title: CUTAC_combo_2h_1_(240722_CD_Hs_1225)

description:
Library name: CUTAC_combo_2h_1
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 2 hours.

value: MDA-MB-231 human breast cancer epthileal cells  (ATCC HTB-26).


title: iPSC-CM, ventricular, WT/WT, rep 1

status: Public on Nov 25 2025

type: SRA

city: Vancouver

first: Kate

last: Huang

state: BC

address: 166-1081 Burrard Street

department: Department of Medicine - Centre for Heart Lung Innovation

country: Canada

institute: University of British Columbia

library_source: transcriptomic

data_processing:
FASTQ files were aligned to the reference transcriptome with STAR version 2.6.0a.
Read counts were quantified with HTSEQ version 0.11.2.
Gene count normalization and differential expression were performed using DESEQ2 version 1.16.1.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes read counts of samples (columns) by transcripts (rows).

molecule: total RNA

organism: Homo sapiens

growth_protocol: hiPSC-derived cardiomyocytes and engineered heart tissue constructs were cultured in RPMI 1640 with B27 supplement media and kept in an incubator at 37°C, 5% CO2.

extract_protocol:
Total RNA of hiPSC-CMs were extracted using the illustra RNAspin Mini Isolation Kit (GE Healthcare). Total RNA of engineered heart tissues were extracted using the Total RNA Purification Kit (Norgen Biotek). RNA integrity was assessed with the TapeStation 4200 (Agilent Technologies) and quantified with the Qubit RNA HS assay (Thermo Fisher Scientific).
200ng of total RNA was used as input for ribosomal RNA depletion using the MGIEasy rRNA Depletion Kit (MGI). Strand-specific libraries were prepared using the MGIEasy RNA Directional Library Prep Kit (MGI). Library quality and size were checked with the TapeStation 4200 D1000 Assay (Agilent Technologies) then quantified using the Qubit dsDNA HS Assay (Thermo Fisher Scientific). Libraries were sequenced on a MGI DNB-G50 sequencer to generate approximately 40 million 100-bp paired-end reads per library.

tag: tissue

tag: cell line

value: Isogenic AF patient iPSCs

tag: cell type

value: ventricular-like

tag: genotype

value: WT/WT


title: WT_saline_2

city: Cambridge

first: Ya-Chieh

last: Hsu

state: MA

address: 7 Divinity Ave, sherman-fairchild

department: Stem Cell and Regenerative Biology

country: USA

institute: Harvard University

description: RNA sequencing of treated and control samples

library_source: transcriptomic single cell

data_processing:
Data was processed using Cell Ranger v7.1.0, including demultiplexing, barcode processing, gene counting, and aggregation of single-cell gene expression data.
Assembly: mm10
Supplementary files format and content: H5 files - gene exression matrix

molecule: polyA RNA

organism: Mus musculus

source_name: Skin

extract_protocol:
Cells were isolated from C57BL/6J mice in first anagen after 12 hr injection with saline (control) or RTX, and after 72 hr injection with RTX. Mouse back skin containing the damaged regions was dissected, and the fat layer was removed by scraping with a surgical scalpel. The dermal fraction was isolated by incubating the skin in a collagenase solution in HBSS on an orbital shaker for 45-60 minutes at 37°C with scraping of the dermis. Following collection of the dermis, the remaining skin was incubated in trypsin-EDTA for 25-30 minutes at 37°C to collect the epidermis. Single cell suspensions of each fraction were obtained by filtering through a 70-mm and 40-mm filter. Cell suspensions were then centrifuged for 8 minutes at 350g at 4°C and resuspended in 5% FBS with a CD16/F32 Fc blocking antibody (BioLegend 101302, 1:100).
Libraries were constructed according to the 10x Genomics Single Cell v3.1 protocol
For scRNAseq, a small aliquot of the epidermal and dermal fractions was set aside containing fibroblasts. The fibroblasts were depleted from the remainder of each fraction by incubating with CD140A-biotin antibody (eBioscience 13-1401-82, 1:200) and then removing CD140A-bound cells with magnetic beads. The aliquoted fractions were then added back to respective samples, and cells were stained for 45-60 minutes on ice using the following antibodies: CD34-e660 (eBioscience 0-0341-82, 1:100), Ly-6A/E (Sca-1)-PerCp-Cy5.5 (eBioscience 45-5981-82, 1:1000), CD45-eF450 (eBioscience 48-0451-82, 1:250), a6-PE (eBioscience 12-0495-82, 1:250). DAPI (1:1000) was used to exclude dead cells. FACS was used to enrich for cell populations of interest at a ratio of 2:1:3:1:2 (immune cells: fibroblasts: hair follicle: general cells: HFSCs) that were isolated as follows: immune cells (CD45+), fibroblasts (Sca1+, CD34+, a6-), hair follicle (Sca1-, CD34-,a6low-high), general cells (DAPI-, CD45-, Sca1-, CD34-,a6-), HFSCs (Sca1-, CD34+,a6+).

value: Skin

tag: strain

tag: age

value: Wild-type

tag: treatment

value: Saline


title: iPSC-CM, atrial, WT/TTNtv, rep 3

value: atrial-like

value: WT/TTNtv (p.Ser21134Trpfs*25)


title: WT_saline_1


title: CUTAC_combo_0h_2_(240722_CD_Hs_1224)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
Library name: CUTAC_combo_0h_2
RNA Polymerase II Serine-5P-based CUTAC in untreated MDA-MB-231 cells for co-treatment series.

library_source: genomic

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments.
4. We used bedtools 2.30.0 "genomecov" to make a normalized count track which is the fraction of counts at each base pair scaled by the size of the reference sequence so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .bw)
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: MDA-MB-231 human breast cancer epthileal cells  (ATCC HTB-26).

tag: antibody

value: Anti-RNA Polymerase CTD repeat YSPTSPS (phospho S5) antibody [4H8] from abcam (ab5408).


title: p00_rbsatb2x_bc546

city: Santa Cruz

first: Bin

last: Chen

state: CA

address: 1156 High St.

department: MCD Biology

institute: University of California Santa Cruz

description: Library name: bc546

data_processing:
Paired end reads were trimmed to 25x25bp and mapped using Bowtie2 against the set of mouse RepeatMasker elements plus the E.coli genome
Paired end reads that mapped to repeat elements or E.coli  were discarded. The remaining reads were mapped to the mm10 genome using Bowtie2 .
The set of Bowtie2 paired-end mappings was filtered, retaining only mappings having  genomic length less than or equal to 120bp.
The bam files of mappings were converted to coverage tracks across the genome with the bedtools programs, using options so that the end-to-end coverage of each paired-end read is used.
The coverage tracks were compressed into bigWig format.
The coverage was merged over groups of 3 samples of the same developmental stage, experiment date, and antibody (including the IgG control antibody).
For each developmental stage and experiment date, the 3-sample coverage of an antibody was compared to the 3-sample coverage of the IgG control antibody using the SEACR program with the "norm" and "stringent" parameters.
The SEACR bed file of peaks was converted to a track in the bigBed format
Assembly: mm10
Supplementary files format and content: bigWig coverage tracks of the end-to-end mappings of the paired-end reads
Supplementary files format and content: bigBed track of SEACR stringent peak loci
Library strategy: CUT&Tag

source_name: cerebral cortex

extract_protocol:
Cortices were dissected, and cells were isolated with the Accumax (Sigma-Aldrich A7089) following the manufacturer’s instructions. 100,000 cells were used for each experiment
CUT&RUN, DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645, E7103) with index primers (NEB, E7335L, E7500L).

value: cerebral cortex

tag: develpmental stage

value: wildtype

value: Cut&Run


title: iPSC-CM, ventricular, WT/WT, rep 3


title: p00_rbsatb2x_bc545

description: Library name: bc545


title: CUTAC_combo_0h_1_(240722_CD_Hs_1223)

description:
Library name: CUTAC_combo_0h_1
RNA Polymerase II Serine-5P-based CUTAC in untreated MDA-MB-231 cells for co-treatment series.


title: WT-PHx48h-1 [snRNA-seq]

city: 上海

first: shuqing

last: Liu

address: 415 Fengyang Road

department: gastroenterology

country: China

institute: shanghai changzheng hospital

data_processing:
The raw FASTQ data of snRNA-seq were processed by CellRanger (5.0.0) to generate the gene expression that was further analyzed using the Seurat package (version 3.2.0)
Assembly: FASTQs  generated  from  Illumina  sequencing  output  were  aligned  to  the  mouse genome, version GRCm38, using the  STAR algorithm
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: nuclear RNA

source_name: liver

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
For 10 × library preparation, each cDNA molecule was tagged on the 3’end of a mRNA transcript with unique molecular identifiers (UMI) and cell labels indicating its cell of origin on cDNA synthesis.

value: liver

value: liver cell

value: 12-week old

value: PHx


title: HKO-PHx48h-1 [snRNA-seq]


title: iPSC-CM, atrial, WT/TTNtv, rep 2


title: iPSC-CM, ventricular, WT/TTNtv, rep 3


title: CDK12_combo_8h_2_(240722_CD_Hs_1222)

description:
Library name: CDK12_combo_8h_2
CUT&Tag targeting CDK12 in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 8 hours.

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments.
4. We used bedtools 2.30.0 "genomecov" to make a normalized count track which is the fraction of counts at each base pair scaled by the size of the reference sequence so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .bw)
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

value: MDA-MB-231 human breast cancer epthileal cells  (ATCC HTB-26).

value: Anti-CDK12 from Millipore Sigma (ABE1861).


title: e13_rbnr2f1x_bc562

description: Library name: bc562


title: CDK12_combo_8h_1_(240722_CD_Hs_1221)

description:
Library name: CDK12_combo_8h_1
CUT&Tag targeting CDK12 in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 8 hours.


title: e13_rbnr2f1x_bc561

description: Library name: bc561


title: iPSC-CM, atrial, WT/WT, rep 1

value: Isogenic AF patient iPSCs


title: WT-PHx48h-2

data_processing:
CLC Genomics Workbench v 11.0.1
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
According to the instructions of the experiment, the purified Total RNA was separated into mRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

value: hepatocyte

value: WT

value: partial hepatectomy (PHx)


title: iPSC-CM, atrial, WT/TTNtv, rep 1


title: iPSC-CM, ventricular, WT/TTNtv, rep 2

value: ventricular-like


title: CDK12_combo_4h_2_(240722_CD_Hs_1220)

description:
Library name: CDK12_combo_4h_2
CUT&Tag targeting CDK12 in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 4 hours.


title: CUTAC_combo_2h_2_(240722_CD_Hs_1226)

description:
Library name: CUTAC_combo_2h_2
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 2 hours.


title: WT-PHx48h-3


title: WT-PHx48h-1


title: iPSC-CM, ventricular, WT/TTNtv, rep 1


title: CDK12_combo_4h_1_(240722_CD_Hs_1219)

description:
Library name: CDK12_combo_4h_1
CUT&Tag targeting CDK12 in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 4 hours.


title: HKO-PHx48h-3

value: HKO


title: p00_wtn_rbbcl11ax_bc917

description: Library name: bc917


title: CDK12_combo_2h_2_(240722_CD_Hs_1218)

description:
Library name: CDK12_combo_2h_2
CUT&Tag targeting CDK12 in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 2 hours.


title: p00_wtn_rbbcl11ax_bc916

description: Library name: bc916


title: CDK12_combo_2h_1_(240722_CD_Hs_1217)

description:
Library name: CDK12_combo_2h_1
CUT&Tag targeting CDK12 in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 2 hours.


title: HKO-PHx48h-2


title: HKO-PHx48h-1


title: p00_wtn_rbbcl11ax_bc915

description: Library name: bc915


title: KP Rosa26-tdTomato/+ tumors harvested at 14 weeks post tumor initiation, repilcate, HTO

city: New York

first: Jason

middle: Earl

last: Chan

state: NY

address: 1275 York Ave, Box 20

department: Medicine

institute: Memorial Sloan Kettering Cancer Center

description:
AdSPC-Cre
IGO15488_2.featureref.csv

library_source: other

data_processing:
FASTQ files of single-cell RNA-sequencing data generated on the 10X Chromium platform were processed using the standard CellRanger pipeline (version >=6.0.0). Reads were aligned to a custom GRCm38 / mm10 reference containing additional transgenes used in the study. The generated cell-gene count matrices were analyzed using a combination of published packages and custom scripts in either the scanpy (v> 1.9.0) / AnnData (v. 0.10.5, Python)
Assembly: GRCm38/mm10
Supplementary files format and content: h5ad
Library strategy: HTO

molecule: protein

source_name: lung

growth_protocol: Cells were isolated from animals. No additional growth was involved.

