description: Library name: ATAC_TSC_Rep2_0h

data_processing:
Raw reads were trimmed using TrimGalore (Cutadapt version 0.4.2_dev). Reads were then aligned to the mm10 genome using bowtie2 (version 2.2.4)with default parameters. Samtools (version 1.9) were used to convert sam files to bam files which were then sorted and indexed using samtools view, sort, and index respectively. Non-primary and supplementary alignments, alongside reads with a MAPQ < 10 were filtered out using the samtools view -F 2304 -b -q 10 command. Read duplicates were detected and removed via the MarkDuplicates command of Picard-tools (https://broadinstitute.github.io/picard/, version 2.3.0). Deeptools bamCoverage (version 3.0.1) was employed to generate bigwig track files for visualization with the following options used:
Raw reads were trimmed using TrimGalore (Cutadapt version 0.4.2_dev). Reads were then aligned to the mm10 genome using bowtie2 (version 2.2.4)with default parameters. Samtools (version 1.9) were used to convert sam files to bam files which were then sorted and indexed using samtools view, sort, and index respectively. Non-primary and supplementary alignments, alongside reads with a MAPQ < 10 were filtered out using the samtools view -F 2304 -b -q 10 command. Read duplicates were detected and removed via the MarkDuplicates command of Picard-tools (https://broadinstitute.github.io/picard/, version 2.3.0). Deeptools bamCoverage (version 3.0.1) was employed to generate bigwig track files for visualization with the following options used: binSize 1 normalizeUsing RPGC effectiveGenomeSize 2150570000 extendReads outFileFormat bigwig
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Briefly, 50,000 cells were harvested, washed with PBS, and re-suspended in 50 μl of cold lysis buffer. After the centrifuge, the cell pellet was kept and proceeded for TDE1-mediated transposition reaction (15027865, Illumina) at 37°C for 30 min, followed by DNA purification using a Qiagen MinElute PCR Purification Kit (28004, QIAGEN).
For library preparation, the transposed DNA fragments were amplified by PCR to add the sequencing barcodes and then purified using an AMpure reagent (A63880, Beckman). The concentration of libraries was measured by Qubit kit (Q32851, Thermo Fisher) and further diluted to 1.8 pM after denaturation. A pair-end sequencing aiming for 40 million reads per sample was run in the NextSeq instrument.

value: Trophoblast stem cells


title: Trophoblast stem cells, biological replicate 1

status: Public on Oct 24 2025

type: SRA

city: Barcelona

first: Thomas

last: Graf

address: Carrer del Dr. Aiguader, 88

country: Spain

institute: Center for Genomic Regulation

description: Library name: ATAC_TSC_Rep1_0h

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Trophoblast stem cells

growth_protocol: ESCs and the CEBPa-ER cell lines were cultured on gelatinized plates in KnockOut DMEM (10829018, Gibco) containing 15% ESC FBS (16141079, Gibco), 1x Penicillin-Streptomycin (15140122, Gibco), 1x L-Glutamine (25030081, Gibco), 1x Non-Essential Amino Acids (11140068, Gibco), 1nM sodium pyruvate (11360070, Gibco), 0.1 mM 2-Mercaptoethanol (31350010, Gibco), and 1000 U/ml fresh leukemia inhibitory factor (LIF) (ESG1106, Sigma-Aldrich).

treatment_protocol: For CEBPa induction, cells were treated with 1 µM Tamoxifen (H7904, Sigma-Aldrich) which shuttles the factor into the cell nucleus.

tag: cell line

tag: treatment

tag: time


title: CHAMP1 RES human myoblast, GM, repeat1

city: Athens

first: Pengpeng

last: Bi

state: GA

address: 315 Riverbend Rd

country: USA

institute: University of Georgia

description: Library name: CHAMP1RES_GM_1

library_source: transcriptomic

data_processing:
For bulk RNASeq, raw sequencing data was processed with initial quality control (QC) using FastQC (version 0.11.9) to assess read quality and MultiQC (version 1.14) was used to aggregate and visualize quality control metrics across all samples. After QC, raw sequencing reads were processed using fastp (version 0.23.2) for adaptor trimming and reads filtering with the following filtering parameters: quality score threshold: 20, maximum proportion of unknown bases (N): 10, maximum percentage of unqualified bases: 30%. A reference human hg38 genome index was constructed using HISAT2 (version 2.2.1) with the provided genome sequence. Cleaned reads were aligned to the reference genome using HISAT2. Alignment outputs were converted to sorted BAM files using SAMtools (version 1.6), and BAM files were indexed for downstream analysis. Gene-level read counts were quantified using featureCounts (Subread version 2.0.3).
Assembly: Hg38
Supplementary files format and content: Raw count from featurecounts output

molecule: polyA RNA

organism: Homo sapiens

source_name: Skeletal muscle

growth_protocol: Human myoblasts are maintained in skeletal muscle cell basal medium (PromoCell, C-23260) supplemented with 15% fetal bovine serum (FBS; Sigma-Aldrich, F2442), 5% growth medium supplement mix (PromoCell, C-39365), GlutaMAX, and 1% gentamicin sulfate. For differentiation, myoblasts were cultured in differentiation medium comprising DMEM supplemented with 2% horse serum, 10 μM DAPT (Cayman, 13197), and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted from human myoblast cells using TRIzol reagent (Thermo Fisher Scientific, 15-596-018) according to the manufacturer’s protocol.
Bulk RNA library will be prepared using NEBNext UltraII directional kit with PolyA selection under manufacturer's protocol.

treatment_protocol: Human myoblasts are differentiated in DM (2% Horse serum in DMEM).

tag: tissue

value: Skeletal muscle

value: Human myoblast

tag: cell type

value: immortalized cell line

tag: genotype

value: GM


title: E1_AP_11

city: Boston

first: Marcos

last: Simoes-Costa

state: Massachusetts

address: 300 Longwood Ave

department: Pathology

institute: Boston Children's Hospital

description: Tomo-seq library

data_processing:
Trimming of adapter sequences and poly(A) tails was performed using BBDuk (version 38.93)
Bam alignment files were indexed using samtools (version 1.10) and reads were counted with htseq-count (version 0.13.5) using a GTF file containing chicken gene annotations
Assembly: galGal6
Supplementary files format and content: raw counts for all the libraries, including the two AP replicates, the LR replicate, and the HH1-3 libraries

molecule: total RNA

organism: Gallus gallus

source_name: AP embryo #E1

growth_protocol: Gastrula stage chicken embryos were obtained from fertilized eggs, dissected in Ringers solution, prepared for cryosectioning in O.C.T.

extract_protocol:
Total RNA for each section  was extracted with the kit RNAqueous®-Micro Kit (ThermoFisher #AM1931) following the manufacturers recommendations.
The RNA-seq libraries were prepared with the kit QuantSeq 3'mRNA-seq Library Prep Kit (FWD) for Illumina (Lexogen #K01596), following the manufacturers recommendations  for low input samples.
3'RNA-seq libraries

treatment_protocol: HH5 chicken embryos were cryosectioned into 100um sections following its antero-posterior or left-right axis. HH1, HH2 and HH3 embryos were hand dissected into equally distributed antero-posterior sections. Each section was collected for RNA extraction.

tag: developmental stage

tag: axis

value: antero-posterior

value: embryo


title: ESC, CEBPa induced, 72h, sorted SSEA1-, clone 2

description: Library name: ATAC_CEBPaER_Clone2_SSEA1_Low_72h

source_name: ESCs expressing CEBPa-ERT2

value: ESCs expressing CEBPa-ERT2

value: tamoxifen


title: E1_AP_10

description: Tomo-seq library


title: CHAMP1 KO human myoblast, GM, repeat3

description: Library name: CHAMP1KO_GM_3


title: CHAMP1 RES human myoblast, DM2d, repeat1

description: Library name: CHAMP1RES_DM2d_1


title: ESC, CEBPa induced, 72h, sorted SSEA1-, clone 1

description: Library name: ATAC_CEBPaER_Clone1_SSEA1_Low_72h


title: E1_AP_09

description: Tomo-seq library


title: CHAMP1 KO human myoblast, GM, repeat2

description: Library name: CHAMP1KO_GM_2


title: ESC, CEBPa induced, 72h, sorted SSEA1+, clone 2

description: Library name: ATAC_CEBPaER_Clone2_SSEA1_High_72h


title: E1_AP_08

description: Tomo-seq library


title: A1 human myoblast, DM6d, repeat2

description: Library name: A1_DM6d_2

data_processing:
Raw sequencing data was processed with initial quality control (QC) using FastQC (version 0.11.9) to assess read quality and MultiQC (version 1.14) was used to aggregate and visualize quality control metrics across all samples. After QC, raw sequencing reads were processed using fastp (version 0.23.2) for adaptor trimming and reads filtering with the following filtering parameters: quality score threshold: 20, maximum proportion of unknown bases (N): 10, maximum percentage of unqualified bases: 30%. A reference human hg38 genome index was constructed using HISAT2 (version 2.2.1) with the provided genome sequence. Cleaned reads were aligned to the reference genome using HISAT2. Alignment outputs were converted to sorted BAM files using SAMtools (version 1.6), and BAM files were indexed for downstream analysis. Gene-level read counts were quantified using featureCounts (Subread version 2.0.3).
Assembly: Hg38
Supplementary files format and content: Raw counts for each sample

extract_protocol:
Total RNA was extracted from human myoblast cells using TRIzol reagent (Thermo Fisher Scientific, 15-596-018) according to the manufacturer’s protocol.
RNA library will be prepared using NEBNext UltraII directional kit with PolyA selection under manufacturer's protocol.

