title: p39_post

city: Frederick

last: Chen

state: MD

address: 8560 Progress Drive

institute: Frederick National Laboratory

description: Library name: 69_662_RNA

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (hg38) and the annotated transcripts using STAR.
Assembly: hg38
Supplementary files format and content: RSEM counts and TXT format

source_name: Ovarian tumor

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) with on-column DNase treatment.
RNA samples were pooled and sequenced on NovaSeq Xplus 1.5B using Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus and paired-end sequencing.

value: Ovarian tumor


title: T24 LPS + Nigericin replicate 3

status: Public on Feb 06 2026

type: SRA

city: Houston

first: Stephen

middle: Qi Rong

last: Wong

state: Texas

address: 6670 Bertner Ave

country: USA

institute: Houston Methodist

description: Library name: SW9

library_source: transcriptomic

data_processing:
Raw sequencing files (.fastq) and mapped sequencing files (.bam) were prepared by LC Sciences (Houston, TX) to generate gene count matrix.
Assembly: hg38
Supplementary files format and content: gene count table in excel format

molecule: total RNA

organism: Homo sapiens

growth_protocol: T24 cells are grown in standard cell culture conditions in DMEM high glucose media supplemented with 1% pen-strep.

extract_protocol:
Cells were washed twice with ice-cold PBS before being scrapped in sufficient volume of PBS. Cell are palleted and sent to Novogene USA for RNA extraction and sequencing.
T24 cells were submitted to LC Sciences (Houston, TX) for RNA extraction and library construction.

treatment_protocol: As described in manuscript.

tag: cell line

tag: cell type

value: Epithelial


title: T24 LPS + Nigericin replicate 2

description: Library name: SW8


title: p157_post

first: Jack

description: Library name: 78_2705_1_RNA

tag: tissue


title: Fy11_Day7

city: Chicago

first: Joao

last: Barroso-Batista

state: IL

address: The University of Chicago, KCBD room 9220E, 900 E 57th Street

institute: The University of Chicago

description: Library name: SPF4.RFy11.Day7

data_processing:
reads were trimmed with trimmomatic to remove adapter sequence and trailing bases with a quality score less than 20
trimmed reads were mapped to the rhesus macaque genome (RheMac8) using the STAR v2.7.10ac two-pass method
read counts were generated for each gene using HTCseq v2.0 based on overlap of any part of a read with an annotated gene exon
Assembly: RheMac8
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

organism: Macaca mulatta

source_name: blood

extract_protocol:
RNA was extracted using miRNAeasy kit (Qiagen). 300 ng of RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep kit (Illumina) according to the manufacturer’s protocol

value: blood

value: PBMCs

tag: treatment

value: Influenza vaccination


title: Fy11_Day3

description: Library name: SPF4.RFy11.Day3


title: T24 LPS + Nigericin replicate 1

description: Library name: SW7


title: p220_post

description: Library name: 74_7401_RNA


title: p211_post

description: Library name: 73_6810_RNA


title: T24 Vehicle replicate 3

description: Library name: SW3


title: p224_post

description: Library name: 75_7622_RNA


title: p90_post

description: Library name: 71_1905_RNA


title: Fy11_Day1

description: Library name: SPF4.RFy11.Day1


title: T24 Vehicle replicate 2

description: Library name: SW2


title: p40_post

description: Library name: 70_665_RNA


title: p99_post

description: Library name: 72_1980_RNA


title: Fy11_Day0

description: Library name: SPF4.RFy11.Day0


title: p182_post

description: Library name: 45_5804_RNA


title: Yr14_Day7

description: Library name: SPF3.RYr14.Day7


title: p161_post

description: Library name: 41_2906_RNA


title: p133_post

description: Library name: 38_9404_RNA


title: p178_post

description: Library name: 43_5605_RNA


title: Yr14_Day3

description: Library name: SPF3.RYr14.Day3


title: p173_post

description: Library name: 42_5504_RNA


title: T24 Vehicle replicate 1

description: Library name: SW1


title: p23_post

description: Library name: 77_411_1_RNA


title: p140_post

description: Library name: 39_9606_RNA


title: Healthy human control

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

description:
Library name: A18-43
FFPE spatial transcrptome sequencing

data_processing:
CellRanger V8 was used to process raw sequencing and imagry to produce RNA expression
Seurat V5 was used to process RNA expression and images
Standard T tests using FindMarkers was used all statistical analyses
Differential gene lists were imported into Ingenuity Pathway Analysis to draw biological inferences
Assembly: GRCh38
Supplementary files format and content: ./276A_aligned_fiducials.jpg - list of spatial barcodes
Supplementary files format and content: ./276A_barcodes.tsv.gz - list of gene IDs
Supplementary files format and content: ./276A_detected_tissue_image.jpg - gene expression count data in Matrix Market Exchange format
Supplementary files format and content: ./276A_features.tsv.gz - aligned fiducials of the tissue image
Supplementary files format and content: ./276A_matrix.mtx.gz - image of tissue and spots
Supplementary files format and content: ./276A_scalefactors_json.json.- scale factors on json format
Supplementary files format and content: ./276A_tissue_hires_image.png - hi-res image of the tissue
Supplementary files format and content: ./276A_tissue_lowres_image.png - low-res image of the tissue
Supplementary files format and content: ./276A_tissue_positions.csv - list of  barcodes and spatial positions
Library strategy: Spatial Transcriptomics

source_name: Hippocampus on autopsy

extract_protocol: 10X library using standard 3' processing on 10X Cytassist machine

value: Hippocampus on autopsy


title: p109_post

description: Library name: 36_8005_RNA


title: Yr14_Day0

description: Library name: SPF3.RYr14.Day0


title: p179_post

description: Library name: 44_5704_RNA


title: p150_post

description: Library name: 40_9904_RNA


title: p39_pre

description: Library name: 47_651_RNA


title: Drug Resistant Mesial Temporal Lobe Epilepsy (MTLE) with Hippocampal Sclerosis (HS)

description:
Library name: EP-276A
FFPE spatial transcrptome sequencing


title: Yr14_Day1

description: Library name: SPF3.RYr14.Day1


title: p107_post

description: Library name: 35_7007_RNA


title: p211_pre

description: Library name: 62_6800_RNA


title: p123_post

description: Library name: 37_9005_RNA


title: Vt12_Day1

description: Library name: SPF3.RVt12.Day1


title: p222_pre

description: Library name: 67_7502_RNA


title: p23_pre

description: Library name: 79_PRST_RNA


title: p116_pre

description: Library name: 53_8701_RNA


title: Vt12_Day7

description: Library name: SPF3.RVt12.Day7


title: Vt12_Day3

description: Library name: SPF3.RVt12.Day3


title: Vt12_Day0

description: Library name: SPF3.RVt12.Day0


title: p157_pre

description: Library name: 76_2701_2_RNA


title: p43_pre

description: Library name: 49_702_RNA


title: p220_pre

description: Library name: 65_7301_RNA


title: p207_pre

description: Library name: 60_6501_RNA


title: Mi12_Day3

description: Library name: SPF3.RMi12.Day3


title: p224_pre

description: Library name: 68_7601_RNA


title: Mi12_Day1

description: Library name: SPF3.RMi12.Day1


title: p166_pre

description: Library name: 54_5200_RNA


title: p209_pre

description: Library name: 61_6700_RNA


title: p204_pre

description: Library name: 58_6251_RNA


title: 786-O_H3K27ac_HiChIP

city: Boston

first: Jeremy

last: Simon

state: MA

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

description: Library name: 786-O_H3K27ac_HiChIP

library_source: genomic

data_processing:
ChIP-seq data for HKC8 (STAT3, H3K4me1, H3K4me3, H3K27ac, input control) and 786-O (STAT3, IgG control) were processed with nf-core/chipseq v2.1.0 using the hg38 reference and GENCODE v43 gene annotations. Default parameters were used except that MACS3 additionally specified “--keep-dup all --nomodel --extsize 147” for peak calling.
H3K27ac HiChIP data were first processed with nf-core/hic using pairtools processing mode (available from https://github.com/nservant/nf-core-hic/tree/dev) with “--no_digestion --min_cis_dist 1000” and bin sizes ranging from 1 Kb to 1 Mb. The 5 Kb contact maps were then used as input for FitHiChIP v11.0 alongside H3K27ac ChIP-seq consensus peaks from GSE102095 as identified above, running in Peak-to-Peak mode with the following parameters: BINSIZE=5000, LowDistThr=5000, UppDistThr=2000000, UseP2PBackgrnd=1, BiasType=2, MergeInt=1, QVALUE=0.1.
Assembly: hg38
Supplementary files format and content: bigWig of ChIP-seq data scaled by sequencing depth
Supplementary files format and content: cooler file of HiChIP contacts at 5kb resolution, bedpe of significant loops
Library strategy: HiChIP

molecule: genomic DNA

growth_protocol: 786-O, HKC8 cells were purchased from the American Type Culture Collection (ATCC). The cell lines used in this study were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco) high glucose medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin unless specifically indicated. All cells were cultured in a humidified incubator at 37 °C with 5% CO2. All cells were tested negative for mycoplasma by using the mycoplasma detectionkit (Lonza, LT07–218) or mycoplasma elimination reagent-plasmocin (Invivogen, ant-mpt).