extract_protocol: Encapsulation and library preparation were performed using the 10X Genomics Chromium Single Cell 3’ Library & Gel bead Kit V3 (10X Genomics, PN-1000121) according to the manufacturer’s protocol. Libraries were sequenced using the Nova-Seq 6000 platform (Illumina).

treatment_protocol: KP mice with either Slc4a11-FSF-MCD/+ or Hopx-FSF-MACD/+ alleles with either Hipp11-FSF-GGCB/+ or Rosa26-FSF-mTmG/+ reporter alleles were infected by adenoviral CMV-FlpO or lentiviral PGK-FlpO recombinase. Mice bearing tumors were treated with either Tamoxifen, Diphtheria toxin, or saline with or without Cisplatin and MRTX1133 as indicated, and tumor cells were isolated, hashed using TotalSeq-B antibodies, and processed for single-cell mRNA sequencing after FACS purification. One dataset contains KP Rosa26-tdTomato/+ tumors used in this study.

value: lung

value: Primary tumor cells

value: Tumor cells


title: sivps35-2+AC

city: Los Angeles

first: Bishuang

last: Cai

address: 675 Charles E. Young Dr South, Rm 1220

institute: University of California, Los Angeles

description:
Library name: GC17
bulk RNA-seq

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality. Reads were pre-processed by Trim Galore (v.0.6.3) and Cutadapt programs.
Reads were aligned to the mouse genome mm10 using STAR (v2.7.6a) with the default settings.
Transcript assembly and differential expression analysis were performed using Cufflinks (v2.2.1). Assembling of novel transcripts was not allowed (-G), other parameters of Cufflinks followed the default setting.
A tab-delimited matrix file containing FPKM+1 values for RefSeq genes in each sample generated using Cufflinks.
Assembly: mm10
Supplementary files format and content: tab-delimited text file

source_name: Bone marrow-derived macrophages

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer’s instructions
RNA-seq library construction was performed at Innomics Inc. with a standard polyA-enrichment protocol.

treatment_protocol: Mouse bone marrow-derived macrophages (BMDMs) were treated with siVps35 and incubated with apoptotic cells (AC).

value: Bone marrow-derived macrophages

value: BMDM

tag: Sex

value: Male

value: 8 weeks

value: BMDMs with siVps35 and AC treatment


title: p00_wtn_rbcux1xxx_bc923

description: Library name: bc923

value: cerebral cortex

value: wildtype

value: Cut&Run


title: sicon-3+AC

description:
Library name: GC6
bulk RNA-seq

value: BMDMs with siControl and AC treatment


title: sivps35-3+AC

description:
Library name: GC18
bulk RNA-seq


title: sivps35-1+AC

description:
Library name: GC16
bulk RNA-seq


title: CDK12_combo_0h_2_(240722_CD_Hs_1216)

description:
Library name: CDK12_combo_0h_2
CUT&Tag targeting CDK12 in untreated MDA-MB-231 cells for co-treatment series.

value: MDA-MB-231 human breast cancer epthileal cells  (ATCC HTB-26).

value: Anti-CDK12 from Millipore Sigma (ABE1861).


title: CDK12_combo_0h_1_(240722_CD_Hs_1215)

description:
Library name: CDK12_combo_0h_1
CUT&Tag targeting CDK12 in untreated MDA-MB-231 cells for co-treatment series.


title: e13_rbnr2f1x_bc560

description: Library name: bc560


title: KP Rosa26-tdTomato/+ tumors harvested at 14 weeks post tumor initiation, replicate, GEX

description:
AdSPC-Cre
IGO15488_2.featureref.csv

data_processing:
FASTQ files of single-cell RNA-sequencing data generated on the 10X Chromium platform were processed using the standard CellRanger pipeline (version >=6.0.0). Reads were aligned to a custom GRCm38 / mm10 reference containing additional transgenes used in the study. The generated cell-gene count matrices were analyzed using a combination of published packages and custom scripts in either the scanpy (v> 1.9.0) / AnnData (v. 0.10.5, Python)
Assembly: GRCm38/mm10
Supplementary files format and content: h5ad


title: p00_wtn_rbcux1xxx_bc922

description: Library name: bc922


title: sicon-2+AC

description:
Library name: GC5
bulk RNA-seq


title: p00_wtn_rbcux1xxx_bc921

description: Library name: bc921


title: KP Rosa26-tdTomato/+ tumors harvested at 14 weeks post tumor initiation, HTO

description:
AdSPC-Cre
IGO15488_1.featureref.csv


title: sicon-1+AC

description:
Library name: GC4
bulk RNA-seq


title: BRG1_combo_8h_2_(240722_CD_Hs_1214)

description:
Library name: BRG1_combo_8h_2
CUT&Tag targeting BRG1 in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 8 hours.

value: Anti-BRG1 antibody [EPNCIR111A] from Abcam (ab110641).


title: e15_gtlhx2xx_bc649

description: Library name: bc649


title: BRG1_combo_4h_2_(240722_CD_Hs_1212)

description:
Library name: BRG1_combo_4h_2
CUT&Tag targeting BRG1 in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 4 hours.


description:
Library name: IGO17721-Hopx-BG-Saline
KPfrt Hopx-MACD/+ BG/+  cell line; tail vein injected, harvested 5 weeks post transplant (1 week Saline), GEX

growth_protocol: Tumors were isolated from animals with transplanted cell lines. No additional growth is involved.

extract_protocol:
Encapsulation and library preparation were performed using the 10X Genomics Chromium Single Cell 3’ Library & Gel bead Kit V3 (10X Genomics, PN-1000121) according to the manufacturer’s protocol. Libraries were sequenced using the Nova-Seq X platform (Illumina).
Encapsulation and library preparation were performed using the 10X Genomics Chromium Single Cell 3’ Library & Gel bead Kit V3 (10X Genomics, PN-1000121) according to the manufacturer’s protocol. Libraries were sequenced using the Nova-Seq X platform (Illumina).

treatment_protocol: Cell line transplants were treated with Saline or Diphtheria toxin as indicated and tumor cells were isolated for single-cell mRNA sequencing after FACS purification.

value: cancer

value: Kras-G12D/+ Trp53-Frt/Frt Hopx-MACD/+ Hipp11-BG/+

value: Saline

tag: batch


title: KPfrt Hopx-MACD/+ Hipp11-GGCB/+ tumor cells harvested 16 weeks PTI, HTO

description:
PGK-FlpO induced tumors
IGO16318.featureref.csv

value: lung

value: Primary tumor cells

value: Kras-G12D/+ Trp53-delta/delta Hopx-MACD/+ Hipp11-GGCB/+


title: e15_gtlhx2xx_bc648

description: Library name: bc648


title: e15_gtlhx2xx_bc647

description: Library name: bc647


title: KPfrt Hopx-MACD/+ Hipp11-GGCB/+ tumor cells harvested 16 weeks PTI, GEX

value: Tumor cells


title: BRG1_combo_4h_1_(240722_CD_Hs_1211)

description:
Library name: BRG1_combo_4h_1
CUT&Tag targeting BRG1 in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 4 hours.


title: KP Rosa26-tdTomato/+ tumors harvested at 14 weeks post tumor initiation, GEX

description:
AdSPC-Cre
IGO15488_1.featureref.csv


title: e12_h3k27me3_bc532

description: Library name: bc532


title: BRG1_combo_2h_2_(240722_CD_Hs_1210)

description:
Library name: BRG1_combo_2h_2
CUT&Tag targeting BRG1 in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 2 hours.


title: KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumors treated and harvested at 17 weeks PTI after 3 weeks of tracing, HTO, rep1

description:
PGK-FlpO induced tumors
IGO16235.featureref.csv

value: Kras-G12D/+ Trp53-delta/delta Slc4a11-MCD/+ Rosa26-mTmG/+

value: Tamoxifen, cisplatin, MRTX1133


title: BRG1_combo_8h_1_(240722_CD_Hs_1213)

description:
Library name: BRG1_combo_8h_1
CUT&Tag targeting BRG1 in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 8 hours.


title: BRG1_combo_2h_1_(240722_CD_Hs_1209)

description:
Library name: BRG1_combo_2h_1
CUT&Tag targeting BRG1 in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 2 hours.


title: RNA extracted from AB1-mCherry sorted cells from pleural tumour, mouse 3.3

city: Crawley

first: M. Lizeth

last: Orozco Morales

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

description:
Library name: CELL_PL3
CELL_TPM.txt

data_processing:
Alignment was performed using Kallisto, mapped to the mouse genome Release M29 (GRCm39)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: Pleural tumour

growth_protocol: AB1-mCherry cells were assessed for mCherry under a fluorescent microscope. 5% brightest AB1-mCherry cells were then sorted using the BD Influx System (USB) hardware and BD FACSTM Software. These cells were then cultured and used for further experiments. Cells were maintained in complete R10 medium, RPMI 1640 (Invitrogen) supplemented with 10% newborn calf serum (NCS; Life Technologies), 20 mM HEPES (Sigma-Aldrich), 0.05 mM 2-mercaptoethanol (pH 7.2; Merck, Kilsyth, Australia), 60 µg/mL penicillin (Life Technologies), 50 µg/mL gentamicin (David Bull Labs). Cells were confirmed mycoplasma negative by polymerase chain reaction. Cells were cultured as a monolayer at 37 C in a humidified atmosphere with 5% CO2. Cells were passaged at approximately 1:10-1:5 every 2-3 days when reaching 75-80% confluence.

extract_protocol:
Whole tumour processing. Tumours were submerged in RNAprotect Tissue Reagent (QIAGEN, 76104) at 4 C for 72 h to allow RNAprotect to penetrate the tissue. Then, tumours were removed from RNAprotect and stored at –80C. RNA extraction was performed with the RNeasy Plus Mini Kit (QIAGEN, 74134) following manufacturer’s instructions for animal tissues. Tumours were dissociated with the TissueRuptor II (QIAGEN, 9002758) and TissueRuptor Disposable Probes (QIAGEN, 990890) in 600 µL of RLT Buffer. Final elution was performed in 30 µL RNAse-free water. Sorted tumour cells processing. After sorting, tumour cells were stored in RNAprotect Cell Reagent (QIAGEN, 76526) at -80 C. RNA extraction was performed with the RNeasy Plus Micro Kit (QIAGEN, 74034) following manufacturer’s instructions for Cells and fine-needle aspirates. 75 µL of RLT Buffer were added to each sample. Final elution was performed in 14 µL RNAse-free water.
Library preparation and sequencing for both whole tumour and tumour cells samples were performed at 50 bp single end reads with Illumina HiSeq standard protocols by Australian Genome Research Facility.

treatment_protocol: No treatment was given to mice

value: Pleural tumour

value: murine mesothelioma

value: untreated

tag: sample collection_day

value: Day 10

value: BALB/c

value: 12 weeks

value: female


title: RNA extracted from AB1-mCherry sorted cells from pleural tumour, mouse 3.5

description:
Library name: CELL_PL5
CELL_TPM.txt


title: RNA extracted from AB1-mCherry sorted cells from pleural tumour, mouse 3.4

description:
Library name: CELL_PL4
CELL_TPM.txt


title: KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumors treated and harvested at 17 weeks PTI after 3 weeks of tracing, GEX, rep1


title: e12_h3k27me3_bc530

description: Library name: bc530

value: cerebral cortex

value: wildtype

value: Cut&Run


description:
Library name: IGO17721-Hopx-BG-DT
KPfrt Hopx-MACD/+ BG/+  cell line; tail vein injected, harvested 5 weeks post transplant (1 week DT), GEX

value: cancer

value: Kras-G12D/+ Trp53-Frt/Frt Hopx-MACD/+ Hipp11-BG/+

value: DT


title: BRG1_combo_0h_2_(240722_CD_Hs_1208)

description:
Library name: BRG1_combo_0h_2
CUT&Tag targeting BRG1 in untreated MDA-MB-231 cells for co-treatment series.

value: MDA-MB-231 human breast cancer epthileal cells  (ATCC HTB-26).

value: Anti-BRG1 antibody [EPNCIR111A] from Abcam (ab110641).


title: KPfrt Slc4a11-MCD/+ Hipp11-GGCB/+ tumor cells harvested 16 weeks PTI after 1 week of ablation, replicate, HTO

description:
PGK-FlpO induced tumors
IGO15342.featureref.csv

value: lung

value: Primary tumor cells

value: Tumor cells

value: Kras-G12D/+ Trp53-delta/delta Slc4a11-MCD/+ Hipp11-GGCB/+


title: RNA extracted from AB1-mCherry sorted cells from pleural tumour, mouse 3.2

description:
Library name: CELL_PL2
CELL_TPM.txt

value: Pleural tumour

value: murine mesothelioma

value: untreated


title: KPfrt Slc4a11-MCD/+ Hipp11-GGCB/+ tumor cells harvested 16 weeks PTI after 1 week of ablation, replicate, GEX


title: e12_h3k4me3x_bc538

description: Library name: bc538


title: RNA extracted from AB1-mCherry sorted cells from pleural tumour, mouse 3.1

description:
Library name: CELL_PL1
CELL_TPM.txt

value: Day 10

value: BALB/c

value: 12 weeks


title: BRG1_combo_0h_1_(240722_CD_Hs_1207)

description:
Library name: BRG1_combo_0h_1
CUT&Tag targeting BRG1 in untreated MDA-MB-231 cells for co-treatment series.