value: WT

value: DM

tag: batch

value: 6 days


title: CHAMP1 KO human myoblast, GM, repeat1

description: Library name: CHAMP1KO_GM_1


title: E1_AP_07

description: Tomo-seq library


title: ESC, CEBPa induced, 48h, sorted SSEA1-, clone 2

description: Library name: ATAC_CEBPaER_Clone2_SSEA1_Low_48h


title: ESC, CEBPa induced, 72h, sorted SSEA1+, clone 1

description: Library name: ATAC_CEBPaER_Clone1_SSEA1_High_72h


title: E1_AP_06

description: Tomo-seq library


title: A1 human myoblast, DM6d, repeat1

description: Library name: A1_DM6d_1


title: ESC, CEBPa induced, 48h, sorted SSEA1-, clone 1

description: Library name: ATAC_CEBPaER_Clone1_SSEA1_Low_48h


description: Library name: CEBPa_ChIP_CEBPaER_Clone2_SSEA1_Low_48h

data_processing:
Raw reads were trimmed using TrimGalore (Cutadapt version 0.4.2_dev). Reads were then aligned to the mm10 genome using bowtie2 (version 2.2.4) with default parameters. Samtools (version 1.9) were used to convert sam files to bam files which were then sorted and indexed using samtools view, sort, and index respectively. Non-primary and supplementary alignments, alongside reads with a MAPQ < 10 were filtered out using the samtools view -F 2304 -b -q 10 command. Read duplicates were detected and removed via the MarkDuplicates command of Picard-tools (https://broadinstitute.github.io/picard/, version 2.3.0). Deeptools bamCoverage (version 3.0.1) was employed to generate bigwig track files for visualization with the following options used:
binSize 1 normalizeUsing RPKM effectiveGenomeSize 2150570000 extendReads 147.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
For chromatin immunoprecipitations, 10 million cells were collected and crosslinked in 1% formaldehyde under rotation for 10 min, followed by glycine-mediated quenching. After the centrifuge, the cell pellet was re-suspended in SDS lysis buffer for 15 min and sonicated for 18 cycles of 30 sec on, and 30 sec off using the Bioruptor Pico (Diagenode). The supernatant was incubated with protein A magnetic beads (10002D, Invitrogen) pre-coupled with CEBPa antibody (8718, Cell Signaling) at 4℃ overnight. The next day, DNA was collected after sequentially washing and elution, followed by Proteinase K treatment and de-crosslinking.
Libraries were prepared using the DNA Library Prep for Illumina kit (E7370, NEB) and amplified by Multiplex Oligos for Illumina kit (E6440, E6442, E6444, E6446, NEB). Libraries were sequenced on the NextSeq2000 instrument (Illumina), obtaining at least 40 million reads per sample.


title: E1_AP_04

description: Tomo-seq library


title: A1 human myoblast, DM2d, repeat1

description: Library name: A1_DM2d_1

value: 2 days


description: Library name: CEBPa_ChIP_CEBPaER_Clone1_SSEA1_Low_48h


title: E1_AP_03

description: Tomo-seq library


title: ESC, CEBPa induced, 48h, sorted SSEA1+, clone 1

description: Library name: ATAC_CEBPaER_Clone1_SSEA1_High_48h


title: ESC, CEBPa induced, 48h, sorted SSEA1+, clone 2

description: Library name: CEBPa_ChIP_CEBPaER_Clone2_SSEA1_High_48h


title: A1 human myoblast, GM, repeat2

description: Library name: A1_GM_2


title: A1 human myoblast, DM2d, repeat2

description: Library name: A1_DM2d_2


title: E1_AP_02

description: Tomo-seq library


title: A1 human myoblast, GM, repeat1

description: Library name: A1_GM_1


description: Library name: CEBPa_ChIP_CEBPaER_Clone1_SSEA1_High_48h


title: ESC, CEBPa non-induced, 0h, clone 2

description: Library name: CEBPa_ChIP_CEBPaER_Clone2_0h


title: E1_AP_01

description: Tomo-seq library


title: ESC, CEBPa non-induced, 0h, clone 2

description: Library name: ATAC_CEBPaER_Clone2_0h


title: HBECs_pool002_ADT

status: Public on Oct 23 2025

city: Somerville

first: Mauricio

last: Cortes

state: MA

address: 101 South Street

institute: Cellarity

description:
Library name: ILD2-035_SRAB0001190
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.

library_source: other

data_processing:
Ingest data per plate: load 10x outputs (Gene Expression and Antibody Capture) for all libraries belonging to a plate into a single AnnData object.
Compute per-cell QC metrics: total UMIs (nCount_RNA), genes detected (nFeature_RNA), mitochondrial fraction (percent_mito), and housekeeping gene checks; derive library-specific thresholds for library size and percent_mito.
Filter cells using per-library QC thresholds to retain high-quality cells only.
Filter genes with very low prevalence (genes detected in too few cells are removed).
Normalize and transform (pre-demultiplexing): store raw counts in a “counts” layer; apply library-wise total count normalization (target_sum = 1e6) and log1p transform to produce the filtered_normalized plate-level matrix.
Demultiplex per library using HTO/CMO counts: compute CLR-normalized hashtag counts; apply per-library thresholding to classify cells (singlet/multiplet/negative); assign singlet cells to a specific hashtag/well; merge assignments across libraries to plate level.
Generate demultiplexed plate object: retain singlets with well and treatment mapping; save as demuxed plate-level AnnData.
Pseudobulk by well: sum gene counts across cells within each well (including vehicle control wells and replicate wells); preserve raw summed counts in a “counts” layer; normalize pseudobulk matrices (target_sum = 1e6, exclude_highly_expressed = True) and log1p transform.
Compute v-scores within each plate: for each perturbation vs DMSO (matched within library_id), compute per-gene v-score as [mean(log1p(y)) − mean(log1p(x))] / sqrt(Var(log1p(x)) + Var(log1p(y))); save as vscores.
Differential expression on pseudobulk: run limma within each plate (perturbation vs DMSO) and export moderated statistics (e.g., logFC, t, p-value, FDR).
Create combined files: concatenate plate-level outputs across all plates to produce combined_demuxed.h5ad, combined_pseudobulk.h5ad, combined_vscores.h5ad, and combined_limma.csv; no additional filtering, normalization, or re-analysis performed.
Assembly: hg38
Supplementary files format and content: SRTPXXXX_raw_feature_bc_matrix.h5 – Raw cell × feature count matrix (HDF5 format) generated by 10x Genomics Cell Ranger. Contains unfiltered UMI counts for all detected barcodes across both gene expression and feature barcoding (including antibody/hashtag features).
Supplementary files format and content: SRTPXXXX_filtered_feature_bc_matrix.h5 – Filtered cell × feature count matrix (HDF5 format) generated by 10x Genomics Cell Ranger. Contains UMI counts for barcodes identified as high-quality cells, across gene expression and feature barcoding modalities.
Supplementary files format and content: SRTPXXXX_metrics_summary.csv – Summary file produced by 10x Genomics Cell Ranger with run-level QC metrics, including sequencing depth, reads per cell, mapping statistics, fraction of reads in cells, and other quality control indicators.
Supplementary files format and content: SRTPXXXX_feature_reference.csv – Feature reference file used in Cell Ranger to define the set of non-gene features included in the library. In this dataset, it specifies hashtag oligos (CMOs/HTOs) used for cell multiplexing; does not include gene annotations.
Supplementary files format and content: ILD1/2-XXX_raw.h5ad - Unfiltered cell x gene count matrix for the entire plate (all libraries from that plate concatenated); pre-QC, pre-normalization, pre-demultiplexing.
Supplementary files format and content: ILD1/2-XXX_filtered_normalized.h5ad - QC-filtered high-quality cells (thresholds applied per library), library-wise total-count normalized and log1p-transformed; produced before demultiplexing; stored as a single plate-level matrix.
Supplementary files format and content: ILD1/2-XXX_demuxed.h5ad - Plate-level AnnData with per-cell assignments to well and treatment; demultiplexing performed per library using CLR-normalized hashtag counts and a mixture model, then merged across libraries for the plate.
Supplementary files format and content: ILD1/2-XXX_pseudobulk.h5ad - Well-level expression for the plate: gene counts summed across cells within each well (vehicle controls such as DMSO and any replicate wells kept as separate entries); includes raw summed counts in a layer and a normalized/log representation.
Supplementary files format and content: ILD1/2-XXX_vscores.h5ad - Gene-level differential statistics within the plate (perturbation vs a matched-library DMSO well). For a comparison x->y: v-score = [mean(log1p(y)) - mean(log1p(x))] / sqrt(Var(log1p(x)) + Var(log1p(y))), where means and variances are over single-cell counts in each well (i.e. computed directly downstream of demuxed.h5ad, before pseudobulking).
Supplementary files format and content: ILD1/2-XXX_limma.csv - limma differential expression results against plate-level DMSO replicates, run on the plate’s well-level pseudobulk matrix; per-gene coefficients and moderated statistics (e.g., logFC, t, p-value, FDR). Results for all wells in the plate are concatenated, with the compound used to treat each well annotated in the "compound name" column.
Supplementary files format and content: combined_demuxed.h5ad - Concatenation of all plates’ demuxed AnnData objects; no additional filtering, normalization, or analysis.
Supplementary files format and content: combined_pseudobulk.h5ad - Concatenation of all plates’ well-level pseudobulk profiles; plate and well provenance retained; no recomputation.
Supplementary files format and content: combined_vscores.h5ad - Concatenation of v-score results from all plates; definitions and comparisons unchanged; no recomputation.
Supplementary files format and content: combined_limma.csv - Concatenation of plate-level limma outputs; same columns as plate files; no recomputation.

