title: CL71-CRE-1

description:
Library name: Sample 65
CL71


title: BAL11_IgG_ChIP

status: Public on Feb 27 2026

type: SRA

city: London

first: Niklas

last: Feldhahn

address: The Commonwealth Building, Hammersmith Hospital, Du Cane Road

department: Department of Medicine

country: United Kingdom

institute: Imperial College London

library_source: genomic

data_processing:
Trimmed fastq files were aligned to the human genome, hg38, using bowtie2 (v2.4.4), using the additional parameter: --no-unal.
SAM files generated by bowtie2 were converted to BAM format using samtools (v1.14) view -S -b.
Bam files were processed using samtools fixmate ‑m, samtools sort -o, samtools markdup -r, samtools collate -o, samtools sort -o
To generate a file for visualisation on a genome browser, the final bam files were processed by deeptools (v3.5.1) suite.
To generate bigwig files, bamCoverage was used with the following parameters: --normalizeUsing RPKM, --extendReads, --effectiveGenomeSize 2913022398 (for hg38), or 2654621783 (for mm39).
Assembly: hg38 or mm39
Supplementary files format and content: RPKM normalised bedGraph files for track visualisation by genome browsers.

molecule: genomic DNA

organism: Homo sapiens

source_name: bone marrow

growth_protocol: Cell lines were grown at a density 0.5-3mio/ml in RPMI1640 media with 20% FBS, 1% Pen/Strep and 1X Glutamax. Ph+B-ALL cells from patient BAL08 were expanded ex vivo on sub-lethally irradiated OP9 cells (0.5x106 OP9 cells/10 cm dish, mitotically inactivated by 13.6 Gy, 25 × 106 B-ALL cells/plate) grown in aMEM media with 20% FBS, 1% Pen/Strep and 1X Glutamax. After ~20 days of co-culture, cells were checked for viability and B-ALL phenotype by flow cytometry and then split to new OP9-coated plates for respective experiments.

extract_protocol:
ChIP-Seq for H3K27ac was done as described in Boulianne et al using anti-Histone H3 (acetyl K27) antibody – ChIP Grade (ab4729) (Abcam) and polyclonal rabbit IgG (isotype control) (sc2027) (Santa Cruz Biotechnologies), with the exception that initial cross-linking was performed at RT. For HA-ChIP-Seq, three lots of 2 x 10^7 cells per sample were separately, sequentially double-crosslinked consisting of a 30 min RT incubation with 2 mM Disuccinimidyl Glutarate (DSG) in PBS followed by a 30 min RT incubation with 1% formaldehyde (prepared in PBS) (rotating during incubation and washes in between), with the remainder done as described in Boulianne et al3 but using 0.8 ug anti-HA-tag antibody (Cell Signalling #3724) per 2 x 10^7 cells.
ChIP-Seq libraries were generated from ChIP immunoprecipitated DNA using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (NEB) and sequenced either at Novogene or at the in-house sequencing facility of the MRC London Institute of Medical Sciences at Imperial College London.

treatment_protocol: Where indicated cells were treated with DMSO or Ponatinib (100nM for human cells, 10nM for mouse cells), 250nM dTAGV-1, or 2.5uM AK-2292. Treatment was for 24h, except for samples labeled BV173_parental_* and BV173_STAT5_2A_NTAG_* that were treated for 48h.

tag: tissue

value: bone marrow

tag: cell line

value: primary cells

tag: cell type

value: B-cell precursors

tag: genotype

tag: treatment

value: no treatment


title: CL69-GFP-2

city: Worcester

first: Sithara Raju

last: Ponny

state: MA

address: 55 N Lake Ave

department: Program in Molecular Medicine

country: USA

institute: UMass Chan Medical School

description:
Library name: Sample 63
CL69

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor and low quality sequences using cutadapt
TPM and Counts were calculated using Salmon
Assembly: mm10
Supplementary files format and content: excel file include read count values for each Sample
Supplementary files format and content: excel file include TPM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA was harvested using RNeasy kit with Dnase I treatment.
PolyA enrichment library preperation by Novogene and libraries were pair end sequenced for 150bp on NovaSeq6000 platform.

value: liver

tag: strain

value: J1 J2 lf/lf

tag: diet

value: HFD

tag: time


title: BAL05_IgG_ChIP


title: CL70-GFP-3

description:
Library name: Sample 64
CL70


title: S_470_D5_Con

city: Canyon

first: Bradly

middle: Isaiah

last: Ramirez

state: Texas

address: 3201 Russel Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

data_processing:
Base calling with Illumina RTA v3
Quality assessed with FastQC 0.11.9-Java-11
Trimming with Trimmomatic 0.39 to remove adapters; phred33; sliding window of 4 bases, minimum quality score 20; minimum length = 28 bases; trimmed leading and trailing bases with quality score less than 3
HISAT2 v2.2.1 used to map and index reads against Bos taurus reference genome ARS-UCD1.3
Reads assembled and quantified with StringTie v2.1.0
Resulting GFFs merged with StringTie v2.1.0
PrepDE3.py3 used to generate read count matrix
Differential expression performed with edgeR v3.38.4 and glmmSeq v0.2.0
Assembly: ARS-UCD1.3
Supplementary files format and content: Tab delineated text file of raw gene counts for each sample

organism: Bos taurus

source_name: Whole blood

extract_protocol:
RNA extracted with Tempus Spin RNA Isolation Kits
RNA libraries were prepared for sequencing using Illumina stranded mRNA library preparation kits, using standard Illumina protocols.

treatment_protocol: Samples collected in Tempus blood RNA tubes and stored same day at -80 C until extraction

value: Whole blood

value: Day 5

value: Control

tag: individual id

tag: disease

value: bovine respiratory disease (BRD)


title: CL67-FLPO-3

description:
Library name: Sample 61
CL67


title: S_466_D15_Con

value: Day 15


title: S_478_D6_Con

value: Day 6


title: S_476_D4_Con

value: Day 4


title: CL64-FLPO-1

description:
Library name: Sample 59
CL64


title: CL68-GFP-1

description:
Library name: Sample 62
CL68


title: S_458_D12_Con

value: Day 12


title: CL63-CRE-3

description:
Library name: Sample 58
CL63


title: BAL11_H3K27ac_ChIP


title: BAL08_PON_IgG_ChIP

value: Ponatinib


title: CL62-CRE-2

description:
Library name: Sample 57
CL62


title: CL65-FLPO-2

description:
Library name: Sample 60
CL65


title: BAL05_H3K27ac_ChIP


title: CL58-GFP-3

description:
Library name: Sample 55
CL58


title: BAL08_PON_H3K27ac_ChIP


title: S_441_D10_Con

value: Day 10


title: CL56-GFP-1

description:
Library name: Sample 53
CL56


title: CL60-CRE-1

description:
Library name: Sample 56
CL60


title: BAL08_DMSO_H3K27ac_ChIP

value: bone marrow

value: DMSO


title: BAL08_DMSO_IgG_ChIP

value: primary cells

value: B-cell precursors


title: S_447_D14_Con

value: Day 14


title: S_438_D4_Con


title: CL54-FLPO-2

description:
Library name: Sample 52
CL54

value: liver

value: J1 J2 lf/lf


title: TOM1_PON_input


title: S_443_D5_Con

value: Whole blood


title: CL52-CRE-3

description:
Library name: Sample 50
CL52

value: HFD


title: S_419_D7_Con

value: Day 7

value: Control


title: CL53-FLPO-1

description:
Library name: Sample 51
CL53


title: CL51-CRE-2

description:
Library name: Sample 49
CL51


title: CL57-GFP-2

description:
Library name: Sample 54
CL57


title: CL50-CRE-1

description:
Library name: Sample 48
CL50


title: S_464_D33_Tula

value: Day 33

value: Tulathromycin

value: bovine respiratory disease (BRD)


title: TOM1_PON_IgG_ChIP


title: TOM1_PON_H3K27ac_ChIP


title: CL49-GFP-3

description:
Library name: Sample 47
CL49


title: TOM1_DMSO_input


title: S_413_D32_Tula

value: Day 32


title: CL48-GFP-2

description:
Library name: Sample 46
CL48


title: CL47-GFP-1

description:
Library name: Sample 45
CL47


title: CL46-FLPO-3

description:
Library name: Sample 44
CL46


title: TOM1_DMSO_IgG_ChIP


title: S_454_D21_Tula

value: Day 21


title: CL45-FLPO-2

description:
Library name: Sample 43
CL45


title: S_476_D0_Con

value: Day 0


title: S_479_D0_Con


title: TOM1_DMSO_H3K27ac_ChIP

value: bone marrow


title: F_3

city: Beijing

first: Xinyi

last: Luo

address: No. 11, North 3rd Ring East Road

department: School of Materia Medica

country: China

institute: Beijing University of Chinese Medicine

description:
Library name: sample 2
Treatment

data_processing:
HTSeq v 0.5.4 p3 was used to count the reads numbers mapped to each gene.
Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped (FPKM).
Assembly: GRCh38
Supplementary files format and content: fpkm_genename.xls

extract_protocol:
TRIzol(Invitrogen, CA, USA)
NEBNext® UltraTM RNA Library Preparation Kit for Illumina® (NEB, USA)

value: breast cancer cell

value: incubated for 24 h with 1μM CEL


title: CL44-FLPO-1

description:
Library name: Sample 42
CL44


title: F_2

description:
Library name: sample 1
Control

value: incubated for 24 h


title: SUPB15_PON_input

value: B-cell precursors

value: Ponatinib


title: S_470_D0_Con


title: MDA-MB231 cells, ERBBride-targeting siRNA-1, biol rep 3

city: Shenzhen

first: Diansheng

last: Zhou

address: 1066 Xueyuan Road, Nanshan District

institute: Shenzhen University

description:
Library name: Sample 6
Column name in All.HTSeq.counts.txt: si1_3

data_processing:
Trimmomatic software were used to remove adapter and low quality reads
STAR is used to align clean reads to reference genome.
Read counts for individual transcripts of each sample were produced with HTSeq-count. Read counts for individual transcripts of each sample were produced with kallisto.
Assembly: hg38_V43_gencode
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was extracted from MDA-MB-231 cells transfected with control siRNA or ERBBride-targeting siRNA-1.
RNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA Library Prep Kit（NEB #E7490）following manufacturer's protocols

value: Breast cancer cells

value: ERBBride knock down


title: CL43-CRE-2

description:
Library name: Sample 41
CL43

value: liver

value: J1 J2 lf/lf

value: HFD


title: MDA-MB231 cells, ERBBride-targeting siRNA-1, biol rep 1

description:
Library name: Sample 4
Column name in All.HTSeq.counts.txt: si1_1


title: MDA-MB231 cells, ERBBride-targeting siRNA-1, biol rep 2

description:
Library name: Sample 5
Column name in All.HTSeq.counts.txt: si1_2


title: SUPB15_PON_H3K27ac_ChIP


title: MDA-MB231 cells, siCTRL, biol rep 2

description:
Library name: Sample 2
Column name in All.HTSeq.counts.txt: sictrl_2

value: WT


title: S_447_D0_Con

value: Whole blood

value: Control


title: CL39-FLPO-4

description:
Library name: Sample 37
CL39


title: CL42-CRE-1

description:
Library name: Sample 40
CL42


title: MDA-MB231 cells, siCTRL, biol rep 1

description:
Library name: Sample 1
Column name in All.HTSeq.counts.txt: sictrl_1


title: DKC1_KD_C6_biol rep2

city: Kanpur

first: Bushra

last: Ateeq

state: Uttar Pradesh

address: Lab-4, BSBE, Indian Institute of Technology Kanpur, Kalyanpur

department: Department of Biological Sciences and Bioengineering

country: India

institute: Indian Institute of Technology Kanpur

description:
Library name: SW620shDKC1C6W2
RNA-seq

data_processing:
Raw reads were trimmed for adapter sequences using Trimmomatic/0.38 to obtain high-quality data (phred score ≥30). Artifacts such as low quality reads, contaminant DNA, or PCR duplicates were removed. Trimmed reads were mapped to Human hg38 genome with HISAT/2.1.0, splice-aware aligner. Transcripts were assembled by StringTie/2.1.3b with aligned reads. Differential expression analysis was performed using DESeq2 R package to identify dysregulated genes (> or < 0.6 log2(fold-change) and adjusted p-value <0.05).
Assembly: hg38
Supplementary files format and content: Raw gene counts have been provided as tab-delimited excel file

source_name: Colorectal

growth_protocol: SW620 cells were obtained from the cell line repository at the National Centre for Cell Sciences, Pune, Maharashtra, India and grown in Leibovitz’s L-15 medium supplemented with 10% fetal bovine serum, 0.5% Penicillin/Streptomycin at 37 °C in a humidified incubator with 0% CO2 as per ATCC recommendations. STR profiling was performed at DNA Forensics Laboratory, New Delhi for cell line identification

extract_protocol:
RNA was isolated from the SW620 cells using TRIzol reagent (Ambion, Life technologies) as per the instructions provided by the manufacturer. Quality of the isolated RNA was assessed using 2100 Bioanalyzer (Agilent Technologies).
Library was prepared using Illumina TruSeq Stranded mRNA Library prep kit (Reference Guide # 1000000040498 v00) as per manufacturer's instructions. Paired-end sequencing was performed at Macrogen Inc. (South Korea) on NovaSeq 6000 platform with a 150bp read length and more than 25M reads recorded per sample.

