title: UTP15_ChIP-seq_Input-1


status: Public on Oct 23 2025

type: SRA

city: Somerville

first: Mauricio

last: Cortes

state: MA

address: 101 South Street

country: USA

institute: Cellarity

description:
Library name: SRTP0002007
Multiome GEX  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.
SRTP0002007_filtered_feature_bc_matrix.h5
multiome_donor_32606_day_4_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad

library_source: transcriptomic 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.

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

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.

tag: tissue

value: peripheral blood

tag: cell type

value: CD34-positive hematopoietic stem and progenitor cell

tag: treatment

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

tag: batch

value: donor 32606

tag: time point

value: Day 4


title: UTP15_CLIP-seq-2

city: Guanzhou

first: dongmei

last: he

address: Yunpu Street

country: China

institute: University of Chinese Academy of Sciences

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

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.

tag: cell line

value: mESC

tag: genotype

tag: chlp antibody

value: FLAG M2(Sigma,F1804)


description:
Library name: SATC0001468
Multiome ATAC-seq  library from mobilized peripheral CD34+ HSPC donor 13176 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_13176_day_2_processed.h5mu
multiome_atac_counts.h5ad
atac_peaks.bed
atac_fragments.tsv.gz
SRTP0001997_atac_fragments.tsv.gz

library_source: genomic single cell

value: donor 13176

value: Day 2


title: UTP15_CLIP-seq-1


description:
Library name: SRTP0002006
Multiome GEX  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.
SRTP0002006_filtered_feature_bc_matrix.h5

value: donor 27678


description:
Library name: SRTP0002005
Multiome GEX  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.
SRTP0002005_filtered_feature_bc_matrix.h5
multiome_donor_31800_day_4_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad

value: donor 31800


title: UTP15_ChIP-seq_Ctrl-2


title: UTP15_AID_24h-2_Nascent-RNA-seq

library_source: transcriptomic

data_processing:
The adapter and low-quality sequences were removed from raw reads using fastp.
Reads were aligned to the mouse reference genome (mm10) or spike-in reference using Hisat2.
UMI-tools was employed to identify UMI and remove PCR duplicates.
featureCounts was assigned aligned reads to genes.
BAM files were converted to bigwig format using bamCoverage
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: bigWig

extract_protocol:
RNA was harvested using TRI Reagent. 200 μg of total RNA was used for nascent RNA enrichment and library construction.
RNA libraries for nascent RNA-seq were constructed using small RNA library construction strategy. Briefly, RNA was ligated with pre-adenylated 3’-adapter and reverse-transcribed. cDNA was isolated to ligate another adapter. Finally, the RNA library was enriched by PCR amplification.

treatment_protocol: Cells were treated with 1 mM EU for 15 minutes after IAA-induced protein degradation at different time points.


title: UTP15_AID_24h-1_Nascent-RNA-seq


description:
Library name: SRTP0002003
Multiome GEX  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.
SRTP0002003_filtered_feature_bc_matrix.h5
multiome_donor_27678_day_3_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad

value: Day 3


description:
Library name: SRTP0002002
Multiome GEX  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.
SRTP0002002_filtered_feature_bc_matrix.h5
multiome_donor_32606_day_3_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad


title: UTP15_ChIP-seq_ActD-1


title: UTP15_AID_4h-2_Nascent-RNA-seq


description:
Library name: SRTP0002001
Multiome GEX  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.
SRTP0002001_filtered_feature_bc_matrix.h5
multiome_donor_13176_day_3_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad


title: UTP15_AID_0h-2_Nascent-RNA-seq


title: UTP15_AID_4h-1_Nascent-RNA-seq


title: P23

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

molecule: polyA RNA

source_name: Placenta

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: Placenta

tag: outcome

value: Preterm

tag: background

tag: Sex

value: Male


description:
Library name: SRTP0002000
Multiome GEX  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.
SRTP0002000_filtered_feature_bc_matrix.h5
multiome_donor_31800_day_2_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad


title: UTP15_AID_0h-1_Nascent-RNA-seq


title: NANOG_AID_24h-1_Nascent-RNA-seq

value: NANOG-AID


description:
Library name: SRTP0001998
Multiome GEX  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.
SRTP0001998_filtered_feature_bc_matrix.h5
multiome_donor_32606_day_2_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad


description:
Library name: SRTP0001999
Multiome GEX  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.
SRTP0001999_filtered_feature_bc_matrix.h5
multiome_donor_27678_day_2_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad


description:
Library name: SRTP0002008
Multiome GEX  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.
SRTP0002008_filtered_feature_bc_matrix.h5
multiome_donor_13176_day_4_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad


title: NANOG_AID_8h-2_Nascent-RNA-seq


description:
Library name: SRTP0001997
Multiome GEX  library from mobilized peripheral CD34+ HSPC donor 13176 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.
SRTP0001997_filtered_feature_bc_matrix.h5
multiome_donor_13176_day_2_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad


title: NANOG_AID_24h-2_Nascent-RNA-seq


title: NANOG_AID_4h-2_Nascent-RNA-seq


description:
Library name: SRAB0002016
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 10
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_31800_day_10.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad

library_source: other

molecule: protein

value: Day 10


description:
Library name: SRAB0002015
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 10
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_27678_day_10.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad

value: peripheral blood


description:
Library name: SRTP0002004
Multiome GEX  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.
SRTP0002004_filtered_feature_bc_matrix.h5
multiome_donor_31800_day_3_processed.h5mu
multiome_rna_counts.h5ad
multiome_alldonors_alldays.h5ad

value: CD34-positive hematopoietic stem and progenitor cell


description:
Library name: SRAB0002014
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 10
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_32606_day_10.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad

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


title: NANOG_AID_4h-1_Nascent-RNA-seq


description:
Library name: SRAB0002013
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 13176 at Day 10
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_13176_day_10.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad


description:
Library name: SRAB0001979
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 7
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_31800_day_7.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad

value: Day 7


title: NANOG_AID_2h-2_Nascent-RNA-seq


title: P22

value: Mock

value: PBS


description:
Library name: SRAB0001978
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 7
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_27678_day_7.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad


title: NANOG_AID_0h-2_Nascent-RNA-seq

value: mESC


description:
Library name: SRAB0001977
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 7
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_32606_day_7.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad

value: donor 32606


title: NANOG_AID_0h-1_Nascent-RNA-seq


description:
Library name: SRAB0001976
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 13176 at Day 7
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_13176_day_7.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad

value: donor 13176


title: UTP15_AID_48h-2_Total-RNA-seq

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 Hisat2.
Picard was employed to remove PCR duplicates.
featureCounts was assigned aligned reads to genes.
BAM files were converted to bigwig format using bamCoverage
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: bigWig

extract_protocol:
RNA was harvested using TRI Reagent. 1 μg of total RNA was used for RNA library construction.
RNA libraries for RNA-seq were constructed using VAHTS Strand mRNA-seq Library Prep Kit for Illumina. rRNA was removed using QIAseq FastSelect-rRNA HMR Kit.

treatment_protocol: Cells were treated 500 μm IAA at different time points.


title: UTP15_AID_24h-2_Total-RNA-seq


description:
Library name: SRAB0001973
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 4
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_32606_day_4.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad

value: Day 4


title: NANOG_AID_8h-1_Nascent-RNA-seq


description:
Library name: SRAB0001975
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 4
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_31800_day_4.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad

value: donor 31800


description:
Library name: SRAB0001974
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 4
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_27678_day_4.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad

value: donor 27678


title: UTP15_AID_0h-2_Total-RNA-seq


description:
Library name: SRAB0001971
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 3
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_31800_day_3.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad

value: Day 3


description:
Library name: SRAB0001972
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 13176 at Day 4
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_13176_day_4.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad


title: UTP15_AID_48h-1_Total-RNA-seq


title: NANOG_AID_48h-2_Total-RNA-seq


title: NANOG_AID_48h-1_Total-RNA-seq


description:
Library name: SRAB0001968
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 13176 at Day 3
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_13176_day_3.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad


title: UTP15_AID_0h-1_Total-RNA-seq


description:
Library name: SRAB0001969
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 3
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_32606_day_3.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad


description:
Library name: SRAB0001970
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 3
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_27678_day_3.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad


title: NANOG_AID_4h-1_Total-RNA-seq


title: NANOG_AID_4h-2_Total-RNA-seq


description:
Library name: SRAB0001967
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 2
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_31800_day_2.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad

value: Day 2


title: NANOG_AID_2h-1_Nascent-RNA-seq


title: NANOG_AID_2h-2_Total-RNA-seq


description:
Library name: SRAB0001965
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 2
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_32606_day_2.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad


description:
Library name: SRAB0001964
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 13176 at Day 2
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_13176_day_2.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad


title: NANOG_AID_2h-1_Total-RNA-seq


title: NANOG_AID_0h-1_Total-RNA-seq


title: NANOG_AID_0h-2_Total-RNA-seq


description:
Library name: SRTP0002015
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 10
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0002015_filtered_feature_bc_matrix.h5
CITE_donor_27678_day_10.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad


description:
Library name: SRTP0002016
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 10
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0002016_filtered_feature_bc_matrix.h5
CITE_donor_31800_day_10.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad


title: UTP15_AID_24h-1_Total-RNA-seq


title: C3H10T1-2_Parental_HiC

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Raw Hi-C reads were trimmed of adapter sequences using Fastp v0.23.3 and aligned to the mm10 assembly using BWA v.0.7.17 with default parameters. Afterwards, ligation junctions (Hi-C pairs) were identified in aligned paired-end sequences using Pairtools v1.1.0. The restriction enzyme specified to Pairtools was the Arima kit, which uses the two restriction enzymes: DpnII and HinfI. Duplicated reads were marked using ‘pairtools dedup’ with the parameters: “--mark-dups --backend cython --output-stats $SAMPLE.stats -o $SAMPLE.dedup.pairs.gz”. Then, duplicated reads were removed and only uniquely-mapped reads were selected using ‘pairtools select’ with the parameters: “--chrom-subset mm10.canon.chroms '(rfrag1!=rfrag2) and ((pair_type=="UU" or pair_type=="RU" or pair_type=="UR"))' -o $SAMPLE.pairs.gz ${samp}.dedup.pairs.gz’. Junctions were subsequently binned and counted using Cooler v0.10.0, in which pairs (.pairs.gz) files were converted to a cooler (.cool) file using “cooler cload pairix --assembly mm10 mm10.canon.sizes:1000 $SAMPLE.pairs.gz $SAMPLE.1000.cool”. The cooler file underwent matrix balancing using “cooler balance $SAMPLE.1000.cool --blacklist $BLACKLIST.bed”. The matrix was then binned into different window sizes contained within a single multi-resolution cooler (.mcool) file using “cooler zoomify --out $SAMPLE.mcool --resolutions 1000,5000,10000,25000,50000,100000,250000,500000,1000000,2500000 --balance --balance-args --max-iters 1000 $SAMPLE.1000.cool”.
Assembly: mm10
Supplementary files format and content: multi-resolution Hi-C contact maps (.mcool)

growth_protocol: C3H10T1/2 mouse mesenchymal stem cells (ATCC) were cultured in DMEM with 10% fetal bovine serum (FBS,) and supplemented with 1% GlutaMax.