extract_protocol:
Immunoprecipitation was performed by incubating chromatin with specific antibodies: STAT3 (CST, 9139), H3K4me1 (Abcam, ab8895), H3K4me3 (Abcam, ab8580), and H3K27ac (Abcam, ab4729), using Protein G magnetic beads at 4°C overnight with rotation. The samples were washed, collected using a magnetic stand, and eluted for cross-link reversal. Proteinase K (Sigma, 3115828001) was used for protein degradation, and RNAse A (Sigma, 70856-3) for RNA degradation. DNA was purified using the Qiagen PCR purification kit (Qiagen, 28106). For HiChIP, Chromatin fragments were incubated with anti-H3K27ac antibody (Cell Signaling Technology, 8173) overnight at 4°C for chromatin immunoprecipitation. The antibody-protein-DNA complex was pulled down with protein A/G-coated magnetic beads. Chromatin ends were repaired and ligated to a biotinylated bridge adapter followed by proximity ligation of adapter containing ends. After proximity ligation, crosslinks were reversed, and the DNA was purified from proteins and converted into a sequencing library.
For ChIP-seq, libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S) and sequenced at the McDermott Center Next Generation Sequencing Core at UT Southwestern. For HiChIP, the sequencing library was generated using Illumina-compatible adapters. Biotin-containing fragments were isolated using streptavidin beads before PCR enrichment of the library. The library was sequenced on Illumina Novaseq platform with paired-end sequencing at 300 million reads per sample.

treatment_protocol: ChIP (Chromatin immunoprecipitation) was performed using SimpleChIP Enzymatic Chromatin IP Kit (CST #9003). Briefly, cells were cross-linked with 1% formaldehyde, followed by treatment with 10X glycine to quench the reaction. Cells were lysed in lysis buffer (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton x-100) and sonicated with a BioRuptor to shear chromatin. The HiChIP experiment was outsourced to Dovetail Genomics (Cantata Bio, LLC) and performed per their established protocol. Briefly, approximately 10 million 786-O cells were collected, and chromatin was subsequently fixed with 3 mM disuccinimidyl glutarate (DSG), followed by another fixation with 1% formaldehyde. The fixed chromatin was digested in situ with micrococcal nuclease (MNase) and then extracted with RIPA lysis buffer.

tag: chip antibody

tag: replicate


title: HKC8_STAT3_ChIP_Rep2

description: Library name: HKC8_STAT3_ChIP_Rep2

data_processing:
ChIP-seq data for HKC8 (STAT3, H3K4me1, H3K4me3, H3K27ac, input control) and 786-O (STAT3, IgG control) were processed with nf-core/chipseq v2.1.0 using the hg38 reference and GENCODE v43 gene annotations. Default parameters were used except that MACS3 additionally specified “--keep-dup all --nomodel --extsize 147” for peak calling.
H3K27ac HiChIP data were first processed with nf-core/hic using pairtools processing mode (available from https://github.com/nservant/nf-core-hic/tree/dev) with “--no_digestion --min_cis_dist 1000” and bin sizes ranging from 1 Kb to 1 Mb. The 5 Kb contact maps were then used as input for FitHiChIP v11.0 alongside H3K27ac ChIP-seq consensus peaks from GSE102095 as identified above, running in Peak-to-Peak mode with the following parameters: BINSIZE=5000, LowDistThr=5000, UppDistThr=2000000, UseP2PBackgrnd=1, BiasType=2, MergeInt=1, QVALUE=0.1.
Assembly: hg38
Supplementary files format and content: bigWig of ChIP-seq data scaled by sequencing depth
Supplementary files format and content: cooler file of HiChIP contacts at 5kb resolution, bedpe of significant loops


title: Mi12_Day7

description: Library name: SPF3.RMi12.Day7


title: p215_pre

description: Library name: 63_7102_RNA


title: p59_pre

description: Library name: 50_151_RNA


title: Mi12_Day0

description: Library name: SPF3.RMi12.Day0


title: HKC8_STAT3_ChIP_Rep1

description: Library name: HKC8_STAT3_ChIP_Rep1


title: p171_pre

description: Library name: 56_5402_RNA


title: Ga13_Day3

description: Library name: SPF3.RGa13.Day3


title: Ga13_Day7

description: Library name: SPF3.RGa13.Day7


title: p168_pre

description: Library name: 55_5300_RNA


title: p90_pre

description: Library name: 51_1900_RNA


title: Ga13_Day1

description: Library name: SPF3.RGa13.Day1


title: HKC8_ChIP_input_Rep1

description: Library name: HKC8_ChIP_input_Rep1

value: input control


title: HKC8_ChIP_input_Rep2

description: Library name: HKC8_ChIP_input_Rep2


title: p99_pre

description: Library name: 52_1976_RNA


title: p221_pre

description: Library name: 66_7350_RNA


title: HKC8_H3K4me3_ChIP_Rep2

description: Library name: HKC8_H3K4me3_ChIP_Rep2


title: p206_pre

description: Library name: 59_6402_1_RNA


title: Ga13_Day0

description: Library name: SPF3.RGa13.Day0


title: p40_pre

description: Library name: 48_657_RNA


title: p219_pre

description: Library name: 64_7251_RNA


title: HKC8_H3K4me1_ChIP_Rep2

description: Library name: HKC8_H3K4me1_ChIP_Rep2


title: HKC8_H3K4me1_ChIP_Rep1

description: Library name: HKC8_H3K4me1_ChIP_Rep1


title: p154_pre

description: Library name: 11_2200_RNA


title: Bw12_Day1

description: Library name: SPF3.RBw12.Day1


title: p135_pre

description: Library name: 6_9500_RNA


title: HKC8_H3K4me3_ChIP_Rep1

description: Library name: HKC8_H3K4me3_ChIP_Rep1


title: HKC8_H3K27ac_ChIP_Rep2

description: Library name: HKC8_H3K27ac_ChIP_Rep2


title: Bw12_Day7

description: Library name: SPF3.RBw12.Day7


title: Bw12_Day0

description: Library name: SPF3.RBw12.Day0


title: p24_pre

description: Library name: 46_401_RNA


title: p202_pre

description: Library name: 34_6100_RNA


title: p231_pre

description: Library name: 31_7802_RNA


title: Bw12_Day3

description: Library name: SPF3.RBw12.Day3


title: HKC8_H3K27ac_ChIP_Rep1

description: Library name: HKC8_H3K27ac_ChIP_Rep1


title: p182_pre

description: Library name: 18_5801_RNA


title: Kk13_Day7

description: Library name: SPF2.RKk13.Day7


title: p223_pre

description: Library name: 27_7552_RNA


title: p229_pre

description: Library name: 29_7700_RNA


title: HM3

city: Wilmington

first: Uciel

last: Chorostecki

state: Delaware

address: 251 Little Falls Drive

institute: Kresko RNA Tech

description: Library name: Sample 3

data_processing:
Adapter sequences were trimmed with cutadapt; reads were quality-filtered with FASTQC; alignment was performed using bowtie2 against curated sRNA references (tRNA, yRNA, rRNA, miRNA). Unknown reads were aligned to GRCh38 or Bos taurus genome with HISAT2.
Assembly: GRCh38 (human) and Bos taurus UMD3.1 assemblies.
Supplementary files format and content: All results described in the manuscript were derived from raw sequencing data.

source_name: Human skim milk sample from healthy lactating donor (3)

extract_protocol:
Skim milk was centrifuged and filtered to remove cells and fat. Total RNA was extracted from the cell-free supernatant using TRIzol reagent following the manufacturer’s protocol
Small RNA libraries were prepared using Illumina TruSeq Small RNA Library Prep Kit, following the manufacturer’s instructions.

value: milk

tag: batch


title: p178_pre

description: Library name: 16_5602_RNA


title: HM2

description: Library name: Sample 2

source_name: Human skim milk sample from healthy lactating donor (2)


title: p133_pre

description: Library name: 5_9400_RNA


title: p230_pre

description: Library name: 30_7750_RNA


title: HM1

description: Library name: Sample 1

source_name: Human skim milk sample from healthy lactating donor (1)


title: p208_pre

description: Library name: 24_6601_RNA


title: Kk13_Day0

description: Library name: SPF2.RKk13.Day0


title: p226_pre

description: Library name: 28_7650_RNA


title: Kk13_Day3

description: Library name: SPF2.RKk13.Day3


title: p161_pre

description: Library name: 13_2901_RNA


city: New York

first: Zihan

last: Xu

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-128
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

