_H3
bigWig file


title: ChIP, H2A, SSRP1-FKBP-E14, DMSO, clone13

description:
Library name: cl-13-dmso_H2A
bigWig file


title: Panel1_CW20047D-1_i


title: ChIP, H3K27AC, SSRP1-FKBP-E14, DMSO, clone13

description:
Library name: cl-13-dmso_H3K27ac
bigWig file


title: Panel1_CW60115F-1_i


title: Panel4_CW20047D-3_i


title: ChIP, input,  SSRP1-FKBP-E14, dTAG-13 3h, clone1

description:
Library name: cl-1-dTAG-3h_input
bigWig file


title: Panel4_CW60219E-4_ii


title: ChIP, input,  SSRP1-FKBP-E14, DMSO, clone1

description:
Library name: cl-1-dmso_input
bigWig file


title: Panel4_CW60220F-4_i


title: Panel1_CW20047D-1_ii


title: ChIP, H2B, SSRP1-FKBP-E14, DMSO, clone1

description:
Library name: cl-1-dmso_H2B
bigWig file


title: ChIP, H3K27AC, SSRP1-FKBP-E14, DMSO, clone1

description:
Library name: cl-1-dmso_H3K27ac
bigWig file


title: Panel4_CW60040F-4_i


title: ChIP, H2A, SSRP1-FKBP-E14, dTAG-13 3h, clone1

description:
Library name: cl-1-dTAG-3h_H2A
bigWig file


title: Panel1_CW20050D-1_i


title: MCC, SSRP1-FKBP-E14, MNase 9U,dTAG3h, clone36, tech rep 2

description:
Library name: MCC-E14-C36-9U-2_dTAG3h
raw ligation junctions
ligation_junctions_MCC-E14-dTAG3h.tsv.gz

data_processing:
The data was analysed using the MCC pipeline (Hamley, 2023). In short, adaptors were trimmed with trim_galore, paired end reads were merged into single read using the central area of overlap (flash). Blat was used to map reads to the 800bp around the capture site. Then, the fastqs were split into one file per viewpoint with MCC_fastq_splitter.pl. The fastq files were then aligned to the mm39 genome using bowtie.
Then MCC_analyser.pl checks that the reads contain the oligo sequence, removes PCR duplicates and derives ligation junctions and up/downstream orientation.
Assembly: mm39
Supplementary files format and content: ligation junction files (tsx.gz)
Supplementary files format and content: probe sequences (csv)

extract_protocol:
40M cells were fixed with 2% FA and permeabilized with 1% digitoning. Then, the chromatin was digested with MNase and ligated. After RNase and Prot K treatment, the DNA was purified with phenol-chloroform extraction and sonicated aiming for 200bp fragments.
Sequencing libraries were prepared with NEBNext Ultra II (NEB 7645S). Regions of interest were captured with biotinylated probes using the HyperCapture Target Enrichment Kit (Roche 9075828001)


title: Panel4_CW20053A-2_i


title: ChIP, H3, SSRP1-FKBP-E14, DMSO, clone1

description:
Library name: cl-1-dmso_H3
bigWig file


title: Panel1_CW20051C-1_i


title: Panel4_CW60230E-4_i


title: Panel4_CW20053A-2_ii


title: Panel4_CW20012E-2_ii


title: Panel4_CW60040F-5_i


title: MCC, SSRP1-FKBP-E14, MNase 8U,dTAG3h, clone36, tech rep 2

description:
Library name: MCC-E14-C36-8U-2_dTAG3h
raw ligation junctions
ligation_junctions_MCC-E14-dTAG3h.tsv.gz


title: ChIP, H2A, SSRP1-FKBP-E14, DMSO, clone1

description:
Library name: cl-1-dmso_H2A
bigWig file


title: Panel4_CW60220F-3_i


title: MCC, SSRP1-FKBP-E14, MNase 9U, dTAG3h, clone1, tech rep 2

description:
Library name: MCC-E14-C1-9U-2_dTAG3h
raw ligation junctions
ligation_junctions_MCC-E14-dTAG3h.tsv.gz


title: MCC, SSRP1-FKBP-E14, MNase 9U, dTAG3h, clone36, tech rep 1

description:
Library name: MCC-E14-C36-9U-1_dTAG3h
raw ligation junctions
ligation_junctions_MCC-E14-dTAG3h.tsv.gz


title: Panel3_CW60040F-4_i


title: MCC, SSRP1-FKBP-E14, MNase 8U, dTAG3h, clone36, tech rep 1

description:
Library name: MCC-E14-C36-8U-1_dTAG3h
raw ligation junctions
ligation_junctions_MCC-E14-dTAG3h.tsv.gz


title: Panel4_CW20041A-2_i


title: MCC, SSRP1-FKBP-E14, MNase 9U, dTAG3h, clone1, tech rep 1

description:
Library name: MCC-E14-C1-9U-1_dTAG3h
raw ligation junctions
ligation_junctions_MCC-E14-dTAG3h.tsv.gz


title: Panel4_CW20012E-2_i


title: MCC, SSRP1-FKBP-E14, MNase 9U, dTAG3h, clone13, tech rep 2

description:
Library name: MCC-E14-C13-9U-2_dTAG3h
raw ligation junctions
ligation_junctions_MCC-E14-dTAG3h.tsv.gz


title: MCC, SSRP1-FKBP-E14, MNase 9U, dTAG3h, clone13, tech rep 1

description:
Library name: MCC-E14-C13-9U-1_dTAG3h
raw ligation junctions
ligation_junctions_MCC-E14-dTAG3h.tsv.gz