molecule: protein

source_name: HBEC

growth_protocol: A375, A549, HepG2, PC3, and HEK293T cell lines were purchased from the American Tissue Culture Collection and cultured in either RPMI or DMEM with fetal bovine serum, as per supplier recommendations. The human embryonic kidney cell line HA1E was obtained from the Cancer Cell Line Encyclopedia at the Broad Institute and maintained under the same conditions. Normal human bronchial epithelial cells (HBECs) were obtained from Lonza from two healthy donors; cells were thawed and grown in PneumaCult medium for three days at 37 °C before plating in 24-well dishes for two days. Peripheral blood mononuclear cells (PBMCs) from two healthy donors were isolated from leukopaks (Miltenyi Biotec), frozen at 1×10^8 cells per vial, then thawed and CD8+ cytotoxic T cells isolated using the CD8+ T Cell Isolation Kit (Miltenyi). T cells were cultured in RPMI supplemented with fetal bovine serum and IL-2, and activated for 72 hours at 37 °C with CD3/CD28 Dynabeads (Life Technologies); beads were removed by magnetic separation before plating. Mobilized human peripheral blood CD34+ cells from healthy donors were obtained from StemCell Technologies, thawed into PBS with 1% human serum albumin, and incubated for 48 hours in StemSpan medium containing CC100 and rhTPO at 37 °C, then replated in fresh medium with CC100 and rhTPO. Human preadipocytes from healthy lean donors (Zen-Bio) were thawed into 24-well plates in plating medium; after incubation at 37 °C for 24 hours, the medium was changed to differentiation medium and cells were incubated for an additional 72 hours.

extract_protocol:
For adherent cell lines and preadipocytes, cells were harvested with 0.05% trypsin and collected with serum-containing medium. HBECs were harvested with ACF Enzymatic Dissociation Solution for 7 minutes according to the manufacturer’s protocol and collected with medium. CD8+ T cells and CD34+ hematopoietic stem cells were harvested by centrifugation for 5 minutes at 300 × g.
Single-cell library generation: Harvested cells were washed with PBS and labeled with TotalSeq-B hashtag antibodies from BioLegend according to manufacturer’s protocol. Briefly, cells were incubated with 250ng of TotalSeq-B antibodies (hashtags 1-10) for 30 minutes at room temperature. Cells were washed with PBS a total of three times and then ten samples with different hashtags were pooled and counted on a Luna Cell Counter. Single-cell libraries were then prepared using the Chromium Single Cell 3’ Feature Barcoding Kit targeting 10,000 cells per library, according to manufacturer’s protocols (10x Genomics; CG000317 Rev B). Following cell encapsulation, RNA is released by lysis within droplets and captured by barcoded gel beads.

treatment_protocol: For adherent cell lines (A375, A549, HepG2, PC3, HEK293T, HA1E), cells were seeded into 24-well dishes, incubated for 24 hours at 37 °C, and then treated with compounds for 24 hours at the maximum tolerated dose previously determined for each line. HBECs were treated in PneumaCult medium with compounds and incubated for 24 hours at 37 °C. CD8+ T cells were plated in 96-well plates in medium containing IL-2; compounds were added at 2× concentration and incubated for 24 hours at 37 °C. CD34+ hematopoietic stem cells were plated in 96-well plates in medium containing CC100 and rhTPO; compounds were added at 2× concentration and incubated for 24 hours at 37 °C. Human preadipocytes in differentiation medium were treated with compounds at 2× concentration and incubated for 24 hours at 37 °C.

value: HBEC

value: Multiplexed treatment with small molecules, one per hashtag. Processed files contain demultiplexed treatment values


title: HBECs_pool003_ADT

description:
Library name: ILD2-036_SRAB0001191
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: HBECs_pool001_ADT

description:
Library name: ILD2-035_SRAB0001189
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: PreAdip_pool003_ADT

description:
Library name: ILD2-034_SRAB0001187
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.

source_name: PAD

value: PAD


title: PreAdip_pool002_ADT

description:
Library name: ILD2-033_SRAB0001186
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.


title: ESC, CEBPa non-induced, 0h, clone 1

description: Library name: ATAC_CEBPaER_Clone1_0h


title: ILD2Ar2_CD34_pool04_ADT

description:
Library name: ILD2-028_SRAB0001321
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.

value: ILD2-028, completed on 9/30/21


title: E1_AP_05

description: Tomo-seq library


title: ILD2Ar2_CD34_pool03_ADT

description:
Library name: ILD2-028_SRAB0001320
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: PreAdip_pool001_ADT

description:
Library name: ILD2-033_SRAB0001185
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.


description: Library name: ATAC_CEBPaER_Clone2_SSEA1_High_48h


title: ILD2Ar2_CD34_pool02_ADT

description:
Library name: ILD2-027_SRAB0001319
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.

value: ILD2-027, completed on 9/30/21


title: ILD2Ar2_CD34_pool01_ADT

description:
Library name: ILD2-027_SRAB0001318
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: ILD2Ar2_preAdip_pool01_ADT

description:
Library name: ILD2-025_SRAB0001314
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: ILD2Ar2_HA1E_pool03_ADT

description:
Library name: ILD2-024_SRAB0001230
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.

value: ILD2-024, completed on 9/8/2021


title: ILD2Ar2_preAdip_pool04_ADT

description:
Library name: ILD2-026_SRAB0001317
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: ILD2Ar2_preAdip_pool03_ADT

description:
Library name: ILD2-026_SRAB0001316
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: ILD2Ar2_HA1E_pool02_ADT

description:
Library name: ILD2-023_SRAB0001229
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.

value: ILD2-023, completed on 9/8/2021


title: HBECs_pool004_ADT

description:
Library name: ILD2-036_SRAB0001192
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: ILD2Ar2_HA1E_pool01_ADT

description:
Library name: ILD2-023_SRAB0001228
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.


title: ILD2Ar2_HepG2_pool04_ADT

description:
Library name: ILD2-022_SRAB0001239
Perturbational single-cell screen with hashtag oligos. for cell line HepG2, replicate2.

value: ILD2-022, completed on 9/8/2021


title: ILD2Ar2_HepG2_pool03_ADT

description:
Library name: ILD2-022_SRAB0001238
Perturbational single-cell screen with hashtag oligos. for cell line HepG2, replicate2.


title: ILD2Ar2_HepG2_pool01_ADT

description:
Library name: ILD2-021_SRAB0001236
Perturbational single-cell screen with hashtag oligos. for cell line HepG2, replicate2.

value: ILD2-021, completed on 9/8/2021


title: ILD2Ar2_HepG2_pool02_ADT

description:
Library name: ILD2-021_SRAB0001237
Perturbational single-cell screen with hashtag oligos. for cell line HepG2, replicate2.


title: ILD2Ar2_A375_pool04_ADT

description:
Library name: ILD2-020_SRAB0001235
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.

value: ILD2-020, completed on 9/8/2021


title: PreAdip_pool004_ADT

description:
Library name: ILD2-034_SRAB0001188
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.


title: ILD2Ar2_A375_pool03_ADT

description:
Library name: ILD2-020_SRAB0001234
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.


title: ILD2Ar2_A375_pool02_ADT

description:
Library name: ILD2-019_SRAB0001233
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.

value: ILD2-019, completed on 9/8/2021


title: ILD2Ar2_PC3_pool02_ADT

description:
Library name: ILD2-017_SRAB0001249
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: ILD2Ar2_PC3_pool03_ADT

description:
Library name: ILD2-018_SRAB0001250
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: ILD2Ar2_A549_pool03_ADT

description:
Library name: ILD2-016_SRAB0001246
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: ILD2Ar2_A549_pool04_ADT

description:
Library name: ILD2-016_SRAB0001247
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: ILD2Ar2_A549_pool02_ADT

description:
Library name: ILD2-015_SRAB0001245
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: HepG2_pool004_ADT

description:
Library name: ILD2-014_SRAB0001156
Perturbational single-cell screen with hashtag oligos. for cell line HepG2, replicate1.


title: ILD2Ar2_HA1E_pool04_ADT

description:
Library name: ILD2-024_SRAB0001231
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.


title: HepG2_pool001_ADT

description:
Library name: ILD2-013_SRAB0001153
Perturbational single-cell screen with hashtag oligos. for cell line HepG2, replicate1.


title: ILD2Ar2_preAdip_pool02_ADT

description:
Library name: ILD2-025_SRAB0001315
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: HepG2_pool003_ADT

description:
Library name: ILD2-014_SRAB0001155
Perturbational single-cell screen with hashtag oligos. for cell line HepG2, replicate1.


title: HepG2_pool002_ADT

description:
Library name: ILD2-013_SRAB0001154
Perturbational single-cell screen with hashtag oligos. for cell line HepG2, replicate1.


title: HEK293T_pool004_ADT

description:
Library name: ILD2-012_SRAB0001152
Perturbational single-cell screen with hashtag oligos. for cell line HEK293T, replicate1.


title: HEK293T_pool003_ADT

description:
Library name: ILD2-012_SRAB0001151
Perturbational single-cell screen with hashtag oligos. for cell line HEK293T, replicate1.


title: HEK293T_pool001_ADT

description:
Library name: ILD2-011_SRAB0001149
Perturbational single-cell screen with hashtag oligos. for cell line HEK293T, replicate1.


title: A549_pool003_ADT

description:
Library name: ILD2-010_SRAB0001147
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.

value: ILD2-010, completed on 8/24/21


title: HEK293T_pool002_ADT

description:
Library name: ILD2-011_SRAB0001150
Perturbational single-cell screen with hashtag oligos. for cell line HEK293T, replicate1.


title: A549_pool001_ADT

description:
Library name: ILD2-009_SRAB0001145
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.

value: ILD2-009, completed on 8/24/21


title: A549_pool002_ADT

description:
Library name: ILD2-009_SRAB0001146
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.


title: A375_pool004_ADT

description:
Library name: ILD2-008_SRAB0001144
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.

value: ILD2-008, completed on 8/24/21


title: A549_pool004_ADT

description:
Library name: ILD2-010_SRAB0001148
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.


title: A375_pool001_ADT

description:
Library name: ILD2-007_SRAB0001141
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.

value: ILD2-007, completed on 8/24/21


title: ILD2Ar2_PC3_pool04_ADT

description:
Library name: ILD2-018_SRAB0001251
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: A375_pool002_ADT

description:
Library name: ILD2-007_SRAB0001142
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.