library_source: other

data_processing:
For PerturbFate Dual-omics libraries, BCL files were demultiplexed into FASTQ files using P7 PCR barcodes. Each FASTQ file contained all RNA and ATAC reads from the same indexing PCR well. During barcode extraction, reads from the oligo-dT/randomN RNA and ATAC modalities were split into separate files based on modality-specific adapter sequence matching. Read1 matching the "TG" sequence at the 41–42 nt position was classified as transcriptome data. Oligo-dT-originated RNA reads required at least 10 consecutive T bases at positions 51–60 nt, while randomN-originated RNA reads did not exhibit this pattern. ATAC read pairs were identified by the Tn5 ME sequence at the 41–50 nt position of Read1.
For the PerturbFate Dual-omics RNA reads, cell barcodes and UMI sequences from Read1 were appended to the headers of each Read2 FASTQ file, and only Read2 was used for subsequent steps. Poly(A) sequences, adapter sequences, and low-quality bases were trimmed from Read2 of oligo-dT reads, while 14 additional bases (potential priming hexamer and UMI sequences) were removed from randomN reads using Trim_Galore (0.6.7). After this step, oligo-dT and randomN reads were combined for further processing. STAR (2.7.9a) was used to map reads to the hg38 reference genome (GRCh38.p13, GENCODE). Reads with a mapping score ≥30 were selected using SAMtools (1.13). Single-cell deduplication was performed based on UMI sequences and alignment locations, and retained reads were split into SAM files per cell. Finally, single-cell gene-to-cell raw count matrices were constructed by assigning reads to genes.
For the PerturbFate Dual-omics ATAC reads, cell barcodes from RNA Read1 were appended to the headers of both ATAC Read1 and Read2 FASTQ files. Adapter sequences were removed in paired-end mode using Trim_Galore (0.6.7). STAR (2.7.9a) was used to map read pairs to the hg38 reference genome (GRCh38.p13, GENCODE). Picard (2.27.4) was used to remove PCR duplicates, and TSV files containing genomic locations and full cell barcodes were generated for SnapATAC2 (2.6.1)
sgRNA reads were matched against constant sequences in Read1 and Read2, allowing a maximum of one mismatch. For each filtered read pair, the cell barcode, sgRNA sequence, and UMI were extracted from designed positions. Extracted sgRNA sequences with at most one mismatch from the sgRNA library were corrected. UMI sequences were used for deduplication by collapsing identical UMIs for each individual sgRNA under a unique cell barcode. Cells with sgRNA UMI counts exceeding 5 were retained, and the sgRNA × cell count matrix was constructed.
For PerturbFate Tri-omics, most computational steps were the same as described above, with minor modifications. In this protocol, nascent and pre-existing transcriptomes from the same cell were amplified separately using distinct P7 PCR barcodes and processed as separate cells (two groups of reads with distinct cell barcodes). These were matched after single-cell gene-to-cell raw count matrices were generated. Additionally, because ATAC DNA underwent secondary tagmentation, the pipeline was modified to process single-end Read1 of ATAC fragments for chromatin accessibility quantification. The sgRNA library from the same cell was amplified from both nascent and pre-existing transcriptome PCR wells but shared a unique cell barcode for matching, achieved by adding the same barcoded sgRNA inner P7-U6 primer to paired nascent and pre-existing transcriptome PCR wells.
Assembly: hg38
Supplementary files format and content: RDS file contains a sparse matrix that can be read into R
Supplementary files format and content: csv file include meta data of cells
Supplementary files format and content: h5ad file include an anndata object containing a peak x count matrix with cell meta data

molecule: other

source_name: A375 cell line

growth_protocol: A375-dCas9-BFP-KRAB cells were transduced with a sgRNA library at a low MOI and BFP+ GFP+ double positive cells were sorted out. Cells were cultured for additional 6 days with either DMSO or 1uM Vemurafenib treatment.

extract_protocol:
After trypsinization, cells in each 6cm dish were collected into a 15ml falcon tube and kept on ice. Cells were spun down at 300xg for 5 minutes (4 °C) and washed once in 3ml ice-cold PBS. Every 1M cells were fixed with 1ml ice-cold 1% FA in PBS for 10 minutes on ice. For every 1mL cell suspension, 20μL of 10% Triton X-100 (0.2% final) was added to the tube to permeabilize cells for 3 min on ice. Spin down tubes at 500g for 3 min at 4 ̊C and quickly aspirate the supernatant. Cells are resuspended in 500uL of PBSI, and mix with 500uL 100 mM Tris-HCl pH8 with 5 μL of 10% Triton-X100. Spin down tubes at 500g for 5 min at 4 ̊C.
Fixed cells underwent Tn5 tagmentation in bulk, reverse transcription in bulk, two rounds of indexing ligation, and finally indexing PCR. SgRNA libraries were further separated and enriched by another round of PCR. A step-by-step experimental protocol of PerturbFate library preparation is included in the supplementary material of the publication.

treatment_protocol: On day6, before the end of the screen, 2.5ml of the original media from each plate was mixed with 2.5uL of 200mM 5EU dissolved in DMSO and was put back for nascent RNA metabolic labeling. After 1 hour of treatment, cells were harvested for PerturbFate profiling.

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


title: p124_pre

description: Library name: 3_8900_RNA


title: p173_pre

description: Library name: 15_5500_RNA


title: p213_pre

description: Library name: 25_6901_RNA


title: Je11_Day7

description: Library name: SPF2.RJe11.Day7


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-126
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-127
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: p140_pre

description: Library name: 7_9601_RNA


title: Kk13_Day1

description: Library name: SPF2.RKk13.Day1


title: p155_pre

description: Library name: 12_2302_RNA


title: Je11_Day1

description: Library name: SPF2.RJe11.Day1


title: p107_pre

description: Library name: 1_7001_RNA


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-125
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: p109_pre

description: Library name: 2_8000_RNA


title: VT033006_12hAPF_PN_plate6

city: Stanford

first: Yunming

last: Wu

state: CA

address: 327 Campus Drive, Bass biology building, rm334

department: Biology

institute: Stanford University

description: Library name: VT033006_12hAPF_PN_plate6

data_processing:
Reads were aligned to the Drosophila melanogaster genome (r6.10) using STAR (2.7.10a) [Dobin et al., 2013]. Gene counts were produced using STAR --quantMode GeneCounts.
Assembly: r6.10
Supplementary files format and content: .tab file of gene counts per cell from STAR output
Supplementary files format and content: h5ad file of the count matrix.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: brain

extract_protocol:
Single cells were prepared using the method described in Li et al. 2017
libraries were constructed using the method described in Picelli et al., 2014

value: brain

tag: strain

value: Projection neuron

value: heterozygote


title: Je11_Day3

description: Library name: SPF2.RJe11.Day3


title: Je11_Day0

description: Library name: SPF2.RJe11.Day0


title: p150_pre

description: Library name: 10_9900_RNA


title: p200_pre

description: Library name: 33_6011_RNA


title: Gl11_Day7

description: Library name: SPF2.RGl11.Day7


title: p146_pre

description: Library name: 9_9802_RNA


title: p233_pre

description: Library name: 32_7852_RNA


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-122
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Gl11_Day3

description: Library name: SPF2.RGl11.Day3


title: p216_pre

description: Library name: 26_7201_RNA


title: p196_pre

description: Library name: 20_5951_RNA


title: Gl11_Day1

description: Library name: SPF2.RGl11.Day1


title: VT033006_12hAPF_PN_plate5

description: Library name: VT033006_12hAPF_PN_plate5


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-124
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: p199_pre

description: Library name: 21_6050_2_RNA


title: p123_pre

description: Library name: 4_9000_RNA


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-123
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: p144_pre

description: Library name: 8_9701_RNA


title: Gl11_Day0

description: Library name: SPF2.RGl11.Day0


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-121
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: p179_pre

description: Library name: 17_5700_RNA


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-119
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-120
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: p162_pre

description: Library name: 14_5100_RNA


title: VT033006_12hAPF_PN_plate7

description: Library name: VT033006_12hAPF_PN_plate7


title: Donor 10 cells perturbed with KDM1A knockdown by CRISPRi

city: Palo Alto

first: Lattice

last: Data Coordination

address: 3165 Porter Drive

department: Genetics

description: Library name: Donor10_KDM1A

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.
Assembly: GRCh38, GENCODE48
Supplementary files format and content: processed data format:csv, processed data content: raw counts, normalized counts (CPM)

growth_protocol: Naive human CD4+ T cells were isolated isolated with the EasySep Human Naive CD4+ T Cell Isolation Kit (catalog no. #19555, STEMCELL Technologies) according to the manufacturer’s protocol from PBMC-enriched leukapheresis products (Leukopaks, STEMCELL Technologies, catalog no. 70500) from healthy donors, after institutional review board–approved informed written consent (STEMCELL Technologies). At day 0, primary naive human CD4+ T cells were seeded at 1 x 106 cells/ml in cXVIVO and 200 IU/ml IL-2 at 150µL/well in 96-well flat bottom plates. Cells were activated using ImmunoCult human CD3/CD28/CD2 T cell activator at 25 µl/ml. The next morning, cells were transduced with 2% v/v concentrated ZIM3KRAB-dCas9-BlastR lentivirus. In the afternoon, cells in each well were transduced with a distinct, individual single gRNA expressing lentivirus at 2% v/v. On day 3, cells were split to ~5 x 105 cells/mL and Blasticidin was added at 10 µg/mL final concentration. At day 5, cells were centrifuged and resuspended with cXVIVO supplemented with 200 IU/mL IL-2, 5 ng/mL IL-7 and 10 µg/mL blasticidin at ~5 x 105 cells/mL. At day 7, cells were counted and diluted to 1 x 106 cells/mL with cXVIVO supplemented with 200 IU/mL IL-2, 5 ng/mL IL-7 and 10 µg/mL blasticidin. At day 8, cells were centrifuged and resuspended at 1 x 106 cells/mL with cXVIVO supplemented with 200 IU/mL IL-2 and 5 ng/mL IL-7. On day 10 morning, cells were centrifuged and resuspended at 2 x 106 cells/ml with cXVIVO supplemented with 200 IU/mL IL-2 and 12.5 µL/mL ImmunoCult human CD3/CD28/CD2 T cell activator for 8 hours.

extract_protocol:
Cells were centrifuged and resuspended in DNA/RNA Shield (Zymo Research) and sent for bulk RNAseq by Plasmidsaurus.
plasmidsaurus library preparation - conversion of mRNA into complementary DNA via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification.

value: CD4-positive, alpha-beta T cells

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of KDM1A

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: A+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: donor ethnicity

value: Pacific Islander

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: JVA_Day3

description: Library name: SPF2.JVA.Day3

tag: tissue

value: blood

tag: cell type

value: PBMCs

tag: treatment

value: Influenza vaccination


title: Donor 10 cells perturbed with SGF29 knockdown by CRISPRi

description: Library name: Donor10_SGF29

treatment_protocol: 200 IU/mL IL-2 and 12.5 µL/mL ImmunoCult human CD3/CD28/CD2 T cell activator for 8 hours

value: CD4-positive, alpha-beta T cells

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown SGF29

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-118
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: cell line