title: Panel3_CW60220F-4_i


title: MCC, SSRP1-FKBP-E14, MNase 8U, dTAG3h, clone1, tech rep 1

description:
Library name: MCC-E14-C1-8U-1_dTAG3h
raw ligation junctions
ligation_junctions_MCC-E14-dTAG3h.tsv.gz


title: MCC, SSRP1-FKBP-E14, MNase 9U, DMSO, clone36, tech rep 2

description:
Library name: MCC-E14-C36-9U-2_DMSO
raw ligation junctions
ligation_junctions_MCC-E14-DMSO.tsv.gz


title: Panel3_CW20053A-2_ii


title: Panel4_CW60219E-4_i


title: MCC, SSRP1-FKBP-E14, MNase 8U, dTAG3h, clone1, tech rep 2

description:
Library name: MCC-E14-C1-8U-2_dTAG3h
raw ligation junctions
ligation_junctions_MCC-E14-dTAG3h.tsv.gz


title: Panel3_CW60219E-4_i


title: MCC, SSRP1-FKBP-E14, MNase 8U, dTAG3h, clone13, tech rep 2

description:
Library name: MCC-E14-C13-8U-2_dTAG3h
raw ligation junctions
ligation_junctions_MCC-E14-dTAG3h.tsv.gz


title: MCC, SSRP1-FKBP-E14, MNase 8U, DMSO, clone36, tech rep 1

description:
Library name: MCC-E14-C36-8U-1_DMSO
raw ligation junctions
ligation_junctions_MCC-E14-DMSO.tsv.gz


title: Panel3_CW20047D-3_i


title: MCC, SSRP1-FKBP-E14, MNase 8U, dTAG3h, clone13, tech rep 1

description:
Library name: MCC-E14-C13-8U-1_dTAG3h
raw ligation junctions
ligation_junctions_MCC-E14-dTAG3h.tsv.gz


title: MCC, SSRP1-FKBP-E14, MNase 8U, DMSO, clone1, tech rep 2

description:
Library name: MCC-E14-C1-8U-2_DMSO
raw ligation junctions
ligation_junctions_MCC-E14-DMSO.tsv.gz


title: Panel3_CW20053A-2_i


title: MCC, SSRP1-FKBP-E14, MNase 9U, DMSO, clone36, tech rep 1

description:
Library name: MCC-E14-C36-9U-1_DMSO
raw ligation junctions
ligation_junctions_MCC-E14-DMSO.tsv.gz


title: Panel3_CW20041A-2_i


title: Panel3_CW20047D-4_i


title: Panel3_CW20012E-2_ii


title: MCC, SSRP1-FKBP-E14, MNase 8U, DMSO, clone36, tech rep 2

description:
Library name: MCC-E14-C36-8U-2_DMSO
raw ligation junctions
ligation_junctions_MCC-E14-DMSO.tsv.gz


title: Panel3_CW60219E-3_ii


title: Panel3_CW60219E-3_i


title: MCC, SSRP1-FKBP-E14, MNase 9U, DMSO, clone1, tech rep 1

description:
Library name: MCC-E14-C1-9U-1_DMSO
raw ligation junctions
ligation_junctions_MCC-E14-DMSO.tsv.gz


title: Panel3_CW60040F-5_i


title: Panel3_CW20012E-2_i


title: Panel3_CW60230E-4_i


title: MCC, SSRP1-FKBP-E14, MNase 8U, DMSO, clone1, tech rep 1

description:
Library name: MCC-E14-C1-8U-1_DMSO
raw ligation junctions
ligation_junctions_MCC-E14-DMSO.tsv.gz


title: MCC, SSRP1-FKBP-E14, MNase 9U, DMSO, clone13, tech rep 1

description:
Library name: MCC-E14-C13-9U-1_DMSO
raw ligation junctions
ligation_junctions_MCC-E14-DMSO.tsv.gz


title: MCC, SSRP1-FKBP-E14, MNase 9U, DMSO, clone13, tech rep 2

description:
Library name: MCC-E14-C13-9U-2_DMSO
raw ligation junctions
ligation_junctions_MCC-E14-DMSO.tsv.gz


title: Panel2_CW60040F-4_i


title: MCC, SSRP1-FKBP-E14, MNase 9U, DMSO, clone1, tech rep 2

description:
Library name: MCC-E14-C1-9U-2_DMSO
raw ligation junctions
ligation_junctions_MCC-E14-DMSO.tsv.gz


title: Panel2_CW20053A-2_i


title: TT-seq, SSRP1-FKBP-E14, dTAG-13 3h, clone36

description:
Library name: TT-SSRP1-FKBP-E14-dTAG3h-36
bigWig file

data_processing:
TT-seq analysis was carried out with the SeqNado pipeline. In short, reads were trimmed QC with trim_galore, aligned to mm39_dm6 suing STAR (v2.4.2a) in paired-end mode using default parameters.
bigWigs were generated with deepTools (v3.5.1) and scaled according to spike-in reads.
Assembly: mm39
Supplementary files format and content: bigWig

extract_protocol:
Fifty million cells were labelled with 500uM 4-thiouridine (4sU) for 5 min and lysed in Trizol. For reference normalization, Drosophila S2 cells were labelled with 500uM 4sU for 5min and lysed in Trizol. Drosophila lysate was added in a ratio of 1:3 (drosophila:mouse). Total RNA was isolated by phenol-chloroform extraction, DNAse treated and sonicated (Covaris ME220). 4sU-labelled transcripts were biotinylated with EZ-link biotin-HPDP (ThermoFisher Scientific), isolated using Streptavidin beads (Miltenyi) and purified with the RNeasy MinElute Cleanup Kit (Qiagen 74204).
Libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit (E7760).