title: C3H10T1-2_TKO_SUV39H1_KD_CUTandRUN_H3K9me3_rep2

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

description: Library name: CUTANDRUN_sample_30

data_processing:
CUT&RUN reads were trimmed of adapter sequences using Fastp v0.23.3. Bowtie v2.5.1 was used to align the reads to the mm10 assembly using the parameters “-I 10 -X 700 --end-to-end --local --very-sensitive-local --no-unal --no-overlap --no-dovetail --no-mixed --no-discordant -1 ${SAMPLE}.R1.fq.gz -2 ${SAMPLE}.R2.fq.gz”. Samtools was used to remove duplicated reads and reads below a cutoff of MAPQ < 3. Samclip was used to filter bacterial sequences prior to alignment. The bamCoverage function from deepTools v3.3.1 was used to normalize CUT&RUN signals by dividing by the total alignments (in millions) (bamCoverage -b $BAM -o $OUTPUT.bigWig --normalizeUsing CPM --centerReads -bs 10 -e 200 -bl $mm10.BLACKLIST.bed).
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

growth_protocol: C3H10T1/2 mouse mesenchymal stem cells (ATCC) were cultured in DMEM with 10% fetal bovine serum (FBS,) and supplemented with 1% GlutaMax. To establish stable knockdown of SUV39H1, a collection of five different mouse SUV39H1 shRNA plasmids were obtained from the McGill University Life Science Complex High-Throughput Screening Facility (Sigma-Aldrich Mission shRNAs: TRCN0000097439, TRCN0000097440, TRCN0000097441, TRCN0000097442 and TRCN0000097443).  Lentiviral particles were produced by transiently transfecting individual lentiviral SUV39H1 or control shRNA vectors together with the helper plasmids psPAX2 and pMD2.G at a ratio of 5:4:1 respectively in HEK293T cells.  Briefly, HEK293T cells were grown to 70% confluence in 60 mm cell culture dishes prior to transfection.  Cells were transfected with the TransIT-LT1 transfection reagent following the manufacturer’s protocol.  The lentivirus-containing supernatants were collected and filtered 72 h later using a 0.45 μm syringe filter and stored at –80°C. To maximize the knockdown of SUV39H1 expression, C3H10T1/2 parental and NSD1/2-SETD2 TKO cells were transduced simultaneously with all five SUV39H1 shRNA lentiviruses.  Cells were grown to 70% confluence in a well of a 6 well plate prior to infection. Cells were infected in DMEM complete media supplemented with 5 mg/ml of polybrene and infected using 125 μl of pooled lentiviral particles.  Media was refreshed 24 hours post-infection, and the cells were allowed to grow for an additional 48 hours prior to selection. The infected cells were selected with puromycin (1 µg/ml) for 7 days, and all surviving cells were pooled to generate stable cell lines with SUV39H1 knockdown. To establish stable overexpression of human SUV39H1, the pCDH-blast-HA-3XFlag-SUV39H1-WT plasmid was provided by the laboratory of Dr. Scott Rothbart. Lentivirus production, infection and establishment of C3H10T1/2 parental and NSD1/2-SETD2-TKO cells overexpressing SUV39H1 was performed as previously described in Liu et al. Mol Cell (2025).

extract_protocol:
CUT&RUN reactions were performed with the Epicypher CUTANA ChIC/CUT&RUN Kit Version 3 (cat# 14-1048) using 550,000 fresh C3H10T1/2 cultured cells and following the manufacturer’s protocol (Epicypher User Manual Version 3.5) for adherent cells. Prior to performing CUT&RUN, optimization of C3H10T1/2 cell permeabilization was performed following Appendix 1.1 (Epicypher User Manual Version 3.5). Cell permeabilization was found to be most optimal using a final working concentration of 0.01% Digitonin (Promega). Successful binding of cells to Concanavalin A beads was confirmed as recommended and outlined by the manufacturer. Manufacturer supplied H3K4me3 positive control and IgG negative control antibodies were used and the reactions were performed in parallel with processed samples. Processed samples were incubated with specific antibodies. Manufacturer also supplied E.coli spike-in DNA, which was used in each reaction for sequencing normalization. Quantification of purified CUT&RUN DNA was performed using the Qubit fluorometer with the 1X dsDNA HS Assay Kit (Invitrogen).
Library preparations were performed using the Epicypher CUTANA CUT&RUN Library Prep Kit Version 1 (cat# 14-1001) following the manufacturer’s protocol. Final CUT&RUN library concentrations were quantified as previously described, and enrichment of mononucleosome-sized fragments was assessed by Bioanalyzer (Agilent) prior to sequencing. CUT&RUN libraries were sequenced at a depth of 15M reads per sample by the McGill University Genome Centre using the Illumina NovaSeq 6000 at 100bp paired-end reads.

value: fibroblast

tag: cut&run antibody

value: H3K9me3 (Abcam, ab8898)


title: ILD2Ar2_PC3_pool01_ADT

description:
Library name: ILD2-017_SRAB0001248
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: PC3_pool004_ADT

description:
Library name: ILD2-006_SRAB0001140
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: C3H10T1-2_TKO_SUV39H1_KD_CUTandRUN_H3K9me3_rep1

description: Library name: CUTANDRUN_sample_29


title: PC3_pool003_ADT

description:
Library name: ILD2-006_SRAB0001139
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: ILD2Ar2_A549_pool01_ADT

description:
Library name: ILD2-015_SRAB0001244
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: C3H10T1-2_Parental_SUV39H1_KD_CUTandRUN_H3K9me3_rep1

description: Library name: CUTANDRUN_sample_27


title: ILD2Ar2_A375_pool01_ADT

description:
Library name: ILD2-019_SRAB0001232
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.


title: C3H10T1-2_TKO_SUV39H1_OE_CUTandRUN_H3K9me3_rep2

description: Library name: CUTANDRUN_sample_26


title: PC3_pool002_ADT

description:
Library name: ILD2-005_SRAB0001138
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: C3H10T1-2_Parental_SUV39H1_KD_CUTandRUN_H3K9me3_rep2

description: Library name: CUTANDRUN_sample_28


title: C3H10T1-2_TKO_SUV39H1_OE_CUTandRUN_H3K9me3_rep1

description: Library name: CUTANDRUN_sample_25


title: C3H10T1-2_Parental_SUV39H1_OE_CUTandRUN_H3K9me3_rep2

description: Library name: CUTANDRUN_sample_24


title: C3H10T1-2_Parental_SUV39H1_OE_CUTandRUN_H3K9me3_rep1

description: Library name: CUTANDRUN_sample_23


title: 1014 CD40-OE, RGS+IgG#3

city: Nashville

first: Chi

last: Yan

state: Tennessee

address: 432A Preston Res Building, 2220 Pierce Ave

institute: Vanderbilt University

description: Library name: 9496-WL-0030

data_processing:
RNA reads were aligned to the reference genome using STAR (RRID:SCR_004463) and quantified by featureCounts (RRID:SCR_012919). The RNA-seq quality was further checked after mapping by RNA-SeQC (RRID:SCR_005120), including alignment and duplication rates, GC bias, rRNA content, regions of alignment, 3’/5’ bias, and number of detectable transcripts. DESeq2 (RRID:SCR_015687) was used to detect differential expression between two conditions, considering technical and biological variability. CIBERSORT(RRID:SCR_016955), based on the LM22 gene signature, was used to estimate immune cells infiltrating the tumor. Benjamini-Hochberg correction was applied to adjust for multiple-testing. Functional enrichment analysis was performed by WebGestalt (RRID:SCR_006786)  and Gene Set Enrichment Analysis (GSEA, RRID:SCR_003199). TCRs were sequenced using the TCR Immunoverse all chain assay per the manufacturer’s protocol (Invitae/ArcherDX). Sequencing results were evaluated using Archer Immunoverse analyzer. CDR3 sequences and frequency tables were extracted from the manufacturers’ analysis platform and imported into R for analysis using the Immunarch package (RRID:SCR_023089, https://immunarch.com) in R.
Assembly: M36 (GRCm39)
Supplementary files format and content: RNAseq_mouse.count, RNAseq_mouse.proteincoding.count
Supplementary files format and content: 9496-WL-0001~0030_TRB.IR_per_clonotype_results.tsv
Library strategy: TCR-Seq

source_name: melanoma tumor

extract_protocol:
RNA was extracted from tumor tissues using the RNeasy Plus Mini Kit (Cat#: 74134, Qiagen) per manufacturer’s protocol.
RNA-Seq was performed using an Illumina next-generation sequencing platform at the Vanderbilt University Medical Center VANTAGE (Vanderbilt Technologies for Advanced Genomics) core facility and analyzed by Vanderbilt Technologies for Advanced Genomics Analysis and Research Design (VANGARD) core facility.

value: melanoma tumor

value: NRAS-mut melanoma

value: Rigosertib+IgG


title: HA1E_pool004_ADT

description:
Library name: ILD2-004_SRAB0001136
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.

value: Multiplexed treatment with small molecules, one per hashtag. Processed files contain demultiplexed treatment values


title: A375_pool003_ADT

description:
Library name: ILD2-008_SRAB0001143
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.