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


title: JVA_Day7

description: Library name: SPF2.JVA.Day7


title: Donor 10 cells perturbed with ATP2A2 knockdown by CRISPRi

description: Library name: Donor10_ATP2A2

value: CRISPRi knockdown ATP2A2

value: No

value: A+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors


title: Donor 10 cells perturbed with Non-targeting control knockdown by CRISPRi

description: Library name: Donor10_NTC

tag: tissue

value: blood

tag: cell type

tag: treatment

tag: experimental perturbation

value: CRISPRi control

tag: donor id

value: Normal

value: Zymo DNA/RNA Shield

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: donor ethnicity

value: Pacific Islander

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: Donor 9 cells perturbed with SGF29 knockdown by CRISPRi

description: Library name: Donor9_SGF29

value: CD4-positive, alpha-beta T cells

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown SGF29

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: Caucasian


title: VT033006_12hAPF_PN_plate3

description: Library name: VT033006_12hAPF_PN_plate3

value: brain

tag: strain

value: Projection neuron

tag: genotype

value: heterozygote

tag: batch


title: VT033006_12hAPF_PN_plate2

description: Library name: VT033006_12hAPF_PN_plate2

tag: tissue

tag: cell type


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-117
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: cell line

value: A375 cell line

value: Melanoma

value: BRAF V600E

tag: treatment

value: DMSO or Vemurafenib


title: Donor 9 cells perturbed with NFKB2 knockdown by CRISPRi

description: Library name: Donor9_NFKB2

value: blood

tag: experimental perturbation

value: CRISPRi knockdown of NFKB2

tag: donor id

value: No

value: A+

value: ACDA

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

tag: genetic perturbation_strategy


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-116
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: genotype


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-115
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Donor 9 cells perturbed with Non-targeting control knockdown by CRISPRi

description: Library name: Donor9_NTC

value: CD4-positive, alpha-beta T cells

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi control

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: Zymo DNA/RNA Shield

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Caucasian

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: Donor 9 cells perturbed with ATP2A2 knockdown by CRISPRi

description: Library name: Donor9_ATP2A2

tag: tissue

value: blood

tag: cell type

tag: treatment

tag: experimental perturbation

value: CRISPRi knockdown ATP2A2

tag: donor id

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection


title: 77_08_Day3

description: Library name: SPF2.77.06.Day3

value: PBMCs

value: Influenza vaccination


title: Donor 10 cells perturbed with CYB5R4 knockdown by CRISPRi

description: Library name: Donor10_CYB5R4

value: CRISPRi knockdown CYB5R4

tag: donor age

value: No

value: A+

value: ACDA

value: STEMCELL technologies

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

value: Pacific Islander

tag: genetic perturbation_strategy


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-114
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: cell line

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


title: JVA_Day1

description: Library name: SPF2.JVA.Day1

tag: tissue


title: VT033006_12hAPF_PN_plate4

description: Library name: VT033006_12hAPF_PN_plate4

value: brain

tag: strain

tag: cell type

value: Projection neuron

value: heterozygote

tag: batch


title: Donor 9 cells perturbed with KDM1A knockdown by CRISPRi

description: Library name: Donor9_KDM1A

value: blood

value: CD4-positive, alpha-beta T cells

tag: treatment

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of KDM1A

tag: donor id

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: Male

value: adult stage

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Caucasian

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: VT033006_12hAPF_PN_plate1

description: Library name: VT033006_12hAPF_PN_plate1


title: 77_09_Day7

description: Library name: SPF2.77.06.Day7

value: PBMCs

value: Influenza vaccination


title: Donor 8 cells perturbed with Non-targeting control 3 knockdown by CRISPRi

description: Library name: Donor8_NTC3

value: CRISPRi control

tag: donor age

value: Yes

value: O+

value: ACDA

value: STEMCELL technologies

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy


title: 77_07_Day1

description: Library name: SPF2.77.06.Day1

tag: tissue

value: blood

tag: cell type

tag: treatment


title: Donor 8 cells perturbed with SGF29 knockdown by CRISPRi

description: Library name: Donor8_SGF29

value: CD4-positive, alpha-beta T cells

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown SGF29

tag: donor id

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: Male

value: adult stage


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-113
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: cell line

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-112
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Donor 9 cells perturbed with CYB5R4 knockdown by CRISPRi

description: Library name: Donor9_CYB5R4

value: CRISPRi knockdown CYB5R4

tag: donor age

value: No

value: A+

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

value: Zymo DNA/RNA Shield

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Caucasian

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: 77_06_Day0

description: Library name: SPF2.77.06.Day0

tag: tissue

value: blood

tag: cell type

value: PBMCs

tag: treatment

value: Influenza vaccination


title: JVA_Day0

description: Library name: SPF2.JVA.Day0


title: Donor 8 cells perturbed with NFKB2 knockdown by CRISPRi

description: Library name: Donor8_NFKB2

value: CD4-positive, alpha-beta T cells

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of NFKB2

tag: donor id

tag: donor weight

tag: donor height

tag: donor smoker

value: Yes

value: O+

value: ACDA

value: STEMCELL technologies

value: Male

value: adult stage

tag: sample preservation_method

tag: suspension depletion_factors

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy


title: Yz6_Day7

description: Library name: SPF1.RYz6.Day7


title: Donor 8 cells perturbed with KDM1A knockdown by CRISPRi

description: Library name: Donor8_KDM1A

value: CRISPRi knockdown of KDM1A

tag: donor age

tag: donor blood_type

tag: anticoagulant

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO


title: Donor 8 cells perturbed with MED24 knockdown by CRISPRi

description: Library name: Donor8_MED24

tag: tissue

value: blood

tag: cell type

tag: treatment

value: CRISPRi knockdown of MED24

tag: donor body_mass_index

tag: donor disease

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: Donor 8 cells perturbed with ELOB knockdown by CRISPRi

description: Library name: Donor8_ELOB

value: CD4-positive, alpha-beta T cells

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of ELOB

tag: donor id

tag: donor weight

tag: donor height

tag: donor smoker

tag: sample preservation_method

tag: suspension depletion_factors


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-111
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: cell line

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


title: Donor 7 cells perturbed with SGF29 knockdown by CRISPRi

description: Library name: Donor7_SGF29

value: CRISPRi knockdown SGF29

tag: donor age

value: No

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy


title: Yz6_Day1

description: Library name: SPF1.RYz6.Day1

tag: tissue

value: blood

tag: cell type

value: PBMCs

tag: treatment

value: Influenza vaccination


title: Donor 7 cells perturbed with Non-targeting control 1 knockdown by CRISPRi

description: Library name: Donor7_NTC1

value: CD4-positive, alpha-beta T cells

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi control

tag: donor id

tag: donor weight

tag: donor height

tag: donor smoker

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

value: Zymo DNA/RNA Shield

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: Yz6_Day3

description: Library name: SPF1.RYz6.Day3


title: Donor 7 cells perturbed with NFKB2 knockdown by CRISPRi

description: Library name: Donor7_NFKB2

value: CRISPRi knockdown of NFKB2

tag: donor age

value: No

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

tag: donor sex

tag: sample preservation_method

tag: suspension depletion_factors


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-109
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: cell line

value: A375 cell line

tag: cell type

value: Melanoma

tag: genotype

value: BRAF V600E

tag: treatment

value: DMSO or Vemurafenib


title: Donor 7 cells perturbed with MEN1 knockdown by CRISPRi

description: Library name: Donor7_MEN1

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of MEN1

tag: donor id

tag: donor weight

tag: donor height

value: STEMCELL technologies

value: Male

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy


title: Donor 7 cells perturbed with MED24 knockdown by CRISPRi

description: Library name: Donor7_MED24

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown of MED24

tag: donor age

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

value: Zymo DNA/RNA Shield

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: CRISPRi

tag: enriched cell_types

tag: library protocol


title: Donor 7 cells perturbed with KDM1A knockdown by CRISPRi

description: Library name: Donor7_KDM1A

tag: tissue

tag: cell type

tag: treatment

tag: experimental perturbation

value: CRISPRi knockdown of KDM1A

value: No

value: O+

value: ACDA

tag: donor sex

tag: sample preservation_method

tag: suspension depletion_factors

value: Plasmidsaurus RNA-Seq


title: Donor 7 cells perturbed with GATA3 knockdown by CRISPRi

description: Library name: Donor7_GATA3

value: blood

value: CD4-positive, alpha-beta T cells

value: CRISPRi knockdown of GATA3

tag: donor id

tag: donor weight

tag: donor height

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor ethnicity

tag: genetic perturbation_strategy


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-107
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: cell line

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-106
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Ss10_Day3

description: Library name: SPF1.RSs10.Day3

value: PBMCs

value: Influenza vaccination


title: Donor 7 cells perturbed with ELOB knockdown by CRISPRi

description: Library name: Donor7_ELOB

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown of ELOB

tag: donor age

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: STEMCELL technologies

value: Male

value: adult stage

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

value: Zymo DNA/RNA Shield

value: Hispanic

tag: enriched cell_types

tag: library protocol


title: Yz6_Day0

description: Library name: SPF1.RYz6.Day0

tag: tissue

value: blood

tag: cell type

tag: treatment


title: Ss10_Day1

description: Library name: SPF1.RSs10.Day1


title: Donor 6 cells perturbed with SGF29 knockdown by CRISPRi

description: Library name: Donor6_SGF29

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown SGF29

tag: donor id

tag: donor weight

tag: donor height

value: No

value: O+

value: ACDA

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: sample preservation_method

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Caucasian

value: CRISPRi

value: Plasmidsaurus RNA-Seq


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-110
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: cell line