title: RNA extracted from AB1-mCherry sorted cells from peritoneal tumour, mouse 2.5

description:
Library name: CELL_IP5
CELL_TPM.txt

source_name: Peritoneal tumour

value: Peritoneal tumour

value: female


title: BRG1_FHT1015_8h_2_(240403_CD_Hs_932)

description:
Library name: BRG1_FHT1015_8h_2
CUT&Tag targeting BRG1 in MDA-MB-231 cells treated with 1uM FHT1015 for 8 hours.


title: KPfrt Slc4a11-MCD/+ Hipp11-GGCB/+ tumor cells harvested 16 weeks PTI after 1 week of ablation, HTO

description:
PGK-FlpO induced tumors
IGO15123.featureref.csv


title: RNA extracted from AB1-mCherry sorted cells from peritoneal tumour, mouse 2.4

description:
Library name: CELL_IP4
CELL_TPM.txt


title: KPfrt Slc4a11-MCD/+ Hipp11-GGCB/+ tumor cells harvested 16 weeks PTI after 1 week of ablation, GEX


title: e12_h3k27me3_bc531

description: Library name: bc531

value: cerebral cortex

value: wildtype

value: Cut&Run


title: RNA extracted from AB1-mCherry sorted cells from peritoneal tumour, mouse 2.3

description:
Library name: CELL_IP3
CELL_TPM.txt


title: CDK12_FHT1015_8h_2_(240403_CD_Hs_931)

description:
Library name: CDK12_FHT1015_8h_2
CUT&Tag targeting CDK12 in MDA-MB-231 cells treated with 1uM FHT1015 for 8 hours.

value: MDA-MB-231 human breast cancer epthileal cells  (ATCC HTB-26).

value: Anti-CDK12 from Millipore Sigma (ABE1861).


title: CUTAC_FHT1015_8h_1_(240403_CD_Hs_930)

description:
Library name: CUTAC_FHT1015_8h_1
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells treated with 1uM FHT1015 for 8 hours.

value: Anti-RNA Polymerase CTD repeat YSPTSPS (phospho S5) antibody [4H8] from abcam (ab5408).


title: e12_h3k27acx_bc541

description: Library name: bc541


title: e12_h3k27acx_bc540

description: Library name: bc540


title: KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+  tumor cells harvested 14 weeks PTI after 2 weeks of tracing, replicates, GEX

description:
PGK-FlpO induced tumors
IGO15771.featureref.csv

value: lung

value: Primary tumor cells

value: Kras-G12D/+ Trp53-delta/delta Slc4a11-MCD/+ Rosa26-mTmG/+

value: Tamoxifen


title: BRG1_FHT1015_8h_1_(240403_CD_Hs_925)

description:
Library name: BRG1_FHT1015_8h_1
CUT&Tag targeting BRG1 in MDA-MB-231 cells treated with 1uM FHT1015 for 8 hours.

value: Anti-BRG1 antibody [EPNCIR111A] from Abcam (ab110641).


title: RNA extracted from AB1-mCherry sorted cells from peritoneal tumour, mouse 2.1

description:
Library name: CELL_IP1
CELL_TPM.txt

value: murine mesothelioma

value: untreated


title: RNA extracted from AB1-mCherry sorted cells from peritoneal tumour, mouse 2.2

description:
Library name: CELL_IP2
CELL_TPM.txt

value: Day 10

value: BALB/c


title: CDK12_FHT1015_8h_1_(240403_CD_Hs_924)

description:
Library name: CDK12_FHT1015_8h_1
CUT&Tag targeting CDK12 in MDA-MB-231 cells treated with 1uM FHT1015 for 8 hours.


title: KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+  tumor cells harvested 14 weeks PTI after 2 weeks of tracing, replicates, HTO

value: Tumor cells


title: CUTAC_FHT1015_8h_2_(240403_CD_Hs_937)

description:
Library name: CUTAC_FHT1015_8h_2
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells treated with 1uM FHT1015 for 8 hours.


title: KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+  tumor cells harvested 8 weeks PTI after 2 weeks of tracing, HTO

description:
PGK-FlpO induced tumors
IGO15601.featureref.csv


title: KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+  tumor cells harvested 14 weeks PTI after 2 weeks of tracing, HTO

description:
PGK-FlpO induced tumors
IGO15600.featureref.csv


title: p00_idnax0915_bc835

description: Library name: bc835

data_processing:
Paired end reads were trimmed to 37x37bp and mapped using Bowtie2 against the set of mouse RepeatMasker elements.
Paired end reads that mapped to repeat elements were discarded. The remaining reads were mapped using Bowtie2 to the mm10 genome.
The mappings were converted to bedGraph coverage using bedTools genomeCoverageBed, and then to bigWig using bedGraphToBigWig
The repeat-filtered control (input DNA) replicate mappings were concatenated into a single set for use in IDR processing.
For each antibody, there were 2 repeat-filtered replicates as well as associated pseudo replicates for use in IDR processing.
Peaks were called for the replicates and pseudo-replicates from each antibody using MACS2 with a very permissive p-value cutoff of 0.5 to generate a large set of peaks for processing by IDR.
The top 100,000 MACS2 peaks for the replicates and pseudo-replicates were processed by IDR and then filtered using  thresholds for the original replicates, self pseudo replicates, and pooled pseudo replicates of 0.01, 0.02, 0.01 respectively
The optimal set of peaks selected by IDR using the above criteria were extracted into a narrowPeak bed file.
Assembly: mm10
Supplementary files format and content: bigwig files of coverage for each sample's genomic mapping
Supplementary files format and content: narrowPeak files from IDR processing of replicates for the 2 different antibodies.

extract_protocol:
P0 wild type cortices were dissected, fixed for 10 min with 1% formaldehyde and neutralized with glycine. The cells were lysed, and the chromatin was sheared into 100∼300 bp fragments. Immunoprecipitation reactions were performed using the Satb2 antibodies
ChIPed DNA and input DNA were used. DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645, E7103) with index primers (NEB, E7335L).

tag: chip antibody

value: input DNA


title: p00_idnax0915_bc834

description: Library name: bc834

value: cerebral cortex


title: KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+  tumor cells harvested 8 weeks PTI after 2 weeks of tracing, GEX


title: RNA extracted from AB1-mCherry sorted cells from subcutaneous tumour, mouse 1.4

description:
Library name: CELL_SC4
CELL_TPM.txt

source_name: Subcutaneous tumour

value: Subcutaneous tumour

value: 12 weeks

value: female


title: RNA extracted from AB1-mCherry sorted cells from subcutaneous tumour, mouse 1.5

description:
Library name: CELL_SC5
CELL_TPM.txt


title: CUTAC_FHT1015_4h_2_(240403_CD_Hs_923)

description:
Library name: CUTAC_FHT1015_4h_2
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells treated with 1uM FHT1015 for 4 hours.

value: MDA-MB-231 human breast cancer epthileal cells  (ATCC HTB-26).


title: e12_h3k4me3x_bc536

description: Library name: bc536

value: wildtype

value: Cut&Run


title: e12_h3k4me3x_bc537

description: Library name: bc537


title: BRG1_FHT1015_4h_2_(240403_CD_Hs_918)

description:
Library name: BRG1_FHT1015_4h_2
CUT&Tag targeting BRG1 in MDA-MB-231 cells treated with 1uM FHT1015 for 4 hours.


title: RNA extracted from AB1-mCherry sorted cells from subcutaneous tumour, mouse 1.3

description:
Library name: CELL_SC3
CELL_TPM.txt


title: p00_idnax0828_bc807

description: Library name: bc807


title: CDK12_FHT1015_4h_2_(240403_CD_Hs_917)

description:
Library name: CDK12_FHT1015_4h_2
CUT&Tag targeting CDK12 in MDA-MB-231 cells treated with 1uM FHT1015 for 4 hours.

value: Anti-CDK12 from Millipore Sigma (ABE1861).


title: p00_idnax0828_bc801

description: Library name: bc801


title: e12_h3k27acx_bc539

description: Library name: bc539


title: KPfrt Slc4a11-MCD/+ Hipp11-GGCB/+ tumor cells harvested 16 weeks PTI after 2 weeks of tracing, HTO

description:
AdCMV-FlpO induced tumors
IGO14143.featureref.csv

value: lung

value: Primary tumor cells

value: Kras-G12D/+ Trp53-delta/delta Slc4a11-MCD/+ Hipp11-GGCB/+


title: RNA extracted from AB1-mCherry sorted cells from subcutaneous tumour, mouse 1.2

description:
Library name: CELL_SC2
CELL_TPM.txt

value: murine mesothelioma


title: KPfrt Slc4a11-MCD/+ Hipp11-GGCB/+ tumor cells harvested 16 weeks PTI after 2 weeks of tracing, GEX

value: Tamoxifen


title: RNA extracted from AB1-mCherry sorted cells from subcutaneous tumour, mouse 1.1

description:
Library name: CELL_SC1
CELL_TPM.txt

value: untreated

value: Day 10


title: CUTAC_FHT1015_4h_1_(240403_CD_Hs_916)

description:
Library name: CUTAC_FHT1015_4h_1
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells treated with 1uM FHT1015 for 4 hours.

value: Anti-RNA Polymerase CTD repeat YSPTSPS (phospho S5) antibody [4H8] from abcam (ab5408).


title: p00_rbpcsatb2_bc816

description: Library name: bc816

value: rabbit polyclonal satb2

value: ChIP-seq


title: p00_rbpcsatb2_bc808

description: Library name: bc808

value: cerebral cortex


title: CDK12_FHT1015_4h_1_(240403_CD_Hs_910)

description:
Library name: CDK12_FHT1015_4h_1
CUT&Tag targeting CDK12 in MDA-MB-231 cells treated with 1uM FHT1015 for 4 hours.


title: liver, RIC_hEV, rep4

city: Shanghai

first: Yichao

last: Zhao

state: China

address: #160 Pujian Road, Shanghai,China

department: Renji Hospital

institute: Shanghai Jiaotong University

data_processing:
Quality control of raw sequencing data was performed using FastQC (v0.11.9)
Raw reads were processed using Trimmomatic (v0.38) according to the quality control report of each sample.
Clean reads were mapped to the genome using hisat2 (v2.2.1) with default parameters.
The number of aligned reads for each gene was counted with the htseq-count (v0.13.5) program.
Differential expression analysis was performed in R (v3.4.1) using DESeq2 (v1.18.1).
Assembly: Assembly: mm10
Supplementary files format and content: Comma separated value files include FPKM values for each sample

growth_protocol: Mice were fed a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) to induce nonalcoholic steatohepatitis (NASH), and were intravenously injected with circulating extracellular vesicles (EVs) isolated from human volunteers subjected to remote limb ischemic conditioning (RIC)  or sham treatment . Liver tissues were harvested and subjected to RNA-sequencing.

extract_protocol:
Total RNA was extracted using the Trizol method following the manufacturer’s protocol
RNA libararies for RNA-seq were prepared using VAHTSUniversalRNA-seqLibraryPrepKitforIllumina following the manufacturer’s protocol

value: liver

value: WT


title: p00_rbmcsatb2_bc817

description: Library name: bc817

value: rabbit monoclonal satb2


title: liver, RIC_hEV, rep3


title: CUTAC_FHT1015_2h_2_(240403_CD_Hs_909)

description:
Library name: CUTAC_FHT1015_2h_2
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells treated with 1uM FHT1015 for 2 hours.

value: MDA-MB-231 human breast cancer epthileal cells  (ATCC HTB-26).


title: liver, RIC_hEV, rep2


title: liver, RIC_hEV, rep1


title: KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+  tumor cells harvested 14 weeks PTI after 2 weeks of tracing, GEX

value: Tumor cells

value: Kras-G12D/+ Trp53-delta/delta Slc4a11-MCD/+ Rosa26-mTmG/+


title: BRG1_FHT1015_2h_2_(240403_CD_Hs_904)

description:
Library name: BRG1_FHT1015_2h_2
CUT&Tag targeting BRG1 in MDA-MB-231 cells treated with 1uM FHT1015 for 2 hours.

value: Anti-BRG1 antibody [EPNCIR111A] from Abcam (ab110641).