title: 1014 CD40-OE, RGS+IgG#2

description: Library name: 9496-WL-0029


title: 1014 CD40-OE, RGS+IgG#1

description: Library name: 9496-WL-0028


title: 1014 Virol ctl, RGS+IgG#2

description: Library name: 9496-WL-0026


title: 1014 Virol ctl, RGS+IgG#1

description: Library name: 9496-WL-0025


title: HA1E_pool002_ADT

description:
Library name: ILD2-003_SRAB0001134
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: 1014 Virol ctl, RGS+IgG#3

description: Library name: 9496-WL-0027


title: HA1E_pool003_ADT

description:
Library name: ILD2-004_SRAB0001135
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: 1014 CD40-OE, aCD40+PD1#2

description: Library name: 9496-WL-0023

value: Agonist CD40+PD1


title: HA1E_pool001_ADT

description:
Library name: ILD2-003_SRAB0001133
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: 1014 CD40-OE, aCD40+PD1#3

description: Library name: 9496-WL-0024


title: 1014 CD40-OE, aCD40+PD1#1

description: Library name: 9496-WL-0022


title: 1014 Virol ctl, aCD40+PD1#2

description: Library name: 9496-WL-0020


title: CD34_pool003_ADT

description:
Library name: ILD2-002_SRAB0001159
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: 1014 Virol ctl, aCD40+PD1#1

description: Library name: 9496-WL-0019


title: 1014 CD40-OE, Vehicle+PD1#3

description: Library name: 9496-WL-0018


title: 1014 CD40-OE, Vehicle+PD1#1

description: Library name: 9496-WL-0016


title: CD34_pool002_ADT

description:
Library name: ILD2-001_SRAB0001158
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: 1014 Virol ctl, Vehicle+PD1#3

description: Library name: 9496-WL-0015


title: PC3_pool001_ADT

description:
Library name: ILD2-005_SRAB0001137
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: 1014 Virol ctl, Vehicle+PD1#2

description: Library name: 9496-WL-0014


title: 1014 Virol ctl, Vehicle+PD1#1

description: Library name: 9496-WL-0013


title: DrugSeq09_24well_hPreadipocytes_rep1_row7_ADT

description:
Library name: ILD1-022_SRAB0000706
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.

value: PAD

value: ILD1-022, completed on 3/4/2021


title: 1014 CD40-OE, Vehicle+aCD40#2

description: Library name: 9496-WL-0011

value: Veh+agonist CD40


title: 1014 CD40-OE, Vehicle+aCD40#3

description: Library name: 9496-WL-0012


title: DrugSeq09_24well_hPreadipocytes_rep1_row6_ADT

description:
Library name: ILD1-022_SRAB0000705
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.


title: 1014 CD40-OE, Vehicle+aCD40#1

description: Library name: 9496-WL-0010


title: DrugSeq09_24well_hPreadipocytes_rep1_row5_ADT

description:
Library name: ILD1-022_SRAB0000704
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.


title: 1014 Virol ctl, Vehicle+aCD40#3

description: Library name: 9496-WL-0009


title: 1014 CD40-OE, Vehicle+IgG#2

description: Library name: 9496-WL-0005

value: Veh+IgG


title: CD34_pool004_ADT

description:
Library name: ILD2-002_SRAB0001160
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: 1014 CD40-OE, Vehicle+IgG#3

description: Library name: 9496-WL-0006


title: 1014 Virol ctl, Vehicle+aCD40#1

description: Library name: 9496-WL-0007


title: DrugSeq15_24well_Preadipocytes_v2_Row7_ADT

description:
Library name: ILD1-019_SRAB0000763
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: 1014 Virol ctl, Vehicle+IgG#2

description: Library name: 9496-WL-0002


title: 1014 Virol ctl, aCD40+PD1#3

description: Library name: 9496-WL-0021


title: 1014 Virol ctl, Vehicle+IgG#1

description: Library name: 9496-WL-0001


title: CD34_pool001_ADT

description:
Library name: ILD2-001_SRAB0001157
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: 1014 CD40-OE, RGS+IgG#3a

description: Library name: 9496-WL-0030a

data_processing:
RNA reads were aligned to the reference genome using STAR (RRID:SCR_004463) and quantified by featureCounts (RRID:SCR_012919). The RNA-seq quality was further checked after mapping by RNA-SeQC (RRID:SCR_005120), including alignment and duplication rates, GC bias, rRNA content, regions of alignment, 3’/5’ bias, and number of detectable transcripts. DESeq2 (RRID:SCR_015687) was used to detect differential expression between two conditions, considering technical and biological variability. CIBERSORT(RRID:SCR_016955), based on the LM22 gene signature, was used to estimate immune cells infiltrating the tumor. Benjamini-Hochberg correction was applied to adjust for multiple-testing. Functional enrichment analysis was performed by WebGestalt (RRID:SCR_006786)  and Gene Set Enrichment Analysis (GSEA, RRID:SCR_003199). TCRs were sequenced using the TCR Immunoverse all chain assay per the manufacturer’s protocol (Invitae/ArcherDX). Sequencing results were evaluated using Archer Immunoverse analyzer. CDR3 sequences and frequency tables were extracted from the manufacturers’ analysis platform and imported into R for analysis using the Immunarch package (RRID:SCR_023089, https://immunarch.com) in R.
Assembly: M36 (GRCm39)
Supplementary files format and content: RNAseq_mouse.count, RNAseq_mouse.proteincoding.count
Supplementary files format and content: 9496-WL-0001~0030_TRB.IR_per_clonotype_results.tsv


title: DrugSeq15_24well_Preadipocytes_v2_Row6_ADT

description:
Library name: ILD1-019_SRAB0000762
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: DrugSeq15_24well_Preadipocytes_v2_Row5_ADT

description:
Library name: ILD1-019_SRAB0000761
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: 1014 CD40-OE, RGS+IgG#1a

description: Library name: 9496-WL-0028a


title: 1014 Virol ctl, RGS+IgG#2a

description: Library name: 9496-WL-0026a


title: 1014 Virol ctl, RGS+IgG#3a

description: Library name: 9496-WL-0027a


title: 1014 CD40-OE, Vehicle+PD1#2

description: Library name: 9496-WL-0017


title: 1014 Virol ctl, RGS+IgG#1a

description: Library name: 9496-WL-0025a


title: 1014 CD40-OE, RGS+IgG#2a

description: Library name: 9496-WL-0029a


title: 1014 CD40-OE, aCD40+PD1#2a

description: Library name: 9496-WL-0023a


title: 1014 CD40-OE, aCD40+PD1#1a

description: Library name: 9496-WL-0022a


title: 1014 Virol ctl, aCD40+PD1#3a

description: Library name: 9496-WL-0021a


title: 1014 Virol ctl, Vehicle+aCD40#2

description: Library name: 9496-WL-0008


title: DrugSeq13_96well_hCD8_v2_row7_ADT

description:
Library name: ILD1-018_SRAB0000728
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate2.


title: 1014 Virol ctl, aCD40+PD1#2a

description: Library name: 9496-WL-0020a


title: DrugSeq13_96well_hCD8_v2_row5_ADT

description:
Library name: ILD1-018_SRAB0000726
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate2.


title: 1014 CD40-OE, Vehicle+PD1#3a

description: Library name: 9496-WL-0018a


title: 1014 CD40-OE, aCD40+PD1#3a

description: Library name: 9496-WL-0024a


title: DrugSeq13_96well_hCD8_v2_row6_ADT

description:
Library name: ILD1-018_SRAB0000727
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate2.


title: 1014 CD40-OE, Vehicle+PD1#2a

description: Library name: 9496-WL-0017a


title: DrugSeq14_96well_hCD34_v2_row6_ADT

description:
Library name: ILD1-017_SRAB0000738
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: 1014 Virol ctl, Vehicle+IgG#3

description: Library name: 9496-WL-0003


title: 1014 CD40-OE, Vehicle+PD1#1a

description: Library name: 9496-WL-0016a


title: DrugSeq14_96well_hCD34_v2_row7_ADT

description:
Library name: ILD1-017_SRAB0000739
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: 1014 Virol ctl, Vehicle+PD1#3a

description: Library name: 9496-WL-0015a


title: 1014 Virol ctl, aCD40+PD1#1a

description: Library name: 9496-WL-0019a


title: DrugSeq14_96well_hCD34_v2_row5_ADT

description:
Library name: ILD1-017_SRAB0000737
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: 1014 Virol ctl, Vehicle+PD1#2a

description: Library name: 9496-WL-0014a


title: 1014 Virol ctl, Vehicle+PD1#1a

description: Library name: 9496-WL-0013a


title: DrugSeq15_24well_Preadipocytes_v2_Row4_ADT

description:
Library name: ILD1-016_SRAB0000760
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: 1014 CD40-OE, Vehicle+aCD40#3a

description: Library name: 9496-WL-0012a


title: DrugSeq15_24well_Preadipocytes_v2_Row3_ADT

description:
Library name: ILD1-016_SRAB0000759
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: 1014 CD40-OE, Vehicle+aCD40#2a

description: Library name: 9496-WL-0011a


title: DrugSeq15_24well_Preadipocytes_v2_Row2_ADT

description:
Library name: ILD1-016_SRAB0000758
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: 1014 CD40-OE, Vehicle+aCD40#1a

description: Library name: 9496-WL-0010a


title: 1014 Virol ctl, Vehicle+aCD40#1a

description: Library name: 9496-WL-0007a


title: 1014 Virol ctl, Vehicle+aCD40#3a

description: Library name: 9496-WL-0009a


title: 1014 CD40-OE, Vehicle+IgG#2a

description: Library name: 9496-WL-0005a


title: 1014 CD40-OE, Vehicle+IgG#1a

description: Library name: 9496-WL-0004a


title: DrugSeq15_24well_Preadipocytes_v2_Row1_ADT

description:
Library name: ILD1-016_SRAB0000757
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: DrugSeq09_24well_hPreadipocytes_rep1_row3_ADT

description:
Library name: ILD1-015_SRAB0000702
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.

value: ILD1-015, completed on 3/4/2021


title: 1014 Virol ctl, Vehicle+aCD40#2a

description: Library name: 9496-WL-0008a


title: DrugSeq09_24well_hPreadipocytes_rep1_row4_ADT

description:
Library name: ILD1-015_SRAB0000703
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.