treatment_protocol: Lentiviral packaging of the shRNA constructs was performed using ViraPower Lentiviral Expression System (Invitrogen, Carlsbad, CA, USA) as per manufacturer's instructions. For stable silencing of DKC1, human lentiviral short-hairpin RNA-targeting DKC1 (shDKC1) and non-targeting scrambled short-hairpin RNA (shSCRM) were cloned in pLV vectors (Cyagen Biosciences, Santa Clara, USA). Stable cells were maintained under selection pressure with 1μg/mL puromycin (Sigma-Aldrich).

value: Colorectal

value: Epithelial cells

value: Knockdown

value: No treatment

tag: batch


title: S_441_D0_Con

value: Day 0

value: bovine respiratory disease (BRD)


title: DKC1_KD_C6_biol rep1

description:
Library name: SW620shDKC1C6W1
RNA-seq


title: S_443_D0_Con


title: SUPB15_DMSO_IgG_ChIP

value: bone marrow

value: DMSO


title: SUPB15_DMSO_H3K27ac_ChIP

value: B-cell precursors


title: CL38-FLPO-3

description:
Library name: Sample 36
CL38


title: HBM01_PCHIC

data_processing:
PCHiC data was processed as described in Freire-Pritchett et al. (doi: 10.1038/s41596-021-00567-5).
Raw fastq files were aligned to the human genome (hg38) using the HiCUP package (v0.7.3), with the range di-tags set between 100 - 850 bp.
The Capture Hi-C Analysis of Genomic Organisation (CHiCAGO) (v1.18.0) was utilised to process HiCUP-generated bam files to produce interaction files, with a score threshold of 5.
Assembly: hg38
Supplementary files format and content: Significant PCHiC interactions (Bait chromosome, bait start, bait end, other-end chromosome coordinate and CHiCAGO score, CHiCAGO score)
Library strategy: PCHiC

source_name: Bone marrow

extract_protocol:
Cells were counted and a total of 20 million cells were harvested to be processed with the promoter-capture HiC protocol as described in Schoenfelder et al. (doi:10.3791/57320). Briefly, paraformaldehyde crosslinked nuclei were digested with HindIII, with the ends labelled with biotin and subsequently ligated. Reverse crosslink was performed and the DNA was sonicated and subsequently purified with streptavidin beads.
Library construction was prepared according to the protocol described in Schoenfelder et al (doi:10.3791/57320). Briefly, xGen Stubby Adapter and UDI primer set was utilised to index each HiC library using the Phusion polymerase. Following sequencing adapter ligation, the library was purified with SPRI beads. To generate PCHiC library, biotinylated RNA probes were used to capture promoter sequences from the HiC library and amplified by PCR and subsequently purified. PCHiC library was sequenced by paired-end sequencing.

treatment_protocol: Cells were treated with either DMSO (vehicle control), or Ponatinib (100 nM) for 24 hours before harvesting the cells.

value: Bone marrow

value: primary cells

value: healthy B-cell precursors

value: normal

value: no treatment


title: MDA-MB231 cells, siCTRL, biol rep 3

description:
Library name: Sample 3
Column name in All.HTSeq.counts.txt: sictrl_3

value: Breast cancer cells

value: WT


title: CL41-GFP2

description:
Library name: Sample 39
CL41

value: liver

value: J1 J2 lf/lf

value: HFD


title: SUPB15_DMSO_input


title: CL40-GFP-1

description:
Library name: Sample 38
CL40


title: SUPB15_PON_IgG_ChIP

value: Ponatinib


title: S_458_D0_Con

value: Whole blood

value: Control


title: DKC1_KD_C3_biol rep2

description:
Library name: SW620shDKC1C3W2
RNA-seq

value: Colorectal

value: Epithelial cells

value: Knockdown

value: No treatment


title: S_413_D0_Tula

value: Day 0

value: Tulathromycin

value: bovine respiratory disease (BRD)


title: BAL08_+DMSO_PCHIC

value: Bone marrow

value: primary cells

value: lymphoid leukaemia

value: DMSO


title: BAL08_+PON_PCHIC


title: CL36-FLPO-1

description:
Library name: Sample 34
CL36

value: liver


title: S_454_D0_Tula


title: S_464_D0_Tula


title: DKC1_KD_C3_biol rep1

description:
Library name: SW620shDKC1C3W1
RNA-seq


title: S_474_D21_Con

value: Day 21


title: Scramble_control_biol rep2

description:
Library name: SW620_shSCRMW2
RNA-seq


title: CL37-FLPO-2

description:
Library name: Sample 35
CL37

value: J1 J2 lf/lf

value: HFD


title: CL33-CRE-1

description:
Library name: Sample 31
CL33


title: S_436_D21_Con

value: Whole blood


title: OCIAML3, 1 µM A485, PU1, rep2

city: Mainz

first: Aarón

last: Gallego Crespo

state: Rhineland-palatinate

address: Langenbeckstraße 1

department: III. Medical Department

country: Germany

institute: University Medical Center of the Johannes Gutenberg University

description: Library name: Sample 91

data_processing:
Libraries were sequenced using Illumina NovaSeq X Plus technology.
ChIP-Seq reads were trimmed using Trim Galore v0.6.5 for adapters removal.
Trimmed reads were aligned to the human reference genome (GRCh38/hg38) using the aligner Bowtie2 v2.5.1 (Parameters: bowtie2 --very-sensitive -k 1). Uniquely mapped and properly paired reads were retained using Picard v2.6.0 for reads deduplication.
Peaks were called with MACS2 v2.2.7.1.
BigWig files were created using DeepTools v3.5.1 for coverage visualization
Assembly: hg38
Supplementary files format and content: Bigwig files

source_name: Blood cells

growth_protocol: RPMI 10% FCS and 1% Pen/Strep; cells were cultured at 37°C with 5% CO2

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes. Crosslinking was terminated with 125mM Glycine for 5 minutes. Cell pellets were washed twice with ice-cold PBS and snap-frozen in liquid nitrogen
ChIP libraries were prepared using NEBNext® Ultra II DNA Library Prep Kit for Illumina. ChIP DNA was amplified using 11 cycles according to the manufacturers instruction. Amplified ChIP libraries were finally size selected using AMPure Beads (Beckman-Coulter) and analyzed via Tapesation (High Sensiticity, Agilent).

treatment_protocol: 24 Hours of Treatment with A-485 or DMSO

value: Blood cells

value: Acute Myeloid Leukemia


title: S_475_D21_Con

value: Control


title: S_473_D21_Con


title: CL35-CRE-3

description:
Library name: Sample 33
CL35


title: OCIAML3, DMSO control, PU1, rep2

description: Library name: Sample 90


title: Scramble_control_biol rep1

description:
Library name: SW620_shSCRMW1
RNA-seq

value: Colorectal

value: Epithelial cells


title: SUP-B15_+DMSO_PCHIC


title: TOM-1_+PON_PCHIC

value: Ponatinib


title: CL34-CRE-2

description:
Library name: Sample 32
CL34


title: CL32-GFP-3

description:
Library name: Sample 30
CL32


title: SUP-B15_+PON_PCHIC


title: TOM-1_+DMSO_PCHIC


title: CL31-GFP-2

description:
Library name: Sample 29
CL31


title: K562_+PON_PCHIC

value: myeloid leukaemia cells


title: S_415_D21_Con


title: OCIAML3, 1 µM A485, PU1, rep1

description: Library name: Sample 89


title: K562_+DMSO_PCHIC


title: S_431_D21_Con


title: S_408_D21_Con


title: BV-173_+PON_rep2

data_processing:
Salmon (v1.10.1) was used to quantify transcript count from RNA-Seq. A full decoy index was generated using whole genome and transcript sequences obtained from GENCODE genes database, with the hg38 (release 43) and mm39 (release 32) genomes, respectively.
Trimmed fastq files were processed using Salmon (v1.10.1) with the following parameters: ‑‑gcbias, ‑‑writeUnmappedNames.
GenomicFeatures(v1.46.5) was used to generate transcript-to-gene objects in R, using GTF files obtained from the GENECODE gene database.
Salmon quantification file was subsequently analysed using DESeq2 (v1.34.0).
Assembly: hg38 or mm39
Supplementary files format and content: quant.sf

extract_protocol:
Cells were washed with PBS, counted and subjected RNA isolation using Qiagen RNAeasy kit. RNA was snap frozen and sent for mRNA sequencing at Novogene.
Libraries were generated by Novogene.

treatment_protocol: Where indicated, cells were treated with DMSO or Ponatinib (100nM for human cells, 10nM for mouse cells), 250nM dTAGV-1, or 2.5uM AK-2292. Treatment was for 24h, except for samples indicated that were treated for 48h.

value: bone marrow

value: cell line

value: B-cell precursor


title: CL30-GFP-1

description:
Library name: Sample 28
CL30


title: OCIAML3, DMSO control, PU1, rep1

description: Library name: Sample 88


title: CL28-FLPO-4

description:
Library name: Sample 27
CL28


title: S_477_D21_Tula

value: Tulathromycin


title: BV-173_+DMSO_rep2

value: DMSO


title: CL26-FLPO-2

description:
Library name: Sample 25
CL26

value: liver


title: S_467_D21_Tula

value: Day 21


title: OCIAML3, DMSO control, FLI1, rep2

description: Library name: Sample 82


title: OCIAML3, 1 µM A485, FLI1, rep1

description: Library name: Sample 81


title: S_459_D21_Tula


title: SUP-B15_+A-485_rep3


title: CL25-FLPO-1

description:
Library name: Sample 24
CL25

value: J1 J2 lf/lf


title: CL27-FLPO-3

description:
Library name: Sample 26
CL27

value: HFD


title: S_465_D21_Tula

value: Whole blood


title: OCIAML3, 1 µM A485, MEF2D, rep1

description: Library name: Sample 85

value: Blood cells


title: CL24-CRE-2

description:
Library name: Sample 23
CL24


title: SUP-B15_+DMSO_rep3


title: TOM-1_+A-485_rep3


title: CL23-CRE-1

description:
Library name: Sample 22
CL23


title: S_451_D21_Tula


title: OCIAML3, DMSO control, MEF2D, rep1

description: Library name: Sample 84

value: Acute Myeloid Leukemia


title: SUP-B15_+DMSO_rep2


title: OCIAML3, 1 µM A485, FLI1, rep2

description: Library name: Sample 83


title: TOM-1_+DMSO_rep3


title: CL22-GFP-4

description:
Library name: Sample 21
CL22


title: OCIAML3, 1 µM A485, STAT1, rep2

description: Library name: Sample 79


title: S_405_D21_Tula


title: OCIAML3, DMSO control, STAT1, rep2

description: Library name: Sample 78


title: TOM-1_+A-485_rep2


title: OCIAML3, 1 µM A485, STAT1,  rep1

description: Library name: Sample 77


title: S_414_D21_Tula


title: S_475_D14_Con

value: Day 14

value: Control


title: CL20-GFP-2

description:
Library name: Sample 19
CL20


title: OCIAML3, DMSO control, FLI1, rep1

description: Library name: Sample 80


title: BV-173_+PON_rep1


title: CL18-FLPO-3

description:
Library name: Sample 17
CL18


title: S_473_D14_Con


title: CL21-GFP-3

description:
Library name: Sample 20
CL21


title: BV-173_+DMSO_rep1


title: S_436_D14_Con


title: CL19-GFP-1

description:
Library name: Sample 18
CL19


title: SUP-B15_+PON_rep1


title: OCIAML3, 1 µM A485, CEBPA, rep2

description: Library name: Sample 71


title: S_431_D14_Con


title: CL16-FLPO-1

description:
Library name: Sample 15
CL16


title: SUP-B15_+DMSO_rep1


title: TOM-1_+DMSO_rep2


title: S_415_D14_Con


title: OCIAML3, 1 µM A485, CEBPB, rep1

description: Library name: Sample 73


title: CL17-FLPO-2

description:
Library name: Sample 16
CL17


title: S_474_D14_Con


title: OCIAML3, DMSO control, STAT1, rep1

description: Library name: Sample 76


title: CL14-CRE-2

description:
Library name: Sample 13
CL14


title: CL15-CRE-3

description:
Library name: Sample 14
CL15


title: OCIAML3, 1 µM A485, CEBPA, rep1

description: Library name: Sample 69


title: TOM-1_+DMSO_rep1


title: TOM-1_+PON_rep1


title: OCIAML3, DMSO control, CEBPA, rep2

description: Library name: Sample 70


title: BAL08_+PON

value: primary


title: S_408_D14_Con


title: OCIAML3, DMSO control, CEBPB, rep1

description: Library name: Sample 72


title: CL13-CRE-1

description:
Library name: Sample 12
CL13


title: S_467_D14_Tula


title: CL12-GFP-3

description:
Library name: Sample 11
CL12


title: S_477_D14_Tula


title: OCIAML3, 1 µM A485, ARID1A, rep1

description: Library name: Sample 65


title: OCIAML3, DMSO control, ARID1A, rep1

description: Library name: Sample 64


title: S_465_D14_Tula


title: CL11-GFP-2

description:
Library name: Sample 10
CL11


title: S_459_D14_Tula


title: S_451_D14_Tula


title: CL8-FLPO-2

description:
Library name: Sample 8
CL8


title: HBM06

value: normal

value: no treatment


title: OCIAML3, DMSO control, CEBPA, rep1

description: Library name: Sample 68


title: HBM04

value: bone marrow


title: OCIAML3, 1 µM A485, SMARCA4, rep1

description: Library name: Sample 61


title: OCIAML3, DMSO control, SMARCA4, rep2

description: Library name: Sample 62


title: S_414_D14_Tula


title: CL10-GFP-1

description:
Library name: Sample 9
CL10


title: SUP-B15_+DMSO_ATAC-Seq

data_processing:
Trimmed fastq files were aligned to the human genome, hg38, using bowtie2 (v2.4.4) using the additional parameter: --no-unal. SAM files were generated by bowtie2 and converted to BAM format using samtools (v1.14) view -S -b.
Bam files were processed using samtools fixmate ‑m, samtools sort -o, samtools markdup -r, samtools collate -o, samtools sort -o.
To generate a file for visualisation on a genome browser, the final bam files were processed by deeptools (v3.5.1) suite.
To generate bigwig files, bamCoverage was used with the following parameters: --normalizeUsing RPKM, --extendReads, --effectiveGenomeSize 2913022398 (for hg38).
Assembly: hg38
Supplementary files format and content: Normalised bigwig files for track visualisation by WashU genome browser.