title: RNA extracted from AB1-mCherry pleural whole tumour, mouse 3.4

description:
Library name: TUM_PL_4
TUM_TPM.txt

value: Pleural tumour

value: BALB/c

value: 12 weeks

value: female


title: RNA extracted from AB1-mCherry pleural whole tumour, mouse 3.7

description:
Library name: TUM_PL_7
TUM_TPM.txt

value: murine mesothelioma

value: untreated


title: RNA extracted from AB1-mCherry pleural whole tumour, mouse 3.5

description:
Library name: TUM_PL_5
TUM_TPM.txt

value: Day 10


title: RNA extracted from AB1-mCherry pleural whole tumour, mouse 3.3

description:
Library name: TUM_PL_3
TUM_TPM.txt


title: CDK12_FHT1015_2h_2_(240403_CD_Hs_903)

description:
Library name: CDK12_FHT1015_2h_2
CUT&Tag targeting CDK12 in MDA-MB-231 cells treated with 1uM FHT1015 for 2 hours.

value: Anti-CDK12 from Millipore Sigma (ABE1861).


title: liver, ctr_hEV, rep4


title: BRG1_FHT1015_4h_1_(240403_CD_Hs_911)

description:
Library name: BRG1_FHT1015_4h_1
CUT&Tag targeting BRG1 in MDA-MB-231 cells treated with 1uM FHT1015 for 4 hours.


title: RNA extracted from AB1-mCherry pleural whole tumour, mouse 3.2

description:
Library name: TUM_PL_2
TUM_TPM.txt


title: CUTAC_FHT1015_2h_1_(240403_CD_Hs_902)

description:
Library name: CUTAC_FHT1015_2h_1
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells treated with 1uM FHT1015 for 2 hours.

value: Anti-RNA Polymerase CTD repeat YSPTSPS (phospho S5) antibody [4H8] from abcam (ab5408).


title: liver, ctr_hEV, rep3


title: BRG1_FHT1015_2h_1_(240403_CD_Hs_897)

description:
Library name: BRG1_FHT1015_2h_1
CUT&Tag targeting BRG1 in MDA-MB-231 cells treated with 1uM FHT1015 for 2 hours.


title: RNA extracted from AB1-mCherry pleural whole tumour, mouse 3.1

description:
Library name: TUM_PL_1
TUM_TPM.txt


title: p00_rbmcsatb2_bc809

description: Library name: bc809

value: cerebral cortex

value: wildtype

value: ChIP-seq


title: liver, ctr_hEV, rep2

value: liver

value: WT


title: RNA extracted from AB1-mCherry peritoneal whole tumour, mouse 2.7

description:
Library name: TUM_IP_7
TUM_TPM.txt

value: Peritoneal tumour


title: CDK12_FHT1015_2h_1_(240403_CD_Hs_896)

description:
Library name: CDK12_FHT1015_2h_1
CUT&Tag targeting CDK12 in MDA-MB-231 cells treated with 1uM FHT1015 for 2 hours.

value: MDA-MB-231 human breast cancer epthileal cells  (ATCC HTB-26).


title: Female Trim24-gRNA rep2

type: RNA

city: Isehara

first: Akihide

last: Kamiya

state: Kanagawa

address: 143 Shimokasuya

country: Japan

institute: Tokai University

description:
Gene expression in female Tim24 knockdown mouse liver
Oct12_2_4-559(normalized)

hyb_protocol: The labelled cRNA was hybridized to the Agilent Whole Mouse Genome Microarray v2 8×60k following manufacture's protocol.

scan_protocol: Arrays were scanned using Agilent Technologies G2600D SG13164306

data_processing:
The scanned images were analyzed with Agilent Feature Extraction 11.5.1.1 (Agilent Technology) using default parameters.
The raw signal intensities were log2 transformed and normalized by 75 percent tile shift using Gene spring GX software (Agilent Technology).

source_name: Female Cas9-knockin mouse (with Trim24 gRNA) rep2

label_protocol: Cy3 labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions. cRNA was quantified with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from liver tissues with Trizol reagents following manufacture's protocol. Extracted RNA quality was checked by the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: whole liver

value: Female

value: Cas9-knockin mouse (with Trim24 gRNA)


title: CUTAC_THZ531_8h_2_(240403_CD_Hs_853)

description:
Library name: CUTAC_THZ531_8h_2
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells treated with 400nM THZ531 for 8 hours.


title: Female Cux2, Sall1, Trim24-gRNA rep2

description:
Gene expression in female Cux2, Sall1, Tim24 knockdown mouse liver
Oct12_2_2-835(normalized)

source_name: Female Cas9-knockin mouse (with Cux2, Sall1, Trim24 gRNA) rep2


title: RNA extracted from AB1-mCherry peritoneal whole tumour, mouse 2.4

description:
Library name: TUM_IP_5
TUM_TPM.txt

value: BALB/c

value: 12 weeks


title: Female Trim24-gRNA rep1

description:
Gene expression in female Tim24 knockdown mouse liver
Oct12_2_3-404(normalized)

source_name: Female Cas9-knockin mouse (with Trim24 gRNA) rep1


title: liver, CDAHFD_RIC, rep4

growth_protocol: Mice were fed a normal chow (NC) or a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) to induce nonalcoholic steatohepatitis (NASH), and were subjected to remote limb ischemic conditioning (RIC) or sham treatment. Liver tissues were harvested and subjected to RNA-sequencing.


title: BRG1_THZ531_8h_2_(240403_CD_Hs_848)

description:
Library name: BRG1_THZ531_8h_2
CUT&Tag targeting BRG1 in MDA-MB-231 cells treated with 400nM THZ531 for 8 hours.

value: Anti-BRG1 antibody [EPNCIR111A] from Abcam (ab110641).


title: RNA extracted from AB1-mCherry peritoneal whole tumour, mouse 2.3

description:
Library name: TUM_IP_4
TUM_TPM.txt

value: murine mesothelioma

value: untreated

value: female


title: RNA extracted from AB1-mCherry peritoneal whole tumour, mouse 2.2

description:
Library name: TUM_IP_3
TUM_TPM.txt

value: Day 10


title: CDK12_THZ531_8h_2_(240403_CD_Hs_847)

description:
Library name: CDK12_THZ531_8h_2
CUT&Tag targeting CDK12 in MDA-MB-231 cells treated with 400nM THZ531 for 8 hours.

value: Anti-CDK12 from Millipore Sigma (ABE1861).


title: liver, CDAHFD_RIC, rep3


title: Male negative control rep2

description:
Gene expression in Male control mouse liver
Oct12_1_4-837(normalized)

source_name: Male Cas9-knockin mouse (negative control) rep2

value: Male

value: Cas9-knockin mouse (negative control)


title: RNA extracted from AB1-mCherry peritoneal whole tumour, mouse 2.1

description:
Library name: TUM_IP_1
TUM_TPM.txt


title: RNA extracted from AB1-mCherry subcutaneous whole tumour, mouse 1.5

description:
Library name: TUM_SC_5
TUM_TPM.txt

value: Subcutaneous tumour


title: BRG1_THZ531_8h_1_(240403_CD_Hs_841)

description:
Library name: BRG1_THZ531_8h_1
CUT&Tag targeting BRG1 in MDA-MB-231 cells treated with 400nM THZ531 for 8 hours.


title: CUTAC_THZ531_8h_1_(240403_CD_Hs_846)

description:
Library name: CUTAC_THZ531_8h_1
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells treated with 400nM THZ531 for 8 hours.

value: Anti-RNA Polymerase CTD repeat YSPTSPS (phospho S5) antibody [4H8] from abcam (ab5408).


title: liver, CDAHFD_RIC, rep1

value: liver

value: WT


title: liver, ctr_hEV, rep1


title: liver, CDAHFD_RIC, rep2


title: liver, CDAHFD_sham, rep4


title: Sir2a H3K14ac ChIP Rep2

city: Paris

first: Sebastian

last: Baumgarten

address: 25, Rue du Dr. Roux

department: Parasites and Insect Vectors

country: France

institute: Institut Pasteur

description: Library name: Sir2a H3K14ac ChIP Rep2

data_processing:
Raw read pre-processing and adapter trimming were performed using bcl2fastq and trimmomatic. A reference genome in which the regions Pf3D7_05_v3:1286689-1300188 (encpdoing for the A1 rDNA locus) and Pf3D7_13_v3:2789345-2808200 (encoding for the S3 rDNA locus) are masked was created using bedtools maskfasta. Trimmed reads were aligned to the masked genome using bowtie2 with settings ‘--no-mixed --no-discordant --end-to-end --sensitive’. Alignments were subsequently filtered for PCR duplicates using samtools ‘fixmate’ and ‘markdup’ and only alignments with a mapping quality ≥ 30 were retained (samtools view -q 30). To calculate differences in HMGB1 occupancy at rDNA loci at 32°C and 37°C, IP/input enrichments were first calculated for both conditions and replicates independently using macs2 ‘callpeak’ with options ‘--nomodel --extsize 120’. The resulting tag numbers, pileup and lambda files for the IP and input samples of each replicate and condition were then used to calculate significant enrichment differences using macs2 ‘bdgdiff ‘. For all ChIP-seq experiments, coverage tracks representing the ratio of IP over Input were generated using deeptool’s (58) ‘bamCompare’ with options ‘-bs 10 --scaleFactorsMethod None --operation ratio --normalizeUsing CPM’. IP/input coverage tracks were visualized using the Integrative Genomics Viewer.
For the analysis of histone PTMs in the wild-type3D7 and Sir2a-KO parasites, raw sequencing reads were pre-processed as described above. The reads were then mapped to the masked P. falciparum genome (plasmoDB v64) using tinymapper, with option '--mode ChIP’ and using the S. cerevisiae S288C genome (version R64) as calibration reference. Only correctly paired reads with a mapping quality >= 30 were retained (bowtie2 option '-f 0x001 -f 0x002’ -q 30) for downstream analysis within tinymapper. Significant peaks for each replicate and histone PTM were identified within tinymapper using macs2 and by using the input sample as background. To calculate quantitative enrichment values for each PTM, for each sample and replicate, the number of ChIP reads mapping to the P. falciparum genome (in counts per million [CPM]) is normalized to the total number of ChIP reads mapping to the S. cerevisiae calibration genome. Overlapping consensus peaks between replicates were identified using bedtool’s ‘intersect’.
Assembly: PlasmoDB v64
Supplementary files format and content: BigWig and BedGraph files with ChIP/input ration tracks
Supplementary files format and content: BigWig files with Spike-in calibrated enrichment tracks

organism: Plasmodium falciparum

growth_protocol: HMGB1-HA and HMGB2-HA cell lines were synchronized by plasmion/sorbitol to a 6h window. After the synchronization, half of the culture was incubated at 32°C. Parasites cultivated at 37°C were collected at 36 h.p.i., while parasites incubated at 32°C were collected at 56 h.p.i., which corresponded to an equivalent developmental stage. For histone PTM ChIP-seq, wild-type P. falciparum (strain 3D7) and Sir2a-KO cell lines were synchronized by plasmion/sorbitol to a 6h window and collected at 16 h.p.i. For the spike in samples, Saccharomyces cerevisiae was grown overnight in yeast peptide dextrose media (Bacteriological peptone 20 g/L, Glucose 20 g/L, Yeast extract 10 g/L) at 30°C with agitation (300 rpm) to reach the stationary phase. The optical density (OD) was measured and the culture was diluted to an OD of 0.4. Cells were collected during the exponential phase at OD = 0.8 by centrifugation (5 min, 30°C, 2500g) and crosslinking was performed by resuspending the cells in 2% formaldehyde and incubating at 25°C for 5 min with rotation. 3M Tris was added to a final concentration of 1.5 M to quench the crosslinking reaction, and the mixture was rotated at 25°C for 1 min. After centrifugation (3 min, 4°C, 2500g), the pellets were washed once with ice-cold PBS, and once with ddH2O. After centrifugation (20 sec, 4°C, 3 300g), the supernatant was removed and the pellets were snap-frozen and stored at -80 °C.