title: Panel2_CW60230E-4_i


title: Panel2_CW20047D-3_i


title: MCC, SSRP1-FKBP-E14, MNase 8U, DMSO, clone13, tech rep 2

description:
Library name: MCC-E14-C13-8U-2_DMSO
raw ligation junctions
ligation_junctions_MCC-E14-DMSO.tsv.gz


title: TT-seq, SSRP1-FKBP-E14, dTAG-13 3h, clone13

description:
Library name: TT-SSRP1-FKBP-E14-dTAG3h-13
bigWig file


title: MCC, SSRP1-FKBP-E14, MNase 8U, DMSO, clone13, tech rep 1

description:
Library name: MCC-E14-C13-8U-1_DMSO
raw ligation junctions
ligation_junctions_MCC-E14-DMSO.tsv.gz


title: TT-seq, SSRP1-FKBP-E14, dTAG-13 3h, clone1

description:
Library name: TT-SSRP1-FKBP-E14-dTAG3h-1
bigWig file


title: TT-seq, SSRP1-FKBP-E14, DMSO, clone36

description:
Library name: TT-SSRP1-FKBP-E14-DMSO-36
bigWig file


title: Panel1_CW60040F-2_i


title: Panel2_CW60220F-3_i


title: Panel1_CW60218E-2_i


title: RNA, SSRP1-FKBP-E14, dTAG-13 6h, clone36

description:
Library name: RNA-DTAG6H-C36
counts from featureCounts

data_processing:
RNA-seq analysis was carried out with the SeqNado pipeline (https://github.com/alsmith151/SeqNado). In short, reads were trimmed QC with trim_galore, aligned to mm39_dm6 suing STAR (v2.4.2a) in paired-end mode using default parameters.
Read counts were obtained with featureCounts (Subread package v2.0.6).
Assembly: mm39
Supplementary files format and content: featureCounts table (tsv)

extract_protocol:
Mouse embryonic stem cells were harvested and Drosophil cells were added in a ratio of 1:3 (drosophila:mouse). Total RNA was extracted with the RNeasy Mini kit (Qiagen 74104). Poly A mRNA was isolated with NEBNext Poly(A) mRNA magnetic isolation module (E7490).
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760)

value: dTAG-13 6h


title: Panel2_CW60219E-2_i


title: Panel2_CW60040F-3_i


title: RNA, WT E14, DMSO, rep2

description:
Library name: RNA-WT-E14-2
counts from featureCounts

value: WT


title: Panel2_CW20012E-2_i


title: RNA, WT E14, DMSO, rep3

description:
Library name: RNA-WT-E14-3
counts from featureCounts


title: RNA, SSRP1-FKBP-E14, DMSO, clone36

description:
Library name: RNA-DMSO-C36
counts from featureCounts


title: Panel1_CW20069F-1_i


title: Panel1_CW60230E-2_i


title: TT-seq, SSRP1-FKBP-E14, DMSO, clone13

description:
Library name: TT-SSRP1-FKBP-E14-DMSO-13
bigWig file


title: Panel1_CW60220F-2_i


title: RNA, WT E14, DMSO, rep1

description:
Library name: RNA-WT-E14-1
counts from featureCounts


title: TT-seq, SSRP1-FKBP-E14, DMSO, clone1

description:
Library name: TT-SSRP1-FKBP-E14-DMSO-1
bigWig file


title: RNA, SSRP1-FKBP-E14, DMSO, clone1

description:
Library name: RNA-DMSO-C1
counts from featureCounts


title: RNA, SSRP1-FKBP-E14, dTAG-13 6h, clone13

description:
Library name: RNA-DTAG6H-C13
counts from featureCounts


title: Panel1_CW60219E-1_i


title: Panel1_CW60230E-1_i


title: ATAC, SSRP1-FKBP-E14, dTAG-13 3h, clone36

description:
Library name: ATAC-SSRP1-FKBP-E14-dTAG3h_36
bigWig files

data_processing:
Data was processed using SeqNado (https://github.com/alsmith151/SeqNado). In short, reads where timmed using trim_galore with Cutadapt (v0.6.10), mapped with Bowtie2 (v2.5.1), PCR duplicates were removed with picard MarkDuplicates (v3.0.0), problematic genomic regions in the ENCODE Blacklist were discarded, bigWig files were generated with deepTools (v3.5.1) normalizing with RPKM.
Assembly: mm39
Supplementary files format and content: bigWig

extract_protocol:
Nuclei were extracted from 50,000 live cells and tagemented with Nextera Tn5 transposase (Illumina 20034197). Resulting DNA fragments were purified with the MinElute Kit (Qiagen 28004)
Tagmented fragments were amplified with 10 cycles of PCR and purified with the MinElute Kit (Qiagen 28004)