extract_protocol:
C3H10T1/2 mouse mesenchymal stem cells (two million cells per sample) were crosslinked and processed using the Arima-HiC+ kit and following the Arima Genomics HiC protocol for Mammalian Cell Lines (A510008). Proximally-ligated DNA was fragmented to an average size of 400 bp using the BioRuptor UCS-300 at low intensity for 10 cycles (30s ON, 90s OFF).
Library preparation of fragmented proximally-ligated DNA was performed using the NEBNext® Ultra™ II DNA Library Prep Kit (E7645S), NEBNext Multiplex Oligos for Illumina (E6440S), and the Arima HiC+ Kit according to manufacturer protocols. Hi-C libraries were sequenced by the McGill University Genome Centre at 150 bp paired-end reads using the Illumina NovaSeq 6000.

value: fibroblast

tag: kit

value: Arima

value: parental


description:
Library name: SRTP0002013
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 13176 at Day 10
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0002013_filtered_feature_bc_matrix.h5
CITE_donor_13176_day_10.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad

value: peripheral blood

value: Day 10


description:
Library name: SRTP0002014
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 10
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0002014_filtered_feature_bc_matrix.h5
CITE_donor_32606_day_10.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad

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


title: C3H10T1-2_NSD1-2-SETD2-TKO_ATACseq_rep2_batch1

data_processing:
Raw ATAC-seq reads were trimmed and filtered for quality using Trimmomatic v0.39 with default parameters. Trimmed reads were mapped to the mm10 genome assembly using Bowtie2 v2.5.1 using default parameters. Afterwards, the reads were adjusted by shifting all positive-strand reads 4 bp downstream and all negative-strand reads 5 bp upstream to the center of the reads on the transposase binding event. Peak calling was performed on each replicate using MACS2 v2.2.6 with ‘-extsize 200 -shift -100 -nomodel’ parameters. To find a set of reproducible peaks across replicates, we calculated the irreproducible discovery rate (IDR) and excluded peaks with an IDR greater than 0.05 across every pair of replicates. Subsequently, the ENCODE blacklist was used to filter the peaks. Coverage tracks were generated using bamCoverage from deepTools v3.3.1 with parameters ‘-b $BAM -o $OUTPUT.bigWig --normalizeUsing CPM --centerReads -e 200 --minMappingQuality 5’’.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
50,000 C3H10T1/2 cultured cells were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at 500 rcf for 5 min in a pre-chilled (4°C) fixed-angle centrifuge. After centrifugation, supernatant was aspirated and cell pellets were then resuspended in 50 μl of ATAC-seq RSB containing 0.1% IGEPAL, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without IGEPAL and digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 rcf in a pre-chilled (4°C) fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50 uL transposition mix (2x TD Buffer, 100 nM final transposase, 16.5 uL PBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, 5 uL H2O) (Illumina Tagment DNA Enzyme and Buffer Small Kit, 20034197). Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1000 rpm. Reactions were cleaned up with DNA Clean and Concentrator 5 columns (Zymo Research)
ATAC-Seq library preparation was performed according to the Omni-ATAC protocol. Illumina Nextera DNA Unique Dual Indexes Set C (Illumina, 20027215) were added and amplified (12 cycles) using NEBNext 2x MasterMix. Sequencing of the ATAC-Seq libraries was performed on the Illumina NovaSeq 6000 system using 100-bp paired-end sequencing.


title: C3H10T1-2_NSD1-2-SETD2-TKO_ATACseq_rep1_batch1


description:
Library name: SRTP0001978
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 7
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0001978_filtered_feature_bc_matrix.h5
CITE_donor_27678_day_7.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad

value: Day 7


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_ATACseq_rep2_batch1


description:
Library name: SRTP0001977
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 7
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0001977_filtered_feature_bc_matrix.h5
CITE_donor_32606_day_7.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad


description:
Library name: SRTP0001979
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 7
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0001979_filtered_feature_bc_matrix.h5
CITE_donor_31800_day_7.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_HiC


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_ATACseq_rep1_batch1


description:
Library name: SRAB0001966
CITE-seq ADT  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 2
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
CITE_donor_27678_day_2.h5mu
citeseq_protein_counts.h5ad
citeseq_alldonors_alldays.h5ad


title: C3H10T1-2_NSD1-2-3-SETD2-NSD1-2-3-SETD2-QKO_ATACseq_rep2_batch2


description:
Library name: SRTP0001975
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 4
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0001975_filtered_feature_bc_matrix.h5
CITE_donor_31800_day_4.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad


description:
Library name: SRTP0001973
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 4
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0001973_filtered_feature_bc_matrix.h5
CITE_donor_32606_day_4.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad


description:
Library name: SRTP0001974
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 4
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0001974_filtered_feature_bc_matrix.h5
CITE_donor_27678_day_4.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_ATACseq_rep2_batch2


description:
Library name: SRTP0001972
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 13176 at Day 4
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0001972_filtered_feature_bc_matrix.h5
CITE_donor_13176_day_4.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_ATACseq_rep1_batch2


description:
Library name: SRTP0001976
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 13176 at Day 7
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0001976_filtered_feature_bc_matrix.h5
CITE_donor_13176_day_7.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad


title: C3H10T1-2_NSD1-2-3-SETD2-NSD1-2-3-SETD2-QKO_ATACseq_rep1_batch2


title: C3H10T1-2_Parental_CUTandRUN_H3K9me3_rep2

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

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.

tag: cut&run antibody

value: H3K9me3 (Abcam, ab8898)


title: ILD2Ar2_HBECs_pool04_ADT

description:
Library name: ILD2-032_SRAB0001342
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.

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.