extract_protocol:
Each sample was resuspended in 2 ml nuclear extraction buffer (10 mM HEPES pH 8, 10 mM KCl, 0.1 mM EDTA pH 8, and complete protease inhibitor (PI, Roche no. 11836170001). IGEPAL CA-630 was added to a final concentration of 0.25% and the cells were lysed with a prechilled douncer homogenizer (200 strokes). The nuclei were pelleted by centrifugation (13,500g, 10 min, 4°C), and the supernatant (cytoplasmic fraction) was removed while the pellet was resuspended in 1.8 mL of cold SDS Lysis buffer (50 mM Tris–HCl pH 8, 10 mM EDTA pH 8, 1% SDS, PI). Chromatin was sheared to ~250 bp fragments by 10 sonication cycles (once cycle: 30s ON / 30s OFF) using a Diagenode Pico Bioruptor. Insoluble materials were removed by centrifugation (10 min at 13,500g at 4°C) and DNA concentration was measured by Qubit. For the wild-type and Sir2a-KO histone-PTM ChIP-seq experiments, P. falciparum and yeast chromatin was mixed at the following ratios (P. falciparum:yeast): H4K16ac: 2.5:1; H3K9ac, H3K14ac, H4K12ac: 1:1. 100ng of DNA was stored as input sample at -20°C for later processing (see below). For each immunoprecipitation, 25 μl of Protein G Dynabeads (Invitrogen 10004D) were pre-washed twice with 1 ml ChIP dilution buffer (16.7 mM Tris–HCl pH 8, 150 mM NaCl, 1.2 mM EDTA pH 8, 1% Triton X-100, 0.01% SDS) and resuspended in 1 ml ChIP dilution buffer. For HMGB1-HA and HMGB2-HA samples, 1 μg of anti-HA (Abcam # ab9110) was added to the beads and incubated at 4°C for 2h with rotation. For the wild-type and Sir2a-KO samples, 1 ug of either anti-H3K9ac (Merck # 07-532), anti-H3K14ac (Abcam # ab52946), anti-H4K12ac (Active Motif # 39066) or anti-H4K16ac (Merck # 07-329) was added and incubated at 4°C for 2h with rotation. The beads were washed twice with 1 ml ChIP dilution buffer and 1μg of chromatin lysate was diluted 10-fold in ChIP dilution buffer, added to the bead-antibody complexes and incubated at 4°C overnight with constant rotation. Following immunoprecipitation, the beads were washed sequentially in 1 ml of low salt wash buffer (20 mM Tris–HCl pH 8, 150 mM NaCl, 2 mM EDTA pH 8, 1% Triton X-100, 0.1% SDS), High salt wash buffer (20 mM Tris–HCl pH 8, 500 mM NaCl, 2 mM EDTA pH 8, 1% Triton X-100, 0.1% SDS), LiCl wash buffer (10 mM Tris–HCl pH 8, 250 mM LiCl, 1 mM EDTA pH 8, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate) and TE wash buffer (10 mM Tris–HCl pH 8, 1 mM EDTA pH 8). For each wash, the beads were rotated for 5 min at 4°C except for the last TE wash, which was performed at room temperature (RT). The beads were then resuspended in 200 μl of elution buffer (50 mM Tris–HCl pH 8 10 mM EDTA pH 8.0, 1% SDS) and protein-DNA complexes were eluted by 30 min incubation at 65°C. The beads were collected on a magnetic rack and the supernatant transferred to a new tube.
The immunoprecipitated DNA and the input DNA were reverse-crosslinked by incubating the samples at 65°C for 10h. 200 μl of TE buffer were added and the samples were treated with RNase A (0.2 mg/mL final concentration) for 2h at 37°C, followed by a 2 h incubation at 55°C with proteinase K (0.2 mg/mL final concentration). DNA was purified by adding 400 μl phenol:chloroform:isoamyl alcohol, and phases were separated by centrifugation (13,500g, 10 min, 4°C) after vigorous vortexing. 16 μl of 5 M NaCl (200 mM final concentration) and 30 μg glycogen were added to the aqueous phase, and DNA was precipitated by adding 800 μl 100% EtOH 4°C and incubating for 30 min at −20°C. DNA was pelleted by centrifugation (20,000g, 10 min, 4°C) and washed with 500 μl 80% EtOH 4°C. After centrifugation, the DNA pellet was air-dried and resuspended in 30 μl of 10 mM Tris-HCl pH 8.0. Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit (NEB E7645S) and sequenced (150 bp paired end) on the NextSeq 500 platform (Illumina).

treatment_protocol: Synchronized parasite cultures were lysed with saponin (0.075% in DPBS), washed with DPBS at 37°C (or 32°C for parasites cultivated at this temperature) and resuspended in DPBS at 25°C. For HMGB1-HA and HMGB2-HA samples, parasites were first cross-linked for 20 min by adding glycolbis(succinimidylsuccinate) (EGS) to a final concentration of 1.5 mM. All samples (pre-corss-linked or not) where cross-linked for 10 min by adding methanol-free formaldehyde (Thermo Fisher # 28908) to 1% final concentration with gentle agitation. The cross-linking reaction was quenched by adding 2.5 M glycine to a final concentration of 0.125 M and incubated at RT for another 5 min. Parasites were centrifuged (3,250g, 5 min, 4°C), washed with DPBS, snap-frozen, and stored at −80°C until further use. For the spike in, yeast cell pellets were thawed on ice and resuspended in 1X yeast ChIP lysis buffer (50 mM Hepes-KOH pH 8, 140 mM NaCl, 1mM EDTA, 1% Triton X100, 0.1% sodium deoxycholate, 1mM PMSF and 1X protease inhibitors). The cell walls were disrupted using a Beads Beater with zirconium beads and samples were recovered by centrifugation. The chromatin was sheared by sonication (8 cycles ‘30sec ON / 30 sec OFF’ in a BioRuptor) and centrifuged (20 min, 21,130g, 4°C). The supernatant was transferred to a new tube, aliquoted and stored at -80°C. Yeast chromatin was mixed with P. falciparum chromatin as described below.


title: liver, CDAHFD_sham, rep5


title: Sir2a H3K14ac ChIP Rep1

description: Library name: Sir2a H3K14ac ChIP Rep1


title: CDK12_THZ531_8h_1_(240403_CD_Hs_840)

description:
Library name: CDK12_THZ531_8h_1
CUT&Tag targeting CDK12 in MDA-MB-231 cells treated with 400nM THZ531 for 8 hours.

value: MDA-MB-231 human breast cancer epthileal cells  (ATCC HTB-26).


title: RNA extracted from AB1-mCherry subcutaneous whole tumour, mouse 1.4

description:
Library name: TUM_SC_4
TUM_TPM.txt


title: Female negative control rep1

description:
Gene expression in female control mouse liver
Oct12_1_1-665(normalized)

source_name: Female Cas9-knockin mouse (negative control) rep1

value: whole liver

value: Female


title: Female Cux2, Sall1, Trim24-gRNA rep1

description:
Gene expression in female Cux2, Sall1, Tim24 knockdown mouse liver
Oct12_2_1-663(normalized)

source_name: Female Cas9-knockin mouse (with Cux2, Sall1, Trim24 gRNA) rep1


title: Sir2a H3K9ac ChIP Rep2

description: Library name: Sir2a H3K9ac ChIP Rep2


title: RNA extracted from AB1-mCherry subcutaneous whole tumour, mouse 1.3

description:
Library name: TUM_SC_3
TUM_TPM.txt

value: BALB/c


title: Sir2a H3K9ac ChIP Rep1

description: Library name: Sir2a H3K9ac ChIP Rep1


title: CUTAC_THZ531_4h_2_(240403_CD_Hs_839)

description:
Library name: CUTAC_THZ531_4h_2
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells treated with 400nM THZ531 for 4 hours.


title: CDK12_THZ531_4h_2_(240403_CD_Hs_833)

description:
Library name: CDK12_THZ531_4h_2
CUT&Tag targeting CDK12 in MDA-MB-231 cells treated with 400nM THZ531 for 4 hours.


title: liver, CDAHFD_sham, rep3


title: Male negative control rep1

description:
Gene expression in Male control mouse liver
Oct12_1_3-405(normalized)

source_name: Male Cas9-knockin mouse (negative control) rep1


title: BRG1_THZ531_4h_2_(240403_CD_Hs_834)

description:
Library name: BRG1_THZ531_4h_2
CUT&Tag targeting BRG1 in MDA-MB-231 cells treated with 400nM THZ531 for 4 hours.


title: liver, CDAHFD_sham, rep2


title: liver, CDAHFD_sham, rep1


title: Sir2a H4K12ac ChIP Rep2

description: Library name: Sir2a H4K12ac ChIP Rep2


title: Female negative control rep2

description:
Gene expression in female control mouse liver
Oct12_1_2-833(normalized)

source_name: Female Cas9-knockin mouse (negative control) rep2


title: CUTAC_THZ531_4h_1_(240403_CD_Hs_832)

description:
Library name: CUTAC_THZ531_4h_1
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells treated with 400nM THZ531 for 4 hours.


title: Sir2a Input Rep4

description: Library name: Sir2a Input Rep4


title: Sir2a H4K12ac ChIP Rep1

description: Library name: Sir2a H4K12ac ChIP Rep1


title: KPfrt Slc4a11-MCD/+ iRFP670-Gluc cell line; tail vein injected, harvested 5 weeks post transplant (1 week DT), GEX

description:
Library name: IGO17483-DT_GEX
10x genomics

data_processing:
FASTQ files of single-cell RNA-sequencing data generated on the 10X Chromium platform were processed using the standard CellRanger pipeline (version >=6.0.0). Reads were aligned to a custom GRCm38 / mm10 reference containing additional transgenes used in the study. The generated cell-gene count matrices were analyzed using a combination of published packages and custom scripts in either the scanpy (v> 1.9.0) / AnnData (v. 0.10.5, Python)
Assembly: GRCm38/mm10
Supplementary files format and content: h5: raw counts
Supplementary files format and content: h5ad: processed file
Supplementary files format and content: csv: featureref for Total Seq B Hash antibodies

extract_protocol:
Encapsulation and library preparation were performed using the 10X Genomics Chromium Single Cell 3’ Library & Gel bead Kit V3 (10X Genomics, PN-1000121) according to the manufacturer’s protocol. Libraries were sequenced using the Nova-Seq 6000 platform (Illumina).
Single cell suspensions were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following QC, the samples were loaded onto Next GEM Chip G (14143, 15123, 15342, 15488, 15600, 15601, 15771) or GEM-X Single Cell Chip (16235, 16318, 16562, 16686, 17402, 17483, 17543) (10X Genomics PN 1000690 & 2000060) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of ~4-50,000 cells proceeded using the Chromium Next GEM Single Cell 3’ Kit v3.1 or GEM-X Single Cell 3’ Kit v4 (10X Genomics PN 1000268 & 1000691) according to the manufacturer’s protocol. cDNA amplification included 11-12 cycles and 78-863 ng of the material was used to prepare sequencing libraries with 8-14 cycles of PCR. Indexed libraries were pooled and sequenced on a NovaSeq 6000 (14143, 16235, 16562) or X (15123, 15342, 15488, 15600, 15601, 15771, 16235, 16318, 16562, 16686, 17402, 17483, 17543) in a PE28/88 run using the NovaSeq 6000 S4 (200 Cycles) or X 10B (100 Cycles) or 25B (300 cycles) Reagent Kit (Illumina).  An average of 38 thousand paired reads was generated per cell.

value: lung

value: AT1401 iRFP670-GLuc

value: Tumor cells

value: Kras-G12D/+ Trp53-delta/delta Slc4a11-MACD/+ iRFP670-Gluc

value: Saline


title: KPfrt Slc4a11-MCD/+ iRFP670-Gluc cell line; tail vein injected, harvested 5 weeks post transplant (1 week Saline), GEX

description:
Library name: IGO17483-Saline_GEX
10x genomics

value: Diphteria toxin


title: KPfrt Hopx-MACD/+ Rosa26-mTmG/+ tumors; harvested at 14 weeks PTI after 14 days of tracing, HTO

description:
Library name: IGO17543_HTO
10x genomics

value: Primary tumor cells

value: Kras-G12D/+ Trp53-delta/delta Hopx-MACD/+ Rosa26-mTmG/+

value: Tamoxifen


title: liver, NC_RIC, rep3


title: Sir2a Input Rep1

description: Library name: Sir2a Input Rep1


title: KPfrt Hopx-MACD/+ Rosa26-mTmG/+ tumors; harvested at 14 weeks PTI after 14 days of tracing, GEX

description:
Library name: IGO17543_GEX
10x genomics


title: KPfrt (Slc4a11-MCD/+ or Hopx-MACD/+) Rosa26-mTmG/+ tumors harvested at (6 or 12) weeks PTI, 3d tracing, HTO

description:
Library name: IGO17402_HTO
10x genomics

value: Kras-G12D/+ Trp53-delta/delta Slc4a11-MCD/+ Rosa26-mTmG/+ and Kras-G12D/+ Trp53-delta/delta Hopx-MACD/+ Rosa26-mTmG/+


title: liver, NC_RIC, rep5


title: KPfrt (Slc4a11-MCD/+ or Hopx-MACD/+) Rosa26-mTmG/+ tumors harvested at (6 or 12) weeks PTI, 3d tracing, GEX

description:
Library name: IGO17402_GEX
10x genomics


title: Sir2a H4K16ac ChIP Rep2

description: Library name: Sir2a H4K16ac ChIP Rep2


title: Sir2a Input Rep2

description: Library name: Sir2a Input Rep2


title: CDK12_THZ531_2h_2_(240403_CD_Hs_819)

description:
Library name: CDK12_THZ531_2h_2
CUT&Tag targeting CDK12 in MDA-MB-231 cells treated with 400nM THZ531 for 2 hours.