title: RNA, SSRP1-FKBP-E14, DMSO, clone13

description:
Library name: RNA-DMSO-C13
counts from featureCounts


title: ATAC, SSRP1-FKBP-E14, dTAG-13 3h, clone1

description:
Library name: ATAC-SSRP1-FKBP-E14-dTAG3h_1
bigWig files


title: MFascicularis_exp1_chip1_GEX

description: Library name: MFascicularis_exp1_chip1_GEX_lib

organism: Macaca fascicularis

value: induced pluripotent stem cell

value: KRAB-dCas9-HA-P2A-mCherry insertion at AAVS1 locus

tag: library type

value: 10x Genomics 5' Gene Expression


title: ATAC, SSRP1-FKBP-E14, DMSO, clone13

description:
Library name: ATAC-SSRP1-FKBP-E14-DMSO_13
bigWig files

value: DMSO


title: Panel1_CW60218E-1_i

value: M


title: RNA, SSRP1-FKBP-E14, dTAG-13 6h, clone1

description:
Library name: RNA-DTAG6H-C1
counts from featureCounts


title: ATAC, SSRP1-FKBP-E14, DMSO, clone1

description:
Library name: ATAC-SSRP1-FKBP-E14-DMSO_1
bigWig files


title: Panel1_CW60040F-1_i

value: control


title: Panel1_CW20053A-1_i

value: case


title: ATAC, SSRP1-FKBP-E14, dTAG-13 3h, clone13

description:
Library name: ATAC-SSRP1-FKBP-E14-dTAG3h_13
bigWig files

value: dTAG-13 3h


title: Panel1_CW20012E-1_i

value: F


title: Panel1_CW60220F-1_i


title: MFascicularis_exp1_chip1_CRISPR

description: Library name: MFascicularis_exp1_chip1_CRISPR_lib

value: 10x Genomics 5' CRISPR Guide Capture


title: DRIPc-seq in RHKI, control without exogenous RNaseH treatment

city: Worcester

first: Chun-Hao

last: Chao

address: 364 Plantation St. LRB560D

department: MCCB

institute: UMass Chan Medical School

description: Library name: DRIP_control_N

data_processing:
Fastq files were trimmed with Trimmomatic v0.39, then aligned by Bowtie2 v2.5.0 with GRCm38. SAM files were sorted and deduplicate by Picard v2.10.0. Reads were filtered by MAPQ > 10 and -f 99, -f 147, -f 83 or -f 163 for the unique mapped reads with Samtools v1.16.1. HOMER v4.11 and Deeptools v3.5.1 were applied on bam file for aggregation plot, heatmap, bedgraph, bigwig and peak annotation.
Assembly: GRCm38 with Gencode vM25 annotation
Supplementary files format and content: control_N.bw is a BigWig file derived from the combined BAM file of DRIPc-seq  in control without exogenous RNaseH treatment
Supplementary files format and content: control_RNaseH.bw is a BigWig file derived from the combined BAM file of DRIPc-seq in control with exogenous RNaseH treatment
Supplementary files format and content: Dox_N.bw is a BigWig file derived from the combined BAM file of DRIPc-seq in Dox treatment
Library strategy: DRIPc-seq

growth_protocol: Cells were detached with accutase and plated at a density of 2–2.5 × 105 cells per 6-cm dish at 37°C in a 5% CO₂ atmosphere. Culture medium was 2i/LIF medium (NDiff 227 supplemented with LIF, 2% FBS, 3 µM CHIR-99021, and 1 µM PD0325901).

extract_protocol:
RHKI cells were lysed in buffer (10 mM Tris, pH 7.5; 10 mM EDTA; 10 mM NaCl; 0.5% sarcosyl) with Proteinase K at 37°C overnight. DNA was extracted via PCI and ethanol precipitation, then digested with BsrGI, EcoRI, HindIII, SspI, and XbaI, followed by RNase III treatment for remove dsRNA (0.5U per 1µg gDNA). DNA was split into aliquots with or without RNase H (and RNase A if needed and 20-25U RNaseH per 1µg gDNA), re-extracted, and immunoprecipitated with 10-15 µg S9.6 antibody in MeDP buffer overnight at 4°C. Complexes were pulled down with Protein G beads, washed, and eluted in 2x STOP buffer (20 mM Tris 8.0, 100 mM NaCl, 20 mM EDTA, 1% SDS) at 65°C. DNA was purified and analyzed by qPCR using SYBR Fast reagent and specific primers. Enrichment was calculated as % input and fold change over negative control.
Input DNA was used for library preparation using a NEBNext Ultra II kit with TruSeq adapters (no USER). Libraries were purified with double-size selection by Ampure XP beads (0.6x-0.9x). Immunoprecipitated RNA/DNA hybrids were digested with 10U DNase I and the RNA was recovered by PCI and ethanol precipitation. Libraries were prepared by NEBNext Ultra II Directional RNA library prep kit with TruSeq Adaptors, purified either with double-size selection by Ampure XP beads (0.6x-0.9x) or gel extraction (150-650 bp) and sequenced (NovaSeq, PE150; 90-100 million reads for DRIP libraries and 20-30 million reads for input libraries).

treatment_protocol: Dox condition was treated with doxycycline 500 ng/ml for 48 hours

value: mouse embryonic stem cell

value: HA-Rnaseh1 knock-in

value: S9.6 antibody (Kerafast)


title: DRIPc-seq in RHKI, Dox treatment without exogenous RNaseH treatment

description: Library name: DRIP_Dox_N


title: Input of DRIPc-seq in RHKI, control with exogenous RNaseH treatment

description: Library name: Input_control_RH


title: Cas9 gSting LNP Lung 2, Day21, RNAseq

city: Guangzhou

first: Yangeng

last: Wang

state: Guangdong

address: No. 777 East Xingye Avenue, Panyu District, Guangzhou, Guangdong, China

institute: South China University of Technology

description:
Library name: Samples 8
Column in 1_genes_fpkm_expression.txt: FPKM.G5_2