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


description:
Library name: SRTP0001971
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 3
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0001971_filtered_feature_bc_matrix.h5
CITE_donor_31800_day_3.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad


title: ILD2Ar2_HBECs_pool03_ADT

description:
Library name: ILD2-032_SRAB0001341
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: C3H10T1-2_Parental_CUTandRUN_H3K9me3_rep1


title: ILD2Ar2_HBECs_pool02_ADT

description:
Library name: ILD2-031_SRAB0001340
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: ILD2Ar2_HEK293_pool04_ADT

description:
Library name: ILD2-030_SRAB0001338
Perturbational single-cell screen with hashtag oligos. for cell line HEK293T, replicate2.


title: C3H10T1-2_Parental_CUTandRUN_H3K4me1_rep2

value: H3K4me1 (Cell Signaling, 5326S)


description:
Library name: SRTP0001969
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 3
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0001969_filtered_feature_bc_matrix.h5
CITE_donor_32606_day_3.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad

value: donor 32606


title: ILD2Ar2_HEK293_pool03_ADT

description:
Library name: ILD2-030_SRAB0001337
Perturbational single-cell screen with hashtag oligos. for cell line HEK293T, replicate2.


description:
Library name: SRTP0001968
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 13176 at Day 3
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0001968_filtered_feature_bc_matrix.h5
CITE_donor_13176_day_3.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad

value: donor 13176


title: ILD2Ar2_HEK293_pool02_ADT

description:
Library name: ILD2-029_SRAB0001336
Perturbational single-cell screen with hashtag oligos. for cell line HEK293T, replicate2.


title: ILD2Ar2_HEK293_pool01_ADT

description:
Library name: ILD2-029_SRAB0001335
Perturbational single-cell screen with hashtag oligos. for cell line HEK293T, replicate2.


title: C3H10T1-2_Parental_CUTandRUN_H3K27me3_rep2

value: H3K27me3 (Cell Signaling, 9733)


title: DrugSeq12_96well_hCD8_v1_row7_ADT

description:
Library name: ILD1-021_SRAB0000699
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate1.

value: ILD1-021, completed on 3/4/2021


description:
Library name: SRTP0001967
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 31800 at Day 2
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0001967_filtered_feature_bc_matrix.h5
CITE_donor_31800_day_2.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad

value: donor 31800

value: Day 2


description:
Library name: SRTP0001966
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 2
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0001966_filtered_feature_bc_matrix.h5
CITE_donor_27678_day_2.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad

value: donor 27678


title: C3H10T1-2_Parental_CUTandRUN_H3K27me3_rep1

value: fibroblast

value: parental


title: C3H10T1-2_NSD1-2-SETD2-TKO_CUTandRUN_H3K4me1_rep2


title: DrugSeq11_96well_hCD34_v1_row6_ADT

description:
Library name: ILD1-020_SRAB0000667
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: DrugSeq11_96well_hCD34_v1_row5_ADT

description:
Library name: ILD1-020_SRAB0000666
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: DrugSeq12_96well_hCD8_v1_row5_ADT

description:
Library name: ILD1-021_SRAB0000697
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate1.


title: DrugSeq12_96well_hCD8_v1_row4_ADT

description:
Library name: ILD1-013_SRAB0000696
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate1.

value: ILD1-013, completed on 3/4/2021


title: DrugSeq12_96well_hCD8_v1_row3_ADT

description:
Library name: ILD1-013_SRAB0000695
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate1.


description:
Library name: SRTP0001965
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 32606 at Day 2
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0001965_filtered_feature_bc_matrix.h5
CITE_donor_32606_day_2.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad

value: peripheral blood

value: CD34-positive hematopoietic stem and progenitor cell


title: ILD2Ar2_HBECs_pool01_ADT

description:
Library name: ILD2-031_SRAB0001339
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: DrugSeq11_96well_hCD34_v1_row7_ADT

description:
Library name: ILD1-020_SRAB0000668
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


description:
Library name: SRTP0001970
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 27678 at Day 3
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0001970_filtered_feature_bc_matrix.h5
CITE_donor_27678_day_3.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad

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

value: Day 3


title: C3H10T1-2_NSD1-2-SETD2-TKO_CUTandRUN_H3K27me3_rep2


description:
Library name: SRTP0001964
CITE-seq GEX  library from mobilized peripheral CD34+ HSPC donor 13176 at Day 2
10x Genomics Single Cell Gene Expression with Feature Barcoding technology (CITE-seq) using TotalSeq-B Human Universal Cocktail V1.0. Time course analysis of mobilized peripheral CD34+ hematopoietic stem and progenitor cells cultured in StemSpan SFEM media with CC100 and TPO. Cells collected at day 2 of 10-day culture period. Cell types include HSC, MasP, MkP, NeuP, MoP, EryP, and BP based on preliminary annotation.
SRTP0001964_filtered_feature_bc_matrix.h5
CITE_donor_13176_day_2.h5mu
citeseq_rna_counts.h5ad
rna_combined_with_velocity_and_refined_annotations.h5ad
citeseq_alldonors_alldays.h5ad