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


title: Ss10_Day7

description: Library name: SPF1.RSs10.Day7

value: PBMCs

value: Influenza vaccination


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-105
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Donor 6 cells perturbed with NFKB2 knockdown by CRISPRi

description: Library name: Donor6_NFKB2

value: blood

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown of NFKB2

tag: donor age

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: source

value: STEMCELL technologies

value: adult stage

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

value: Zymo DNA/RNA Shield

tag: donor ethnicity

tag: genetic perturbation_strategy


title: Donor 7 cells perturbed with ATP2A2 knockdown by CRISPRi

description: Library name: Donor7_ATP2A2

tag: tissue

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

tag: experimental perturbation

value: CRISPRi knockdown ATP2A2

tag: donor id

tag: donor weight

tag: donor height

value: No

value: O+

value: ACDA

value: Male

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Hispanic

tag: enriched cell_types

tag: library protocol


title: Donor 6 cells perturbed with Non-targeting control 3 knockdown by CRISPRi

description: Library name: Donor6_NTC3

value: CRISPRi control

tag: donor age

tag: donor smoker

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: sample preservation_method

tag: suspension depletion_factors

value: Caucasian

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: Donor 6 cells perturbed with MEN1 knockdown by CRISPRi

description: Library name: Donor6_MEN1

value: blood

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown of MEN1

tag: donor blood_type

tag: anticoagulant

tag: source

value: STEMCELL technologies

value: adult stage

tag: donor body_mass_index

tag: donor disease

tag: donor ethnicity

tag: genetic perturbation_strategy


title: Ss10_Day0

description: Library name: SPF1.RSs10.Day0

tag: tissue

tag: cell type

value: PBMCs

tag: treatment

value: Influenza vaccination


title: Donor 8 cells perturbed with GATA3 knockdown by CRISPRi

description: Library name: Donor8_GATA3

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of GATA3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: Yes

value: O+

value: TRUE

value: Normal

value: Zymo DNA/RNA Shield

tag: enriched cell_types

tag: library protocol


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-108
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: cell line

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-104
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Donor 6 cells perturbed with MED24 knockdown by CRISPRi

description: Library name: Donor6_MED24

value: blood

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown of MED24

tag: donor smoker

value: No

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: sample preservation_method

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Caucasian

value: CRISPRi

value: Plasmidsaurus RNA-Seq


title: Donor 6 cells perturbed with KDM1A knockdown by CRISPRi

description: Library name: Donor6_KDM1A

tag: tissue

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

tag: experimental perturbation

value: CRISPRi knockdown of KDM1A

tag: donor id

value: O+

value: STEMCELL technologies

value: adult stage

value: TRUE

tag: donor body_mass_index

tag: donor disease

tag: donor ethnicity

tag: genetic perturbation_strategy


title: Donor 6 cells perturbed with GATA3 knockdown by CRISPRi

description: Library name: Donor6_GATA3

value: CRISPRi knockdown of GATA3

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: Normal

value: Zymo DNA/RNA Shield

tag: enriched cell_types

tag: library protocol


title: Sd4_Day3

description: Library name: SPF1.RSd4.Day3

value: blood

value: PBMCs

value: Influenza vaccination


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-103
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: cell line

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


title: Donor 5 cells perturbed with ELOB knockdown by CRISPRi

description: Library name: Donor6_ELOB

tag: tissue

tag: cell type

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown of ELOB

value: No

tag: anticoagulant

value: ACDA

tag: source

tag: donor sex

value: Female

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: sample preservation_method

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Caucasian

value: CRISPRi

value: Plasmidsaurus RNA-Seq


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-102
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: treatment


title: Sd4_Day1

description: Library name: SPF1.RSd4.Day1


title: Sd4_Day7

description: Library name: SPF1.RSd4.Day7


title: Donor 5 cells perturbed with Non-targeting control 3 knockdown by CRISPRi

description: Library name: Donor5_NTC3

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi control

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

value: O+

value: STEMCELL technologies

value: Male

value: adult stage

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

value: Zymo DNA/RNA Shield

tag: donor ethnicity

tag: genetic perturbation_strategy


title: Donor 5 cells perturbed with CYB5R4 knockdown by CRISPRi

description: Library name: Donor6_CYB5R4

tag: tissue

value: blood

tag: cell type

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown CYB5R4

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

tag: enriched cell_types

tag: library protocol


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-101
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: cell line

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

tag: treatment

value: DMSO or Vemurafenib


title: Sd4_Day0

description: Library name: SPF1.RSd4.Day0

value: PBMCs

value: Influenza vaccination


title: Donor 5 cells perturbed with MEN1 knockdown by CRISPRi

description: Library name: Donor5_MEN1

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of MEN1

tag: donor id

tag: donor age

value: No

value: ACDA

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: sample preservation_method

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Caucasian

value: CRISPRi

value: Plasmidsaurus RNA-Seq


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-100
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: cell type


title: Qt8_Day7

description: Library name: SPF1.RQt8.Day7

tag: tissue

value: blood


title: Donor 5 cells perturbed with MED24 knockdown by CRISPRi

description: Library name: Donor5_MED24

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown of MED24

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: O+

tag: anticoagulant

value: STEMCELL technologies

value: Male

value: adult stage

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

value: Zymo DNA/RNA Shield

tag: donor ethnicity

tag: genetic perturbation_strategy


title: Qt8_Day3

description: Library name: SPF1.RQt8.Day3

value: PBMCs

tag: treatment

value: Influenza vaccination


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-98
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: cell line

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


title: Patient 15 - pre treatment

city: Madison

first: Huy

last: Dinh

state: WI

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

description: Library name: Pt15_Pre

library_source: transcriptomic single cell

data_processing:
Raw FASTQs were run through Cellranger v7.1.0, using the GRCh38 human genome for alignment and otherwise default parameters.
10x genomics flex (probe-based) samples were aligned using the Cellranger “multi” function with human probe set v1 and using the patient-specific barcodes to deconvolute multiplexed samples.
Assembly: GRCh38 human genome & human probe set v1
Supplementary files format and content: Cell Ranger Feature Barcode Matrices (HDF5 Format)

source_name: PBMC

extract_protocol:
Cryopreserved peripheral blood mononuclear cells (PBMC) from trial participants were stored long-term in liquid phase LN2. For sample preparation, cryotubes were partially submerged in a 37°C water bath until mostly thawed, then transferred to 15mL conical tubes with 9mL of pre-warmed, filter-sterilized RPMI Media (Gibco Cat# 11875093) and 10% by-volume fetal bovine serum (FBS; Hyclone Cat# SH30071.01HI). Cells were centrifuged for 5 minutes at 400g at room temperature, decanted, then resuspended in 1mL chilled (4°C) phosphate-buffered saline (PBS; Gibco Cat# 14190144) + 0.04% bovine serum albumin (BSA; Gibco Cat# 15260037) with 0.2U/µl of RNAse inhibitor (Sigma Cat# 3335399001). Initial cell counting and viability were performed using a Countess II automated cell counter (Invitrogen Cat# AMQAX1000) with a 1:1 dilution of trypan blue (0.4% solution, Gibco Cat# 15250061) to confirm sufficient cell yields and greater than 80% viability. Samples were then processed using the following 10X Genomics protocols.
Single cells were captured and barcoded using the 10X Chromium controller using its 3’ or 10x Flex (probe-based) whole transcriptome kits. Gel Bead-In EMulsions (GEMs) were prepared, followed by cDNA amplification and size-based cleanup. Final libraries were sent for sequencing using NovaSeq and NovaSeqX platforms to target at least 20k reads per cell.

value: PBMC


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-97
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Donor 5 cells perturbed with GATA3 knockdown by CRISPRi

description: Library name: Donor5_GATA3

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of GATA3

tag: donor id

tag: donor age

value: No

value: ACDA

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: Caucasian

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq


title: Qt8_Day1

description: Library name: SPF1.RQt8.Day1

tag: tissue

tag: cell type


title: Donor 5 cells perturbed with KDM1A knockdown by CRISPRi

description: Library name: Donor5_KDM1A

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

value: CRISPRi knockdown of KDM1A

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

value: O+

tag: anticoagulant

value: STEMCELL technologies

value: Male

value: adult stage

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-99
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: cell line

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

tag: treatment

value: DMSO or Vemurafenib


title: Patient 14 - pre treatment

description: Library name: Pt14_Pre

value: PBMC


title: Patient 14 - post treatment

description: Library name: Pt14_Post


title: Patient 15 - post treatment

description: Library name: Pt15_Post


title: Donor 5 cells perturbed with NFKB2 knockdown by CRISPRi

description: Library name: Donor5_NFKB2

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: CRISPRi knockdown of NFKB2

tag: donor id

tag: donor age

value: No

value: ACDA

tag: source

tag: donor sex

tag: donor dev_stage

tag: donor living_at_sample_collection

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: donor ethnicity

value: Caucasian

tag: genetic perturbation_strategy


title: Ht8_Day7

description: Library name: SPF1.RHt8.Day7

tag: tissue

tag: cell type

value: PBMCs

value: Influenza vaccination


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-95
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Patient 11 - post treatment

description: Library name: Pt11_Post


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-96
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Qt8_Day0

description: Library name: SPF1.RQt8.Day0


title: Patient 11 - pre treatment

description: Library name: Pt11_Pre


title: Patient 12 - pre treatment

description: Library name: Pt12_Pre


title: Patient 12 - post treatment

description: Library name: Pt12_Post


title: Ht8_Day3

description: Library name: SPF1.RHt8.Day3


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-94
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Patient 10 - pre treatment

description: Library name: Pt10_Pre


title: Patient 9 - pre treatment

description: Library name: Pt9_Pre


title: Patient 10 - post treatment

description: Library name: Pt10_Post


title: Ht8_Day0

description: Library name: SPF1.RHt8.Day0


title: Ht8_Day1

description: Library name: SPF1.RHt8.Day1


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-93
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-92
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Patient 8 - post treatment