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used Ensembl (ftp://ftp.ensembl.org/pub/release-107/fasta/homo_sapiens/dna/) to map reads to the reference genome of homo sapiens Ensembl_v107. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: homo_sapiens Ensembl_v107
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

source_name: Lung

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.  The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.   Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.  e6150, USA) under 94℃ 5-7min.   Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.   1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.  m0209, USA), RNase H (NEB, cat.  m0297, USA) and dUTP Solution (Thermo Fisher, cat.  R0133, USA）.   An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters.   Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.   Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.   After the heat-labile UDG enzyme (NEB, cat.  m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min;   8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec;   and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 400±50 bp.   At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ X Plus (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Lung

value: Cas9/gSting LNP treatment

tag: time

value: Day 21


title: genomic DNA from white matter 17

type: genomic

first: Leonille

last: Schweizer

address: Charitépl. 1

institute: Charité - Universitätsmedizin

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Methylation array data were processed in R (version 3.5.0) applying Bioconductor packages minfi (version 1.28.4)

label: Cy3 and Cy5

source_name: white matter 17

label_protocol: standard Illumina protocol

extract_protocol: Genomic DNA extraction of formalin-fixed and paraffin embedded (FFPE) tissue was conducted from white matter areas with increased cell density avoiding cortical regions with neuronal cells using the Maxwell Tissue DNA Purification Kit (Promega) according to the manufacturer´s protocol.

value: white matter

value: male

tag: case

value: p

tag: multiregion


title: DRIPc-seq in RHKI, control with exogenous RNaseH treatment

description: Library name: DRIP_control_RH


title: ATAC, SSRP1-FKBP-E14, DMSO, clone36

description:
Library name: ATAC-SSRP1-FKBP-E14-DMSO_36
bigWig files

value: Embryo

value: E14 Tg2a IV

value: mouse embryonic stem cells


title: genomic DNA from white matter 18

source_name: white matter 18

tag: Sex


title: genomic DNA from white matter 15

source_name: white matter 15


title: Input of DRIPc-seq in RHKI, control without exogenous RNaseH treatment

description: Library name: Input_control_N

tag: cell type


title: Pulmonary fibrosis lung tissue 1, Day 21, RNA-seq

description:
Library name: Samples 4
Column in 1_genes_fpkm_expression.txt: FPKM.G2_1

value: WT

value: Bleomycin treatment


title: Cas9 gSting LNP Lung 3, Day21, RNAseq

description:
Library name: Samples 9
Column in 1_genes_fpkm_expression.txt: FPKM.G5_3


title: Pulmonary fibrosis lung tissue 2, Day 21, RNA-seq

description:
Library name: Samples 5
Column in 1_genes_fpkm_expression.txt: FPKM.G2_2


title: Cas9 gSting LNP Lung 1, Day21, RNAseq

description:
Library name: Samples 7
Column in 1_genes_fpkm_expression.txt: FPKM.G5_1


title: genomic DNA from white matter 14

source_name: white matter 14

value: female


title: genomic DNA from white matter 11

source_name: white matter 11


title: Pulmonary fibrosis lung tissue 3, Day 21, RNA-seq

description:
Library name: Samples 6
Column in 1_genes_fpkm_expression.txt: FPKM.G2_3


title: Control lung tissue (saline 2), Day 21, RNA-seq

description:
Library name: Samples 2
Column in 1_genes_fpkm_expression.txt: FPKM.G1_2

value: Saline control


title: genomic DNA from white matter 10

source_name: white matter 10

value: r


title: genomic DNA from white matter 9

source_name: white matter 9


title: genomic DNA from white matter 13

source_name: white matter 13


title: H2A.Z CUT&Tag in ZX-1, Dox, rep5

description: Library name: ZX-1_H2A.Z_Dox_rep5

data_processing:
Fastq files were trimmed with Trimmomatic, then aligned by Bowtie2 with GRCm38. SAM files were sorted and deduplicate by Picard. Reads were filtered by MAPQ > 10 and -f 99, -f 147, -f 83 or -f 163 for the unique mapped reads. HOMER and deeptools were applied on bam file for aggregation plot, heatmap, bedgraph, bigwig and peak annotation.
Peakcalling of H2A.Z was perform through getDifferentialPeaksReplicates.pl from HOMER with IgG as background signal and '-style histone -tagThreshold 40'.
Assembly: GRCm38 with Gencode vM25 annotation
Supplementary files format and content: ZX_H2AZ_control.bedGraph.gz is bedGraph file derived from the combined BAM file of all replicates in ZX-1 control experiment
Supplementary files format and content: ZX_H2AZ_Dox.bedGraph.gz is bedGraph file derived from the combined BAM file of all replicates in ZX-1 Dox experiment
Library strategy: CUT&Tag

source_name: cell line

extract_protocol:
Cells were bound on ConA beads and incubate with the primary antibody or proteins overnight in antibody buffer. For CUT&Tag, cells were incubated with secondary antibody and pA-Tn5 sequentially and then tagmented with tagmentation buffer. Tagmentation was stopped by EDTA buffer and DNA were then recovered and directly subjected to library amplification. For CUT&RUN, cells were incubated with pA-MNase and digested on ice-water in buffer containing CaCl2. Digestion was stopped by 2X STOP buffer and DNA were recovered by high speed spin, Proteinase K/SDS digestion and PCI extraction. For MapR, cell were directly applied for digestion and the rest step as described in CUT&RUN.
For CUT&Tag, tagmented DNA was recovered and directly PCR with Nextera primer for library amplification. For CUT&RUN and MapR, NEBNext Ultra II DNA library prep was used for library construction with 14 cycle of library amplification.

