title: CD4i_R2L40_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L40_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

value: 48 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

value: no, no, no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

tag: description donor_sex

tag: suspension type

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

value: pooled:D1 - Hispanic or Latin American, D2 - African American, D3 - African American, D4 - Asian

value: CRISPR interference

value: constitutive

value: CD4-positive, alpha-beta T cell

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: 10x Gene Expression Flex


title: seCLIP_U2O2MYCtetOn_MYC_IP_R1_DOX

status: Public on Feb 06 2026

type: SRA

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

library_source: transcriptomic

data_processing:
For seCLIP experiments, the analysis was performed according to the Skipper workflow (Boyle et al 2023). Fastq files of CLIP and input samples were normalized to sequencing depth using seqtk. Per condition, the same input subsampled using different random seeds was provided. For samples spiked with cDNA, reads mapping to the DNA spike-in were identified using STAR (Dobin et al. 2013). Accordingly, fastq files were normalized according to the number of reads mapping to the spike-in in each sample. Multiplexed eCLIPs were demultiplexed using UMItools (Smith et al. 2017) and used without further normalization. Subsequently, samples were trimmed utilizing skewer (Jiang et al. 2014) and extracts unimolecular identifiers (UMIs) using fastp (Chen et al 2018) and aligned to the human genome version GRCh38 for all MYC seCLIP and eCLIP experiments or to the murine genome version GRCm38 for TLR3 seCLIPs using STAR (Dobin et al. 2013). PCR duplicates were removed by using UMItools (Smith et al. 2017). To identify genomic regions with enriched signal in the CLIP over the SMI input, the automated Skipper analysis pipeline was used 46. The GENCODE version 38 gene annotations were obtained from gencodegenes.org. Transcripts were filtered based on total RNA-seq data in K562 cells with a minimum expression level of one transcript per million. A custom parse_gff.R script (Boyle et al 2023) was used to define RNA feature and transcript types (CDS_START ‘Start codon’, CDS_STOP ‘Stop codon’, CDS ‘CDS’ (of protein coding genes), UTR5 ‘5’ UTR’, UTR3 ‘3’ UTR’, EXON_SMALL ‘ncRNA’ (including snoRNA, snRNA, scaRNA, scRNA, miRNA, vault_RNA, rRNA, rRNA_pseudogene, Mt_rRNA, Mt_tRNA, ribozyme, sRNA, misc_RNA), INTRON ‘Intron’, EXON_LNCRNA ‘lncRNA’ (including lncRNA, processed_transcript), EXON_MRNA ‘Other’ (including Immunoglobulin (Ig) variable chain and T-cell receptor (TcR) genes, retaind_intron, non_stop_decay, protein_cidubg_LoF, nonsense_mediated_decay, TEC), PSEUDO ‘Pseudogene’ (including inactivated immunoglobulin genes, pseudogene, polymorphic_pseudogene, translated_pseudogene, translated_unprocessed_pseudogene, pseudogene, transcribed_unprocessed_pseudogene, transcribed_processed_pseudogene, transcribed_unitary_pseudogene, unitary_pseudogene, processed_pseudogene, unprocessed_pseudogene), PRIMIRNA ‘pri-miRNA’, SS3_ADJ ‘3’ splice site adj. (100 bp intronic region downstream of the 3’ splice site), SS3_ADJ ‘5’ splice site adj. (100 bp intronic region upstream of the 5’ splice site), SSB_ADJ ‘Branch