description: Library name: Pt8_Post


title: Patient 5 - post treatment

description: Library name: Pt5_post


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-91
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Wm14_Day3

description: Library name: NSPF5.RWm14.Day3


title: Patient 8 - pre treatment

description: Library name: Pt8_pre


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-90
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Patient 6 - pre treatment

description: Library name: Pt6_pre


title: Patient 5 - pre treatment

description: Library name: Pt5_pre


title: Patient 7 - post treatment

description: Library name: Pt7_post


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-89
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Patient 6 - post treatment

description: Library name: Pt6_post


title: Patient 9 - post treatment

description: Library name: Pt9_Post


title: Wm14_Day7

description: Library name: NSPF5.RWm14.Day7


title: Patient 4 - pre treatment

description: Library name: Pt4_pre


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-88
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Patient 4 - post treatment

description: Library name: Pt4_post


title: Wm14_Day0

description: Library name: NSPF5.RWm14.Day0


title: Patient 3 - post treatment

description: Library name: Pt3_Post


title: Wm14_Day1

description: Library name: NSPF5.RWm14.Day1


title: Patient 3 - pre treatment

description: Library name: Pt3_Pre


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-87
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Fn14_Day1

description: Library name: NSPF5.RFn14.Day1


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-86
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Lung immune ane epithelial cells from RA_3 patient

city: Los Angeles

first: Kensuke

last: Suga

state: California

address: 8700 Beverly Blvd

department: Department of Rheumatology

institute: Kao Autoimmunity Institute

description: Library name: RA_3

data_processing:
The CellRanger v9.0.0 software was used with the default settings for demultiplexing, aligning reads with STAR software to a human GRCh38-2024A transcriptome reference genome (provided by 10X Genomics).
Assembly: GRCh38-2024A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Human Lung

extract_protocol:
Frozen lung tissues in cryovials were thawed at 37℃ for 2 minutes in a water bath, washed in Hank’s balanced salt solution (HBSS), and then centrifuged for 5 minutes at 500g and 4℃. After that, lung tissues were put in 10cm petri dishes and finely minced. Subsequently, the minced tissues were incubated in HBSS containing 1X Liberase TM (0.25 U/mL) and DNaseI (0.5 mg/ml), and agitated at 360 rpm at 37℃ for 30 minutes. For enriching epithelial cells and immune cells, the dissociated single-cell suspensions were stained with antibodies for EPCAM, CD45, and CD31 and sorted using fluorescence-activated cell sorting (FACS) with a BD Influx cell sorter. The viability of the cells was determined by staining the cell preparation with DAPI 30 minutes prior to cell sorting.
Library was performed according to the manufacter's protocol (10X Chromium GEM-X Single Cell 3’ kit v4).

value: Human Lung

value: Immune and epithelial cells

tag: subject status

value: RA-ILD patient


title: Fn14_Day3

description: Library name: NSPF5.RFn14.Day3


title: Fn14_Day7

description: Library name: NSPF5.RFn14.Day7


title: Lung immune ane epithelial cells from RA_5 patient

description: Library name: RA_5


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-85
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

value: A375 cell line


title: Lung immune ane epithelial cells from RA_4 patient

description: Library name: RA_4


title: Lung immune ane epithelial cells from CTD_2 patient

description: Library name: CTD_2

value: Non-RA Connective tissue disease (CTD)-ILD patient


title: Lung immune ane epithelial cells from RA_1 patient

description: Library name: RA_1


title: Cv9_Day7

description: Library name: NSPF5.RCv9.Day7


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-83
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

value: Melanoma

value: BRAF V600E


title: Lung immune ane epithelial cells from CTD_3 patient

description: Library name: CTD_3


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-82
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

value: DMSO or Vemurafenib


title: Lung immune ane epithelial cells from CTD_1 patient

description: Library name: CTD_1


title: Patient 2 - post treatment

description: Library name: Pt2_Post

value: PBMC


title: Fn14_Day0

description: Library name: NSPF5.RFn14.Day0

value: blood


title: Lung immune ane epithelial cells from Control_4 patient

description: Library name: Control_4

value: Control


title: Cv9_Day1

description: Library name: NSPF5.RCv9.Day1


title: Lung immune ane epithelial cells from Control_3 patient

description: Library name: Control_3


title: Lung immune ane epithelial cells from Control_1 patient

description: Library name: Control_1


title: Cv9_Day0

description: Library name: NSPF5.RCv9.Day0


title: Cv9_Day3

description: Library name: NSPF5.RCv9.Day3


title: Lung immune ane epithelial cells from RA_2 patient

description: Library name: RA_2


title: A549_Sm22mut cells, TGFβ treatment, Day5, biological repeat 3

city: Richardson

first: John

middle: Tran

last: Nguyen

state: TX

address: 800 W Campbell Rd

department: Bioengineering

institute: The University of Texas at Dallas

description:
Library name: Sample Sm22mutTGFb biol rep 3
Column name in normalized_counts.csv: S1TGFb3

data_processing:
Data analysis for differential gene expression between sample conditions was performed with a pipeline consisted of HISAT2, StringTie, featureCounts, and DESeq2.
Assembly: human genome GRCh38.p14
Supplementary files format and content: csv file include gene name and normalized counts for each sample

growth_protocol: Cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum, 5 mL of 10,000 U/mL penicillin-streptomycin (Gibco, catalog no. 15140122) and 0.1 mM MEM non-essential amino acids (Gibco, catalog no. 11140050). Cells were maintained at 37C, 100% humidity, and 5% CO2.

extract_protocol:
Total RNAs were harvested using RNeasy Mini kit and sample quality was evaluated using OD260/OD280 (1.8-2.2). 2 µg of total RNAs in 10 µL nuclease-free water per sample submission.
RNA libraries for RNA-seq were prepared internally at Genewiz.

treatment_protocol: In experiments, the cells were stimulated with 10 ng/mL TGFβ in complete culture medium.

value: lung adenocarcinoma epithelial cell line

value: miR22/SNAI1 target site KO

value: 10 ng/mL TGFβ

tag: time

value: Day 5


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-81
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Lung immune ane epithelial cells from Control_2 patient

description: Library name: Control_2


title: A549_Sm22mut cells, TGFβ treatment, Day5, biological repeat 2

description:
Library name: Sample Sm22mutTGFb biol rep 2
Column name in normalized_counts.csv: S1TGFb2


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-80
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: DV2J_Day3

description: Library name: NSPF5.DV2J.Day3

value: PBMCs


title: DV2J_Day7

description: Library name: NSPF5.DV2J.Day7

value: Influenza vaccination


title: A549_Sm22mut cells, TGFβ treatment, Day5, biological repeat 1

description:
Library name: Sample Sm22mutTGFb biol rep 1
Column name in normalized_counts.csv: S1TGFb1


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-79
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: A549_Sm22mut cells, no treatment, Day5, biological repeat 3

description:
Library name: Sample Sm22mut biol rep 3
Column name in normalized_counts.csv: S13


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-78
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: A549_Sm22mut cells, no treatment, Day5, biological repeat 2

description:
Library name: Sample Sm22mut biol rep 2
Column name in normalized_counts.csv: S12


title: DV2J_Day1

description: Library name: NSPF5.DV2J.Day1


title: DV2J_Day0

description: Library name: NSPF5.DV2J.Day0


title: A549_WT cells, no treatment, Day5, biological repeat 3

description:
Library name: Sample Wildtype biol rep 3
Column name in normalized_counts.csv: WT3

value: WT


title: A549_WT cells, TGFβ treatment, Day5, biological repeat 2

description:
Library name: Sample WildtypeTGFb biol rep 2
Column name in normalized_counts.csv: WTTGFb2


title: A549_WT cells, TGFβ treatment, Day5, biological repeat 1

description:
Library name: Sample WildtypeTGFb biol rep 1
Column name in normalized_counts.csv: WTTGFb1


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-77
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: A549_Sm22mut cells, no treatment, Day5, biological repeat 1

description:
Library name: Sample Sm22mut biol rep 1
Column name in normalized_counts.csv: S11


title: A549_WT cells, TGFβ treatment, Day5, biological repeat 3

description:
Library name: Sample WildtypeTGFb biol rep 3
Column name in normalized_counts.csv: WTTGFb3


title: Tr13_Day7

description: Library name: NSPF4.RTr13.Day7


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-76
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-75
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Tr13_Day3

description: Library name: NSPF4.RTr13.Day3


title: Tr13_Day1

description: Library name: NSPF4.RTr13.Day1


title: A549_WT cells, no treatment, Day5, biological repeat 1

description:
Library name: Sample Wildtype biol rep 1
Column name in normalized_counts.csv: WT1


title: MKKD2_GLC1

city: Omaha

first: Brian

last: North

state: NE

address: 2500 California Plaza

department: Biomedical Science

institute: Creighton University School of Medicine

description: Library name: Sample 7

data_processing:
Data processing was performed at Novogene facility. featureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene and then FPKM of each gene was calculated. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: Hisat2 v2.0.5
Supplementary files format and content: Tab-delimited txt file contains FPKM values for all samples.