value: cell line

value: mouse embryonic stem cell

value: anti-H2A.Z(Active Motif 39113)


title: Control lung tissue (saline 3), Day 21, RNA-seq

description:
Library name: Samples 3
Column in 1_genes_fpkm_expression.txt: FPKM.G1_3

value: Lung


title: genomic DNA from white matter 16

source_name: white matter 16


title: genomic DNA from white matter 6

source_name: white matter 6


title: genomic DNA from white matter 8

source_name: white matter 8


title: Control lung tissue (saline 1), Day 21, RNA-seq

description:
Library name: Samples 1
Column in 1_genes_fpkm_expression.txt: FPKM.G1_1


title: Input of DRIPc-seq in RHKI, Dox treatment without exogenous RNaseH treatment

description: Library name: Input_Dox_N

value: HA-Rnaseh1 knock-in


title: genomic DNA from white matter 12

source_name: white matter 12


title: genomic DNA from white matter 19

source_name: white matter 19


title: hTERT-RPE1 cells, knockdown ccnd1, dox, 1440, rep2

city: Stanford

first: Dong Shin

last: You

address: 327 Campus Drive

institute: Stanford University

description: Library name: shccnd1_1440_rep2

data_processing:
Data was analyzed using the SLAMdunk pipeline, as outlined on https://github.com/t-neumann/slamdunk/blob/bluebee-rc1/LICENSE
Assembly: hg38
Supplementary files format and content: .tsv file containing output file of SLAMdunk pipeline, as outlined on https://t-neumann.github.io/slamdunk/docs.html#tcount-file. Columns of particular interest are 'ConversionsOnTs' and 'CoverageOnTs', which are respectively the cumulative number of T>C conversions and cumulative coverage on all Ts in the mapped gene

growth_protocol: Cells were cultured at 37℃ and 5% CO2 in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F-12 (Corning; 10-092-CV) supplemented with 10% heat-inactivated fetal bovine serum (Corning; 35-011-CV) and 1% penicillin/streptomycin (Gibco; 15140-122).

extract_protocol:
At each collection timepoint, the cells were washed once with PBS, and lysed with TRIReagent.
RNA quality control, library preparation, sequencing and initial data processing were performed by Lexogen NGS Services, Lexogen GmBH, Austria. In brief, samples were characterized by UV-Vis spectrophotometry (Nanodrop 2000c, ThermoFisher) and RNA integrity was assessed on a Fragment Analyzer System using the DNF-471 RNA Kit (15nt) (Agilent). The libraries were constructed using Lexogen’s QuantSeq 3’ mRNA-Seq Library Prep Kit FWD V2. RNA input to the library preparation was normalized to 75ng across all samples. Prepared libraries were quality controlled on a Fragment Analyzer System using the DNF-474 using the HS-DNA kit (1-6000bp) (Agilent). cDNA libraries were sequenced with an Illumina NovaSeq X platform using 100nt single end read length, with 40 million reads on average per sample.

treatment_protocol: Cells were induced with 0.5 ug/mL doxycycline for the entire duration of the experiment to either knockdown or overexpress Cyclin D1. On day 4 of induction, 10µM 4-thiouridine (s4U) (Selleck Chemicals; E1292) was added to the growth medium. A separate replicate was also made at the same time that instead received 10µM uridine (negative control)(Sigma Aldrich; U3003-5G). Media was exchanged every 3 hours for 24 hours. After 24 hours of s4U addition, cells were washed twice with PBS, and growth media with 1mM uridine was applied. At this time, the negative control and 0 hour timepoint samples were collected, and the chase was started.

value: epithelial cell

value: inducible ccnd1 knockdown

value: doxycycline-induced ccnd1 knockdown

tag: chase time_(min)