extract_protocol:
Cells were washed with PBS, counted and subjected to the ATAC-Seq protocol.
ATAC-Seq was performed according to the Omni-ATAC-seq protocol (https://doi.org/10.1038/protex.2017.096). In brief, cells were lysed using NP40, Tween-20 and Digitonin, and nuclei were treated with transposase followed by PCR-amplification of transposed fragments using NEBNext 2x MasterMix.

value: cell line


title: BAL08_+DMSO

value: B-cell precursor


title: S_405_D14_Tula

value: Tulathromycin


title: HBM05


title: CL7-FLPO-1

description:
Library name: Sample 7
CL7


title: OCIAML3, 1 µM A485, SMARCA4, rep2

description: Library name: Sample 63


title: S_475_D7_Con

value: Day 7


title: OCIAML3, 1 µM A485, IRF2BP2, rep2

description: Library name: Sample 59


title: TOM-1_+PON_ATAC-Seq

value: 100nM Ponatinib


title: OCIAML3, DMSO control, SMARCA4, rep1

description: Library name: Sample 60

value: DMSO


title: S_474_D7_Con


title: CL4-CRE-1

description:
Library name: Sample 4
CL4

value: liver

value: J1 J2 lf/lf


title: CL5-CRE-2

description:
Library name: Sample 5
CL5

value: HFD


title: CL6-CRE-3

description:
Library name: Sample 6
CL6


title: S_473_D7_Con

value: Whole blood


title: TOM-1_+DMSO_ATAC-Seq


title: SUP-B15_+PON_ATAC-Seq


title: BAL08_+PON_ATAC-Seq


title: CL2-GFP-2

description:
Library name: Sample 2
CL2


title: BAL08_+DMSO_ATAC-Seq


title: OCIAML3, DMSO control, IRF2BP2, rep2

description: Library name: Sample 58

value: Blood cells

value: Acute Myeloid Leukemia


title: OCIAML3, DMSO control, IRF2BP2, rep1

description: Library name: Sample 56


title: day 1 adult, ev, Teriflunomide 250 uM, batch2, rep4

city: LAUSANNE

first: Johan

last: Auwerx

address: Station 15

department: SV-IBI

country: Switzerland

institute: Ecole Polytechnique Fédérale de Lausanne EPFL

description:
Library name: Teriflunomide_2_4
Column name in raw_counts_all_samples.txt: Teriflunomide_2_4

data_processing:
Raw sequencing reads underwent quality control using FastQC (fastqcr R package, version 0.11.7).
Reads were then aligned to the Caenorhabditis elegans WBcel235.89 genome using STAR (version 2.7.3a) with the --quantMode TranscriptomeSAM GeneCounts option. The output was sorted by coordinate and stored in BAM format.
Gene expression counts were extracted from STAR ReadsPerGene.out.tab, and genes with zero counts across all samples were removed.
Differential gene expression analysis was performed using DESeq2 (version 1.40.2).
Assembly: WBcel235.89
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

organism: Caenorhabditis elegans

source_name: worm

growth_protocol: Worms were cultured and maintained at 20 ̊C and fed with E. coli OP50 on Nematode Growth Media (NGM) plates, prior to experiments.

extract_protocol:
Total RNA was extracted by adding 1 mL of TriPure Isolation Reagent (Cat. 11667165001, Roche) to each worm pellet. We then freeze-thawed the sample eight times (alternatively frozen in dry ice and then thawed in a 37°C water bath) in order to disrupt cell membranes.  RNA was then extracted using the Macherey-Nagel column-based RNA extraction kit (Cat. 740955.250)
RNA sequencing was carried out by the Beijing Genomics Institute (BGI) on the BGISEQ-500 platform.

treatment_protocol: Larval stage L1 worms were isolated using a pluriStrainer® 10 µm filter (SKU 43-50010-50). Approximately 3,000 L1 worms were transferred onto E. coli HT115-seeded plates and fed with an empty vector (EV) control, unless otherwise specified. In the dhod-1 RNAi condition, worms were instead fed dhod-1 RNAi bacteria. The plates contained 2 mM IPTG, 25 mg/mL carbenicillin, and 10 µM 5-FU, along with the compounds of interest. Worms were grown to the Day 1 adult stage, then collected and washed three times with M9 buffer. Worm pellets were snap-frozen in liquid nitrogen and stored at -80°C until use. We collected four biological replicates per condition.

tag: age

value: day 1 adult

value: worm

tag: compound treatment

value: Teriflunomide 250 uM

tag: bacteria feeding

value: ev

tag: replicate


title: S_436_D7_Con

value: Control


title: OCIAML3, DMSO control, CREBBP, rep1

description: Library name: Sample 52


title: day 1 adult, ev, Teriflunomide 250 uM, batch2, rep3

description:
Library name: Teriflunomide_2_3
Column name in raw_counts_all_samples.txt: Teriflunomide_2_3


title: CL3-GFP-3

description:
Library name: Sample 3
CL3


title: OCIAML3, 1 µM A485, P300, rep1

description: Library name: Sample 49


title: S_431_D7_Con


title: S_415_D7_Con


title: day 1 adult, ev, Teriflunomide 250 uM, batch2, rep2

description:
Library name: Teriflunomide_2_2
Column name in raw_counts_all_samples.txt: Teriflunomide_2_2


title: WT2year3

city: Changchun

first: Hanlan

last: Yin

state: Jilin

address: 2699, Qianjin street

institute: Jilin University

description: Library name: Sample 12

data_processing:
Illumina Casava2.19 software used for basecalling.
Rawdata(raw reads) of fastq format were firstly processed through fastp  software. In this step, clean data (clean reads) were obtained by  removing reads containing adapter, reads containing ploy-N and low  quality reads from raw data.
Reference genome and gene model annotation files were downloaded  from genome website directly. Index of the reference genome was built  using Hisat2 v2.0.5 and paired-end clean reads were aligned to the  reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped  to each gene. And then FPKM of each gene was calculated based on the  length of the gene and reads count mapped to this gene.
Assembly: GRCm39
Supplementary files format and content: gene_count.xls
Supplementary files format and content: gene_fpkm.xls

source_name: brain

growth_protocol: Animals were housed in ventilated microisolator cages (4-6 mice/cage) under specific pathogen-free conditions with 12:12 light-dark cycles, ad libitum access to autoclaved food and water.

extract_protocol:
Muscle tissue was removed, rapidly frozen on dry ice, and RNA was extracted using Trizol reagent.
Messenger RNA was purified from total RNA using poly-T oligo-attached  magnetic beads. After fragmentation, the first strand cDNA was  synthesized using random hexamer primers followed by the second  strand cDNA synthesis. The library was ready after end repair, A-tailing,  adapter ligation, size selection, amplification, and purification. The  library was checked with Qubit and real-time PCR for quantification and  bioanalyzer for size distribution detection

treatment_protocol: At 60 days postnatal, ALS mice received an intramuscular injection of BI1 plasmid (30 μg) to restore BI1 expression, while ALS controls were administered an equal volume of PBS.

value: brain


title: CL1-GFP-1

description:
Library name: Sample 1
CL1


title: S_477_D7_Tula


title: day 1 adult, ev, Teriflunomide 250 uM, batch2, rep1

description:
Library name: Teriflunomide_2_1
Column name in raw_counts_all_samples.txt: Teriflunomide_2_1


title: WT2year2

description: Library name: Sample 11


title: OCIAML3, 1 µM A485, IRF2BP2, rep1

description: Library name: Sample 57


title: S_408_D7_Con


title: OCIAML3, 1 µM A485, CREBBP, rep1

description: Library name: Sample 53


title: WT2year1

description: Library name: Sample 10


title: WT1year3

description: Library name: Sample 9


title: day 1 adult, ev, Doxycycline 50 uM, batch2, rep4

description:
Library name: Doxycycline_2_4
Column name in raw_counts_all_samples.txt: Doxycycline_2_4

value: Doxycycline 50 uM


title: S_465_D7_Tula

value: Tulathromycin


title: MOLM13, DMSO control, PU1, rep1

description: Library name: Sample 32


title: day 1 adult, ev, Doxycycline 50 uM, batch2, rep3

description:
Library name: Doxycycline_2_3
Column name in raw_counts_all_samples.txt: Doxycycline_2_3


title: S_467_D7_Tula

value: Day 7


title: MOLM13, DMSO control, CEBPA, rep1

description: Library name: Sample 13


title: day 1 adult, ev, Doxycycline 50 uM, batch2, rep2

description:
Library name: Doxycycline_2_2
Column name in raw_counts_all_samples.txt: Doxycycline_2_2


title: WT1year2

description: Library name: Sample 8


title: MOLM13, 1 µM A485, CEBPB, rep1

description: Library name: Sample 17


title: MOLM13, 1 µM A485, CEBPA, rep1

description: Library name: Sample 14


title: MOLM13, DMSO control, FLI1, rep1

description: Library name: Sample 28


title: S_451_D7_Tula


title: ALSCON_2

description: Library name: Sample 5

source_name: muscle

value: muscle


title: day 1 adult, ev, DMSO, batch2, rep3

description:
Library name: DMSO_2_3
Column name in raw_counts_all_samples.txt: DMSO_2_3

value: DMSO


title: S_459_D7_Tula


title: S_405_D7_Tula


title: ALSCON_3

description: Library name: Sample 6


title: MOLM13, 1 µM A485, FLI1, rep1

description: Library name: Sample 29


title: ALSCON_1

description: Library name: Sample 4


title: ALSBI1_3

description: Library name: Sample 3


title: S_475_D0_Con

value: Day 0


title: S_474_D0_Con


title: day 1 adult, ev, DMSO, batch2, rep1

description:
Library name: DMSO_2_1
Column name in raw_counts_all_samples.txt: DMSO_2_1


title: ALSBI1_2

description: Library name: Sample 2


title: S_473_D0_Con


title: day 1 adult, ev, Miglustat 250 uM, batch1, rep4

description:
Library name: Miglustat_1_4
Column name in raw_counts_all_samples.txt: Miglustat_1_4

value: Miglustat 250 uM


title: day 1 adult, ev, DMSO, batch2, rep2

description:
Library name: DMSO_2_2
Column name in raw_counts_all_samples.txt: DMSO_2_2


title: OCIAML3, DMSO control, P300, rep1

description: Library name: Sample 48


title: S_414_D7_Tula


title: day 1 adult, ev, Doxycycline 50 uM, batch2, rep1

description:
Library name: Doxycycline_2_1
Column name in raw_counts_all_samples.txt: Doxycycline_2_1


title: MOLM-13, 1 µM Inobrodib, rep2

description: Library name: Sample 14

data_processing:
Libraries were sequenced using Illumina NovaSeq X Plus technology.
Adapters sequences were trimmed from raw reads using Trim Galore.
Trimmed reads were aligned to the human reference genome (GRCh38/hg38) using STAR
Transcripts read counts were extracted with SAMtools
Assembly: hg38
Supplementary files format and content: Tab-delimited txt file with raw counts for each sample.