title: Detroit562_H3K36M_OE_HiC

description: Library name: HiC_sample_7

data_processing:
Raw Hi-C reads were trimmed of adapter sequences using Fastp v0.23.3 and aligned to the mm10 or hg38 assembly using BWA v.0.7.17 with default parameters. Afterwards, ligation junctions (Hi-C pairs) were identified in aligned paired-end sequences using Pairtools v1.1.0. The restriction enzyme specified to Pairtools was the Arima kit, which uses the two restriction enzymes: DpnII and HinfI. Duplicated reads were marked using ‘pairtools dedup’ with the parameters: “--mark-dups --backend cython --output-stats $SAMPLE.stats -o $SAMPLE.dedup.pairs.gz”. Then, duplicated reads were removed and only uniquely-mapped reads were selected using ‘pairtools select’ with the parameters: “--chrom-subset mm10.canon.chroms '(rfrag1!=rfrag2) and ((pair_type=="UU" or pair_type=="RU" or pair_type=="UR"))' -o $SAMPLE.pairs.gz ${samp}.dedup.pairs.gz’. Junctions were subsequently binned and counted using Cooler v0.10.0, in which pairs (.pairs.gz) files were converted to a cooler (.cool) file using “cooler cload pairix --assembly mm10 mm10.canon.sizes:1000 $SAMPLE.pairs.gz $SAMPLE.1000.cool”. The cooler file underwent matrix balancing using “cooler balance $SAMPLE.1000.cool --blacklist $BLACKLIST.bed”. The matrix was then binned into different window sizes contained within a single multi-resolution cooler (.mcool) file using “cooler zoomify --out $SAMPLE.mcool --resolutions 1000,5000,10000,25000,50000,100000,250000,500000,1000000,2500000 --balance --balance-args --max-iters 1000 $SAMPLE.1000.cool”.
Assembly: mm10 for C3H10T1/2, hg38 for Cal27 and Detroit562
Supplementary files format and content: multi-resolution Hi-C contact maps (.mcool)

growth_protocol: C3H10T1/2 mouse mesenchymal stem cells (ATCC) were cultured in DMEM with 10% fetal bovine serum (FBS,) and supplemented with 1% GlutaMax. Cal27 (ATCC, CRL-2095) and Detroit562 (ATCC, CCL-138) HNSCC cells were cultured in DMEM (F12) (Invitrogen) with 10% FBS and penicillin-streptomycin. Epitope-tagged H3.3 was previously cloned into pCDH-EF1-MCS-Puro lentiviral vector and site-directed mutagenesis techniques were used to generate the H3K36M mutation. To produce lentivirus, 293T cells were transfected with a lentiviral vector containing H3.3K36M (provided by Dr. Chao Lu) and helper plasmids (psPAX2 and pMD2.G). Supernatant containing lentivirus was collected after 48h, filtered and used to infect Cal27 and Detroit562 cells. Transduced cells were grown under puromycin selection (1 μg/ml) for 48 h after transduction.

extract_protocol:
C3H10T1/2 mouse mesenchymal stem and HNSCC cells (two million cells per sample) were crosslinked and processed using the Arima-HiC+ kit and following the Arima Genomics HiC protocol for Mammalian Cell Lines (A510008). Proximally-ligated DNA was fragmented to an average size of 400 bp using the BioRuptor UCS-300 at low intensity for 10 cycles (30s ON, 90s OFF).
Library preparation of fragmented proximally-ligated DNA was performed using the NEBNext® Ultra™ II DNA Library Prep Kit (E7645S), NEBNext Multiplex Oligos for Illumina (E6440S), and the Arima HiC+ Kit according to manufacturer protocols. Hi-C libraries were sequenced by the McGill University Genome Centre at 150 bp paired-end reads using the Illumina NovaSeq 6000.

value: patient-derived head and neck squamous cell carcinoma cell line

value: Arima


title: DrugSeq11_96well_hCD34_v1_row4_ADT

description:
Library name: ILD1-011_SRAB0000665
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.

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


title: DrugSeq12_96well_hCD8_v1_row2_ADT

description:
Library name: ILD1-013_SRAB0000694
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate1.


title: DrugSeq12_96well_hCD8_v1_row1_ADT

description:
Library name: ILD1-013_SRAB0000693
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate1.


title: C3H10T1-2_NSD1-2-SETD2-TKO_CUTandRUN_H3K27me3_rep1


title: C3H10T1-2_Parental_CUTandRUN_H3K4me1_rep1

value: H3K4me1 (Cell Signaling, 5326S)


title: Detroit562_Parental_HiC

description: Library name: HiC_sample_6


title: DrugSeq12_96well_hCD8_v1_row6_ADT

description:
Library name: ILD1-021_SRAB0000698
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate1.


title: DrugSeq11_96well_hCD34_v1_row3_ADT

description:
Library name: ILD1-011_SRAB0000664
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: Cal27_H3K36M_OE_HiC

description: Library name: HiC_sample_5


title: DrugSeq11_96well_hCD34_v1_row1_ADT

description:
Library name: ILD1-011_SRAB0000662
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_CUTandRUN_H3K4me1_rep2


title: DrugSeq16_24well_BronchialEpithelium_v2_row1_ADT

description:
Library name: ILD1-010_SRAB0000747
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.

value: HBEC


title: DrugSeq11_96well_hCD34_v1_row2_ADT

description:
Library name: ILD1-011_SRAB0000663
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_CUTandRUN_H3K4me1_rep1


title: DrugSeq16_24well_BronchialEpithelium_v2_row2_ADT

description:
Library name: ILD1-010_SRAB0000746
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: DrugSeq16_24well_BronchialEpithelium_v2_row3_ADT

description:
Library name: ILD1-010_SRAB0000745
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: C3H10T1-2_NSD1-2-SETD2-TKO_CUTandRUN_H3K4me1_rep1


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_CUTandRUN_H3K27me3_rep2

value: H3K27me3 (Cell Signaling, 9733)


title: Cal27_Parental_HiC_rep1

description: Library name: HiC_sample_3


title: Cal27_Parental_HiC_rep2

description: Library name: HiC_sample_4


title: DrugSeq16_24well_BronchialEpithelium_v2_row4_ADT

description:
Library name: ILD1-010_SRAB0000744
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: Detroit562_H3K36M_OE_ATACseq_rep2