title: H2A.Z CUT&Tag in ZX-1, Dox, rep4

description: Library name: ZX-1_H2A.Z_Dox_rep4


title: genomic DNA from white matter 5

source_name: white matter 5

value: white matter

value: male


title: hTERT-RPE1 cells, knockdown ccnd1, dox, 720, rep2

description: Library name: shccnd1_720_rep2

tag: genotype


title: genomic DNA from white matter 1

source_name: white matter 1

value: p


title: genomic DNA from white matter 3

source_name: white matter 3


title: H2A.Z CUT&Tag in ZX-1, Dox, rep3

description: Library name: ZX-1_H2A.Z_Dox_rep3


title: genomic DNA from white matter 2

source_name: white matter 2


title: H2A.Z CUT&Tag in ZX-1, Dox, rep2

description: Library name: ZX-1_H2A.Z_Dox_rep2


title: H2A.Z CUT&Tag in ZX-1, control, rep5

description: Library name: ZX-1_H2A.Z_control_rep5


title: H2A.Z CUT&Tag in ZX-1, Dox, rep1

description: Library name: ZX-1_H2A.Z_Dox_rep1


title: hTERT-RPE1 cells, knockdown ccnd1, dox, 180, rep2

description: Library name: shccnd1_180_rep2


title: hTERT-RPE1 cells, knockdown ccnd1, dox, 360, rep2

description: Library name: shccnd1_360_rep2


title: hTERT-RPE1 cells, knockdown ccnd1, dox, 90, rep2

description: Library name: shccnd1_90_rep2


title: hTERT-RPE1 cells, knockdown ccnd1, dox, 45, rep2

description: Library name: shccnd1_45_rep2


title: H2A.Z CUT&Tag in ZX-1, control, rep4

description: Library name: ZX-1_H2A.Z_control_rep4


title: H2A.Z CUT&Tag in ZX-1, control, rep3

description: Library name: ZX-1_H2A.Z_control_rep3


title: H2A.Z CUT&Tag in ZX-1, control, rep1

description: Library name: ZX-1_H2A.Z_control_rep1


title: hTERT-RPE1 cells, knockdown ccnd1, dox, no label, rep2

description: Library name: shccnd1_nolabel_rep2


title: H2A.Z CUT&Tag in ZX-1, control, rep2

description: Library name: ZX-1_H2A.Z_control_rep2


title: hTERT-RPE1 cells, knockdown ccnd1, dox, 20, rep2

description: Library name: shccnd1_20_rep2


title: hTERT-RPE1 cells, knockdown ccnd1, dox, 0, rep2

description: Library name: shccnd1_0_rep2


title: IgG CUT&Tag, Dox, rep3

description: Library name: IgG_Dox_rep3

data_processing:
Fastq files were trimmed with Trimmomatic, then aligned by Bowtie2 with GRCm38. SAM files were sorted and deduplicate by Picard. Reads were filtered by MAPQ > 10 and -f 99, -f 147, -f 83 or -f 163 for the unique mapped reads. HOMER and deeptools were applied on bam file for aggregation plot, heatmap, bedgraph, bigwig and peak annotation.
Peakcalling of H2A.Z was perform through getDifferentialPeaksReplicates.pl from HOMER with IgG as background signal and '-style histone -tagThreshold 40'.
Assembly: GRCm38 with Gencode vM25 annotation
Supplementary files format and content: H2AZ_peak.bed is a BED file containing consensus ATAC-seq peaks identified from overlapping peak regions across all replicates.
Supplementary files format and content: Downpeak_annotation.csv is the significant down peaks with annotation in Dox treatment condition
Supplementary files format and content: Uppeak_annotation.csv is the significant up peaks with annotation in Dox treatment condition
Supplementary files format and content: H2A.Z_control_rep1.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_control_rep2.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_control_rep3.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_control_rep4.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_Dox_rep1.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_Dox_rep2.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_Dox_rep3.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_Dox_rep4.bw is the bigwig file for the corresponded condition
Library strategy: CUT&Tag

value: rabbit IgG (ab37415)


title: hTERT-RPE1 cells, knockdown ccnd1, dox, 10, rep2

description: Library name: shccnd1_10_rep2


title: hTERT-RPE1 cells, knockdown ccnd1, dox, 1440, rep1

description: Library name: shccnd1_1440_rep1


title: IgG CUT&Tag, Dox, rep2

description: Library name: IgG_Dox_rep2


title: IgG CUT&Tag, control, rep3

description: Library name: IgG_control_rep3


title: hTERT-RPE1 cells, knockdown ccnd1, dox, 180, rep1

description: Library name: shccnd1_180_rep1


title: IgG CUT&Tag, Dox, rep4

description: Library name: IgG_Dox_rep4


title: hTERT-RPE1 cells, knockdown ccnd1, dox, 720, rep1

description: Library name: shccnd1_720_rep1


title: IgG CUT&Tag, Dox, rep1

description: Library name: IgG_Dox_rep1


title: hTERT-RPE1 cells, knockdown ccnd1, dox, no label, rep1

description: Library name: shccnd1_nolabel_rep1


title: hTERT-RPE1 cells, knockdown ccnd1, dox, 360, rep1

description: Library name: shccnd1_360_rep1


title: IgG CUT&Tag, control, rep4

description: Library name: IgG_control_rep4


title: hTERT-RPE1 cells, knockdown ccnd1, dox, 45, rep1

description: Library name: shccnd1_45_rep1


title: hTERT-RPE1 cells, overexpression ccnd1, dox, 360, rep2

description: Library name: wtccnd1_360_rep2

value: inducible ccnd1 knockdown; inducible ccnd1 overexpression


title: genomic DNA from white matter 7

source_name: white matter 7


title: RNAP2Ser2P CUT&Tag, control, rep1

description: Library name: RNAP2_control_rep1

value: anti-RNAP2Ser2P (CST 13499)


title: IgG CUT&Tag, control, rep1

description: Library name: IgG_control_rep1


title: H4ac CUT&Tag, control, rep1

description: Library name: H4ac_control_rep1

value: anti-H4ac (Millipore 06-866)