title: 1014 CD40-OE, Vehicle+IgG#3a

description: Library name: 9496-WL-0006a


title: 1014 Virol ctl, Vehicle+IgG#3a

description: Library name: 9496-WL-0003a


title: 1014 Virol ctl, Vehicle+IgG#2a

description: Library name: 9496-WL-0002a


title: DrugSeq13_96well_hCD8_v2_row4_ADT

description:
Library name: ILD1-014_SRAB0000725
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate2.


title: DrugSeq09_24well_hPreadipocytes_rep1_row2_ADT

description:
Library name: ILD1-015_SRAB0000701
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.


title: 4.5W_Ddx20cKO2

city: Niigata City

first: Norihisa

last: Bizen

address: 757 Ichibancho, Asahimachi-dori, Chuo Ward

department: Graduate School of Medical and Dental Sciences

country: Japan

institute: Niigata University

description: Library name: 4.5W_Ddx20cKO2

data_processing:
alignment with STAR
to have BAM file
transcript level  with RSEM
Assembly: mm39
Supplementary files format and content: .txt, gene_id, gene_symbol, raw count

source_name: spinal cord

growth_protocol: Ddx20 knock-out mice, Ddx20flox/flox mice were crossed with Plp-CreER transgenic mice.

extract_protocol: Total RNA was extracted from the spinal cords of control and Ddx20 cKO mice at 4 and 4.5 weeks after tamoxifen administration, with three independent biological replicates for each group. RNA extraction was performed using QIAzol reagent, and mRNA libraries were subsequently constructed by Novogene using the Illumina TruSeq RNA Sample Prep Kit v2.

value: spinal cord

value: Ddx20 cKO


title: 4.5W_Ctrl2

description: Library name: 4.5W_Ctrl2

value: Control


title: DrugSeq13_96well_hCD8_v2_row3_ADT

description:
Library name: ILD1-014_SRAB0000724
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate2.


title: 4.5W_Ctrl3

description: Library name: 4.5W_Ctrl3


title: 4.5W_Ctrl1

description: Library name: 4.5W_Ctrl1


title: 4W_Ddx20cKO3

description: Library name: 4W_Ddx20cKO3


title: DrugSeq13_96well_hCD8_v2_row2_ADT

description:
Library name: ILD1-014_SRAB0000723
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate2.


title: 4W_Ddx20cKO2

description: Library name: 4W_Ddx20cKO2


title: 4W_Ddx20cKO1

description: Library name: 4W_Ddx20cKO1


title: 4W_Ctrl2

description: Library name: 4W_Ctrl2


title: 4W_Ctrl3

description: Library name: 4W_Ctrl3


title: DrugSeq13_96well_hCD8_v2_row1_ADT

description:
Library name: ILD1-014_SRAB0000722
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate2.


title: 4W_Ctrl1

description: Library name: 4W_Ctrl1


title: U14

city: Houston

first: Samantha

last: Ottinger

state: TX

address: 1 Baylor Plaza

department: Molecular Virology and Microbiology

institute: Baylor College of Medicine

data_processing:
Original reads were converted by CASAVA base recognition. Alignment and mapping were performed using HISAT2 (v2.0.5) to genome GRCm39 by Novogene.
Read qunatification was performed using featureCounts (v1.5.0-p3) by Novogene.
Raw count values were normalized and differential gene expression was determined using DESeq2 (v1.42.0) in R Studio (v2023.12.0-369.
Assembly: GRCm39
Supplementary files format and content: comma delimited text file contains normalized read counts for each sample.
Supplementary files format and content: comma delimited text file contains raw counts for each sample

source_name: Uterus

growth_protocol: Pregnant mice and nonpregnant controls were infected with 5e7 CFU UTI89 in 50uL sterile PBS or PBS alone for mock controls. Four hours later, mice were euthanized and bladders, placenta, and uterus were resected.

extract_protocol:
Samples were extracted using Qiagen RNeasy Plus Mini kit (Wiagen 74134).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. cDNA was synthesized using random hexamer priners, followed by second strand cDNA synthesis using dUTP for directional library. Performed by Novogene.

treatment_protocol: Tissues were lysed with 2mm silica beads in 500uL RNA Protect (Qiagen) at 6000 rpm for 3 minutes in a Roche magnalyzer.

value: Uterus

tag: outcome

value: Term

tag: background

tag: Sex

value: female

value: UTI89 RFP


title: U13


title: U11

value: Mock

value: PBS


title: U9


title: DrugSeq14_96well_hCD34_v2_row4_ADT

description:
Library name: ILD1-012_SRAB0000736
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: 1014 Virol ctl, Vehicle+IgG#1a

description: Library name: 9496-WL-0001a

value: melanoma tumor

value: NRAS-mut melanoma


title: DrugSeq14_96well_hCD34_v2_row3_ADT

description:
Library name: ILD1-012_SRAB0000735
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.

value: Multiplexed treatment with small molecules, one per hashtag. Processed files contain demultiplexed treatment values


title: U12

value: Preterm


title: DrugSeq09_24well_hPreadipocytes_rep1_row1_ADT

description:
Library name: ILD1-015_SRAB0000700
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.

value: PAD


title: 4.5W_Ddx20cKO3

description: Library name: 4.5W_Ddx20cKO3


title: U10


title: 1014 CD40-OE, Vehicle+IgG#1

description: Library name: 9496-WL-0004


title: U8


title: 4.5W_Ddx20cKO1

description: Library name: 4.5W_Ddx20cKO1


title: U6


title: U7


title: U2


title: DrugSeq14_96well_hCD34_v2_row1_ADT

description:
Library name: ILD1-012_SRAB0000733
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: U1


title: U4


title: P28

source_name: Placenta

value: Placenta

value: Female


title: U3


title: DrugSeq14_96well_hCD34_v2_row2_ADT

description:
Library name: ILD1-012_SRAB0000734
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: U5


title: P26


title: P25


title: P27


title: P24


title: P21


title: P20

value: Male


title: P15


title: P18


title: P16


title: P19


title: P14


title: P13


title: P9


title: P8


title: P11


title: P12


title: P10


title: P7


title: P4


title: P3


title: P6


title: P5


title: B13

source_name: Bladder

value: Bladder


title: B14


title: B17


title: B15


title: B12


title: B16


title: P17


title: B10


title: B6

value: Nonpregnant


title: B9


title: B8


title: B5


title: B4


title: B7


title: P2


title: B18


title: B3


title: KO testosterone rep6

city: Turku

first: Petra

last: Sipilä

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

data_processing:
Quality control: FastQC tool version 0.11.14
The reads were aligned to the UCSC mm10 mouse genome reference, derived from Illumina iGenomes, using Rsubread package (version 2.0.0) and its inbuilt Refseq gene annotation
Normalization was performed using the calcNormFactors function from the edgeR package version 3.28.0, implementing the trimmed mean of M-values (TMM) normalization method
Assembly: mm10
Supplementary files format and content: Text file containing normalized genewise read counts, reads per kilobase million

source_name: kidney

extract_protocol:
Pregnant dams were sacrificed on 16.5 dpc, two hours after final treatment. E16.5 fetuses were dissected from the uterus and sacrificed, tissue samples collected for genotyping, and kidneys collected and snap frozen in liquid nitrogen. Total RNA was isolated from tissue homogenates by using Trisure reagent (Bioline, USA) according to manufacturer’s instruction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Pregnant dams were treated with testosterone propionate in corn oil, 20 mg/kg, or corn oil as vehicle. Treatment was done as s.c. injections once daily from 14.5-16.5 days post coitum.

value: kidney

value: male

value: Hsd17b3 del/del

value: Testosterone


title: KO vehicle rep5

value: Vehicle


title: B2

value: female


title: WT vehicle rep3

value: WT


title: WT testosterone rep4


title: KO vehicle rep3


title: KO vehicle rep6


title: P1


title: KO vehicle rep2


title: KO vehicle rep1


title: KO testosterone rep5


title: WT vehicle rep2


title: WT testosterone rep3


title: WT testosterone rep2


title: WT vehicle rep1


title: KO testosterone rep4


title: B11


title: WT testosterone rep1


title: KO testosterone rep3


title: KO testosterone rep2


title: Day 7_Lib 3_ADT

description:
Library name: SRAB0006817
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad

data_processing:
Basecalling and FASTQ generation with bcl2fastq v2.20.0.422.
Read alignment and gene counting with Cell Ranger v5.0.1 (10x Genomics) using STAR v2.7.0a against GRCh38.
Initial QC for hashed (Days 1–7) data prior to demultiplexing: retain cells with total counts between 5,000 and 80,000 and mitochondrial fraction <20 percent.
Demultiplex hashed libraries using CLR-normalized hashtag counts and a Gaussian mixture model; classify singlets, multiplets, negatives; retain singlets and assign to wells/perturbations.
Additional per-cell QC after demultiplexing: remove cells with <2,500 or >60,000 counts and cells with <1,600 or >9,000 detected genes.
Per-cell normalization to 10,000 counts and natural log transform (Scanpy v1.9.3).
Reference mapping and label transfer: construct a batch-corrected PC space with harmony; project the query time course into the reference time course CITE-seq PC space; integrate in the reference’s harmony-corrected PC space; transfer cell type labels with SymphonyPy v0.2.1 KNN classifier.
Label transfer validation: evaluate weighted Mahalanobis distance to mapped reference clusters, cosine similarity across highly variable genes between matched types, and expression of canonical markers.
Assemble outputs for GEO: Day 0 raw counts (unhashed); Days 1–7 raw counts (hashed, pre-demultiplexing) and demultiplexed counts (singlets with well assignments); normalized counts across Days 0–7 with transferred cell type annotations.
Assembly: GRCh38
Supplementary files format and content: day0_raw_counts.h5ad - Day 0 single-cell raw count matrix (genes x cells), unhashed and untreated; includes basic per-cell QC metrics; no demultiplexing.
Supplementary files format and content: day1-7_raw_counts.h5ad - Days 1, 2, 5, and 7 hashed single-cell raw count matrices combined prior to demultiplexing; pre-demux QC applied (counts 5,000–80,000; mitochondrial fraction <20 percent); includes hashtag count data and per-cell QC metrics.
Supplementary files format and content: day1-7_demuxed_counts.h5ad - Demultiplexed singlet cells for Days 1, 2, 5, and 7; cells assigned to wells/perturbations via Gaussian mixture modeling on CLR-normalized hashtags; additional QC applied (<2,500 or >60,000 counts; <1,600 or >9,000 genes filtered); includes per-cell well/treatment metadata.
Supplementary files format and content: day0-7_normalized_counts_with_celltype_annotations.h5ad - Normalized (10,000 counts per cell; natural log transformed) cell-by-gene matrix spanning Days 0–7 with transferred cell type annotations obtained by mapping to a reference time course using harmony-corrected PCs and SymphonyPy KNN label transfer; includes validation metrics supporting label robustness.