description: Library name: ATACseq_sample_30

data_processing:
Raw ATAC-seq reads were trimmed and filtered for quality using Trimmomatic v0.39 with default parameters. Trimmed reads were mapped to the mm10 or hg38 genome assembly using Bowtie2 v2.5.1 using default parameters. Afterwards, the reads were adjusted by shifting all positive-strand reads 4 bp downstream and all negative-strand reads 5 bp upstream to the center of the reads on the transposase binding event. Peak calling was performed on each replicate using MACS2 v2.2.6 with ‘-extsize 200 -shift -100 -nomodel’ parameters. To find a set of reproducible peaks across replicates, we calculated the irreproducible discovery rate (IDR) and excluded peaks with an IDR greater than 0.05 across every pair of replicates. Subsequently, the ENCODE blacklist was used to filter the peaks. Coverage tracks were generated using bamCoverage from deepTools v3.3.1 with parameters ‘-b $BAM -o $OUTPUT.bigWig --normalizeUsing CPM --centerReads -e 200 --minMappingQuality 5 -bs 10’’.
Assembly: mm10 for C3H10T1/2, hg38 for Cal27 and Detroit562
Supplementary files format and content: bigWig

extract_protocol:
50,000 cultured cells were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at 500 rcf for 5 min in a pre-chilled (4°C) fixed-angle centrifuge. After centrifugation, supernatant was aspirated and cell pellets were then resuspended in 50 μl of ATAC-seq RSB containing 0.1% IGEPAL, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without IGEPAL and digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 rcf in a pre-chilled (4°C) fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50 uL transposition mix (2x TD Buffer, 100 nM final transposase, 16.5 uL PBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, 5 uL H2O) (Illumina Tagment DNA Enzyme and Buffer Small Kit, 20034197). Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1000 rpm. Reactions were cleaned up with DNA Clean and Concentrator 5 columns (Zymo Research)
ATAC-Seq library preparation was performed according to the Omni-ATAC protocol. Illumina Nextera DNA Unique Dual Indexes Set C (Illumina, 20027215) were added and amplified (12 cycles) using NEBNext 2x MasterMix. Sequencing of the ATAC-Seq libraries was performed on the Illumina NovaSeq 6000 system using 100-bp paired-end sequencing.


title: DrugSeq16_24well_BronchialEpithelium_v2_row5_ADT

description:
Library name: ILD1-010_SRAB0000743
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: DrugSeq16_24well_BronchialEpithelium_v2_row6_ADT

description:
Library name: ILD1-010_SRAB0000742
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_CUTandRUN_c1_H3K9me3_rep1

value: H3K9me3 (Abcam, ab8898)


title: DrugSeq10_24well_hBronchialEpithelium_v1_row6_ADT

description:
Library name: ILD1-009_SRAB0000661
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: Detroit562_Parental_ATACseq_rep2

description: Library name: ATACseq_sample_28


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_CUTandRUN_c1_H3K9me3_rep2


title: DrugSeq10_24well_hBronchialEpithelium_v1_row2_ADT

description:
Library name: ILD1-009_SRAB0000657
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: Detroit562_Parental_ATACseq_rep1

description: Library name: ATACseq_sample_27


title: DrugSeq10_24well_hBronchialEpithelium_v1_row4_ADT

description:
Library name: ILD1-009_SRAB0000659
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_CUTandRUN_H3K9me3_rep1


title: DrugSeq10_24well_hBronchialEpithelium_v1_row5_ADT

description:
Library name: ILD1-009_SRAB0000660
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: Detroit562_H3K36M_OE_ATACseq_rep1

description: Library name: ATACseq_sample_29


title: DrugSEQ06_24well_PC3_Replicate2_row5_ADT

description:
Library name: ILD1-008_SRAB0000609
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: Cal27_H3K36M_OE_ATACseq_rep1

description: Library name: ATACseq_sample_25


title: DrugSeq10_24well_hBronchialEpithelium_v1_row3_ADT

description:
Library name: ILD1-009_SRAB0000658
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_CUTandRUN_H3K9me3_rep2


title: DrugSEQ06_24well_PC3_Replicate2_row2_ADT

description:
Library name: ILD1-008_SRAB0000606
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: DrugSeq10_24well_hBronchialEpithelium_v1_row1_ADT

description:
Library name: ILD1-009_SRAB0000656
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_CUTandRUN_H3K27me3_rep1


title: DrugSEQ06_24well_PC3_Replicate2_row6_ADT

description:
Library name: ILD1-008_SRAB0000610
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_CUTandRUN_H3K4me1_rep2


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_CUTandRUN_H3K27me3_rep2


title: DrugSEQ06_24well_PC3_Replicate2_row3_ADT

description:
Library name: ILD1-008_SRAB0000607
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: DrugSEQ06_24well_PC3_Replicate2_row1_ADT

description:
Library name: ILD1-008_SRAB0000605
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: Cal27_H3K36M_OE_ATACseq_rep2

description: Library name: ATACseq_sample_26


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_CUTandRUN_H3K4me1_rep1


title: Cal27_Parental_ATACseq_rep2

description: Library name: ATACseq_sample_24


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_CUTandRUN_H3K27me3_rep1


title: DrugSEQ07_24well_HA1E_replicate2_row6_ADT

description:
Library name: ILD1-007_SRAB0000616
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.


title: DrugSEQ06_24well_PC3_Replicate2_row4_ADT

description:
Library name: ILD1-008_SRAB0000608
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: Cal27_Parental_ATACseq_rep1

description: Library name: ATACseq_sample_23


title: C57BL/6 female mice, treated with VCD, biological repeat 3

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.