title: H4ac CUT&Tag, Dox, rep2

description: Library name: H4ac_Dox_rep2


title: IgG CUT&Tag, control, rep2

description: Library name: IgG_control_rep2


title: hTERT-RPE1 cells, overexpression ccnd1, dox, 45, rep2

description: Library name: wtccnd1_45_rep2


title: hTERT-RPE1 cells, overexpression ccnd1, dox, 0, rep2

description: Library name: wtccnd1_0_rep2


title: RNAP2Ser2P CUT&Tag, Dox, rep2

description: Library name: RNAP2_Dox_rep2


title: RNAP2Ser2P CUT&Tag, Dox, rep1

description: Library name: RNAP2_Dox_rep1


title: hTERT-RPE1 cells, knockdown ccnd1, dox, 0, rep1

description: Library name: shccnd1_0_rep1


title: hTERT-RPE1 cells, overexpression ccnd1, dox, 720, rep2

description: Library name: wtccnd1_720_rep2


title: hTERT-RPE1 cells, overexpression ccnd1, dox, 1440, rep2

description: Library name: wtccnd1_1440_rep2


title: RNAP2Ser2P CUT&Tag, control, rep2

description: Library name: RNAP2_control_rep2


title: hTERT-RPE1 cells, overexpression ccnd1, dox, 180, rep2

description: Library name: wtccnd1_180_rep2


title: hTERT-RPE1 cells, overexpression ccnd1, dox, no label, rep2

description: Library name: wt_ccnd1_nolabel_rep2


title: H3.3 CUT&Tag, Dox, rep1

description: Library name: H3.3_Dox_rep1

data_processing:
Fastq files were trimmed with Trimmomatic, then aligned by Bowtie2 with GRCm38. SAM files were sorted and deduplicate by Picard. Reads were filtered by MAPQ > 10 and -f 99, -f 147, -f 83 or -f 163 for the unique mapped reads. HOMER and deeptools were applied on bam file for aggregation plot, heatmap, bedgraph, bigwig and peak annotation.
Peakcalling of H2A.Z was perform through getDifferentialPeaksReplicates.pl from HOMER with IgG as background signal and '-style histone -tagThreshold 40'.
Assembly: GRCm38 with Gencode vM25 annotation
Supplementary files format and content: H2AZ_peak.bed is a BED file containing consensus ATAC-seq peaks identified from overlapping peak regions across all replicates.
Supplementary files format and content: Downpeak_annotation.csv is the significant down peaks with annotation in Dox treatment condition
Supplementary files format and content: Uppeak_annotation.csv is the significant up peaks with annotation in Dox treatment condition
Supplementary files format and content: H2A.Z_control_rep1.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_control_rep2.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_control_rep3.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_control_rep4.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_Dox_rep1.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_Dox_rep2.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_Dox_rep3.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_Dox_rep4.bw is the bigwig file for the corresponded condition
Library strategy: CUT&Run

value: anti-H3.3(Active Motif 91191)


title: H3.3 CUT&Tag, Dox, rep2

description: Library name: H3.3_Dox_rep2


title: H4ac CUT&Tag, Dox, rep1

description: Library name: H4ac_Dox_rep1


title: H4ac CUT&Tag, control, rep2

description: Library name: H4ac_control_rep2


title: hTERT-RPE1 cells, overexpression ccnd1, dox, 20, rep2

description: Library name: wtccnd1_20_rep2


title: hTERT-RPE1 cells, overexpression ccnd1, dox, 720, rep1

description: Library name: wtccnd1_720_rep1


title: H3.3 CUT&Tag, control, rep2

description: Library name: H3.3_control_rep2


title: hTERT-RPE1 cells, overexpression ccnd1, dox, 1440, rep1

description: Library name: wtccnd1_1440_rep1


title: hTERT-RPE1 cells, overexpression ccnd1, dox, 10, rep2

description: Library name: wtccnd1_10_rep2


title: H3.3 CUT&Tag, control, rep1

description: Library name: H3.3_control_rep1


title: hTERT-RPE1 cells, overexpression ccnd1, dox, 360, rep1

description: Library name: wtccnd1_360_rep1


title: hTERT-RPE1 cells, overexpression ccnd1, dox, 180, rep1

description: Library name: wtccnd1_180_rep1


title: hTERT-RPE1 cells, overexpression ccnd1, dox, 0, rep1

description: Library name: wtccnd1_0_rep1


title: H3K36me3 CUT&Tag, control, rep3

description: Library name: H3K36me3_control_rep3


title: hTERT-RPE1 cells, overexpression ccnd1, dox, no label, rep1

description: Library name: wtccnd1_nolabel_rep1


title: H3K36me3 CUT&Tag, Dox, rep3

description: Library name: H3K36me3_Dox_rep3


title: H3K36me3 CUT&Tag, Dox, rep1

description: Library name: H3K36me3_Dox_rep1


title: H3K27me3 CUT&Tag, Dox, rep4

description: Library name: H3K27me3_Dox_rep4


title: hTERT-RPE1 cells, overexpression ccnd1, dox, 20, rep1

description: Library name: wtccnd1_20_rep1


title: H3K36me3 CUT&Tag, control, rep4

description: Library name: H3K36me3_control_rep4


title: H3K36me3 CUT&Tag, control, rep1

description: Library name: H3K36me3_control_rep1


title: hTERT-RPE1 cells, overexpression ccnd1, dox, 90, rep1

description: Library name: wtccnd1_90_rep1


title: FF sample 38738

city: Washington

first: Bernard

last: Kwabi-Addo

state: DC

address: 520 W. Street N.W.

department: Biochemistry and Molecular Biology

institute: Howard University College of Medicine

description:
Genomic DNA from FF sample 38738
203991390137_R08C01

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (iScan) and standard recommended Illumina scanner setting

data_processing:
Illumina GenomeStudio Methylation Module V2011.1
[processed value definition] Average Beta

label: Cy3, Cy5

source_name: Prostate

label_protocol: Standard Illumina Protocol

extract_protocol: DNA extracted from fresh frozen samples using Qiagen DNA Mini kit according to standard instructions

tag: disease state

value: Normal

value: Prostate

tag: gleason

tag: psa

tag: recurrence


title: FF sample 56766

description:
Genomic DNA from FF sample 56766
203991390161_R08C01

tag: tissue