value: Anti-CDK12 from Millipore Sigma (ABE1861).


title: liver, NC_RIC, rep4

value: liver


title: 3D7 H3K14ac ChIP Rep2

description: Library name: 3D7 H3K14ac ChIP Rep2


title: Sir2a Input Rep3

description: Library name: Sir2a Input Rep3


title: CUTAC_THZ531_2h_2_(240403_CD_Hs_825)

description:
Library name: CUTAC_THZ531_2h_2
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells treated with 400nM THZ531 for 2 hours.

value: Anti-RNA Polymerase CTD repeat YSPTSPS (phospho S5) antibody [4H8] from abcam (ab5408).


title: BRG1_THZ531_4h_1_(240403_CD_Hs_827)

description:
Library name: BRG1_THZ531_4h_1
CUT&Tag targeting BRG1 in MDA-MB-231 cells treated with 400nM THZ531 for 4 hours.

value: MDA-MB-231 human breast cancer epthileal cells  (ATCC HTB-26).

value: Anti-BRG1 antibody [EPNCIR111A] from Abcam (ab110641).


title: RNA extracted from AB1-mCherry subcutaneous whole tumour, mouse 1.2

description:
Library name: TUM_SC_2
TUM_TPM.txt

value: Subcutaneous tumour

value: murine mesothelioma

value: untreated

value: Day 10

value: 12 weeks

value: female


title: RNA extracted from AB1-mCherry subcutaneous whole tumour, mouse 1.1

description:
Library name: TUM_SC_1
TUM_TPM.txt

value: BALB/c


title: BRG1_THZ531_2h_1_(240403_CD_Hs_813)

description:
Library name: BRG1_THZ531_2h_1
CUT&Tag targeting BRG1 in MDA-MB-231 cells treated with 400nM THZ531 for 2 hours.


title: BRG1_THZ531_2h_2_(240403_CD_Hs_820)

description:
Library name: BRG1_THZ531_2h_2
CUT&Tag targeting BRG1 in MDA-MB-231 cells treated with 400nM THZ531 for 2 hours.


title: liver, NC_sham, rep3

value: WT


title: liver, NC_RIC, rep1


title: CDK12_THZ531_2h_1_(240403_CD_Hs_812)

description:
Library name: CDK12_THZ531_2h_1
CUT&Tag targeting CDK12 in MDA-MB-231 cells treated with 400nM THZ531 for 2 hours.


title: 3D7 H3K9ac ChIP Rep2

description: Library name: 3D7 H3K9ac ChIP Rep2


title: liver, NC_sham, rep5


title: KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumors treated with Tamoxifen and harvested at 12 weeks PTI after 3d tracing, HTO

description:
Library name: IGO16686_HTO
10x genomics

value: lung

value: Primary tumor cells

value: Tumor cells

value: Kras-G12D/+ Trp53-delta/delta Slc4a11-MCD/+ Rosa26-mTmG/+


title: CUTAC_THZ531_2h_1_(240403_CD_Hs_818)

description:
Library name: CUTAC_THZ531_2h_1
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells treated with 400nM THZ531 for 2 hours.


title: liver, NC_sham, rep4


title: CDK12_THZ531_4h_1_(240403_CD_Hs_826)

description:
Library name: CDK12_THZ531_4h_1
CUT&Tag targeting CDK12 in MDA-MB-231 cells treated with 400nM THZ531 for 4 hours.

value: Anti-CDK12 from Millipore Sigma (ABE1861).


title: KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumors treated with Tamoxifen and harvested at 12 weeks PTI after 3d tracing, GEX

description:
Library name: IGO16686_GEX
10x genomics

value: Tamoxifen


title: CUTAC_control_0h_2_(240403_CD_Hs_811)

description:
Library name: CUTAC_control_0h_2
RNA Polymerase II Serine-5P-based CUTAC in untreated MDA-MB-231 cells for single-treatment series.

value: Anti-RNA Polymerase CTD repeat YSPTSPS (phospho S5) antibody [4H8] from abcam (ab5408).


title: liver, NC_RIC, rep2

value: liver


title: grtRmutant

city: Jinju-si

first: Yongsung

last: Kang

state: Gyeongsangnam-do

address: 1 Gyeongsangdae-ro

department: Institute of Agriculture and Life Science

country: South Korea

institute: Gyeongsang National University

description:
Library name: SAMPLE 5
Column name in GrtKR RNAseq_Dataset.xlsx: grtR_0180181

data_processing:
CLRNASeqTM program (CJ Bioscience, South Korea)
Relative transcript abundance was measured in fragments as reads per kilobase of exon sequence per million mapped sequence reads (FPKM).
The eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) database was used to cluster genes into functionally related groups and the KEGG (Kyoto Encyclopedia of Genes and Genomes) database was used to analyze metabolic pathways.
Assembly: Sequence data for the reference genome was obtained from the NCBI database. Quality-filtered reads were aligned to the reference-genome sequence using Bowtie2
Supplementary files format and content: GrtKR RNAseq.xlsx file Includes FPKM values for each Sample.
Supplementary files format and content: GrtKR RNAseq.xlsx file includes information about the GenBank assembly accession and RefSeq assembly accession for Burkholderia glumae BGR1.

organism: Burkholderia glumae

growth_protocol: B. glumae BGR1, BGRK1 (BGR1 grtK::Tn3-gus24), and BGRR1 (BGR1 grtR::Tn3-gus54) grown in LB medium [1% (w/v) tryptone and 0.5% (w/v) of yeast extract at 37°C for 12 h after subculture

extract_protocol:
Total RNA was isolated from B. glumae wild-type BGR1, the grtK mutant (BGR1 grtK::Tn3-gus24) and the grtR mutant (BGR1 grtR::Tn3-gus54), using the RNeasy Mini Kit (Qiagen, Venlo, Netherland) according to the manufacturer’s instructions. To remove genomic DNA completely, the isolated RNA was treated with DNaseI (Ambion, Austin, TX, USA) for 1 h at 37 °C according to the supplier’s instructions. The quantity and quality of the total RNA were evaluated using RNA electropherograms (Agilent 2100 Bioanalyzer, Santa Clara, CA) and by assessing the RNA integrity number (RIN). The NEBNext rRNA Depletion Kit (Bacteria) (New England BioLabs, UK) was used for ribosomal RNA depletion according to the manufacturer's instructions.
Libraries for Illumina sequencing were made with the TruSeq stranded mRNA library prep (Illumina, USA) following the manufacturer’s protocol.

value: Bacterial cell

value: BGR1 grtR::Tn3-gusA54

value: broth culture


title: grtKmutant

description:
Library name: SAMPLE 3
Column name in GrtKR RNAseq_Dataset.xlsx: grtK_0180180

value: BGR1 grtK::Tn3-gusA24


title: liver, NC_sham, rep2


title: Sir2a H4K16ac ChIP Rep1

description: Library name: Sir2a H4K16ac ChIP Rep1


title: BRG1_control_0h_2_(240403_CD_Hs_806)

description:
Library name: BRG1_control_0h_2
CUT&Tag targeting BRG1 in untreated MDA-MB-231 cells for single-treatment series.

value: MDA-MB-231 human breast cancer epthileal cells  (ATCC HTB-26).

value: Anti-BRG1 antibody [EPNCIR111A] from Abcam (ab110641).


title: BGR1control

description:
Library name: SAMPLE 1
Column name in GrtKR RNAseq_Dataset.xlsx: BGR1_0180179


title: 3D7 H3K9ac ChIP Rep1

description: Library name: 3D7 H3K9ac ChIP Rep1


title: liver, NC_sham, rep1


title: BRG1_control_0h_1_(240403_CD_Hs_799)

description:
Library name: BRG1_control_0h_1
CUT&Tag targeting BRG1 in untreated MDA-MB-231 cells for single-treatment series.


title: CUTAC_control_0h_1_(240403_CD_Hs_804)

description:
Library name: CUTAC_control_0h_1
RNA Polymerase II Serine-5P-based CUTAC in untreated MDA-MB-231 cells for single-treatment series.


title: 3D7 H4K12ac ChIP Rep2

description: Library name: 3D7 H4K12ac ChIP Rep2


title: 3D7 H4K16ac ChIP Rep1

description: Library name: 3D7 H4K16ac ChIP Rep1


title: 3D7 Input Rep4

description: Library name: 3D7 Input Rep4


title: liver, AAV-miR-181d-5p, rep3

growth_protocol: Mice were fed a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) to induce nonalcoholic steatohepatitis (NASH), and were intravenously injected with control AAVs or AAVs encoding miR-181d-5p. Liver tissues were harvested and subjected to RNA-sequencing.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol
RNA libararies for RNA-seq were prepared using TruSeq Stranded mRNA LTSample Prep Kit following the manufacturer’s protocol


title: 3D7 H3K14ac ChIP Rep1

description: Library name: 3D7 H3K14ac ChIP Rep1


title: pannier-Gal4 domain warts knock-down

city: Houston

first: Shinya

last: Yamamoto

state: TX

address: 1250 Moursund St

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description:
Library name: WTS
10x Genomics

data_processing:
The sequencing fastq files were alligned and processed by Cell Ranger software v7.2.0
Assembly: dm6.31
Supplementary files format and content: .h5ad matrix file

organism: Drosophila melanogaster

source_name: Head

growth_protocol: In bottles, using 10 males of the UAS-RNAi lines (control; UAS-lacZ-RNAi and experimental; UAS-wts-RNAi [Nig-Japan: 12702R-1]) and ~30 virgin females (pnr-GAL4,UAS-CD8::GFP/TM3, Sb) crosses were set at 25°C. White pupae were moved to separate tubes at 25°C and after aging for 90 hours, dissected.

extract_protocol:
Single-nucleus suspensions were prepared following the protocol described previously [PMID: 35620068] with the adaptation of 20 strokes with the loose Dounce pestle and 20 strokes with the tight Dounce pestle120. Next, we used the BD AriaIII FACS sorter to collect nuclei. Nuclei were stained by Hoechst-33342 on ice (1:1000; >5min). Hoechst+ nuclei were collected during sorting. Individual nuclei were collected into one 1.5ml RNase-free Eppendorf tube with 200µl 1x PBS with 0.5% BSA as the receiving buffer (RNase inhibitor added).
For each 10x Genomics run, 100k nuclei were collected. Nuclei were spun down for 10 min at 950g at 4°C and then resuspended using 80µl or desired amount of 1x PBS with 0.5% BSA (RNase inhibitor added). 2µl of nucleus suspension was used for counting the nuclei with hemocytometers to calculate the concentration. We loaded 40K nuclei to the 10x controller to target >20k nuclei for each channel. Next, we performed snRNA-seq using the 10x Genomics platform with the Chromium Next GEM Single Cell 3' HT (high-throughput) Reagent Kits v3.1 (Dual Index) with the following settings. All PCR reactions were performed using the BioRad C1000 Touch Thermal cycler with a 96-deep Well Reaction Module. The recommended cycle numbers from the 10x protocol were used for cDNA amplification and sample index PCR. As per the 10x protocol, 1:10 dilutions of amplified cDNA and final libraries were evaluated on a bioanalyzer. The final library was sent to Novogene Corporation Inc. for Illumina NovaSeq PE150 S4 lane sequencing with the dual index configuration Read 1 28 cycles, Index 1 (i7) 10 cycles, Index 2 (i5) 10 cycles, and Read 2 90 cycles. A PhiX control library was spiked in at 0.2 to 1% concentration. The sequencing depth is about 26-30K reads per nucleus.

treatment_protocol: 90 hours post-white pupariation (WPP), pupae were placed on double sided tape on a slide, dorsal side up. First the operculum was removed, and then slits made down the left and right sides of the pupal casing, the pupal casing was pulled back to expose the anterior half of the pupa. The thorax was removed from the head and abdomen and then the ventral half of the thorax was removed including the legs and wings. The dorsal half of the thorax was placed immediately into a 1.5ml RNAase free Eppendorf tube on dry ice until flash-frozen using liquid nitrogen.  20 thoraces of each genotype were used for each sample and stored at -80°C until further preparation for sn-RNA-seq.

value: Head

value: pannier-Gal4 domain warts knock-down


title: pannier-Gal4 domain control knock-down

description:
Library name: LACZ
10x Genomics

value: pannier-Gal4 domain control knock-down


title: 3D7 H4K12ac ChIP Rep1

description: Library name: 3D7 H4K12ac ChIP Rep1


title: Po_Sup_2

city: Minneapolis

first: Ryan

middle: C

last: Hunter

state: MN

address: 689 23rd Ave SE

institute: University of Minnesota

scan_protocol: RNA was submitted to the UMN Genomics Center where it was hybridized to our custom Nanostring codeset.