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: female

tag: strain

value: VCD


title: DrugSEQ07_24well_HA1E_replicate2_row5_ADT

description:
Library name: ILD1-007_SRAB0000615
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.


title: DrugSEQ07_24well_HA1E_replicate2_row4_ADT

description:
Library name: ILD1-007_SRAB0000614
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.


title: LJR0179

city: Shanghai

first: Peng

last: Jin

address: Ruijin Rd. II

department: Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description:
Library name: AML_Patient_142
AML_Patient_142

data_processing:
Trim-galore was employed to remove the adapter sequences.
The clean reads were aligned with STAR and quantified with HT-Seq using the GRCh38 human assembly.
The differential expression assessment was conducted using the DESeq2 package.
Gene expression levels were normalized to Transcripts Per Kilobase of exon model per Million mapped reads (TPM) using a customed script.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw count values for each Sample.

source_name: Bone. Marrow

extract_protocol:
Bone marrow mononuclear cells from AML patients were isolated after Ficoll–Isopaque density gradient centrifugation. Genomic mRNA were extracted from the patients’ BM using the AllPrep PowerFecal RNA Kit in accordance with the manufacturer’s instructions.
Libraries were prepared using the KAPA RNA HyperPrep kit in accordance with the manufacturer’s instructions (KAPA). High-throughput sequencing was performed on the NovaSeq 6000 platform in accordance with the manufacturer’s protocol (paired-end 2 × 150 bp).

value: Bone. Marrow

value: Primary patient cells

tag: disease state

value: Acute Myeloid Leukemia

value: Aza-Ven

value: Cohort 2


title: DrugSEQ07_24well_HA1E_replicate2_row3_ADT

description:
Library name: ILD1-007_SRAB0000613
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.


title: DrugSEQ08_24well_A549_Replicate2_repeat_row2_ADT

description:
Library name: ILD1-006_SRAB0000633
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: DrugSEQ08_24well_A549_Replicate2_repeat_row1_ADT

description:
Library name: ILD1-006_SRAB0000632
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: C57BL/6 female mice, treated with VCD, biological repeat 4


title: LJR0174

description:
Library name: AML_Patient_137
AML_Patient_137


title: DrugSEQ07_24well_HA1E_replicate2_row1_ADT

description:
Library name: ILD1-007_SRAB0000611
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.


title: DrugSEQ08_24well_A549_Replicate2_repeat_row6_ADT

description:
Library name: ILD1-006_SRAB0000637
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: C57BL/6 female mice, treated with VCD, biological repeat 2


title: DrugSEQ08_24well_A549_Replicate2_repeat_row5_ADT

description:
Library name: ILD1-006_SRAB0000636
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: DrugSEQ08_24well_A549_Replicate2_repeat_row4_ADT

description:
Library name: ILD1-006_SRAB0000635
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: LJR0173

description:
Library name: AML_Patient_136
AML_Patient_136


title: LJR0178

description:
Library name: AML_Patient_141
AML_Patient_141


title: DrugSEQ07_24well_HA1E_replicate2_row2_ADT

description:
Library name: ILD1-007_SRAB0000612
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.


title: LJR0177

description:
Library name: AML_Patient_140
AML_Patient_140


title: DrugSEQ05_24well_A375_replicate2_row3_ADT

description:
Library name: ILD1-005_SRAB0000601
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.


title: C57BL/6 female mice, treated with vehicle control, biological repeat 1

value: Vehicle


title: DrugSEQ08_24well_A549_Replicate2_repeat_row3_ADT

description:
Library name: ILD1-006_SRAB0000634
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: LJR0172

description:
Library name: AML_Patient_135
AML_Patient_135


title: C57BL/6 female mice, treated with VCD, biological repeat 1


title: DrugSEQ01_24well_PC3_row6_ADT

description:
Library name: ILD1-004_SRAB0000498
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.

value: ILD1-004, completed on 11/3/20


title: LJR0175

description:
Library name: AML_Patient_138
AML_Patient_138


title: C57BL/6 female mice, treated with vehicle control, biological repeat 3


title: DrugSEQ05_24well_A375_replicate2_row6_ADT

description:
Library name: ILD1-005_SRAB0000604
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.


title: LJR0176

description:
Library name: AML_Patient_139
AML_Patient_139


title: DrugSEQ01_24well_PC3_row4_ADT

description:
Library name: ILD1-004_SRAB0000496
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: DrugSEQ05_24well_A375_replicate2_row4_ADT

description:
Library name: ILD1-005_SRAB0000602
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.


title: DrugSEQ05_24well_A375_replicate2_row2_ADT

description:
Library name: ILD1-005_SRAB0000600
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.


title: DrugSEQ01_24well_PC3_row3_ADT

description:
Library name: ILD1-004_SRAB0000495
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: LJR0169

description:
Library name: AML_Patient_132
AML_Patient_132


title: LJR0171

description:
Library name: AML_Patient_134
AML_Patient_134


title: DrugSEQ01_24well_PC3_row2_ADT

description:
Library name: ILD1-004_SRAB0000494
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: DrugSEQ05_24well_A375_replicate2_row1_ADT

description:
Library name: ILD1-005_SRAB0000599
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.


title: Esrra_shRNA_3F

description: C57BL/6 female mice, injected with ESRRA shRNA in the left dorsal hippocampus and the medial prefrontal cortex. Transduced tissues were harvested using GFP signals under the microscope; Esrra shRNA Sample 3

source_name: Transduced tissues from left dorsal hippocampus and the medial prefrontal cortex

treatment_protocol: AAV9 viral particles containing hSyn-EGFP-MIR-ESRRA shRNA shuttle and scrambled control were purchased from Shanghai GeneChem. P30-P45 mice were anesthetized with isoflurane (2–5%) (RWD life Science Co, Shanghai, China) and had their scalp immobilized in a stereotaxic apparatus (RWD). After a precise craniotomy, the AAV was loaded in a Hamilton syringe, which was slowly targeted for injection into the dorsal hippocampus CA2 (Left: M/L: −1.70 mm, A/P: − 1.55 mm, D/V: − 1.70 mm) and the medial prefrontal cortex (Left: M/L: −0.5 mm, A/P: 2.10, D/V: −2.0 mm). 1012 vg/ml (~100 nl) AAV particles were injected with a syringe pump (KD Scientific, Holliston, USA) into the targeted region at 10 nl/min. The needle was gradually withdrawn 20 min after injection. To prevent hypothermia after anaesthesia, the mice were positioned on a heating pad through the procedure until fully awake. The injected mice were monitored daily for recovery status, body weight and infection. Mice were allowed to recover for 30 days prior any behavioural tests and for tissue collection.