source_name: peripheral blood

growth_protocol: Dual-mobilized (Neupogen + Mozobil) peripheral blood CD34+ HSPCs (AllCells) were thawed and cultured in StemSpan SFEM supplemented with TPO (100 ng/mL) and CC100 (Stemcell Technologies). On day 0 (48 h post-thaw), cells were plated in 96-well plates: for megakaryocyte differentiation, 60,000 cells per well in round-bottom plates; for erythroid differentiation, 30,000 cells per well in flat-bottom plates. Cells were passaged 1:4 on day 2 and media were refreshed on day 5.

extract_protocol:
Single-cell RNA was captured directly in droplets per the 10x Genomics Single Cell 3’ v3.1 workflow; no separate bulk RNA extraction was performed.
On days 1, 2, 5, and 7, samples were multiplexed with cell multiplexing oligos (CMOs; 10x Genomics) following the manufacturer’s protocol. Briefly, cells were washed in Cell Staining Buffer (BioLegend), counted, incubated with CMOs for 5 min at room temperature, then washed three times with 4% HSA (Grifols). Twelve CMO-tagged samples were pooled per library by combining ~100,000 cells from each well. Pooled cells were washed once in 4% HSA, counted, and resuspended in Cell Staining Buffer at 1.2e6 cells/mL. Each compound was sequenced in duplicate with duplicates distributed across libraries. Each library included positive and negative controls and a mixture of hit and non-hit compounds. Single-cell 3’ libraries were prepared with Chromium Single Cell 3’ Reagent Kit v3.1 (10x Genomics, 1000268) and sequenced on an Illumina NovaSeq 6000 (paired-end).

treatment_protocol: Compounds (Frontier Scientific; 10 mM stocks in DMSO) were arrayed by Hamilton Microlab STAR. For screening, compounds were arrayed at 0.1, 1, or 10 mM in triplicate; for target deconvolution, 10 mM stocks were serially diluted 3-fold for 8 concentrations and duplicated. Plates were stored at −80 C. On treatment days, plates were thawed at 37 C for 10 min, diluted with IMDM, and transferred with an Integra VIAFLO384 to achieve a final 1,000x dilution in culture. Treatments were applied on days 0, 2, and 5. In this dataset, cells from one donor were analyzed at a final concentration of 1 uM per compound or DMSO control.

value: peripheral blood

value: CD34+ HSPCs

value: Day 7


title: Day 7_Lib 4_GEX

description:
Library name: SRTP0006818
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad

value: Multiplexed treatment with small molecules, one per hashtag. Processed files contain demultiplexed treatment values


title: Day 7_Lib 3_GEX

description:
Library name: SRTP0006817
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: KO vehicle rep4


title: B1

value: Preterm


title: Day 7_Lib 2_GEX

description:
Library name: SRTP0006816
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: KO testosterone rep1


title: 3xTg female mice, treated with VCD in Cycle 14; biological repeat 5

city: Sha Tin

first: Jacquelyne

last: Sun

state: New Territories

address: Room 612A, Mong Man Wai Building,

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
The FASTQ files were first checked for quality using FastQC - as samples all passed our benchmarks, the clean raw data files were subsequently aligned using the STAR alignment software to the mouse genome provided by Gencode M34.
featureCounts was then used to quantify the sequencing data, which is the raw counts file provided in this GEO accession.
Assembly: mm39
Supplementary files format and content: Tab delimited text file containing the raw counts for each samples.
Supplementary files format and content: Metadata file with sample names and treatment is also provided.

source_name: Total cortex

extract_protocol:
Total RNA was extracted using the TRIzol method, and the RNA was resuspended in DNase/Rnase free water. The samples were subsequently sent to Novogene for sequencing using the Illumina NovaSeq 6000 platform. The FASTQ files were returned to us from the sequencing company.
According to the manufacturer's quality control report, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesised using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, enzyme digestion, amplification and purification.

treatment_protocol: Full details can be found in the publication. In brief, 3-month-old C57BL/6 female mice were treated with either vehicle control or VCD treatment for a duration of 15 days at 160mg/kg. The mice were harvested at experimental day 90.

value: Total cortex

value: VCD


title: 3xTg female mice, treated with VCD in Cycle 14; biological repeat 4


title: Day 7_Lib 2_ADT

description:
Library name: SRAB0006816
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: Day 5_Lib 4_GEX

description:
Library name: SRTP0006814
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad

value: Day 5


title: Day 7_Lib 1_ADT

description:
Library name: SRAB0006815
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: 3xTg female mice, treated with VCD in Cycle 14; biological repeat 3


title: Day 7_Lib 1_GEX

description:
Library name: SRTP0006815
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: 3xTg female mice, treated with VCD in Cycle 14; biological repeat 2


title: Day 5_Lib 3_ADT

description:
Library name: SRAB0006813
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: Day 5_Lib 4_ADT

description:
Library name: SRAB0006814
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: Day 5_Lib 3_GEX

description:
Library name: SRTP0006813
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: 3xTg female mice, treated with vehicle control in Cycle 14; biological repeat 5


title: Day 7_Lib 4_ADT

description:
Library name: SRAB0006818
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: 3xTg female mice, treated with vehicle control in Cycle 14; biological repeat 4


title: 3xTg female mice, treated with vehicle control in Cycle 14; biological repeat 3


title: Day 5_Lib 2_GEX

description:
Library name: SRTP0006812
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: Day 5_Lib 2_ADT

description:
Library name: SRAB0006812
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: 3xTg female mice, treated with vehicle control in Cycle 14; biological repeat 2


title: Day 5_Lib 1_ADT

description:
Library name: SRAB0006811
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: Day 5_Lib 1_GEX

description:
Library name: SRTP0006811
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: 3xTg female mice, treated with vehicle control in Cycle 14; biological repeat 1


title: 3xTg female mice, treated with VCD, biological repeat 3


title: Day 2_Lib 4_ADT

description:
Library name: SRAB0006810
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad

value: Day 2


title: 3xTg female mice, treated with VCD, biological repeat 4


title: Day 2_Lib 4_GEX

description:
Library name: SRTP0006810
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: 3xTg female mice, treated with VCD, biological repeat 2


title: 3xTg female mice, treated with VCD in Cycle 14; biological repeat 1


title: Day 2_Lib 3_GEX

description:
Library name: SRTP0006809
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: Day 2_Lib 3_ADT

description:
Library name: SRAB0006809
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: 3xTg female mice, treated with VCD, biological repeat 1


title: 3xTg female mice, treated with vehicle control in Cycle 14; biological repeat 6


title: 3xTg female mice, treated with vehicle control, biological repeat 3


title: Day 2_Lib 2_GEX

description:
Library name: SRTP0006808
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: Day 2_Lib 2_ADT

description:
Library name: SRAB0006808
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: 3xTg female mice, treated with vehicle control, biological repeat 1


title: 3xTg female mice, treated with vehicle control, biological repeat 2


title: 3xTg female mice, treated with P4 in Cycle 14, biological repeat 5


title: Day 2_Lib 1_GEX

description:
Library name: SRTP0006807
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: 3xTg female mice, treated with P4 in Cycle 14, biological repeat 4


title: Day 1_Lib 4_ADT

description:
Library name: SRAB0006806
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad

value: Day 1


title: 3xTg female mice, treated with P4 in Cycle 14, biological repeat 3


title: Day 1_Lib 4_GEX

description:
Library name: SRTP0006806
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: Day 1_Lib 3_ADT

description:
Library name: SRAB0006805
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: 3xTg female mice, treated with P4 in Cycle 14, biological repeat 1


title: Day 1_Lib 2_ADT

description:
Library name: SRAB0006804
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: 3xTg female mice, treated with P4 in Cycle 14, biological repeat 2


title: 3xTg female mice, treated with vehicle control in Cycle 14, biological repeat 6


title: Day 1_Lib 3_GEX

description:
Library name: SRTP0006805
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: 3xTg female mice, treated with vehicle control in Cycle 14, biological repeat 5


title: Day 1_Lib 2_GEX

description:
Library name: SRTP0006804
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: Day 1_Lib 1_ADT

description:
Library name: SRAB0006803
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: 3xTg female mice, treated with vehicle control in Cycle 14, biological repeat 3


title: 3xTg female mice, treated with vehicle control in Cycle 14, biological repeat 1


title: 3xTg female mice, treated with vehicle control in Cycle 14, biological repeat 4


title: Day 1_Lib 1_GEX

description:
Library name: SRTP0006803
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


title: Day 2_Lib 1_ADT

description:
Library name: SRAB0006807
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day1-7_raw_counts.h5ad
day1-7_demuxed_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad


description:
Library name: SATC0001487
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 10
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_31800_day_10_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002020_atac_fragments.tsv.gz

library_source: genomic single cell

data_processing:
Raw sequencing reads were processed using Cell Ranger for CITE-seq samples and Cell Ranger ARC  for Multiome samples to generate count matrices.
Quality control filtering was applied to remove low-quality cells and genes. Cells with high mitochondrial gene expression or low total gene counts were excluded.
Count matrices were normalized and log-transformed. For CITE-seq protein data CLR (centered log-ratio) normalization was applied.
Cell type annotation was performed using gene expression signatures based on reference: https://www.nature.com/articles/ncb3493. Cell types identified include: HSC (Hematopoietic Stem Cell) MasP (Mast Cell Progenitor) MkP (Megakaryocyte Progenitor) NeuP (Neutrophil Progenitor) MoP (Monocyte Progenitor) EryP (Erythrocyte Progenitor) and BP (B-Cell Progenitor).
Assembly: GRCh38 (hg38)
Supplementary files format and content: H5AD files contain single-cell count matrices in AnnData format with cells as observations and genes/proteins/peaks as variables. Includes metadata for cell types donors time points and quality metrics.