data_processing: Expression data were analyzed using nSolver software

organism: Staphylococcus aureus

growth_protocol: Overnight LB cultures of S. aureus were diluted 1:500 and grown to an OD600 of ~0.2-0.3.

extract_protocol: Lysates were dissolved in 1 mL of TRIzol Reagent for 5 minutes, followed by addition of 200 μL chloroform. Samples were agitated for 15 seconds, incubated for 5 minutes, then centrifuged at 12,000 rpm for 15 minutes at 4°C. The aqueous phase was mixed with an equal volume of 95% ethanol and vortexed for 5 seconds. The mixture was then subjected to on-column DNase I treatment and the Zymo RNA Clean & Concentrator kit

treatment_protocol: Cells were pelleted by centrifugation at 14,000 rpm for one minute, resuspended in 50 μL of LB plus 20 mg/mL lysostaphin (Sigma-Aldrich), and incubated at 37°C for 15 minutes


title: CDK12_control_0h_2_(240403_CD_Hs_805)

description:
Library name: CDK12_control_0h_2
CUT&Tag targeting CDK12 in untreated MDA-MB-231 cells for single-treatment series.

source_name: MDA-MB-231 human breast cancer epthileal cells  (ATCC HTB-26).


title: Po_Sup_3


title: 3D7 H4K16ac ChIP Rep2

description: Library name: 3D7 H4K16ac ChIP Rep2


title: FESS_3

source_name: FESS


title: liver, AAV-miR-181d-5p, rep4

source_name: liver

value: WT


title: 3D7 Input Rep2

description: Library name: 3D7 Input Rep2


title: FESS_2


title: FESS_1


title: HEK cells expressing 273H p53 RNA-seq replicate 3

city: Jupiter

first: Wuyue

last: Zhou

address: 110 Scripps Way

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description:
Library name: Sample-09
column name in RNAseq_p53_expression_matrix.tsv: "TTCYJP_9_count"

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: HEK 293

growth_protocol: Stable HEK293T cells expressing mutant and wt p53 were cultured as a monolayer in DMEM, supplemented with 10% v/v FBS, 100 U mL-1 penicillin, 100 µg mL-1 streptomycin, and 1.5 µg/mL Puromycin.

extract_protocol:
Cells were lysed with Zymo DNA/RNA Shield and submitted to Plasmidsaurus (Louisville, KY) for RNA-seq analysis
we convert mRNA into complementary DNA (cDNA) via reverse transcription and second-strand synthesis, followed by tagmentation and library indexing and amplification.

treatment_protocol: Cells were washed once with PBS and harvested with trypsin digestion.

value: HEK 293

value: epithelial cell

value: R273H p53 overexpression


title: Fn_Sup_3


title: HEK cells expressing 273H p53 RNA-seq replicate 1

description:
Library name: Sample-07
column name in RNAseq_p53_expression_matrix.tsv: "TTCYJP_7_count"


title: liver, AAV-miR-181d-5p, rep2


title: 3D7 Input Rep3

description: Library name: 3D7 Input Rep3


title: Po_Sup_1


title: liver, AAV-miR-181d-5p, rep5


title: HEK cells expressing 273H p53 RNA-seq replicate 2

description:
Library name: Sample-08
column name in RNAseq_p53_expression_matrix.tsv: "TTCYJP_8_count"


title: liver, control AAV, rep3

value: control AAV


title: HMGB2 37C Input Rep1

description: Library name: HMGB2 37C Input Rep1


title: HEK cells expressing 245S p53 RNA-seq replicate 2

description:
Library name: Sample-05
column name in RNAseq_p53_expression_matrix.tsv: "TTCYJP_5_count"

value: G245S p53 overexpression


title: liver, AAV-miR-181d-5p, rep1


title: Fn_Sup_2


title: CDK12_control_0h_1_(240403_CD_Hs_798)

description:
Library name: CDK12_control_0h_1
CUT&Tag targeting CDK12 in untreated MDA-MB-231 cells for single-treatment series.

value: Anti-CDK12 from Millipore Sigma (ABE1861).


title: HMGB2 37C ChIP Rep2

description: Library name: HMGB2 37C ChIP Rep2


title: 3D7 Input Rep1

description: Library name: 3D7 Input Rep1


title: liver, control AAV, rep5

value: liver


title: HEK cells expressing wt p53 RNA-seq replicate 3

description:
Library name: Sample-03
column name in RNAseq_p53_expression_matrix.tsv: "TTCYJP_3_count"

value: wt p53 overexpression


title: Fn_Sup_1


title: Brucella_Broth_3


title: HMGB2 37C ChIP Rep1

description: Library name: HMGB2 37C ChIP Rep1


title: HMGB2 37C Input Rep2

description: Library name: HMGB2 37C Input Rep2


title: HEK cells expressing 245S p53 RNA-seq replicate 3

description:
Library name: Sample-06
column name in RNAseq_p53_expression_matrix.tsv: "TTCYJP_6_count"


title: Brucella_Broth_2


title: HEK cells expressing 245S p53 RNA-seq replicate 1

description:
Library name: Sample-04
column name in RNAseq_p53_expression_matrix.tsv: "TTCYJP_4_count"


title: liver, control AAV, rep1


title: HEK cells expressing wt p53 RNA-seq replicate 2

description:
Library name: Sample-02
column name in RNAseq_p53_expression_matrix.tsv: "TTCYJP_2_count"


title: HMGB1 32C Input Rep2

description: Library name: HMGB1 32C Input Rep2


title: Brucella_Broth_1


title: plasma extracellular vesicles, RIC, rep4

data_processing:
Low quality reads were filtered, and the reads with 5’ primer contaminants and poly (A) were removed. The reads without 3’adapter and insert tag, the reads shorter than 15 nt or longer than 41 nt from the raw data were filtered, and the clean reads were obtained.
For primary analysis, the length distribution of the clean sequences in the reference genome was determined. Non-coding RNAs were annotated as rRNAs, tRNAs, small nuclear RNAs (snRNAs), and so on. These RNAs were aligned and then subjected to the Bowtie search against Rfam v.10.1.
The known miRNAs were identified by aligning against miRBase v22 database (http://www.mirbase.org/), and the known miRNA expression patterns in different samples were analyzed.
Unannotated reads were analyzed by mirdeep2 to predict novel miRNAs.
Differential expression analysis was performed in R (v3.4.1) using DESeq2 (v1.18.1).
Assembly: mm10, miRBase v22
Supplementary files format and content: Comma separated value files include normalized counts for each sample

source_name: plasma extracellular vesicles

growth_protocol: Mice were subjected to Remote limb ischemic conditioning (RIC) or sham treatment.

extract_protocol:
RNAs were extracted using exoRNeasy Serum/Plasma Starter Kit following the manufacturer’s protocol
Small RNA libraries were prepared using TruSeq Small RNA Sample Prep Kits following the manufacturer’s protocol

value: plasma extracellular vesicles

value: Remote limb ischemic conditioning


title: liver, control AAV, rep4


title: HEK cells expressing wt p53 RNA-seq replicate 1

description:
Library name: Sample-01
column name in RNAseq_p53_expression_matrix.tsv: "TTCYJP_1_count"


title: HMGB1 32C Input Rep1

description: Library name: HMGB1 32C Input Rep1


title: plasma extracellular vesicles, RIC, rep3


title: HMGB1 32C ChIP Rep2

description: Library name: HMGB1 32C ChIP Rep2


title: liver, control AAV, rep2


title: HMGB1 32C ChIP Rep1

description: Library name: HMGB1 32C ChIP Rep1


title: plasma extracellular vesicles, RIC, rep1


title: KOREF2-P-2

type: protein

city: Ulsan

first: Jong

middle: Hwa

last: Bhak

address: 50, UNIST-gil

institute: UNIST

description: Proteomic profile of 7,596 proteins in KOREF2

hyb_protocol: Per SomaLogic protocols. Full details available at PMID: 23023596 and PMID: 23139410

scan_protocol: SomaLogic uses an Agilent custom microarray and the Agilent SureScan Microarray Scanner. Full details available at PMID: 23023596 and PMID: 23139410

data_processing: Raw data undergoes several normalization and calibration steps, including hybridization normalization where each microarray is scaled according to the signal of 12 control aptamers to account for technical variability in individual microarrays, interpolate median signal normalization and plate scaling, calibration of each aptamer to the median value observed in Calibrator Control samples, and adaptive normalization to a reference using Adaptive Normalization by Maximum Likelihood (ANML) to adjust for inter-sample variability in total signal within and between runs.

label: SOMAmer reagent

source_name: EDTA Plasma

extract_protocol: Whole blood was collected in EDTA tubes, followed by immediate centrifugation to separate blood components.

tag: individual

value: Male


title: KOREF1-P-3Rep

description: Proteomic profile of 7,596 proteins in KOREF1

label_protocol: Per SomaLogic protocols. Full details available at PMID: 23023596 and PMID: 23139410


title: HMGB1 37C Input Rep1

description: Library name: HMGB1 37C Input Rep1


title: HMGB1 37C Input Rep2

description: Library name: HMGB1 37C Input Rep2


title: plasma extracellular vesicles, sham, rep4

value: sham


title: KOREF2-P-3


title: plasma extracellular vesicles, sham, rep3


title: HMGB1 37C ChIP Rep2

description: Library name: HMGB1 37C ChIP Rep2


title: plasma extracellular vesicles, sham, rep1


title: plasma extracellular vesicles, RIC, rep2


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day8, Lot.2

status: Public on Nov 24 2025

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

data_processing:
By using the celseq2 pipeline (https://github.com/yanailab/celseq2), demultiplexing of the raw data was performed, and also UMI counts were calculated.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include UMI count values of all samples.

source_name: Umbilical Vein

growth_protocol: hiHepPCs were cultured in DMEM/F12 and Fibrolife mixture medium with 4% FBS, 1 µg/ml insulin, 10^-7 M dexamethasone, 10 mM nicotinamide, 2 mM L-glutamine, 50 µM 2-mercaptoethanol, and penicillin/streptomycin, containing 20 ng/ml HGF, 1 µM A83-01, 2 µM SB431542, and 5 µM Y27632.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen)
Detailed protocol is described in "CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq (PMID: 27121950)".

treatment_protocol: Induction of hiHepPCs was carried out with or without 3 µM CHIR99021.

value: Umbilical Vein

value: Primay Cells

value: Endothelial Cells

value: Forced expression of FOXA3, HNF1A and HNF6

tag: time

value: Day 8


title: plasma extracellular vesicles, sham, rep2

value: WT


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day8, Lot.1


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day4, Lot.2

value: Day 4


title: KOREF1-P-2


title: KOREF1-P-3


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day4, Lot.1


title: H1299 cells, shPPP2R2A-2 repeat3

city: Columbus

first: Zhaojun

last: Qiu

state: Ohio

address: 460 West 12th Ave

institute: The Ohio State University

description: Library name: H-s-2_3_R1.fastq.gz

data_processing:
Quality control was conducted by retaining high-quality sequences (Q ≥ 30) and excluding low-quality reads based on fastq file reports. Data quality was assessed using FastQC (v0.11.8), followed by adapter trimming with fastq-mcf program (v1.05) and cutadapt (v2.5). Contamination removal was performed using Bowtie2 (version—2.5.1) and paired-end reads were aligned to the reference human genome (GRCh37/hg19) using STAR-v2.7.3a. Reads mapping to ribosomal and mitochondrial genomes were excluded prior to alignment. Raw read counts were estimated using HTSeq (v0.11.2) and normalized using DESeq2. Additionally, gene expression levels were determined using cufflinks (v2.2.1), with expression values reported in FPKM (Fragments per kilobase per million).
Assembly: GRCh37/hg19
Supplementary files format and content: excel file includes raw and normalized counts for each sample

source_name: lung

growth_protocol: A549 and H1299 cells were cultured in DMEM medium (Hyclone) supplemented with 10 % fetal bovine serum (Gibco) and 1 % antibiotic amtimycotic cocktail (Hyclone) in humidified atmosphere with 5 % CO2 at 37o C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construciton of sequencing libraries.
The RNA-sequencing libraries were prepared using the Illumina TruSeq stranded mRNA kit, followed by sequencing on the NovaSeq 6000 PE100 platform at a depth of 40 million reads per sample.

value: lung

value: lung cancer


title: KOREF2-P-1


title: KOREF1-P-1


title: iPSCs (small bioreactor), Q6-7

type: genomic

city: Kyoto

first: Yoshiki

last: Nakashima

state: Kyoto

address: Kyoto Research Park KISTIC Building Room 501, 5th floor, KISTIC building,  134 Chudoji Minami-cho, Shimogyo-ku

department: Research and Development Center

institute: Kyoto University Center for iPS Cell Research and Application Foundation (CiRA Foundation)

hyb_protocol: Arrays were washed and stained using a GeneChip Fluidics Station 450 (Thermo Fisher Scientific) and scanned using a GeneChip Scanner 3000 7G (Thermo Fisher Scientific).