growth_protocol: Cells were cultured at 37°C with 5% CO2 in RPMI with 10% FCS and 1% Pen/Strep

extract_protocol:
RNA was extracted using Qiagens RNeasy Mini Kit (#74106)
cDNA libraries were constructed in Novogenes facilities

treatment_protocol: 1 Mio Cells were treated for 24 Hours with A-485 or Inobrodib or DMSO

value: Inobrodib


title: MOLM-13, 1 µM Inobrodib, rep3

description: Library name: Sample 15


title: MOLM-13, 1 µM Inobrodib, rep1

description: Library name: Sample 13


title: ALSBI1_1

description: Library name: Sample 1


title: S_436_D0_Con

value: Whole blood


title: day 1 adult, ev, Miglustat 250 uM, batch1, rep3

description:
Library name: Miglustat_1_3
Column name in raw_counts_all_samples.txt: Miglustat_1_3


title: S_431_D0_Con


title: S_415_D0_Con


title: MOLM-13, DMSO control, rep3

description: Library name: Sample 12

value: Blood cells


title: RA13-Cre-3

description: Library name: Sample 6

data_processing:
Sequenced reads were trimmed for adaptor and low quality sequences using cutadapt
Clean reads were then mapped to mm10 genome using STAR
TPM and Counts were calculated using SALMON
Assembly: mm10
Supplementary files format and content: tab separated files include read count values for each Sample
Supplementary files format and content: tab separated files include TPM values for each Sample

value: liver

value: RXRa f/f Alb cre+/-

value: HFD


title: S_408_D0_Con


title: day 1 adult, dhod-1 RNAi , DMSO, batch1, rep4

description:
Library name: dhod1_1_4
Column name in raw_counts_all_samples.txt: dhod1_1_4

value: day 1 adult

value: worm

value: dhod-1 RNAi


title: MOLM-13, DMSO control, rep1

description: Library name: Sample 10

value: Acute Myeloid Leukemia


title: OCI-AML3, 1 µM Inobrodib, rep3

description: Library name: Sample 9


title: day 1 adult, ev, Miglustat 250 uM, batch1, rep2

description:
Library name: Miglustat_1_2
Column name in raw_counts_all_samples.txt: Miglustat_1_2

value: ev


title: S_467_D0_Tula

value: Tulathromycin


title: day 1 adult, dhod-1 RNAi , DMSO, batch1, rep2

description:
Library name: dhod1_1_2
Column name in raw_counts_all_samples.txt: dhod1_1_2


title: RA4-WT-3

description: Library name: Sample 3

value: Alb cre +/-


title: RA10-Cre-1

description: Library name: Sample 4


title: OCI-AML3, 1 µM Inobrodib, rep2

description: Library name: Sample 8


title: day 1 adult, ev, Miglustat 250 uM, batch1, rep1

description:
Library name: Miglustat_1_1
Column name in raw_counts_all_samples.txt: Miglustat_1_1


title: RA1-WT-1

description: Library name: Sample 1


title: MOLM-13, DMSO control, rep2

description: Library name: Sample 11


title: OCI-AML3, 1 µM Inobrodib, rep1

description: Library name: Sample 7


title: S_477_D0_Tula


title: day 1 adult, dhod-1 RNAi , DMSO, batch1, rep3

description:
Library name: dhod1_1_3
Column name in raw_counts_all_samples.txt: dhod1_1_3


title: RA11-Cre-2

description: Library name: Sample 5


title: RA2-WT-2

description: Library name: Sample 2


title: day 1 adult, dhod-1 RNAi , DMSO, batch1, rep1

description:
Library name: dhod1_1_1
Column name in raw_counts_all_samples.txt: dhod1_1_1


title: S_465_D0_Tula


title: WT_M_572_citrate

city: New York

first: Abigail

last: Xie

state: New York

address: 430 E 67th St

institute: Memorial Sloan Kettering Cancer Center

description: Library name: WT_M_572_citrate

data_processing:
FASTQ files were aligned to the reference genome using DRAGEN v3.10 (Illumina) to generate BAM files.
Raw counts matrix was generated using featureCounts/subread.
Assembly: mm39
Supplementary files format and content: Processed data files include raw counts for each sample in CSV format.

molecule: polyA RNA

source_name: kidney

extract_protocol:
RNA was isolated using TRIzol (Thermo Fisher Scientific, 15596018) according to the manufacturer’s instructions.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA with RIN values of 7.3-10 underwent polyA selection and library preparation using the TruSeq Stranded mRNA LT Kit (Illumina catalog # RS-122-2102) according to instructions provided by the manufacturer with 8 cycles of PCR.

treatment_protocol: Mice were given 3% sodium citrate in drinking water or normal drinking water starting 7 days prior to tamoxifen and were then maintained on 3% sodium citrate or normal water for duration of experiments. Mice were administered 50 mg/kg tamoxifen intraperitoneally for 5 consecutive days.

value: kidney

value: WT

value: citrate


title: OCI-AML3, 1 µM A-485, rep3

description: Library name: Sample 6


title: S_459_D0_Tula

value: Day 0


title: day 1 adult, ev, Brequinar 500 uM , batch1, rep4

description:
Library name: Brequinar_1_4
Column name in raw_counts_all_samples.txt: Brequinar_1_4

value: Brequinar 500 uM


title: WT_M_571_citrate

description: Library name: WT_M_571_citrate


title: S_405_D0_Tula

value: Whole blood


title: day 1 adult, ev, Brequinar 500 uM , batch1, rep3

description:
Library name: Brequinar_1_3
Column name in raw_counts_all_samples.txt: Brequinar_1_3


title: OCI-AML3, 1 µM A-485, rep2

description: Library name: Sample 5

value: Blood cells


title: day 1 adult, ev, Brequinar 500 uM , batch1, rep2

description:
Library name: Brequinar_1_2
Column name in raw_counts_all_samples.txt: Brequinar_1_2


title: S_451_D0_Tula


title: WT_M_489_citrate

description: Library name: WT_M_489_citrate


title: OCI-AML3, 1 µM A-485, rep1

description: Library name: Sample 4


title: H1-hESC differentiation Day 28, Replicate 3

city: Singapore

first: Roger

last: Foo

address: 14 Medical Drive, MD6

country: Singapore

institute: National University of Singapore

description: Library name: Day28_3

data_processing:
Raw fastq files were trimmed using the trim-galore tool (v0.65) from Babraham Bioinformatics, to sequence length of 50. Paired-end reads were mapped and aligned to the human reference genome GrCh38/hg38 using STAR aligner (v2.7.0) as per default settings, and using gene annotations from GENCODE v38. Aligned gene counts were mapped using Htseq-count, and normalized to Counts per Million (CPM) by sequencing depth. The normalized gene expression count matrix was normalized by gene length.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

growth_protocol: hESCs were maintained in mTesR1 media, and hESC-CMs were maintained RPMI with Insulin in humidified incubator with 5% CO2 at 37°C

extract_protocol:
Directed differentiation into cardiomyocytes were performed and Total RNA were isolated at Day 0, 1, 3, 5, 7, 10, 14, and 28. Total RNA was extracted using Trizol Reagent (15596026, ThermoFisher) and Direct-Zol RNA miniprep Kit (Zymo Research, R2050) according to manufacturer’s protocol. RNA quality and yield was accessed using Agilent RNA 6000 pico kit (50167-1513, Agilent) for quality.
RNA quality and yield was accessed using Agilent RNA 6000 pico kit (50167-1513, Agilent) for quality. Bulk RNA-seq library preparations were prepared using TruSeq Stranded Total RNA library Prep HMR kit (20020596, Illumina). cDNA libraries were quantified using the Agilent DNA1000 kit (5067-1505, Agilent), prior to sequencing on Illumina NextSeq Sequencing platform by Macrogen Asia Pacific Pte. Ltd.

value: Cardiomyocyte


title: MOLM13, 1 µM A485, PU1, rep1

description: Library name: Sample 33


title: WT_F_498_citrate

description: Library name: WT_F_498_citrate


title: day 1 adult, ev, BAY2402234 500 uM , batch1, rep4

description:
Library name: BAY2402234_1_4
Column name in raw_counts_all_samples.txt: BAY2402234_1_4


title: day 1 adult, ev, Brequinar 500 uM , batch1, rep1

description:
Library name: Brequinar_1_1
Column name in raw_counts_all_samples.txt: Brequinar_1_1


title: WT_F_454_citrate

description: Library name: WT_F_454_citrate


title: OCI-AML3, DMSO control, rep1

description: Library name: Sample 1

value: DMSO


title: day 1 adult, ev, BAY2402234 500 uM , batch1, rep3

description:
Library name: BAY2402234_1_3
Column name in raw_counts_all_samples.txt: BAY2402234_1_3


title: H1-hESC differentiation Day 28, Replicate 2

description: Library name: Day28_2


title: OCI-AML3, DMSO control, rep2

description: Library name: Sample 2


title: WT_F_460_citrate

description: Library name: WT_F_460_citrate


title: FL_M_629_citrate

description: Library name: FL_M_629_citrate

value: FL


title: day 1 adult, ev, BAY2402234 500 uM , batch1, rep2

description:
Library name: BAY2402234_1_2
Column name in raw_counts_all_samples.txt: BAY2402234_1_2

value: day 1 adult


title: day 1 adult, ev, DMSO, batch2, rep4

description:
Library name: DMSO_2_4
Column name in raw_counts_all_samples.txt: DMSO_2_4

value: worm


title: FL_M_491_citrate

description: Library name: FL_M_491_citrate


title: sgACO2/CS, pyruvate (24 h), rep2

description: Library name: sgACO2_CS_pyruvate_2

data_processing:
FASTQ files were aligned to the reference genome using DRAGEN v3.10 (Illumina) to generate BAM files.
Raw counts matrix was generated using featureCounts/subread.
Assembly: hg38
Supplementary files format and content: Processed data files include raw counts for each sample in CSV format.

growth_protocol: A549 CRISPR-edited lines were maintained in DMEM with 10% fetal bovine serum. This medium was also used for experiments.

extract_protocol:
RNA was isolated using TRIzol (Thermo Fisher Scientific, 15596018) according to the manufacturer’s instructions.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA with RIN values of 9.3-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR.

treatment_protocol: Cells were treated with vehicle control (water) or sodium pyruvate (5mM, Sigma-Aldrich) for 24 hours.

value: pyruvate


title: H1-hESC differentiation Day 28, Replicate 1

description: Library name: Day28_1


title: FL_M_398_citrate

description: Library name: FL_M_398_citrate


title: FL_F_655_citrate

description: Library name: FL_F_655_citrate


title: day 1 adult, ev, BAY2402234 500 uM , batch1, rep1

description:
Library name: BAY2402234_1_1
Column name in raw_counts_all_samples.txt: BAY2402234_1_1


title: H1-hESC differentiation Day 14, Replicate 3

description: Library name: Day14_3


title: day 1 adult, ev, Terbinafine 31.5 uM , batch1, rep3

description:
Library name: Terbinafine_1_3
Column name in raw_counts_all_samples.txt: Terbinafine_1_3

value: Terbinafine 31.5 uM


title: sgACO2/CS, pyruvate (24 h), rep1

description: Library name: sgACO2_CS_pyruvate_1


title: sgACO2, pyruvate (24 h), rep2

description: Library name: sgACO2_pyruvate_2


title: sgACO2/CS, vehicle (water, 24 h), rep2

description: Library name: sgACO2_CS_vehicle_2

value: vehicle


title: FL_M_405_citrate

description: Library name: FL_M_405_citrate


title: day 1 adult, ev, Terbinafine 31.5 uM , batch1, rep4

description:
Library name: Terbinafine_1_4
Column name in raw_counts_all_samples.txt: Terbinafine_1_4

value: ev


title: H1-hESC differentiation Day 14, Replicate 2

description: Library name: Day14_2


title: S_414_D0_Tula

value: Tulathromycin


title: H1-hESC differentiation Day 14, Replicate 1

description: Library name: Day14_1


title: day 1 adult, ev, Terbinafine 31.5 uM , batch1, rep1

description:
Library name: Terbinafine_1_1
Column name in raw_counts_all_samples.txt: Terbinafine_1_1


title: day 1 adult, ev, Terbinafine 31.5 uM , batch1, rep2

description:
Library name: Terbinafine_1_2
Column name in raw_counts_all_samples.txt: Terbinafine_1_2


title: FL_F_495_citrate

description: Library name: FL_F_495_citrate

value: kidney


title: sgACO2, pyruvate (24 h), rep1

description: Library name: sgACO2_pyruvate_1


title: H1-hESC differentiation Day 10, Replicate 1

description: Library name: Day10_1

value: WT


title: FL_F_492_citrate

description: Library name: FL_F_492_citrate

value: citrate


title: OCI-AML3, DMSO control, rep3

description: Library name: Sample 3

value: Acute Myeloid Leukemia


title: sgACO2, vehicle (water, 24 h), rep2

description: Library name: sgACO2_vehicle_2


title: H1-hESC differentiation Day 10, Replicate 2

description: Library name: Day10_2


title: WT_F_469_water

description: Library name: WT_F_469_water

value: water


title: H1-hESC differentiation Day 7, Replicate 3

description: Library name: Day7_3

value: Cardiac progenitors


title: sgACO2, vehicle (water, 24 h), rep1

description: Library name: sgACO2_vehicle_1


title: day 1 adult, ev, DMSO, batch1, rep3

description:
Library name: DMSO_1_3
Column name in raw_counts_all_samples.txt: DMSO_1_3


title: sgACO2/CS, vehicle (water, 24 h), rep1

description: Library name: sgACO2_CS_vehicle_1


title: H1-hESC differentiation Day 7, Replicate 1

description: Library name: Day7_1


title: WT_M_457_water

description: Library name: WT_M_457_water


title: sgAAVS1, pyruvate (24 h), rep2

description: Library name: sgAAVS1_pyruvate_2


title: H1-hESC differentiation Day 5, Replicate 3

description: Library name: Day5_3


title: WT_F_435_water

description: Library name: WT_F_435_water


title: day 1 adult, ev, DMSO, batch1, rep1

description:
Library name: DMSO_1_1
Column name in raw_counts_all_samples.txt: DMSO_1_1


title: WT_M_418_water

description: Library name: WT_M_418_water


title: day 1 adult, ev, DMSO, batch1, rep4

description:
Library name: DMSO_1_4
Column name in raw_counts_all_samples.txt: DMSO_1_4


title: H1-hESC differentiation Day 5, Replicate 2

description: Library name: Day5_2


title: WT1year1

description: Library name: Sample 7

value: brain


title: Zebrafish Larvae_Treated Input

city: Coimbatore

first: Ekambaram

last: Perumal

address: Maruthamalai Main Road

institute: Bharathiar University

description: Library name: Treated-Input

data_processing:
Based on the quality report, the adaptor sequences and low quality bases are trimmed using AdapterRemoval-v2 (version 2.2.0, any parameters modified for the tool used in analysis: minlength 30,–trimqualities–minquality 20).  Peak calling was performed for the filtered alignment file using MACS (version-3.0) software  with default options
Assembly: The pre-processed reads were used for reference-based pairwise alignment with Danio rerio reference genome d from Ensembl (http://ftp.ensembl.org/pub/release 107/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna.toplevel.fa.gz). The alignment was performed using the Bowtie2 program (version 2.4.1).
Supplementary files format and content: The differential peaks identified were annotated based on the reference gene model using Homer annotatePeaks.pl program.