point prox. (500 bp intronic region centered around the branch point), SS3_PROX ‘3’ splice site prox. (500 bp intronic region downstream of the 3’ splice site), SS5_PROX ‘5’ splice site prox. (500 bp intronic region upstream of the 5’ splice site), SSB_PROX ‘Branch point prox. (500 bp intronic region centered around the branch point)). Each feature was tiled into evenly spaced windows of maximum 100 nucleotides in length and then tested for enrichment in immunoprecipitated over SMI samples using a beta-binomial distribution that accounts for overdispersion in read counts and GC bias. For the analysis of TLR3 seCLIPs by Skipper, statistical thresholds calculated from the fit of the beta-binomial distribution were derived from the automated Skipper pipeline (only windows passing a 20% false discovery rate in both replicates of each experiment were considered enriched), while for MYC seCLIP experiments the statistical thresholds were customized. Within individual replicates, windows that passed a p value threshold p<0.05 were considered enriched windows. Of these, windows that were identified in both replicates and passed a 20% FDR in at least one of the replicates were designated as reproducibly enriched windows. Windows that were called in more than 17% of all K562 and HepG2 ENCODE eCLIP samples were blacklisted and removed. For calling TLR3 reproducible enriched windows in the TLR3-IPs, reproducible enriched windows identified in IgG and NXL controls were blacklisted additionally. Reproducible windows were fine mapped by centering them around the local maximum of binding enrichment per window and adjusted to a fixed size of 75 nt. For RNA motif identification the HOMER script findMotifsGenome.pl (http://homer.ucsd.edu/homer/) was run with the following options: -preparsedDir <directory> -size given -rna -nofacts -S 20 -len 5,6,7,8,9 -nlen 1 -bg <background windows>. A random RNA background was specified by selecting random 75 nt windows belonging to the same RNA feature group. To visualize similarities in binding characteristics to different RNA transcript types in a t-SNE plot, performed MYC seCLIP data was pooled with ENCODE reference RBP eCLIP data, and plotted together in a two-dimensional space using the Rtsne package (https://lvdmaaten.github.io/tsne/). Several random seeds were tested to confirm a reproducible association of the queried protein with a certain feature type. Enrichment odds ratios (ORs), represented by the enrichment of observed CLIP enrichment over a baseline CLIP enrichment per RNA feature type, were calculated based on the call_enriched_windows.R script (Boyle et al 2023). For metagenes and heatmaps, log2FCs of CLIP/input were determined based on deduplicated bam files using bamCompare and plotted using deeptools (Ramirez et al. 2014) using the –sortUsingSamples and --averageTypeSummaryPlot mean options. Intersections between different sets of reproducible enriched windows were generated and visualized using intervene (Khan et al. 2014). Publicly available ENCODE eCLIP and control datasets were downloaded and log2 ratios of CLIP over SMIs were calculated using bamCompare and plotted over called windows of interest using deeptools (Ramirez et al. 2014).
Assembly: GRCh38 (MYC seCLIPs/eCLIPs) or GRCm38 (TLR3 seCLIPs)
Supplementary files format and content: bedgraph files