extract_protocol:
Total RNA was extracted using Qiagen RNA Extraction Kit.
Library construction was performed at Novogene facility. The first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: Cancer cell line

value: shRNA MAPKAPK2 #2, Replicate 1

value: Glucose 20 mM


title: MKKD2_GLC2

description: Library name: Sample 8

value: shRNA MAPKAPK2 #2, Replicate 2


title: MKKD1_GLC2

description: Library name: Sample 6

value: shRNA MAPKAPK2 #1, Replicate 2


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-73
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

value: A375 cell line

value: Melanoma

value: BRAF V600E


title: MKKD1_GLC1

description: Library name: Sample 5

value: shRNA MAPKAPK2 #1, Replicate 1


title: A549_WT cells, no treatment, Day5, biological repeat 2

description:
Library name: Sample Wildtype biol rep 2
Column name in normalized_counts.csv: WT2


title: Tr13_Day0

description: Library name: NSPF4.RTr13.Day0

value: blood


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-74
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

value: DMSO or Vemurafenib


title: SC_NOGLC2

description: Library name: Sample 4

value: shRNA Control, Replicate 2

value: Glucose 0 mM


title: SC_NOGLC1

description: Library name: Sample 3

value: shRNA Control, Replicate 1


title: SC_GLC2

description: Library name: Sample 2


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-72
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-71
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Tm13_Day7

description: Library name: NSPF4.RTm13.Day7

value: PBMCs


title: Tm13_Day3

description: Library name: NSPF4.RTm13.Day3

value: Influenza vaccination


title: Tm13_Day1

description: Library name: NSPF4.RTm13.Day1


title: Microvasculature_49WT_rep2

city: Stockholm

first: Michael

last: Vanlandewijck

address: Blickagången 6

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

description: Library name: 49

data_processing:
Standard methods for processing and analysis of 10X Genomics-generated scRNA-seq data were applied. Sequencing data were first demultiplexed and then aligned to the mouse genome (GRm38/mm10) using Cell Ranger v6.1.2 software (10X Genomics).
Assembly: GRm38/mm10
Supplementary files format and content: tab-separated value files and gene expression matrix files

organism: Mus musculus

source_name: Brain

extract_protocol:
Brain halves were mechanically and enzymatically digested with Collagenase type II (1 mg/mL, cat. #C6885, Sigma). On ice, the washed microvascular fragments were isolated using sheep anti-rat magnetic Dynabeads (50 mL/brain, cat. #11035, Invitrogen) bound to rat anti-mouse PECAM1 antibody (10 mL/brain, cat. #553370, BD Biosciences) and a DynaMag 2 magnet (Invitrogen). The washed microvessels were then further dissociated with Collagenase IV (1 mg/mL, cat. #17104-019, Gibco) and TrypLE (cat. #A1217701, Gibco) to remove the magnetic beads and obtain single cell solutions.
Isolated microvascular fragments (n=2) were dissociated into single-cell suspensions, the viability and cell count was determined using LUNA-FLÔ Dual Fluorescence cell counter (Logos Biosystems). All samples showed above 92% cell viability. The single-cell suspensions were processed using Next Gem Single Cell 3’ Reagent kit v3.1 with dual indexes (10X Genomics). The samples were prepared to capture ~5000 cells per sample and loaded according to the manufacturer’s recommendations. The prepared cDNA libraries were subsequently sequences on a Next seq200 sequencer equipped with a P3 100 cycles flow cell.

value: Brain

tag: age

value: 3 months

tag: Sex

value: Male

value: endothelial cell


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-70
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: cell line

tag: genotype


title: Microvasculature_50KO_rep2

description: Library name: 50


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-69
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

tag: treatment


title: SC_GLC1

description: Library name: Sample 1

value: Cancer cell line

value: Glucose 20 mM


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-84
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

value: A375 cell line


title: P3 digit, LNR

city: Dallas

first: Sneha

last: Korlakunta

address: 6000 Harry Hines Blvd

department: Surgery

institute: UT Southwestern Medical Center

description:
Library name: LNR
10x Genomics

data_processing:
Cellranger pipeline (v6.1.2) was used for demultiplexing and counting as recommended by 10X Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq)
Assembly: GRCm39-2024-A
Supplementary files format and content: Tab-separated value files and matrix files

source_name: P3 digit

extract_protocol:
Digits from ten mice were pooled for each sample. A scalpel blade was used to sever hindlimb digits 2-4 at the proximal end of the 2nd phalangeal element. Each digit was divided down the midline along its length to maximize the exposure of internal tissue surface area to media. A single cell suspension was generated following these techniques: Briefly, digit tissue was subjected to enzymatic digestion using Collagenase I at 3 mg/mL (Thermo Fisher Scientific, 17100-017), Collagenase II at 2 mg/mL (Thermo Fisher Scientific, 17101-015), and Dispase at 3mg/mL (MilliporeSigma, D4693) per 1mL of DMEM (Thermo Fisher Scientific, 11960044) for 45 minutes at 37°C under constant agitation at 150 rpm. Digestions were then quenched with DMEM containing 10% FBS (Gibco, 10437028), filtered through 40um mesh and pelleted via centrifugation for 5min at 400xG at 4⁰C.Supernatant was removed and red blood cells were lysed by resuspending the pellets with 2ml of ACK Lysis Buffer (Gibco A10492-01) and incubating for 2 minutes at room temp. Cell viability was assessed with Trypan blue exclusion on a Countess III (Thermo Fisher Scientific) automated counter and only samples with >75% viability were processed for further sequencing.
Single Cell 3' v3

value: P3 digit

value: 6-8 weeks

value: female

tag: strain

value: Lymph Node removal

tag: batch


title: P3 digit, control

description:
Library name: LNR-Control
10x Genomics

value: No treatment


title: Pt8_Day7

description: Library name: NSPF4.RPt8.Day7

value: blood


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-67
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

value: Melanoma

value: BRAF V600E

value: DMSO or Vemurafenib


title: Pt8_Day3

description: Library name: NSPF4.RPt8.Day3

value: PBMCs

value: Influenza vaccination


title: Tm13_Day0

description: Library name: NSPF4.RTm13.Day0


title: Microvasculature_43WT_rep1

description: Library name: 43

value: Brain

value: 3 months

value: Female


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-68
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Pt8_Day1

description: Library name: NSPF4.RPt8.Day1


title: DRIPc_siExosc10_WT_r1

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

description: Library name: DRIPc_siExosc10_WT_r1

data_processing:
Fastq files of DRIPc-Rx samples were mapped separately to either murine GRCm39 or human GRCh38 genome and to the fly dm6 genome using STAR (Dobin et al., 2013). Subsequently, aligned reads were spike-normalized by dividing the number of mapped reads aligned to GRCm39 or GRCh38 by the number of reads mapped to dm6 for each sample and multiplying this ratio with the smallest number of reads aligned to dm6 for any sample. Peaks were called using MACS (Zhang et al., 2008) with default broad peak settings. For metagenes and heatmaps, log2FC of DRIPs over inputs were determined based on bam files using bamCompare and plotted using deeptools (Ramirez et al., 2014). Samples marked with an asterisk (*) do not contain the Drosophila spike-in and were therefore read-normalized.
Assembly: GRCh38, GRCm39 and dm6
Supplementary files format and content: bedgraph files

source_name: PDAC

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
DRIPc-sequencing was adapted from Sanz and Chédin, 2019. Cells were lysed rotating overnight at 37°C in TE buffer (pH 8) supplemented with 10% SDS and 10 µL proteinase K (10 mg/mL). For spike-normalization 10% Drosophila S2 cells were added according to the cell number. DNA was isolated by phenol/chloroform extraction using MaXtract High Density Tubes (Qiagen) and fragmented with a mixture of restriction enzymes. For this DNA was incubated overnight with 60 U of BsrGI, EcoRI, HindIII, SSpI and Xbal (New England Biolabs) at 37°C. DNA was cleaned up again with phenol/chloroform and fragmentation was validated by agarose gel electrophoresis to ensure successful digestion of the DNA to a size below 1 kb. Subsequently, 200 µg of DNA was treated with 30 U of RNaseT1 (Thermo Fisher Scientific) at 37°C for 30 min to eliminate ssRNA. To avoid potential dsRNA contamination the DNA was treated with 3 U RNaseIII (Thermo Fisher Scientific) for 1 h at 37°C. Samples were then incubated for 6 h at 37°C with or without 60 U of RNaseH1 (New England Biolabs) to ensure specificity of the following immunoprecipitation step. For this DNA in 1 x DRIP binding buffer (10 x DRIP binding buffer: 100 mM Sodium phosphate, 1.4 M NaCl, 0.5 % Triton X-100) was split into two tubes and incubated overnight with 4 µL of S9.6 antibody (New England Biolabs) while rotating. For total input samples, 10 % of DNA was taken before the immunoprecipitation. On the next day wash 40 µL/IP of Protein A and Protein G-coupled Dynabeads (Thermo Fisher Scientific), add to the DNA/antibody mix and incubate for 4 h on a rotating wheel at. 4°C Immunoprecipitated complexes were then washed 3 times each with ice-cold 1 x DRIP binding buffer. Finally, DNA was eluted by adding DRIP elution buffer (50 mM TRIS pH 8,10 mM EDTA, 0.5 % SDS) and roteinase K for 45 min at 55°C while shaking at 900 rpm. DNA was purified with phenol/chloroform extraction and finally eluted in 50 µl TE buffer. Before proceeding to library preparation, 4 µL were used to test enrichment by qPCR.
DNA:RNA hybrids were then treated with DNase (Thermo Fisher Scientific) for 45 min at 37°C. DNase was inactivated by inactivation buffer (Thermo Fisher Scientific) for 5 min at room temperature. After 5 min of centrifugation at 10’000 rpm the supernatant was transferred to a new PCR tube and libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s instructions.

treatment_protocol: Treatment as indicated

value: PDAC

value: KPCshMYC

value: KPC cells

value: Ptf1a-Cre, KRasG12D/+, Tp53R172H/+, pInd20 WTMYC-HA

value: doxycycline (1 µg/ml, 36 h), siExosc10 (36 h)