organism: Danio rerio

source_name: Whole larvae

extract_protocol:
Whole larvae were crosslinked with 1% formaldehyde and quenched with glycine. Further, the chromatin was ultrasonicated under optimal conditions. Around 300-500 bp chromatin fragments were used for immunoprecipitation.
Library was constructed for immunoprecipitated DNA using NEBNext Ultra DNA Library Preparation Kit and the sequencing was performed with the Illumina NovaSeq 6000/ HiSeq X (2x150, paired-end).

value: Whole larvae

value: Esculin


title: sh3_PLUS-KD_3

city: Manchester

first: Carlos

last: Lopez Garcia

state: Greater Manchester

address: Paterson Building, Wilmslow Rd

department: TLCB

institute: CRUK-MI

description: Library name: AM16_30_JS14_S30

data_processing:
Reads were quality-checked using FastQC and adapters were trimmed, reads were aligned to the human genome (GRCh38) using STAR aligner, and read counts generated using feature Counts with Ensemble GTF annotation (Homo_sapiens.GRCh38.75.gtf).
Assembly: Homo_sapiens.GRCh38.75.gtf
Supplementary files format and content: counts.tsv [Count file][.tsv]

source_name: H358 LUAD

growth_protocol: Cells cultured in RPMI 1640 growth medium with 5% Fetal bovine serum (FBS).

extract_protocol:
and RNA extracted using the RNeasy Mini kit (Qiagen) with sample homogenisation by QIAshredder (Qiagen) as per manufacturer’s protocols.
libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD with UDI (Lexogen) on a Bravo NGS Workstation Option B (Agilent Technologies). ). Single read 100bp sequencing was performed by loading 220pM pooled libraries on a NovaSeq 6000 sequencer (Illumina) with standard loading.

treatment_protocol: Pretreated with -/+ 10ng/ml doxycycline for 72 hours prior to seeding at equal low density with fresh media and -/+ 10ng/ml doxyclcine. Fresh media -/+ doxycycline added at 7 days. At 10 days, media removed, cells washed with PBS.

value: H358 LUAD

value: KD


title: Zebrafish Larvae_Treated IP-Nrf2

description: Library name: Treated-IP


title: H1-hESC differentiation Day 7, Replicate 2

description: Library name: Day7_2


title: Zebrafish Larvae_Control IP-Nrf2

description: Library name: Control-IP


title: sgAAVS1, vehicle (water, 24 h), rep1

description: Library name: sgAAVS1_vehicle_1


title: H1-hESC differentiation Day 5, Replicate 1

description: Library name: Day5_1


title: FL_F_164_water

description: Library name: FL_F_164_water

value: FL


title: FL_M_169_water

description: Library name: FL_M_169_water


title: sgAAVS1, pyruvate (24 h), rep1

description: Library name: sgAAVS1_pyruvate_1

value: pyruvate


title: H1-hESC differentiation Day 3, Replicate 2

description: Library name: Day3_2

value: Cardiac mesoderm


title: day 1 adult, ev, DMSO, batch1, rep2

description:
Library name: DMSO_1_2
Column name in raw_counts_all_samples.txt: DMSO_1_2

value: day 1 adult

value: worm

value: DMSO


title: FL_M_417_water

description: Library name: FL_M_417_water

value: kidney


title: sh3_MINUS-WT_3

description: Library name: AM16_28_JS7_S28

value: WT


title: sgAAVS1, vehicle (water, 24 h), rep2

description: Library name: sgAAVS1_vehicle_2

value: vehicle


title: Zebrafish Larvae_Control Input

description: Library name: Control-Input


title: FL_F_161_water

description: Library name: FL_F_161_water


title: H1-hESC differentiation Day 3, Replicate 3

description: Library name: Day3_3


title: H1-hESC differentiation Day 3, Replicate 1

description: Library name: Day3_1


title: WT_M_160_water

description: Library name: WT_M_160_water


title: sh2_PLUS-KD_3

description: Library name: AM16_25_JS22_S25


title: HIR_Lip1

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

description: Library name: Sample3

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed with 10X Genomics Cell Ranger (v8.0.1) using the default parameters and aligned to the Ensembl_release104 Sscrofa 11.1 reference genomes. The gene expression matrix was processed and analyzed by Seurat package (v4.1.0). To filter out low-quality cells, the investigation removed reads from cells in which less than 240 and over 3,600 genes were detected, cells with more than 16,000 UMIs, and cells with more than 10% share of mitochondrial gene expression.
Assembly: Ensembl_release104 Sscrofa 11.1 reference genomes
Supplementary files format and content: Tab-separated values files and matri files

molecule: nuclear RNA

organism: Sus scrofa

source_name: Liver

extract_protocol:
The liver tissue samples were subjected to nuclear isolation, sequencing, and library preparation following the 10X Genomics protocol. Approximately 500 mg of hepatic tissue was dissociated into a singular nuclear suspension via tissue homogenization in a chilled lysis buffer (0.25 M sucrose, 5 mM CaCl2, 3 mM MgAc2, 10 mM Tris-HCl pH 8.0, 1 mM DTT, 0.1 mM EDTA, 1 × Protease Inhibitor and 1U/µL RiboLock RNase Inhibitor (Thermo Scientifc, cat no. O0381) with pestle strokes. The resulting homogenate was subsequently filtered through a 70 µm cell strainer, yielding a nuclear fraction collected in a 15ml centrifuge tube, with a 1 ml volume. This nuclear fraction was mixed with an equal volume of 50% iodixanol solution (0.16 M sucrose, 10 mM NaCl2, 3 mM MgCl2, 10 mM Tris-HCl pH 7.4, 1 U/µL RiboLock RNase Inhibitor, 1 mM DTT and 0.1 mM PMSF Protease Inhibito (Thermo Scientifc, cat no. 36978), yielding a final concentration of 25%, and supplemented with 1 mL of 33% iodixanol solution at the tube's base and 30% iodixanol solution at the top. The solution centrifugation at 500 × g for 8 min at 4℃, subsequent to myelin layer removal from the gradient’s apex. Nuclei were harvested from the 30% iodixanol interface, resuspended in nuclear wash and resuspension buffers, and centrifuge (0.04% bovine serum albumin, 0.2 U/µL RiboLock RNase inhibitor, 500 mM mannitol and 0.1 mM PMSF protease inhibitor in PBS) at 500 × g and 4℃ for 5 min. Filtration through a 40 µm cell filter eliminated cell debris and sizable aggregates. The nuclei’s total count, concentration, and integrity ratio were ascertained via hemocytometer-assisted microscopic examination of trypan-stained samples. Ultimately, the nuclear concentration was regulated to 700-1,200 nuclei/µL, with nuclei inspected using the 10X Chromium platform.
Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Using Chromium Next GEM Single Cell 3'Reagent Kit v3.1 for Library Generation and Sequencing of cDNA. Upon dissolution of the Gel Bead in a GEM, primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10 × Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence were released and mixed with cell lysate and Master Mix. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction. R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. A Single Cell 5’ Library comprised standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 5′ 16 bp 10X Barcode and 10 bp UMI were encoded in Read 1, while Read 2 was used to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 were standard Illumina® sequencing primer sites used in paired-end sequencing.

value: Liver

value: Lip-1 treatment group (Lip-1)


title: H1-hESC differentiation Day 1, Replicate 3

description: Library name: Day1_3

value: Mesendoderm


title: sh2_MINUS-WT_3

description: Library name: AM16_23_JS16_S23


title: FL_F_153_water

description: Library name: FL_F_153_water

value: water


title: HIR_40Gy

description: Library name: Sample2

value: 40 Gy


title: H1-hESC differentiation Day 1, Replicate 2

description: Library name: Day1_2


title: FL_M_147_water

description: Library name: FL_M_147_water


title: R_PLUS-CTRL_3

description: Library name: AM16_21_JS1_S21

value: CTRL


title: WT_0Gy

description: Library name: Sample1

value: non-irradiated controls (0 Gy)


title: H1-hESC differentiation Day 1, Replicate 1

description: Library name: Day1_1


title: C57BL/6 Fibroblast TGF‑β1 24 h,RNA‑seq (Fib_TGFβ1_24h)

city: Wuxi

first: yunjuan

last: Nie

state: Jiangsu

address: 1800 Lihu Avenue

department: Wuxi School of Medicine

institute: Jiangnan University

description:
Library name: Fib_TGFβ1_24h
Lung‑derived primary fibroblasts stimulated with TGF‑β1 for 24 h

data_processing:
Raw FASTQ reads were trimmed with Trimmomatic, then aligned to the Mus musculus reference genome mm39 (Ensembl release) using STAR. Gene-level counts were obtained with featureCounts. The count matrix was imported into DESeq2, normalized using the median-of-ratios method, and transformed via the rlog() function (regularized log) to generate the final rlog-normalized expression matrix.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes rlog-transformed expression values for each Sample

source_name: lung

growth_protocol: Alveolar macrophages (AMs):BALF from C57BL/6 mice was centrifuged (200 ×g, 4°C, 15 min). Cell pellets underwent RBC lysis (Beyotime, #C3702), followed by 1-hr adhesion. Adherent AMs were collected by gentle scraping after washing with Ca²⁺/Mg²⁺-free PBS. pulmonary fibroblasts:WT mouse lungs were minced and digested in DMEM/5% FBS/collagenase IV (1 mg/mL)/DNase I (30 μg/mL) for 30 min. Washed cells were cultured in DMEM/10% FBS/penicillin-streptomycin for 7-14 days. Tissue fragments were removed pre-experiment.

extract_protocol:
Total RNA was extracted, and sequencing libraries were then prepared for RNA‑seq.
RNA of samples was extracted from the tissues by CTAB Kit, Sequencing libraries were generated using VAHTS Universal V8 RNA-seq Library Prep Kit for MGI (NRM605,VAZYME, CHINA) following the manufacturer’s recommendations

treatment_protocol: After cell preparation, cells were treated with IL‑33 (10 ng/mL), TGF‑β1 (10 ng/mL), or their combination, and Trizol samples were collected at the indicated time points (0, 3, 6, 12, 24, 48, 72, and 96 h).