molecule: total RNA

organism: Homo sapiens

source_name: Bone

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

extract_protocol:
seCLIP (single-end enhanced cross-linking and immunoprecipitation) sequencing was performed as described in Van Nostrand et al. and Blue et al. All seCLIP experiments were conducted in duplicates with one pooled size-matched inputs per condition. Per IP sample, 30-40 million cells were crosslinked with UV-C light (254 nm, 2 min, 400 mJ/ cm2). Not UV-crosslinked cells were used as negative control. Cells were lysed in seCLIP lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% (vol/vol) Igepal CA-630, 0.1% (vol/vol) SDS and 0.5% (wt/vol) sodium deoxycholate) supplemented with a protease inhibitor cocktail (Sigma-Aldrich) and 440 U/ml murine RNase inhibitor (NEB), and 10% of crosslinked murine NIH 3T3 cells were added to each sample as spike-in. Samples were sonicated using the M220 Focused-ultrasonicator (Covaris) for 3 min. Next, samples were treated with 40 U RNase I (Thermo Fisher Scientific) and 10 U Turbo DNase for 5 min at 37  °C shaking at 1200 rpm. After centrifugation at 15,000 g for 10 min at 4 °C, supernatants were added to pre-coupled protein A/G Dynabeads (62.5 µl each per IP) to the antibody of interest (10 µg per sample) and incubated rotating at 4 °C overnight. 2% v/v of the lysate (20 µl) including beads were taken as SMInput, both for the RNA gel and for the diagnostic western blot. The remaining lysate was magnetically separated and washed 2 times with high-salt wash buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1% (vol/vol) Igepal CA-630, 1 mM EDTA, 0.1% (vol/vol) SDS and 0.5% (wt/vol) sodium deoxycholate), followed by a transition wash which was conducted by adding 500 µl of high-salt wash buffer, mixing and then adding 500 µl of wash buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, 0.2% (vol/vol) Tween-20 and 5 mM NaCl). Three more washes with wash buffer were conducted, before the immunoprecipitated RNA was dephosphorylated on-beads using the FastAP and PNK enzymes. Therefore, 1X FastAP buffer (Thermo Fisher Scientific), 80 U murine RNase inhibitor (NEB), 4 U Turbo DNase (NEB) and 3 U FastAP enzyme (Thermo Fisher Scientific) were added in a total volume of 50 µl and incubated for 20 min at 37 °C shaking at 1,200 rpm. Without removing the phosphorylation mix, 150 µl PNK master mix (1x PNK7 buffer (700 mM Tris-HCl pH 7, 100 mM MgCl2), 40 U PNK4 enzyme) were added and incubated for another 20 min at 37 °C (shaking at 1,200 rpm). Samples were then washed with 200 µl seCLIP high-salt wash buffer once, followed by a transition wash and three further washings with seCLIP wash buffer. 10% of the IP samples were saved for biotin-labeling to visualize the RNA cross-linked to the protein of interest. To the remaining RNA, InvRiL19 RNA adapters (IDT) were ligated by incubating the samples with 25 µl 3’RNA linker mix (1.2x RNA ligase buffer (no DTT), 1.2 µM ATP, 3.6% DMSO, 0.024% v/v Tween-20, 18% w/v PEG 8000, 0.8 U murine RNase inhibitor (NEB), 72 U T4 RNA ligase high-concentration enzyme) rotating at RT for 75 min. Beads were then washed as follows: 1x wash buffer, transition wash to high-salt wash buffer, 1x high-salt wash buffer, transition wash to wash buffer, 3x wash buffer. After the final wash, 20% per IP sample was kept for the diagnostic western blot. To all IP and SMInput samples, NuPAGE LDS buffer (Thermo Fisher Scientific) containing DTT (98 mM, freshly prepared) was added before samples were incubated at 70 °C for 10 min. After magnetically separating the beads from the lysates, RNA-protein complexes were separated by gel electrophoresis using 8% Bis-Tris gels, and transferred onto nitrocellulose or methanol-activated PVDF membranes for the RNA gels and western blots, respectively. The diagnostic western blot was used as a guide to cut out the region of the membrane starting from the observed size of the protein of interest and extending until the maximal expected size of the RNA-protein complexes (but at least ~75 kDa larger). Membrane pieces were then sliced into ~2 mm x 2 mm squares and transferred into a fresh tube. To digest the protein, membranes were incubated with 24 U proteinase K (Roth) in PKS buffer for 20 min at 37 °C followed by an incubation at 50 °C for another 20 min. RNA was extracted using the RNA Clean and Concentrator-5 kit (Zymo) following the manufacturer’s instructions, and RNA was eluted in 10 µl H2O. Next, SMInput samples were dephosphorylated by incubating each SMInput RNA sample with 20 µl of dephosphorylation master mix (1x FastAP buffer (Thermo