scan_protocol: Scanned data files were generated using the GeneChip Command Console software program and analyzed using the Chromosome Analysis Suite v4.3 (ChAS), considering 1-2 MB for gains/losses and 5 MB for LOH(heterozygosity)/AOH(absence of heterozygosity).

data_processing: We used the KaryoStat™ assay service provided by Life Technologies Corporation (Carlsbad, CA, USA) [Regen Med 14, 505-524 (2019)]. We used the PluriTest™ analysis service from Life Technologies Corporation (Carlsbad, CA, USA)[Regen Med 14, 505-524 (2019)]. This assay assesses 36,000 transcripts and variants against a reference set of >450 samples for gene expression analysis. The transcriptomes of all samples were analyzed and processed in the PluriTest™ algorithm to generate pluripotency and novelty scores. The pluripotency score is based on many samples (pluripotent, somatic, and tissue) in the stem cell model matrix, which consists of an extensive reference set of >450 cell/tissue types, including 223 hESC lines (Stem Cell Matrix-2’ (SCM2) database)[Nat Methods 8, 315-317 (2011)] lines, 41 iPSC lines, somatic cells, and tissues.The final quantitative data file can be viewed on proprietary software provided by Life Technologies Corporation (Carlsbad, CA, USA).[https://assets.thermofisher.com/TFS-Assets/BID/Flyers/Stem-Characterization-Services-Flyer.pdf]

label: Biotin

source_name: iPSCs (CFiS-S01)

label_protocol: gDNA was processed according to the manufacturer's protocol. Briefly, 250 ng of gDNA was digested with the restriction enzyme NspI. The digested DNA was then ligated to the NspI adapter and amplified by PCR. The PCR products were purified and fragmented with DNase I. The fragmented products were end-labeled with biotin and hybridized overnight to KaryoStat arrays (Thermo Fisher Scientific) in a GeneChip Hybridization Oven 645 (Thermo Fisher Scientific).

growth_protocol: (Cultivation of hiPSCs in the small bioreactor) The Quantum system was seeded with 5.2 × 106 hiPSCs suspended in 60 mL of mTeSR Plus-cGMP medium (STEMCELL Technologies), which contained CloneR2 (STEMCELL Technologies) at manufacturer-recommended concentration.   (Cultivation of hiPSCs in the standard bioreactor) The Quantum system was seeded with 5.5 × 107 hiPSCs suspended in 100 mL of mTeSR Plus - cGMP (STEMCELL Technologies) medium containing CloneR2 (STEMCELL Technologies).

extract_protocol: RNA purification with this system involves cell preparation using a PureLink™ RNA Mini Kit (Catalog #12183025;(Thermo Fisher Scientific, Waltham, MA, USA) and quantification using the NanoDrop™2 (Thermo Fisher Scientific, Waltham, MA, USA). The GeneChip® for the PluriTest™ is prepared using 100 ng of total RNA. Genomic DNA (gDNA) was prepared using the Genomic DNA Purification Kit (Catalog K 0512;(Qiagen, Hilden, Germany) and quantified using the Qubit™ dsDNA BR Assay Kit (Catalog Q 32850GeneChip® Preparation;(Thermo Fisher Scientific, Waltham, MA, USA). A total of 250 ng of gDNA was used to prepare the GeneChip® for KaryoStat™ according to the instructions, which is an array that looks for copy number variants and single nucleotide polymorphisms across the genome.

treatment_protocol: (Cultivation of hiPSCs in the small bioreactor)  The flow rates used were an IC circulation flow rate of 0 mL/min and EC circulation flow rate of 18 mL/min. The cells were allowed to adhere for 24 hours with the IC circulation halted and the EC circulating at a flow rate of 0.02 mL/min for gas exchange. Then a volume of culture medium equivalent to 2.5 times the reactor volume was loaded at flow rates of 2 mL/min for the IC and 10 mL/min for the EC. Following this, perfusion culture was initiated through the EC at a flow rate of 0.02 mL/min. On days 3, 5, and 6, mTeSR Plus-cGMP medium (STEMCELL Technologies) equivalent to 1.5 times the reactor volume was loaded into both the IC and EC compartments at the same respective flow rates. The culture was maintained for a total of 7 days. The harvesting process involves the following steps: 1. Wash the system with PBS. 2. Add 60 mL of Accutase (STEMCELL Technologies). 3. Incubate for 4 minutes. To account for the potential impact of the dissociation reagent on the cells, the total exposure time—including the introduction phase—was set to 13 minutes. 4. Flush the cells into harvest bags using mTeSR Plus - cGMP (STEMCELL Technologies) medium containing CloneR2 (STEMCELL Technologies).  (Cultivation of hiPSCs in the standard bioreactor) The flow rates used were an IC circulation flow rate of 150 mL/min and EC circulation flow rate of 30 mL/min. The cells were allowed to adhere for 24 hours with the IC circulation halted and the EC circulating at a flow rate of 0.04 mL/min for gas exchange. Then, a volume of culture medium equivalent to 2.5 times the reactor volume was loaded at flow rates of 4.2 mL/min for the IC space and 74 mL/min for the EC space. Following this, perfusion culture was initiated through the EC compartment at a flow rate of 0.04 mL/min. On days 3, 5, and 6, mTeSR Plus-cGMP medium (STEMCELL Technologies) equivalent to 1.5 times the reactor volume was loaded into both the IC and EC compartments at the same respective flow rates. The culture was maintained for a total of 7 days. The harvesting process involves the same steps used in the small bioreactor but using greater reagent volumes: 1. Wash the system with PBS. 2. Add 180 mL of Accutase (STEMCELL Technologies). 3. Incubate for 10 minutes. This duration was set so that the total exposure time of the cells to the dissociation reagent, including the time during which the reagent was being introduced, would be 13 minutes—consistent with the small-scale reactor where fluids need to be added at lower rates to avoid excessive fluid pressure in the system. 4. Flush the cells into harvest bags using mTeSR Plus - cGMP (STEMCELL Technologies) medium containing CloneR2 (STEMCELL Technologies).

value: iPSCs

tag: group

value: small bioreactor


title: H1299 cells, shPPP2R2A-2 repeat2

description: Library name: H-s-2_2_R1.fastq.gz


title: iPSCs (standard bioreactor), Q5-5

value: standard bioreactor


title: H1299 cells, shPPP2R2A-2 repeat1

description: Library name: H-s-2_1_R1.fastq.gz


title: H1299 cells, shcon repeat3

description: Library name: H-p3_R1.fastq.gz


title: iPSCs (small bioreactor), Q6-6


title: H1299 cells, shPPP2R2A-1 repeat1

description: Library name: H-s-1_1_R1.fastq.gz


title: H1299 cells, shcon repeat2

description: Library name: H-p2_R1.fastq.gz


title: H1299 cells, shPPP2R2A-1 repeat2

description: Library name: H-s-1_2_R1.fastq.gz


title: H1299 cells, shcon repeat1

description: Library name: H-p1_R1.fastq.gz


title: iPSCs (small bioreactor), Q6-5


title: HMGB1 37C ChIP Rep1

description: Library name: HMGB1 37C ChIP Rep1


title: A549 cells, shPPP2R2A-2 repeat2

description: Library name: A-s-2_2_R1.fastq.gz


title: A549 cells, shPPP2R2A-1 repeat3

description: Library name: A-s-1_3_R1.fastq.gz


title: A549 cells, shPPP2R2A-2 repeat3

description: Library name: A-s-2_3_R1.fastq.gz


title: A549 cells, shcon repeat1

description: Library name: A-p1_R1.fastq.gz


title: A549 cells, shPPP2R2A-1 repeat2

description: Library name: A-s-1_2_R1.fastq.gz


title: A549 cells, shPPP2R2A-2 repeat1

description: Library name: A-s-2_1_R1.fastq.gz


title: A549 cells, shPPP2R2A-1 repeat1

description: Library name: A-s-1_1_R1.fastq.gz


title: KOREF1-P-1Rep


title: A549 cells, shcon repeat3

description: Library name: A-p3_R1.fastq.gz


title: A549 cells, shcon repeat2

description: Library name: A-p2_R1.fastq.gz


title: H1299 cells, shPPP2R2A-1 repeat3

description: Library name: H-s-1_3_R1.fastq.gz


title: Bulk RNAseq of HBECs (U30_KD_C2)

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

description: Library name: U30_KD_C2

data_processing:
Bulk RNA Sequencing
Alignment to GRCh38 using Salmon 1.5.2
Differential expression analysis using DESeq2
Assembly: GRCh38 release 101
Supplementary files format and content: Digital gene expression count matrix generated by Salmon.

source_name: Bronchus

growth_protocol: As previously described (11, 12, 49, 53), primary HBE cells were seeded on transwells and maintained in ALI culture until the cells were well-differentiated. We used primary HBE cells from thirteen distinct donors with no history of smoking or lung disease (Supplementary Table).

extract_protocol:
As we previously described (12), we isolated total RNA from HBE cells (n = 3 donors without a history of lung disease) using the RNeasy Mini Kit (Qiagen, Hilden, Germany). Bulk RNA sequencing was performed on a NovaSeq instrument (Illumina, San Diego, CA, USA) by the Bauer Core Facility at Harvard University.
Bulk RNA Seq

treatment_protocol: To mimic bronchoconstriction, well-differentiated HBE cells were exposed to apical-to-basal pressure with a magnitude of 30cm H2O for 3 hrs, as previously described (11, 12, 49, 53). Time-matched control cells received 0cm H2O pressure. Cells and conditioned media were collected between 3 and 72 hrs. In experiments using recombinant human (rh) TGF-β1 (Cell Signaling Technologies, Danvers, MA), we spiked 10 ng/ml into the basolateral media of HBE cells in ALI cultures. Cells were collected between 24 and 72 hrs for further analysis. To determine the signaling pathways that regulate mechanical compression-induced Hic-5 protein expression, we used pharmacological inhibitors of the TGF-β receptor (SB431542; 10 µM, Tocris, Bristol, UK), MEK (U0126; 10 µM, Tocris), and EGFR (AG1478; 10 µM, Tocris). Each inhibitor was added to the basolateral media of HBE cells 1 hr prior to exposure to mechanical compression or TGF- β. As a control, 0.1% DMSO was used.To knock down Hic-5 expression in HBE cells, we used antisense oligonucleotides designed and provided by Ionis Pharmaceuticals. We initially tested five ASOs targeting TGFB1I1(denoted as Hic-5 ASO). Then, we  selected the most effective ASO and used for subsequent experiments. HBE cells maintained in ALI culture were treated with 10µM of either a non-targeting control (scrambled) ASO or Hic-5 ASO between ALI days 9 and 20 prior to the application of mechanical compression. We confirmed the knockdown efficiency of the Hic-5 ASO in well-differentiated HBE cells by RT-qPCR and western blot analysis.

value: Bronchus

value: KD

value: Airway epithelial cells

value: Wild type

value: Control


title: Bulk RNAseq of HBECs (U16_KD_P1)

description: Library name: U16_KD_P1

value: Pressure


title: iPSCs (standard bioreactor), Q5-4


title: Bulk RNAseq of HBECs (U30_KD_C1)

description: Library name: U30_KD_C1


title: Bulk RNAseq of HBECs (U30_KD_P2)

description: Library name: U30_KD_P2


title: Bulk RNAseq of HBECs (U19_KD_P1)

description: Library name: U19_KD_P1


title: Bulk RNAseq of HBECs (U30_KD_P1)

description: Library name: U30_KD_P1


title: Bulk RNAseq of HBECs (U16_KD_P2)

description: Library name: U16_KD_P2


title: Bulk RNAseq of HBECs (U16_KD_C2)

description: Library name: U16_KD_C2


title: Bulk RNAseq of HBECs (U30_WT_P2)

description: Library name: U30_WT_P2


title: Bulk RNAseq of HBECs (U30_WT_P1)

description: Library name: U30_WT_P1


title: Bulk RNAseq of HBECs (U19_KD_C1)

description: Library name: U19_KD_C1


title: Bulk RNAseq of HBECs (U16_WT_P2)

description: Library name: U16_WT_P2


title: iPSCs (standard bioreactor), Q5-6


title: Bulk RNAseq of HBECs (U16_WT_P1)

description: Library name: U16_WT_P1


title: Bulk RNAseq of HBECs (U19_WT_P2)

description: Library name: U19_WT_P2


title: Bulk RNAseq of HBECs (U30_WT_C2)

description: Library name: U30_WT_C2


title: Bulk RNAseq of HBECs (U16_WT_C1)

description: Library name: U16_WT_C1


title: Bulk RNAseq of HBECs (U16_WT_C2)

description: Library name: U16_WT_C2


title: Bulk RNAseq of HBECs (U19_WT_P1)

description: Library name: U19_WT_P1