value: lung

value: primary fibroblast

value: TGF‑β1 10 ng/mL, 24 h


title: H1-hESC Day 0, Replicate 3

description: Library name: Day0_3

value: Stem Cell


title: R_MINUS-CTRL_3

description: Library name: AM16_20_JS18_S20

value: H358 LUAD


title: WT_F_144_water

description: Library name: WT_F_144_water


title: C3/C3 M2/+ male 3

city: Ithaca

first: Mumingjiang

last: Munisha

state: NY

address: 618 Tower Rd, CVM 14 T1-010 VRT

institute: Cornell University

description: Library name: MM15

data_processing:
reads were trimmed for low quality and adaptor sequences with TrimGalore v0.6.0,
Unwanted reads were removed with STAR v 2.7.0e using parameters: --outReadsUnmapped Fastx
final reads were mapped to the mouse reference genome Ensembl GRCm38 using STAR v2.7.0e.
SARTools and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression
Assembly: Ensembl GRCm38
Supplementary files format and content: raw counts for each sample

source_name: Placenta

extract_protocol:
Total RNA was isolated from E13.5 placentae using Zymo Quick-RNA mini-prep Kit
1000ng input total RNA with polyA enrichment is used for library prep using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs)

value: Placenta

tag: Sex

value: Male

tag: Stage


title: C57BL/6 AMs IL‑33 24 h,RNA‑seq (AMs_IL33_24h_3)

description:
Library name: AMs_IL33_24h_3
AMs stimulated with IL‑33 for 24 h

tag: tissue

value: Alveolar macrophages (AMs)

value: IL‑33 10 ng/mL, 24 h


title: sh3_PLUS-KD_2

description: Library name: AM16_18_JS24_S18

tag: cell line

value: KD


title: sh3_MINUS-WT_2

description: Library name: AM16_16_JS23_S16

value: WT


title: H1-hESC Day 0, Replicate 2

description: Library name: Day0_2

tag: cell type


title: sh2_PLUS-KD_2

description: Library name: AM16_14_JS5_S14

tag: genotype


title: C57BL/6 AMs IL‑33 0 h,RNA‑seq (AMs_IL33_0h_3)

description:
Library name: AMs_IL33_0h_3
AMs stimulated with IL‑33 for 0 h

tag: treatment

value: IL‑33 10 ng/mL, 0 h


title: H1-hESC Day 0, Replicate 1

description: Library name: Day0_1


title: C57BL/6 AMs IL‑33 24 h,RNA‑seq (AMs_IL33_24h_2)

description:
Library name: AMs_IL33_24h_2
AMs stimulated with IL‑33 for 24 h


title: sh2_MINUS-WT_2

description: Library name: AM16_13_JS17_S13


title: C3/C3 M2/+ male 1

description: Library name: MM13


title: C3/C3 M2/+ male 2

description: Library name: MM14R


title: C57BL/6 AMs IL‑33 96 h,RNA‑seq (AMs_IL33_96h)

description:
Library name: AMs_IL33_96h
AMs stimulated with IL‑33 for 96 h

value: IL‑33 10 ng/mL, 96 h


title: H1-hESC-CM, Control GapmeR, Replicate 5

description:
Library name: CTNR_5
Clipper Control Rep5

extract_protocol:
Directed differentiation into cardiomyocytes were performed. Beating hESC-CMs were transfected 9 days after the initiation of differentiation with 50 nM of either Control or CLIPPER-GapmeRs using Lipofectamine™ RNAiMAX Transfection Reagent (Thermo Fisher #13778150), and harvested 48 hours later for transcriptomic analysis. Total RNA was extracted using Trizol Reagent (15596026, ThermoFisher) and Direct-Zol RNA miniprep Kit (Zymo Research, R2050) according to manufacturer’s protocol. RNA quality and yield was accessed using Agilent RNA 6000 pico kit (50167-1513, Agilent) for quality.
RNA quality and yield was accessed using Agilent RNA 6000 pico kit (50167-1513, Agilent) for quality. Bulk RNA-seq library preparations were prepared using TruSeq Stranded Total RNA library Prep HMR kit (20020596, Illumina). cDNA libraries were quantified using the Agilent DNA1000 kit (5067-1505, Agilent), prior to sequencing on Illumina NextSeq Sequencing platform by Macrogen Asia Pacific Pte. Ltd.

value: Cardiomyocyte


title: C3/C3 M2/+ female 3

description: Library name: MM18

value: Female


title: R_PLUS-CTRL_2

description: Library name: AM16_12_JS9_S12

value: CTRL


title: C57BL/6 AMs IL‑33 0 h,RNA‑seq (AMs_IL33_0h_2)

description:
Library name: AMs_IL33_0h_2
AMs stimulated with IL‑33 for 0 h


title: H1-hESC-CM, Control GapmeR, Replicate 3

description:
Library name: CTNR_3
Clipper Control Rep3


title: H1-hESC-CM, Control GapmeR, Replicate 4

description:
Library name: CTNR_4
Clipper Control Rep4


title: C3/C3 M2/+ female 1

description: Library name: MM16


title: R_MINUS-CTRL_2

description: Library name: AM16_11_JS8_S11


title: sh3_PLUS-KD_1

description: Library name: AM16_09_JS21_S9


title: H1-hESC-CM, Control GapmeR, Replicate 1

description:
Library name: CTNR_1
Clipper Control Rep1


title: sh3_MINUS-WT_1

description: Library name: AM16_08_JS13_S8


title: H1-hESC-CM, Control GapmeR, Replicate 2

description:
Library name: CTNR_2
Clipper Control Rep2


title: WT male 3

description: Library name: MM5


title: C57BL/6 AMs IL‑33 24 h,RNA‑seq (AMs_IL33_24h_1)

description:
Library name: AMs_IL33_24h_1
AMs stimulated with IL‑33 for 24 h


title: C3/C3 M2/+ female 2

description: Library name: MM17


title: H1-hESC-CM, Clipper GapmeR Knockdown, Replicate 5

description:
Library name: CLIP_5
Clipper KD Rep5

value: GapmeR Knockdown


title: WT male 2

description: Library name: MM4


title: C57BL/6 AMs IL‑33 72 h,RNA‑seq (AMs_IL33_72h)

description:
Library name: AMs_IL33_72h
AMs stimulated with IL‑33 for 72 h

value: lung

value: IL‑33 10 ng/mL, 72 h


title: sh2_PLUS-KD_1

description: Library name: AM16_07_JS2_S7


title: H1-hESC-CM, Clipper GapmeR Knockdown, Replicate 4

description:
Library name: CLIP_4
Clipper KD Rep4


title: sh2_MINUS-WT_1

description: Library name: AM16_06_JS15_S6


title: WT female 3

description: Library name: MM6R


title: C57BL/6 AMs IL‑33 48 h,RNA‑seq (AMs_IL33_48h)

description:
Library name: AMs_IL33_48h
AMs stimulated with IL‑33 for 48 h

value: IL‑33 10 ng/mL, 48 h


title: WT male 1

description: Library name: MM2


title: R_PLUS-CTRL_1

description: Library name: AM16_03_JS6_S3


title: C57BL/6 AMs IL‑33 12 h,RNA‑seq (AMs_IL33_12h)

description:
Library name: AMs_IL33_12h
AMs stimulated with IL‑33 for 12 h

value: IL‑33 10 ng/mL, 12 h


title: WT female 1

description: Library name: MM1


title: C57BL/6 AMs IL‑33 3 h,RNA‑seq (AMs_IL33_3h)

description:
Library name: AMs_IL33_3h
AMs stimulated with IL‑33 for 3 h

value: IL‑33 10 ng/mL, 3 h


title: R_MINUS-CTRL_1

description: Library name: AM16_01_JS10_S1

value: H358 LUAD


title: C57BL/6 AMs IL‑33 0 h,RNA‑seq (AMs_IL33_0h_1)

description:
Library name: AMs_IL33_0h_1
AMs stimulated with IL‑33 for 0 h


title: WT female 2

description: Library name: MM3

value: Placenta


title: H1-hESC-CM, Clipper GapmeR Knockdown, Replicate 1

description:
Library name: CLIP_1
Clipper KD Rep1


title: WSU_AML_R3

status: Public on Feb 26 2026

type: genomic

city: Little Rock

first: Akhilesh

last: Kaushal

state: Arkansas

address: One Children’s Way, Slot 512-43

department: Hematology/Oncology

institute: University of Arkansas for Medical Sciences

description: WSU AML

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

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

data_processing: The raw iDAT files were imported and processed using the minfi and sesame R packages. The data were normalized using the Subset-quantile Within Array Normalization (SWAN) package. The SWAN method is known to reduce technical variability between probe types while maintaining biological differences. DNAm levels for each probe were quantified as beta (β) values, calculated as the proportion of methylated signal (M) to the methylated plus unmethylated (U) signal from probes, with a constant c = 100 (β=  M⁄((M+U+c))). Probes with cross-hybridization, high detection p-values (> 0.01), β > 0.8 or < 0.2 across all samples, and those near single-nucleotide polymorphisms were excluded from the downstream analyses. The preprocessed and filtered β-values were log-transformed to M values using the approximation 〖log〗_2 [β⁄((1-β)]), to ensure a better fit to statistical model assumptions. The limma4 package in R was used to assess the statistical significance of differences in DNAm across groups. Probes with an absolute percentage difference in β-values > 5% and FDR p-value < 0.05 were considered significant.

label: Cy3 and Cy5

source_name: WSU AML

label_protocol: Standard Illumina Protocol

growth_protocol: The KG-1A (# CCL-246.1, ATCC), KASUMI-1 (# CRL-2724, ATCC), ME-1 (# ACC 537, DSMZ), M-07e (# ACC 104, DSMZ), and WSU-AML cell lines were included in this study. KASUMI-1, ME-1, M-07e, and WSU-AML cells were maintained in RPMI-1640 supplemented with 20% heat-inactivated (h.i) FBS. The M-07e culture was additionally supplemented with GM-CSF. KG-1A cells were cultured in IMDM media supplemented with 20% h.i FBS.

extract_protocol: Genomic DNA was extracted from AML cell lines cells using the AllPrep DNA/RNA Kits, Qiagen, following the manufacturer’s instructions. DNA purity and concentration were assessed using a Qubit fluorometer. The integrity of the extracted DNA was evaluated using a bioanalyzer. 500 ng of genomic DNA was bilsulfite converted using the EZ DNA Methylation kit from Zymo Research. Bisulfite converted and processed on Infinium Infinium MethylationEPIC v2.0 Kit.

value: WSU AML


title: H1-hESC-CM, Clipper GapmeR Knockdown, Replicate 3

description:
Library name: CLIP_3
Clipper KD Rep3


title: WSU_AML_R1

description: WSU AML


title: ME1-R2


title: WSU_AML_R2

description: WSU AML


title: C57BL/6 AMs IL‑33 6 h,RNA‑seq (AMs_IL33_6h)

description:
Library name: AMs_IL33_6h
AMs stimulated with IL‑33 for 6 h

value: Alveolar macrophages (AMs)

value: IL‑33 10 ng/mL, 6 h


title: M07e-R3


title: ME1-R1


title: M07e-R1


title: ME1_R3


title: H1-hESC-CM, Clipper GapmeR Knockdown, Replicate 2

description:
Library name: CLIP_2
Clipper KD Rep2


title: KG1A-R2


title: M07e-R2


title: KASUMI1-R2


title: CD41+ MK-R3

description: CD41+ MK

source_name: CD41+ MK

value: CD41+ MK


title: KG1A-R3


title: CD41+ MK-R2

description: CD41+ MK


title: CD34+ HSC-R2

description: CD34+ HSC

source_name: CD34+ HSC

value: CD34+ HSC


title: CD41+ MK-R1

description: CD41+ MK


title: KASUMI1_R3


title: KG1A-R1


title: AML_5967_sgRNA

city: Philadelphia

first: Jacqueline

middle: J

last: Peng

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

description:
Library name: Sample 27
in vitro CRISPR screen

data_processing:
10X Cell Ranger (verion 6.1.2) mkfastq for scRNA and sgRNA (if applicable)
10X Cell Ranger (verion 6.1.2) mkcount
Assembly: hg38 with GFP and mCherry
Supplementary files format and content: filtered_feature_bc_matrix from 10X Cell Ranger mkcount

source_name: Primary AML sample

growth_protocol: The primary AML samples/PDX samples were obtained from the Stem Cell and Xenograft Core Facility at The Perelman School of Medicine at the University of Pennsylvania or xxx, after informed consent in accordance with the Declaration of Helsinki. Protocols used for this study were approved by the University Pennsylvania’s institutional review board. The primary AML samples were frozen in FCS and 10% DMSO in liquid nitrogen for long-term storage. Patient clinical info is included in Table Sx. For short-term in vitro maintenance, cells were cultured in BM media (IMDM supplemented with 15% Fetal Bovine Serum (FBS), 1% P/S, 1% GlutaMAX) supplemented with human cytokines including 10ng/μl human IL-3 (200-03), 10ng/μl human FLT3 (300-19), 100ng/μl humanSCF (300-07), 20ng/μl humanIL-6 (200-06) and 10 ng/μl humanTPO (300-18) (all from Peprotech). Co-culture with stromal “feeder” cells (e.g. OP-9) may be recommended to maintain the primary cells (ref), although we did not see an obvious difference in cell growth with or without the feeder cells for specimens we studied.

extract_protocol:
For scRNA-seq, primary cells were thawed in PBS+5% FBS and treated with DNase I (AMPD1-1KT, Sigma) for 5 min at room temperature. Cells were washed and resuspended with PBS+0.04% BSA. Viability was checked by Trypan Blue (Thermo), and if viability was lower than 95%, live cells were purified by the Dead cell removal kit (MACS). Viable cells were subject to scRNA-seq following the Chromium Next GEM Single Cell 5' v2 protocol. For in vitro Perturb-seq, ells were transduced as described above and maintained in a dish for 9-14 days. For in vivo Perturb-seq, leukemia cells were harvested from BM on day 12 post-transplant. Sorted GFP/mCherry+ leukemia cells were washed 3 times and resuspended in PBS+0.04% BSA and checked for viability. Viable cells were subject to scRNA-seq following the Chromium Next GEM Single Cell 5' v2 protocol with spike-in of sgRNA amplification oligos.
For scRNA-seq, samples were prepared following the Chromium Next GEM Single Cell 5' v2 protocol. For Perturb-seq, samples were subject to the Perturb-seq protocol adapted from ECCITE-seq with small modifications, without antibody-hashtag labelling. Briefly, 2μM sg_RT_v4 (AGCAAGTGAGAAGCATCGTGTCAAAGCACCGACTCGGTGCCAC) oligo was spiked in to the cell suspension containing 20,000 live cells. Cells were barcoded on the 10xGenomics platform following the Chromium Next GEM Single Cell 5' v2 protocol. sgRNA was amplified together with cDNA using a spike-in Guide-tag_additive (AGCAAGTGAGAAGCATCGTGTC), and separated from cDNA by 0.6x SPRIselect beads (Beckman) (beads bind cDNA while supernatant contains sgRNAs). sgRNA was further amplified with primers incorporated with TotalSeq_A_Dual_Index, and purified by 1.2x SPRIselect beads (Beckman). cDNA was amplified and purified following the 10x Genomics protocol. Libraries were analyzed using the Qubit dsDNA HS assay kit (Thermo Fisher) and a High Sensitivity DNA Bioanalyzer Kit (Agilent), and quantified by NEBNext Library Quant Kit for Illumina. Libraries were pooled consisting of 90% cDNA and 10% sgRNA, and pair-end sequenced on a Nova-seq 6000 in Read 1 26, i7 index 10, i5 index 10, Read 2 90bp format.