Fisher Scientific), 40 U murine RNase inhibitor (NEB), 2 U FastAP enzyme (Thermo Fisher Scientific) incubating at 37 °C for 20 min shaking at 1,200 rpm, followed by another 20 min incubation at 37 °C (1,200 rpm) in PNK master mix (1.05x PNK7 buffer, 5.26 mM DTT, 2 U Turbo DNase (NEB), 40 U T4 PNK enzyme). RNA was purified using the Clean & Concentrator 5 kit (Zymo) as described before. To append the SMInput RNA with 3’ RNA adapters, 1.5 µl 100% DMSO and 0.5 µl InvRil19 adapter were added per sample and incubated at 65 °C for 2 min. 13.5 µl of SMInput RNA ligation master mix (0.976x RNA ligase buffer (NEB), 0.976 mM ATP, 2.93% DMSO, 0.02% v/v Tween-20, 14.63 w/v PEG 8000, 12 U murine RNase inhibitor, 36 U T4 RNA ligase high-concentration enzyme) were added and samples were incubated at RT for 60 min on a rotating wheel. To purify the RNA, 15 µl MyOne Silane Dynabeads per sample were washed ones with RLT buffer (Qiagen), resuspended in RLTW buffer (RLT + 0.025% v/v Tween-20) and added to the RNA. An equal volume of 100% EtOH was added and samples were incubated at RT for 10 min, before samples were washed three times with 80% v/v EtOH. After the final wash, beads were tried and subsequently eluted in 9.5 µl of TT elution buffer (10 mM Tris-HCl pH 7.4, 0.1 mM EDTA, 0.01% (vol/vol) Tween-20). All IP and SMInput samples were next reverse transcribed using the SuperScript III enzyme. For that, 1 µl of 5 µM InvAR17 RT primer  and 1 µl of 10 mM dNTPs were added per RNA sample and incubated for 2 min at 65 °C. 10 µl of reverse transcription master mix (1x first strand buffer (Invitrogen), 5 mM DTT, 8 U murine RNase inhibitor (NEB), 120 U Superscript III enzyme (Invitrogen)) were added to each sample and incubated at 55 °C for 20 min. 2.5 µl ExoSAP-IT (Thermo Fisher Scientific) were used to remove unincorporated dNTPs and RT primers (37 °C, 15 min) before 1 µl of 0.5 M EDTA was added. To remove RNA stands, 3 µl of 1 M sodium hydroxide were added and incubated at 70 °C for 10 min. 3 µl of 1 M hydrochloric acid were added to neutralize the sodium hydroxide. RNAs were again purified using MyOne Silane beads as described earlier. After drying, 2.5 µl of 5’ adapter master mix (4.66 µM InvRand3Tr3 adapter and 7.77% DMSO in TT elution buffer) were directly added to the beads and incubated at 70 °C for 2 min before 7.8 µl of ligation master mix (0.097% RNA ligase buffer (NEB), 1.94 mM DTT, 0.97 mM ATP, 0.019% v/v Tween-20, 17.48% PEG 8000, 30 U T4 RNA ligase high-concentration enzyme (NEB), 5’ deadenylase enzyme (NEB)) and incubated at RT overnight. RNA was subsequently purified using MyONE silane beads as described earlier. To estimate the number of cycles required for the final PCR, qPCRs were conducted. For multiplexing of eCLIPs, each RNA adapters containing unique barcodes (RNA_A01, RNA_B06, RNA_C01, RNA_D08, RNA_X1A, RNA_X1B) based on 44 were ligated to the RNA after immunoprecipitation. At least one third of each sample was mixed and further processed as a pool. SMI were separately run through the gel and barcoded RNA adapters were ligated after RNA isolation from the nitrocellulose membranes. As for the IP samples, inputs were merged to a pool and processed together. For total input samples, 20 µl of lysate were taken before the immunoprecipitation. Using the eCLIP adapter strategy 44, the in-line barcode on read 1 was later used to demultiplex the samples bioinformatically. Samples labeled with * contain 10% murine spike-in (NIH 3T3) that has not been used for further analysis.
cDNA libraries were amplified using a three-step, six cycle amplification followed by a two-step amplification bringing each sample to its calculated number of cycles. The final libraries were either purified using an agarose gel-based strategy cutting out gel pieces corresponding to 175-300 bp in size and purifying the DNA using the Qiagen MiniElute gel extraction kit following the manufacturer’s instructions. Alternatively, samples were cleaned using a two-sided selection with SPRI beads (0.7x right-sided, followed by a 1x left-sided selection). The quality and quantity of the libraries were assessed using the Fragment Analyzer (Agilent). To account for different cycle number used during final PCR amplification (e.g. for IgG controls), a DNA spike-in containing adaptors for the Illumina index primers used in the final PCR was generated and equal amounts were added to the immunoprecipitation samples prior to the final PCR for indicated experiments, resulting in different relative ratios of CLIP:DNA spike-in in the final libraries as observed upon measurement using the fragment analyzer.