value: Esrra shRNA


title: LJR0167

description:
Library name: AML_Patient_130
AML_Patient_130


title: Control_shRNA_3F

description: C57BL/6 female mice, injected with scrambled shRNA in the left dorsal hippocampus and the medial prefrontal cortex. Transduced tissues were harvested using GFP signals under the microscope; Control Sample 3

value: Transduced tissues from left dorsal hippocampus and the medial prefrontal cortex

value: Scrambled shRNA


title: drugSEQ04_24well_HA1Ev2_row3_ADT

description:
Library name: ILD1-003_SRAB0000562
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: DrugSEQ05_24well_A375_replicate2_row5_ADT

description:
Library name: ILD1-005_SRAB0000603
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.


title: C57BL/6 female mice, treated with vehicle control, biological repeat 2


title: Esrra_shRNA_2F

description: C57BL/6 female mice, injected with ESRRA shRNA in the left dorsal hippocampus and the medial prefrontal cortex. Transduced tissues were harvested using GFP signals under the microscope; Esrra shRNA Sample 2


title: DrugSEQ01_24well_PC3_row5_ADT

description:
Library name: ILD1-004_SRAB0000497
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: LJR0170

description:
Library name: AML_Patient_133
AML_Patient_133


title: Esrra_shRNA_1F

description: C57BL/6 female mice, injected with ESRRA shRNA in the left dorsal hippocampus and the medial prefrontal cortex. Transduced tissues were harvested using GFP signals under the microscope; Esrra shRNA Sample 1


title: drugSEQ04_24well_HA1Ev2_row2_ADT

description:
Library name: ILD1-003_SRAB0000561
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: DrugSEQ01_24well_PC3_row1_ADT

description:
Library name: ILD1-004_SRAB0000493
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: Control_shRNA_4F

description: C57BL/6 female mice, injected with scrambled shRNA in the left dorsal hippocampus and the medial prefrontal cortex. Transduced tissues were harvested using GFP signals under the microscope; Control Sample 4


title: drugSEQ04_24well_HA1Ev2_row6_ADT

description:
Library name: ILD1-003_SRAB0000565
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: drugSEQ04_24well_HA1Ev2_row1_ADT

description:
Library name: ILD1-003_SRAB0000560
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: DrugSEQ02_24well_A549_row5_ADT

description:
Library name: ILD1-002_SRAB0000503
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.


title: LJR0168

description:
Library name: AML_Patient_131
AML_Patient_131


title: drugSEQ04_24well_HA1Ev2_row5_ADT

description:
Library name: ILD1-003_SRAB0000564
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: DrugSEQ02_24well_A549_row4_ADT

description:
Library name: ILD1-002_SRAB0000502
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.


title: LJR0163

description:
Library name: AML_Patient_126
AML_Patient_126


title: DrugSEQ02_24well_A549_row3_ADT

description:
Library name: ILD1-002_SRAB0000501
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.


title: DrugSEQ02_24well_A549_row2_ADT

description:
Library name: ILD1-002_SRAB0000500
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.


title: drugSEQ04_24well_HA1Ev2_row4_ADT

description:
Library name: ILD1-003_SRAB0000563
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: Control_shRNA_2F

description: C57BL/6 female mice, injected with scrambled shRNA in the left dorsal hippocampus and the medial prefrontal cortex. Transduced tissues were harvested using GFP signals under the microscope; Control Sample 2


title: LJR0165

description:
Library name: AML_Patient_128
AML_Patient_128


title: Control_shRNA_1F

description: C57BL/6 female mice, injected with scrambled shRNA in the left dorsal hippocampus and the medial prefrontal cortex. Transduced tissues were harvested using GFP signals under the microscope; Control Sample 1


title: DrugSEQ03_24well_A375v2_row6_ADT

description:
Library name: ILD1-001_SRAB0000511
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.


title: DrugSEQ02_24well_A549_row6_ADT

description:
Library name: ILD1-002_SRAB0000504
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.


title: LG321_59

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

description: mRNA expression in mouse hippocampus

data_processing:
Gene counts were obtained by aligning reads to the mouse genome (mm10) with Cell Ranger software (v.3.1.0) (10× Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than two cells, cells with a unique gene count over 8000 or less than 300, and cells with a high fraction of mitochondrial reads (>5%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Seurat v3.0.182 R package used for analysis
Assembly: mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

molecule: nuclear RNA

source_name: hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

value: hippocampus

value: Female

tag: age

value: DAP12 KO:-/-;PSUK:Tg/Tg


title: DrugSEQ03_24well_A375v2_row5_ADT

description:
Library name: ILD1-001_SRAB0000510
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.


title: LJR0164

description:
Library name: AML_Patient_127
AML_Patient_127


title: LG321_NY_54

description: mRNA expression in mouse hippocampus


title: DrugSEQ02_24well_A549_row1_ADT

description:
Library name: ILD1-002_SRAB0000499
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.


title: LJR0162

description:
Library name: AML_Patient_125
AML_Patient_125


title: LG321_NY_60

description: mRNA expression in mouse hippocampus

value: DAP12 KO:+/+;PSUK:Tg/Tg


title: LJR0161

description:
Library name: AML_Patient_124
AML_Patient_124


title: DrugSEQ03_24well_A375v2_row4_ADT

description:
Library name: ILD1-001_SRAB0000509
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.


title: LG321_NY_68

description: mRNA expression in mouse hippocampus


title: DrugSEQ03_24well_A375v2_row3_ADT

description:
Library name: ILD1-001_SRAB0000508
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.