treatment_protocol: For PDX/primary cell transduction, Retronectin (Takara) was used to avoid the cytotoxicity effect caused by the polybrene following the manufacturer’s instructions with minor modifications. Briefly, 12-well non-treated plates were coated with 1ml of 20ng/μl Rectronectin for 2 hr at 37°C or overnight at 4°C. The Retronectin was collected, and the plates were blocked with 1ml of 2% BSA for 30 min at RT. The BSA was aspirated, and the plates were washed with 1ml PBS or HBSS. Plates would be ready to use or can be stored at 4°C for up to a week. Retronectin can be recycled for up to 5 times. To boost the infection efficiency for large vectors (e.g. Cas9), 1ml virus containing supernatant was first applied to the plates and spun down at at 750 x g for 30 minutes to allow the virus to attach on the bottom. The supernatant was aspirated, and the above steps can be repeated multiple times to further enrich the virus. To transduce the cells, cells were mixed with virus, adjusted FBS (15% final) and human cytokines described above and 1:500 dilution of LentiBlast Premium (LBPX1500, OZBiosciences, which also enhances hematopoietic cell transduction), and the media was replenished the next day with BM media supplemented with cytokines.

tag: post infection

value: patient ID:5967


title: CD34+ HSC-R3

description: CD34+ HSC


title: MCF7_scramble_Biol_rep_2

city: San Francisco

first: Carolina

last: Di Benedetto

state: CA

address: 2340 Sutter Street, S371

institute: University of California, San Francisco

description: Library name: scr_2

data_processing:
For transcripts assembly, Cutadapt and perl scripts were first used to remove the reads that contained adaptor contamination low quality bases and undetermined bases. Sequence quality was verified using FastQC
HISAT2 was used to map reads to the reference genome. Mapped reads of each sample were assembled using StringTie
All transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare.
StringTie and ballgow were used to estimate the expression levels of all transcripts.
Assembly: GRCh38 (hg38)
Supplementary files format and content: xlsx files include FPKM values for each sample

source_name: breast

growth_protocol: Cells were cultured in RPMI medium supplemented with 10% heat inactivated FBS, 100 units/mL Penicillin and 100 µg/mL Streptomycin. Cells were grown at 37°C in a humified atmosphere at 5% CO2.

extract_protocol:
RNeasy PLUS kit (Qiagen)
llumina’s TruSeq-stranded-mRNA sample preparation protocol.

treatment_protocol: The germline insertion variant rs58296163 was deleted by CRISPR. Clones M11 (MCF7Δ#1) and M46 (MCF7Δ#2) with the desired DNA modification were identified by PCR and DNA sequencing. RNA-seq of two biological replicates per condition was performed. For LINC00636 overexpression by CRISPRa, MCF7 cells stably expressing dCas9-VP64 were transfected with two different sgRNAs targeting LINC00636 TSS (sgRNA1 or sgRNA2) or scramble negative control at a final concentration of 50nM. After 48 hours, cells were collected for RNA extracion. RNA-seq of three biological replicates per condition was performed.

value: breast

value: breast cancer cell

value: dCas9-VP64 overexpressing cells

value: control


title: MCF7_sgRNA2_Biol_rep_1

description: Library name: sgRNA2_1

value: LINC00636 overexpression


title: AML_6481_cDNA

description:
Library name: Sample 31
in vitro CRISPR screen

value: patient ID:6481


title: AML_6481_sgRNA

description:
Library name: Sample 28
in vitro CRISPR screen


title: AML_5967_cDNA

description:
Library name: Sample 30
in vitro CRISPR screen


title: KASUMI1-R1


title: MCF7_scramble_Biol_rep_1

description: Library name: scr_1


title: MCF7_sgRNA1_Biol_rep_2

description: Library name: sgRNA1_2


title: MCF7_sgRNA1_Biol_rep_3

description: Library name: sgRNA1_3


title: MCF7_sgRNA2_Biol_rep_2

description: Library name: sgRNA2_2


title: M11_Biol_Replicate_2

description: Library name: M11_2

value: Insertion-deleted


title: MCF7_parental_Biol_Replicate_2

description: Library name: MCF7_2

value: WT


title: MCF7_scramble_Biol_rep_3

description: Library name: scr_3


title: AML_7575_sgRNA

description:
Library name: Sample 29
in vitro CRISPR screen

value: patient ID:7575


title: MCF7_parental_Biol_Replicate_1

description: Library name: MCF7_1


title: MCF7_sgRNA1_Biol_rep_1

description: Library name: sgRNA1_1


title: NE_Ctrl_RNA_Rep1

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description: Library name: D2_iNE_1

data_processing:
Sequencing reads were aligned to combined genome of hg38 and dm6. Only uniquely mapped reads were retained for downstream analysis.
Read count mapped to each gene was measured using featureCounts with options ‘-O --fracOverlap 0.8’.
Assembly: hg38 + dm6
Supplementary files format and content: Excel file containing read counts per human genes. Columns names matche with sample titles.

source_name: Neuroectoderm

growth_protocol: Human induced pluripotent stem cells (72.3, male, RRID: CVCL_A1BW) were obtained from the CCHMC Pluripotent Stem Cell Facility (PSCF) and cultured under feeder-free condition in mTeSR1 medium (85850, StemCell Technologies) on plates coated with either hESC-qualified Matrigel (354277, Corning) or Cultrex Stem Cell Qualified Reduced Growth Factor Basement Membrane Extract (3434-010-02, Biotechne). hPSCs were cultured in a humidified incubator at 37℃ with 5% CO2.

extract_protocol:
1.0x106 cultured cells were dissociated into single cells using Accutase and were mixed with 100,000 Drosophila Schneider 2 (S2) cells for a spike-in control. Cells were lysed with Aurum Total RNA Lysis Solution (7326802, BioRad). Total RNA was extracted using Aurum™ Total RNA Mini Kit (7326820, BioRad).
The sequencing libraries were prepared by Novogene.

treatment_protocol: For Paraxial mesoderm (PM) differentiation, hPSCs were plated on Matrigel- or Culturex SCQ-coated plates (dilution factor as per hPSC culture) one day before induction. For mesendoderm (ME) differentiation, hPSCs were cultured in CDM2 medium supplemented with 33 ng/ml ActivinA (800-0, Shenandoah; or GFH6, Cell Guidance Systems), 4 uM CHIR99021 (SML1046-25MG, Sigma-Aldrich), 20 ng/ml bFGF (PHG0261, Thermo Fisher Scientific), and 100 nM PIK90 (528117, EMD Millipore) for 24 hours. For subsequent PM differentiation, ME cells were briefly washed with DMEM/F12 and cultured in CDM2 medium supplemented with 1 uM A83-01 (SML0788-5MG, Sigma-Aldrich), 3 uM CHIR99021, 20 ng/ml bFGF, and 250 nM LDN193189 for 24 hours.  For definitive endoderm (DE) differentiation, hPSCs were plated on Matrigel- or Culturex SCQ-coated plates (dilution factor as per hPSC culture) one day before induction. For ME induction, hPSCs were cultured in CDM2 medium supplemented with 100 ng/ml ActivinA, 2 uM CHIR99021, and 50 nM PI103 (SML0559-5MG, Sigma-Aldrich) for 24 hours. For subsequent DE differentiation, ME cells were briefly washed with DMEM/F12 and cultured in CDM2 medium supplemented with 100 ng/ml ActivinA and 250 nM LDN193189 for 24 hours.  For neuroectoderm (NE) differentiation, hPSCs were plated on Matrigel- (1:50 dilution) or Culturex SCQ-coated cell culture plates one day before differentiation. NE was induced by E6 medium (A1516401, Thermo Fisher Scientific) supplemented with 500 nM LDN193189 (SML0559-5MG, Sigma-Aldrich), 10 uM, SB431542 (S4317-5MG, Sigma-Aldrich), and 5 uM XAV931 (X3004-5MG, Sigma-Aldrich). Cells were cultured in this medium for 48 hours with daily media changes.  For inhibiting MEK/ERK signaling, cells were treated with 1 uM of PD0325901 (MEK inhibitor; 72182, STEMCELL Technologies) or DMSO (vehicle control) for two days during differentiation from hPSC into NE, PM, and DE.

value: Neuroectoderm

value: Ctrl


title: M46_Biol_Replicate_2

description: Library name: M46_2


title: PM_Ctrl_RNA_Rep2

description: Library name: iMeso_2

source_name: Paraxial Mesoderm

value: Paraxial Mesoderm


title: MCF7_sgRNA2_Biol_rep_3

description: Library name: sgRNA2_3


title: PM_Ctrl_RNA_Rep1

description: Library name: iMeso_1


title: M46_Biol_Replicate_1

description: Library name: M46_1


title: NE_Ctrl_ChIP_Input_Rep2

description: Library name: NEd2_ChIP_Input_R2

data_processing:
Sequencing reads were aligned to combined genome of hg38 and dm6 using STAR aligner. Only uniquely mapped reads were retained for downstream analysis.
BigWig files were generated using reads aligned to hg38 using bedtools and UCSC toolkit in a RPM scale (*.rpm.bw). For ChIP samples, additional bigwig files were generated by normalizing by spike-in counts, i.e. read per 0.1 million spike-in count (*.rpsm.bw).
Assembly: hg38 + dm6
Supplementary files format and content: bigwig in RPM scale (*.rpm.bw); bigwig in spike-in normalized scale (*.rpsm.bw)

extract_protocol:
Cells were crosslinked with 1% formaldehyde in 1x PBS for 10 min at room temperature. The crosslinking reaction was quenched by adding 0.125 M glycine for 5 min at room temperature. Crosslinked cells were centrifuged at 600 x g for 5 min at 4°C, and the supernatant was removed. The cell pellet was washed with ice-cold 1x PBS, centrifuged again at 600 x g for 5 min at 4°C, and the supernatant was aspirated. This wash step was repeated once more. The final cell pellet was frozen on dry ice and stored at -80°C until use.  Crosslinked human cells were resuspended in Lysis Buffer1 (10 mM Tris-HCl [pH 8.0], 10 mM NaCl, 0.5% NP-40, and 1x Complete Protease Inhibitor EDTA-free) and incubated on ice for 10 min. For Drosophila S2 spike-in controls, crosslinked S2 cells were resuspended in 100 uL Lysis Buffer1 at a final concentration of 2.0x105 or 4.0x105 cells/uL, and 25% of the S2 cells were mixed with human cells. The mixed cell suspension was centrifuged at 665 x g for 5 min at 4℃, and the supernatant was removed. The cell pellet was then resuspended in Lysis Buffer2 (50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 0.32% SDS, 1x Complete Protease Inhibitor EDTA-free) and incubated on ice for 10 min. The cell lysate was then diluted in IP Dilution Buffer (20 mM Tris-HCl [pH 8.0], 150 mM NaCl, 2 mM EDTA, 1% TritonX-100, 1x Complete Protease Inhibitor EDTA-free) and transferred to a milliTUBE ATA Fiber (Covaris). Chromatin was sonicated using a Covaris S220 (Covaris) for 5.5 min. Insoluble debris was removed by centrifugation at 12,000 x g for 5 min at 4℃. The supernatant containing sonicated chromatin was transferred to a new tube and stored at -80℃ until use.  Dynabeads Protein-G (10004D, Thermo Fisher Scientific) (25 - 80 uL) were washed twice with PBS-T (0.02% Tween-20 in 1x PBS). The desired amounts of H3K9me3 (ab8898, Abcam) antibodies were conjugated to washed Dynabeads by incubating for 2 to 6 hours at 4°C with rotation. Meanwhile, frozen sonicated chromatin was thawed on ice. A desired amount of chromatin (Table S3, based on DNA quantity) was diluted with IP dilution buffer at a 4:1 ratio. Antibody-conjugated Dynabeads were washed twice with IP Dilution Buffer (without protease inhibitor), resuspended in the diluted chromatin, and incubated overnight at 4°C with rotation. The next day, ChIPed beads were washed four times using the following washing buffers: (1) FA Lysis Buffer (50 mM HEPES-KOH [pH 7.5], 150 mM NaCl, 2 mM EDTA, 1% TritonX-100, 0.1% Sodium deoxycholate, 1x Complete protease inhibitor EDTA-free); (2) NaCl Buffer (50 mM HEPES-KOH [pH 7.5], 500 mM NaCl, 2 mM EDTA, 1% TritonX-100, 0.1% Sodium deoxycholate); (3) LiCl Buffer (100 mM Tris-HCl [pH 8.0], 500 mM LiCl, 1% NP-40, 1% Sodium deoxycholate); (4) 10 mM Tris-HCl [pH 8.0]. Following washing steps, chromatin was eluted with TES buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 1% SDS) for 15 min at 65℃ while shaking at 1,000 rpm in ThermoMixer F1.5 (Eppendorf). The ChIP and Input chromatin were reverse-crosslinked by adding NaCl to a final concentration of 200 mM and incubating for 8 hours at 65°C. Samples were then treated with 50 ng/uL RNaseA (EN0531, ThermoFisher Scientific) for 30 min at 37°C, followed by treatment with 0.2 mg/mL Protease K (03115828001, Roche) for 2 hours at 37°C. DNA was purified using phenol-chloroform extraction, followed by ethanol precipitation. DNA concentration was measured using Quantus fluorometer (Promega).
Multiplexed libraries were prepared from ChIP and Input samples (two replicates) using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB), following the manufacturer’s protocol with the following modifications. After adaptor ligation, cleanup was performed using AMPure XP Beads (A63880, Beckman Coulter), MagBind Magnetic Beads (M1378-01, Omega), or homemade Sera-mag beads (Rohland et al., Genome Res. 2012) without size selection. After RCR enrichment of the adaptor-ligated library, two rounds of size selection were performed using the AMPure XP Beads or MagBind Magnetic Beads.