growth_protocol: Mobilized peripheral CD34+ hematopoietic stem and progenitor cells (HSPCs) were obtained from four healthy human donors. Cells were cultured in StemSpan SFEM media supplemented with CC100 cytokine cocktail and thrombopoietin (TPO) at 37¬∞C with 5% CO2. Media was changed every 2-3 days during the 10-day culture period. No additional media supplements were added to the cell culture conditions.

extract_protocol:
Total RNA was extracted from single cells using the 10x Genomics protocol. For CITE-seq samples cell surface proteins were captured using TotalSeq-B Human Universal Cocktail V1.0 antibodies before cell lysis. For Multiome samples nuclei were isolated for ATAC-seq library preparation following the 10x Genomics protocol.
CITE-seq libraries were prepared using 10x Genomics Single Cell Gene Expression with Feature Barcoding technology version 3.1. Two libraries were generated per sample: gene expression (GEX) using standard 3' single cell RNA-seq and surface protein detection using antibody-derived tags (ADT) with TotalSeq-B antibodies. Multiome libraries were prepared using 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression technology generating paired GEX and ATAC libraries from the same cells.

treatment_protocol: Cells were maintained in standard culture conditions with StemSpan SFEM media supplemented with CC100 and thrombopoietin (TPO). No additional treatments or stimulations were applied. Cells were sampled at five time points: day 2 day 3 day 4 day 7 and day 10 of culture.

value: CD34-positive hematopoietic stem and progenitor cell

value: StemSpan SFEM media supplemented with CC100 and thrombopoietin (TPO), cultured for 10 days with media changes every 2-3 days

value: donor 31800

tag: time point

value: Day 10


description:
Library name: SATC0001484
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 13176 at Day 10
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_13176_day_10_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002017_atac_fragments.tsv.gz

value: donor 13176


description:
Library name: SATC0001485
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 10
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_32606_day_10_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002018_atac_fragments.tsv.gz

value: donor 32606


title: polII_ChIP-seq_4h_ser5-1

city: Guanzhou

first: dongmei

last: he

address: Yunpu Street

country: China

institute: University of Chinese Academy of Sciences

data_processing:
The adapter and low-quality sequences were removed from raw reads using fastp.
Reads were aligned to the mouse reference genome (mm10) using bowtie2.
Picard was employed to remove PCR duplicates.
ChIP-seq peaks were called using MACS2 with a P-value < 0.05
For CLIP-seq,The raw data were processed to obtain unique CLIP tags using the CTK pipeline,Reads were aligned to the mouse reference genome (mm10) reference using BWA,CTK scripts were then utilized to parse alignments and call peak.
Assembly: mm10
Supplementary files format and content: peak
Supplementary files format and content: bigWIg

growth_protocol: E14TG2a cells were maintained in DMEM supplemented with 15% fetal bovine serum (FBS), GlutaMAX, nonessential amino acids (NEAA), sodium pyruvate, penicillin-streptomycin, 2-mercaptoethanol, and 1000U ml-1 Leukemia inhibitory factor (LIF) on plates coated with 0.2% gelatin.

extract_protocol:
Cells were fixed with 3% formaldehyde for 10 minutes. After quenching and cell lysis, Chromatin was sonicated using Bioruptor plus (Diagenode). Protein-DNA complexes were isolated with antibody.
Cells were crosslinked with 254 nm UV at 0.15 J/cm2. After cell lysis, RNA was digested with RNase T1. CLIP-seq protein-RNA complexes were isolated with antibody.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following manufacture’s protocols.
CLIP-seq libraries were prepared using SMART-Seq® Stranded Kit according to the manufacturer’s instructions.

value: mESC

tag: chlp antibody

value: polII S5P(Abcam,AB5131)


description:
Library name: SATC0001486
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 10
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_27678_day_10_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002019_atac_fragments.tsv.gz

value: peripheral blood

value: donor 27678


title: polII_ChIP-seq_4h_ser5-2


title: polII_ChIP-seq_0h_ser5-2


title: polII_ChIP-seq_0h_ser5-1


description:
Library name: SATC0001483
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 7
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_31800_day_7_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002012_atac_fragments.tsv.gz

value: Day 7


title: polII_ChIP-seq_4h_ser2-2

value: polII S2P(Abcam,AB5095)


description:
Library name: SATC0001481
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 7
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_32606_day_7_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002010_atac_fragments.tsv.gz


title: polII_ChIP-seq_4h_ser2-1


description:
Library name: SATC0001480
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 13176 at Day 7
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_13176_day_7_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002009_atac_fragments.tsv.gz


title: polII_ChIP-seq_0h_ser2-2


description:
Library name: SATC0001479
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 13176 at Day 4
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_13176_day_4_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002008_atac_fragments.tsv.gz

value: Day 4


title: polII_ChIP-seq_0h_ser2-1


title: polII_ChIP-seq_4h_NTD-2

value: polII NTD(CST,14958S)


title: 3xTg female mice, treated with vehicle control in Cycle 14, biological repeat 2

value: Total cortex

value: Vehicle


description:
Library name: SATC0001477
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 4
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002006_atac_fragments.tsv.gz


title: polII_ChIP-seq_4h_NTD-1


description:
Library name: SATC0001476
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 4
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_31800_day_4_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002005_atac_fragments.tsv.gz


title: polII_ChIP-seq_0h_NTD-2


title: polII_ChIP-seq_0h_NTD-1


description:
Library name: SATC0001475
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 3
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_31800_day_3_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002004_atac_fragments.tsv.gz

value: Day 3


description:
Library name: SATC0001474
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 3
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_27678_day_3_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002003_atac_fragments.tsv.gz

value: CD34-positive hematopoietic stem and progenitor cell


description:
Library name: SATC0001473
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 3
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_32606_day_3_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002002_atac_fragments.tsv.gz

value: StemSpan SFEM media supplemented with CC100 and thrombopoietin (TPO), cultured for 10 days with media changes every 2-3 days


description:
Library name: SATC0001482
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 7
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_27678_day_7_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002011_atac_fragments.tsv.gz


title: polII_ChIP-seq_4h_Input-1


description:
Library name: SATC0001471
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 2
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_31800_day_2_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002000_atac_fragments.tsv.gz

value: donor 31800

value: Day 2


title: polII_ChIP-seq_0h_Input-1


title: polII_ChIP-seq_4h_Input-2


title: UTP15_ChIP-seq_NANOG_AddIAA-2

value: NANOG-AID

value: FLAG M2(Sigma,F1804)


description:
Library name: SATC0001469
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 2
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_32606_day_2_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0001998_atac_fragments.tsv.gz

value: donor 32606


title: UTP15_ChIP-seq_NANOG_AddIAA-1

value: mESC


description:
Library name: SATC0001478
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 4
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_32606_day_4_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002007_atac_fragments.tsv.gz

value: peripheral blood


description:
Library name: SRTP0002020
Multiome GEX  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 10
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0002020_filtered_feature_bc_matrix.h5
multiome_donor_31800_day_10_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad

library_source: transcriptomic single cell

value: Day 10


title: UTP15_ChIP-seq_NANOG_NoIAA-1


title: UTP15_ChIP-seq_NANOG_NoIAA-2


title: UTP15_ChIP-seq_Ctrl-1


description:
Library name: SRTP0002019
Multiome GEX  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 10
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0002019_filtered_feature_bc_matrix.h5
multiome_donor_27678_day_10_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad

value: donor 27678


description:
Library name: SRTP0002018
Multiome GEX  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 10
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0002018_filtered_feature_bc_matrix.h5
multiome_donor_32606_day_10_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad


description:
Library name: SRTP0002017
Multiome GEX  library from mobilized peripheral CD34+ HSPC donor 13176 at Day 10
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0002017_filtered_feature_bc_matrix.h5
multiome_donor_13176_day_10_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad

value: donor 13176


title: UTP15_ChIP-seq_ActD-2


description:
Library name: SRTP0002012
Multiome GEX  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 7
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0002012_filtered_feature_bc_matrix.h5
multiome_donor_31800_day_7_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad

value: Day 7


description:
Library name: SATC0001472
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 13176 at Day 3
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_13176_day_3_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0002001_atac_fragments.tsv.gz


title: polII_ChIP-seq_0h_Input-2


description:
Library name: SRTP0002011
Multiome GEX  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 7
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0002011_filtered_feature_bc_matrix.h5
multiome_donor_27678_day_7_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad


title: UTP15_ChIP-seq_IP-2


description:
Library name: SRTP0002010
Multiome GEX  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 7
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0002010_filtered_feature_bc_matrix.h5
multiome_donor_32606_day_7_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad


title: UTP15_ChIP-seq_IP-1


description:
Library name: SATC0001470
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 2
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
multiome_donor_27678_day_2_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0001999_atac_fragments.tsv.gz


description:
Library name: SRTP0002009
Multiome GEX  library from mobilized peripheral CD34+ HSPC donor 13176 at Day 7
10x Chromium Single Cell Multiome ATAC + Gene Expression technology. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO.  Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0002009_filtered_feature_bc_matrix.h5
multiome_donor_13176_day_7_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad


title: UTP15_ChIP-seq_Input-2