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-66
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

value: A375 cell line


title: DRIPc_siNTC_RBRIIImut_r1

description: Library name: DRIPc_siNTC_RBRIIImut_r1

value: Ptf1a-Cre, KRasG12D/+, Tp53R172H/+, pInd20 RBRIIIMUTMYC

value: doxycycline (1 µg/ml, 36 h), siNTC (36 h)


title: DRIPc_siNTC_WT_r1

description: Library name: DRIPc_siNTC_WT_r1


title: DRIPc_siNTC_RBRIIImut_r2

description: Library name: DRIPc_siNTC_RBRIIImut_r2


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-65
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: DRIPc_siExosc10_RBRIIImut_r2

description: Library name: DRIPc_siExosc10_RBRIIImut_r2


title: DRIPc_siExosc10_RBRIIImut_r1

description: Library name: DRIPc_siExosc10_RBRIIImut_r1


title: Microvasculature_45KO_rep1

description: Library name: 45

value: endothelial cell


title: DRIPc_RNaseH_siNTC_WT

description: Library name: DRIPc_RNaseH_siNTC_WT


title: Iv8_Day7

description: Library name: NSPF4.RIv8.Day7

value: blood


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-63
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

value: Melanoma

value: BRAF V600E


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-62
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

value: DMSO or Vemurafenib


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-64
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: DRIPc_RNaseH_siExosc10_RBRIIImut

description: Library name: DRIPc_RNaseH_siExosc10_RBRIIImut


title: DRIPc_RNaseH_siNTC_RBRIIImut

description: Library name: DRIPc_RNaseH_siNTC_RBRIIImut


title: DRIPc_RNaseH_siExosc10_WT

description: Library name: DRIPc_RNaseH_siExosc10_WT


title: Iv8_Day3

description: Library name: NSPF4.RIv8.Day3

value: PBMCs

value: Influenza vaccination


title: DRIPc_input_siNTC_WT

description: Library name: DRIPc_input_siNTC_WT


title: Pt8_Day0

description: Library name: NSPF4.RPt8.Day0


title: DRIPc_input_siExosc10_WT

description: Library name: DRIPc_input_siExosc10_WT


title: Iv8_Day1

description: Library name: NSPF4.RIv8.Day1


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-60
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: DRIPc_input_siExosc10_RBRIIImut

description: Library name: DRIPc_input_siExosc10_RBRIIImut


title: DRIPc_input_siNTC_RBRIIImut

description: Library name: DRIPc_input_siNTC_RBRIIImut


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-61
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: Gu10_Day7

description: Library name: NSPF4.RGu10.Day7


title: Gu10_Day3

description: Library name: NSPF4.RGu10.Day3


title: Gu10_Day1

description: Library name: NSPF4.RGu10.Day1


title: KPC_MYC_ChIPseq_RBRIII_IP_r1

description: Library name: KPC_MYC_ChIPseq_RBRIII_IP_r1

data_processing:
ChIP-Rx samples were mapped separately to the human GRCh38 genome and to the murine GRCm39 genome using Bowtie2 with -N 1 parameters. Subsequently, aligned reads were spike-normalized by dividing the number of mapped reads aligned to GRCh38 by the number of reads mapped to GRCm39 for each sample and multiplying this ratio with the smallest number of reads aligned to GRCm39 for any sample. For murine samples, human reads mapped to the t2t genome were used for spike normalization. For ChIPseqs performed using the HA antibody (*), samples were read normalized.
Assembly: GRCh38
Supplementary files format and content: bedgraph files for each condition and replicate.

extract_protocol:
To crosslink cells following treatment, 1% v/v formaldehyde was added to the cell culture medium and incubated 5 min rotating at RT. 125 mM glycine were added to stop the reaction and incubated for 5 min rotating at RT. Cells were then harvested in ice-cold PBS containing protease and phosphatase inhibitors (Sigma Aldrich). Cells were centrifuged (1,500 rpm, 20 min, 4°C) and the pellet was resuspended in ChIP lysis buffer I (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40). For spike-normalization, 10% murine NIH3T3 cells were added based on the cell number. After 20 min incubation on ice, nuclei were pelleted by centrifugation (1,500 rpm, 20 min, 4°C) and subsequently lysed by incubation in ChIP lysis buffer II (10 mM Tris pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate, 0.1% SDS) for 10 min on ice. The chromatin was fragmented using the Covaris Focused Ultrasonicator M220 (50 min; cycles/burst, 200; peak power, 75; duty factor, 10), and the required fragment size of 150-300 bp was validated by agarose gel electrophoresis. The fragmented chromatin was collected by centrifugation (14,000 rpm, 20 min, 4°C). For each IP, 100 µl of each Protein A and Protein G-coupled Dynabeads (Thermo Fisher Sientific) were pre-incubated overnight with 15 µg antibody in the presence of 5 mg/mL BSA at 4°C. Subsequently, beads were added to the chromatin and incubated overnight at 4°C on a rotating wheel. Immunoprecipitated protein-chromatin complexes were washed 3 times each with ice-cold ChIP wash buffer I (20 mM Tris pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), ChIP wash buffer II (20 mM Tris pH 8.1, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), ChIP wash buffer III (10 mM Tris pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate; including a 5 min incubation at 4°C), and once with ice-cold TE buffer. Protein-chromatin complexes were eluted twice by incubating in 150 µl elution buffer 100 mM NaHCO3, 1% SDS) for 15 min at RT. To remove potential RNA contaminations, IP and input samples were treated with RNase A for 1 h at 37°C. Samples were de-crosslinked by incubation at 65°C shaking overnight, and then treated with Proteinase K for 2 h at 45°C to degrade the protein. The amount of DNA was quantified using Quant-iT PicoGreen dsDNA assay (Thermo Fisher Scientific)
Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s instructions.

value: KPC shMYC

value: Ptf1a-Cre, KRasG12D/+, Tp53R172H/+, pInd20 RBRIIIMUTMYC-HA

value: doxycycline (1 µg/ml, 48 h)


title: KPC_MYC_ChIPseq_WT_IP_r2

description: Library name: KPC_MYC_ChIPseq_WT_IP_r2

value: PDAC


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-58
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: KPC_MYC_ChIPseq_WT_IP_r1

description: Library name: KPC_MYC_ChIPseq_WT_IP_r1

value: KPC cells


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-57
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities


title: KPC_MYC_ChIPseq_IgG

description: Library name: KPC_MYC_ChIPseq_IgG

value: Ptf1a-Cre, KRasG12D/+, Tp53R172H/+, merge


title: KPC_ChIPseq_input_pool_r2

description: Library name: KPC_ChIPseq_input_pool_r2

value: Ptf1a-Cre, KRasG12D/+, Tp53R172H/+, pInd20 WTMYC-HA/RBRIIIMUTMYC-HA


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-59
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

value: A375 cell line


title: brain vasc_Tg100_9 months, rep 2

description: Library name: 20210225_4

data_processing:
The data was sequenced on an Illumina NextSeq2000 sequencer and sequencing output files were demultiplexed and aligned using the Cellranger pipeline (v7.0.0, 10xGenomics). Mapping was done to the mouse mm10 transcriptome where the mouse Clec7a, and human NOTCH3 genes were manually added
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated files and matrix expression files

growth_protocol: All mice were housed in cages of 3-5 mice  with access to ad libitum food and water and kept under a 12h light dark circle at 50% humidity. Animal caretakers inspected animals daily.

extract_protocol:
Cells were extracted using our previously published protocol for microvascular isolation (PMID 37056377). In short, brains were digested into microvascular fragments, which were isolated using magnetic beads coupled to CD31 antibodies. These fragments were then washed and redigested into single cells, which were then loaded onto a 10x Genomics Chromium controller or Chromium iX.
Libraries were contructed according to manufacturers' instructions, using the 10x Genomics NextGEM single cell gene expression kit, v3.2

treatment_protocol: The mice were untreated and were analysed at their respective timepoints

tag: experimental condition

value: Control

tag: gender

value: female

value: 9 months


title: Iv8_Day0

description: Library name: NSPF4.RIv8.Day0

data_processing:
reads were trimmed with trimmomatic to remove adapter sequence and trailing bases with a quality score less than 20
trimmed reads were mapped to the rhesus macaque genome (RheMac8) using the STAR v2.7.10ac two-pass method
read counts were generated for each gene using HTCseq v2.0 based on overlap of any part of a read with an annotated gene exon
Assembly: RheMac8
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

value: blood


title: KPC_ChIPseq_input_pool_r1

description: Library name: KPC_ChIPseq_input_pool_r1


title: Gu10_Day0

description: Library name: NSPF4.RGu10.Day0


title: KPC_MYC_ChIPseq_RBRIII_IP_r2

description: Library name: KPC_MYC_ChIPseq_RBRIII_IP_r2


title: Lo9_Day7

description: Library name: NSPF3.RLo9.Day7


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-56
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

value: Melanoma


title: brain vasc_Tg100_6 months, rep 1

description: Library name: 20210616_1

value: 6 months


title: brain vasc_Tg100_6 months, rep 2

description: Library name: 20210616_4

value: male


description:
Library name: PerturbFate pooled screen Tri-omics Old RNA and ATAC-55
PerturbFate Tri-omics single-cell library containing Pre-existing RNA and ATAC modalities

value: BRAF V600E

value: DMSO or Vemurafenib


title: brain vasc_Tg100_6 months, rep 3

description: Library name: 20210618_2


title: brain vasc_Tg100_9 months, rep 1

description: Library name: 20210225_1


title: Lo9_Day3

description: Library name: NSPF3.RLo9.Day3

value: PBMCs

value: Influenza vaccination