title: M11_Biol_Replicate_1

description: Library name: M11_1


title: NE_Ctrl_ChIP_Input_Rep1

description: Library name: NEd2_ChIP_Input_R1


title: PM_Ctrl_ChIP_Input_Rep2

description: Library name: PM_ChIP_Input_R2

source_name: Paramesoderm

value: Paramesoderm


title: NE_Ctrl_RNA_Rep2

description: Library name: D2_iNE_2


title: PM_Ctrl_RNA_Rep3

description: Library name: iMeso_3


title: NE_Ctrl_RNA_Rep3

description: Library name: D2_iNE_3


title: PM_Ctrl_ChIP_Input_Rep1

description: Library name: PM_ChIP_Input_R1


title: PM_Ctrl_ChIP_H3K9me3_Rep2

description: Library name: PM_ChIP_H3K9me3_R2


title: CD34+ HSC-R1

description: CD34+ HSC


title: PM_Ctrl_ChIP_H3K9me3_Rep1

description: Library name: PM_ChIP_H3K9me3_R1


title: hPSC_Ctrl_ChIP_Input_Rep1

description: Library name: hPSC_Ctl_OCT4CRISPRi_ChIP_Input_Clone10

source_name: hPSC

value: hPSC


title: DE_Ctrl_ChIP_H3K9me3_Rep1

description: Library name: DE_Ctrl_ChIP_H3K9me3_CloneA6

source_name: Definitive endoderm

value: Definitive endoderm


title: NE_Ctrl_ChIP_H3K9me3_Rep2

description: Library name: NEd2_ChIP_H3K9me3_R2


title: hCiPSC_S6D40,scRNA-seq

city: Beijing

first: Jingxiao

last: Cao

state: Beijing

address: No.5 Yiheyuan Road, Yanyuan Street, Haidian District, Beijing

department: Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.

institute: Peking University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19, hg19-and-mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: iPSC-islets

extract_protocol:
CiPSC-derived islets were dissociated into single cells using Accutase, collected and resuspended at 1 × 106 cells per mL in 1× PBS with 0.04% BSA.
Using Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics, 1000268) and Chromium Next GEM Chip G Single Cell Kit (10x Genomics, 1000120), the cell suspension (700–1200 living cells per μL determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In brief, CiPSC-derived islets were dissociated into single cells using Accutase, collected and resuspended at 1 × 106 cells per mL in 1× PBS with 0.04% BSA. About 8 × 103 cells were added to each channel, and the target cell will be recovered was estimated to be about 5 × 103 cells. Captured cells were lysed and the released RNA was barcoded through reverse transcription in individual gel beads in emulsion (GEMs). Reverse transcription was performed on a T100 Touch Thermal Cycler (Bio-Rad) at 53 °C for 45 min, followed by 85 °C for 5 min, and then held at 4 °C. The cDNA was generated and then amplified, and quality-assessed using the Qsep1 system. According to the manufacturer’s instructions, scRNA-seq libraries were constructed using the Library Construction Kit . The libraries were quality-assessed using the Qsep1 system . The libraries were finally sequenced using the Illumina NovaSeq 6000 sequencer with a sequencing depth of at least 2 × 105 reads per cell with a paired-end 150 bp (PE150) reading strategy.

value: iPSC-islets


title: DE_Ctrl_ChIP_Input_Rep1

description: Library name: DE_Ctrl_ChIP_Input_CloneA6


title: hCiPSC_S6D50,scRNA-seq

description: 10x Genomics


title: hPSC_Ctrl_ChIP_H3K9me3_Rep2

description: Library name: hPSC_Ctl_OCT4CRISPRi_ChIP_H3K9me3_Clone11


title: hCiPSC_24 wpt,scRNA-seq

description: 10x Genomics


title: hCiPSC_48 wpt,scRNA-seq

description: 10x Genomics


title: hCiPSC_16 wpt,scRNA-seq

description: 10x Genomics


title: DE_Ctrl_ChIP_Input_Rep2

description: Library name: DE_Ctrl_ChIP_Input_CloneH5


title: NE_Ctrl_ChIP_H3K9me3_Rep1

description: Library name: NEd2_ChIP_H3K9me3_R1


title: DE_Ctrl_ChIP_H3K9me3_Rep2

description: Library name: DE_Ctrl_ChIP_H3K9me3_CloneH5


title: hPSC_Ctrl_ChIP_H3K9me3_Rep1

description: Library name: hPSC_Ctl_OCT4CRISPRi_ChIP_H3K9me3_Clone10


title: hPSC_Ctrl_ChIP_Input__Rep2

description: Library name: hPSC_Ctl_OCT4CRISPRi_ChIP_Input_Clone11


title: hCiPSC_8 wpt,scRNA-seq

description: 10x Genomics


title: Dataset 1: Patient #415-Normal-Epithelium fraction (EpCAM+ CD10- CD45-)

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

institute: Dana-Farber Cancer Institute

description: 10X Genomics

data_processing:
The sequenced reads were aligned to either the human reference genome hg18 or the rat reference genome Rn6. Demultiplexing, barcode calling, gene counting, and group aggregation were subsequently performed. These procedures were all carried out using the 10X Genomics Cell Ranger 7.0.1 and Cell Ranger Aggr. v7.0.1 on 10X Cloud (https://cloud.10xgenomics.com/)
For preprocessing and quality-control, the filtered count matrix files were processed in R using Seurat package. Stringent filtering parameters were set to filter out low-quality reads and dead cells (2000 <nCount < 60000 & percent mt < 20 & percent ribo RPS/RPL < 40). Doublets were identified and removed using DoubletFinder.
The data were normalized using SCTransform and integrated using SCTIntegration prior to decomposing into 30-dimension PCA, clustering and dimensional reduction by UMAP. Subclusters of immune, epithelial, stroma and subsequent T cells, myeloid, and fibroblast clusters were further subsetted and reclustered at same dimension but higher resolution.
DEGs of each seurat cluster at each step were computed using Seurat FindMarkers function. Cell identities were identified and annotated using up to a combination of three methods (1) DEGs of lineage markers, (2) gene modules from previous studies, (3) reference cell atlas such as Celltypist, ProjecTIL.
Downstream analyses relevant to the study include Milo neighborhood analysis, Trajectory analysis Monocle3, FCoEx, single-cell GSEA (Escape), ProjecTIL, CellChat, Gini index quantification, etc.
Assembly: hg18 (Dataset 1), rn6 (Dataset 2-3)
Supplementary files format and content: barcodes.tsv.gz (barcodes), features.tsv.gz (gene IDs), matrix.mtx.gz (gene expression count matrix), filtered_feature_bc_matrix.h5 (combined features, barcodes, matrix)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Normal mammary tissues

extract_protocol:
For dataset 1, clinical specimens were shipped in DMEM media via dry ice and digested immediately upon arrival to the lab. For dataset 2-3, rats were sacrificed and tumors were extracted and minced gently prior to tissue digestion protocol. For both human and rat tissues, the minced tissues were placed in 2 mg/mL collagenase 4, 2 mg/kg hyaluronidase, 2 mg/mL BSA (5-6 fold-greater than tissue volume) and incubated with shaking at 37*C for 60 min (human tumor tissues and rat mammary gland tissue) or 80-90 min (rat tumor tissues). The digested tumors were serially filtered from 500um and 100um strainers and centrifuged at 1700 rpm for 7 min and resuspended in DMEM. For dataset 1 and 2, tissues were stained with FACS markers (CD45+, EpCAM+, CD10+, Live/Dead Aqua, 30min), washed, and filtered, and were subjected to FACS sorting at low speed followed by single-cell library construction targeting 5000 cells/sample. For dataset 3, the entired tumor tissues were digested briefly with TryLE Express Enzyme (7 min) and submited for scRNAseq library construction targeting 5000 cells/sample.
For dataset 1-2, cell and library construction were performed via the 10X Chromium NEXT GEM Single Cell 3' HT v3 protocol targeting 5000 cells per sample. For dataset 3, cell and library construction were performed via the 10X Chromium NEXT GEM Single Cell 5' HT Reagent Kit v2 (Dual Index) protocol.
Equimolar libraries were sequenced on an Illumina NovaSeq6000 at the DFCI Molecular Biology Core Facility with at least 25000 reads per cells.

treatment_protocol: For dataset 2-3, tumor induction in Sprague-Dawley rats was performed via two injection of N-Nitroso-N-Methylurea(NMU, 50mg/kg, 7 days apart). Tumor volumes were measured daily following first detection of palpable tumors in the mammary areas.

value: Normal mammary tissues

value: Breast normal epithelium

value: Untreated


title: Dataset 1: Patient #436-Normal-Immune fraction (CD45+ EpCAM- CD10-)

description: 10X Genomics

value: Breast immune cells


title: Dataset 1: Patient #415-Normal-Stroma fraction (CD45- EpCAM- CD10-)

description: 10X Genomics

value: Breast stromal cells


title: Dataset 1: Patient #415-Normal-Myoepithelium fraction 2 (EpCAM+ CD10+ CD45-)

description: 10X Genomics

value: Breast myoepithelium


title: Human islet_2,scRNA-seq

description: 10x Genomics

source_name: primary islets

value: primary islets


title: Dataset 1: Patient #415-Normal-Myoepithelium fraction 1 (EpCAM+ CD10+ CD45-)

description: 10X Genomics


title: Dataset 1: Patient #389-Normal-Myoepithelium fraction  (EpCAM+ CD10+ CD45-)

description: 10X Genomics


title: Dataset 1: Patient #436-Normal-Epithelium fraction (EpCAM+ CD10- CD45-)

description: 10X Genomics


title: Dataset 1: Patient #436-Normal-Stroma fraction (EpCAM- CD10- CD45-)

description: 10X Genomics


title: Dataset 1: Patient #39-DCIS-Mixed fraction

description: 10X Genomics

source_name: Breast carcinoma in situ

value: Breast carcinoma in situ

value: Mixed breast cells


title: Dataset 1: Patient #389-Normal-Immune fraction (CD45+ EpCAM- CD10-)

description: 10X Genomics


title: Dataset 1: Patient #37-DCIS-Immune fraction (CD45+ EpCAM- CD10-)

description: 10X Genomics


title: Dataset 1: Patient #37-DCIS-Myoepithelium fraction  (EpCAM+ CD10+ CD45-)

description: 10X Genomics


title: Dataset 1: Patient #32-DCIS-Epithelium fraction (EpCAM+ CD10- CD45-)

description: 10X Genomics

value: Breast cancer epithelium


title: Dataset 1: Patient #389-Normal-Stroma fraction  (EpCAM- CD10- CD45-)

description: 10X Genomics


title: Dataset 1: Patient #37-DCIS-Epithelium fraction (EpCAM+ CD10- CD45-)

description: 10X Genomics


title: Dataset 1: Patient #22-DCIS-Mixed fraction

description: 10X Genomics


title: Dataset 1: Patient #29-DCIS-Immune fraction (CD45+ EpCAM- CD10-)

description: 10X Genomics


title: Dataset 1: Patient #36-DCIS-Stroma fraction (EpCAM- CD10- CD45-)

description: 10X Genomics


title: Dataset 1: Patient #23-DCIS-Mixed fraction

description: 10X Genomics


title: Dataset 1: Patient #449-DCIS-Myoepithelium fraction (CD10+EpCAM+CD45-)

description: 10X Genomics


title: Dataset 1: Patient #415-Normal-Immune fraction (CD45+ EpCAM- CD10-)

description: 10X Genomics