treatment_protocol: Treatment as indicated

tag: tissue

value: Bone

tag: cell line

tag: cell type

value: Osteosarcoma cell line

tag: genotype

value: MYC-Tet-On

tag: treatment

value: doxycycline (1 µg/ml, 24 h)


title: Galns m/m, 8 dpf, rep  4

city: Greenwood

first: Heather

last: Flanagan-Steet

state: South Carolina

address: 113 Gregor Mendel Cir.

department: J.C. Self Research Institute

country: USA

institute: Greenwood Genetic Center

description:
Library name: HOM-4
GalnsHOM.4

data_processing:
Sequence reads were trimmed using Trimmomatic v.0.36. The trimmed reads were mapped to the  Danio rerio GRCz10.89 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
From the resulting BAM files, unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
The gene hit counts table was used for downstream differential expression analysis.
Assembly: GRCz10.89
Supplementary files format and content: csv text file contains raw gene hit counts for each sample

molecule: polyA RNA

organism: Danio rerio

source_name: whole animal

growth_protocol: Animals were maintained following standard zebrafish husbandry protocols. The galns mutant line (sa31602) was generated by the Sanger Center Tilling Screen and ultimately acquired from the Zebrafish International Resources Center (ZIRC). Gene specific primers were used to amplify a region surrounding the galns c.539+1G>A (Accession:NM_001080641) mutation, and galns+/m were identified by high resolution melt analysis of genomic DNA (gDNA). Heterozygous animals were outcrossed with the hybrid wild type strain (TLAB) 5 generations prior to experimental analyses.

extract_protocol:
Embryos were genotyped and collected at 8 dpf. Each sample for sequencing was comprised of 15 larvae, collected in 0.5 mL TRIzol reagent (Thermo), and snap frozen on dry ice. Frozen samples were shipped on dry ice to Azenta Life Sciences to complete RNA extraction, library extraction, and sequencing.
Libraries for RNA-seq were generated by Azenta Life Sciences. In short, mRNA was selected through poly-A enrichment, fragmented, and randomly primed. First and second strand cDNA synthesis was performed, followed by end repair, 5' phosphorylation, and dA-tailing. Finally, adapters were ligated and enriched via PCR prior to sequencing.

value: whole animal

value: galns m/m

tag: time

value: 8 dpf


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 New RNA-13
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

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

value: BRAF V600E

value: DMSO or Vemurafenib


title: CD4i_R2L38_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description: Library name: CD4i_R2L38_GEX_lib

library_source: transcriptomic single cell

data_processing:
Raw data from pooled samples were processed by Cell Ranger v9.0.1 using the 2024-A probe set reference. UMI counts were demultiplexed back to each individual donor and stimulation condition using the barcodes in the sample_name: sample_probe_barcode metadata column.
raw_matrix_genome_annotation:Chromium Human Transcriptome Probe Set v1.1.0: 2024-A , raw_matrix_value_units:UMI, raw_matrix_assays: scRNA-seq, CRISPR interference, raw_matrix_feature_keys:gene symbol for scRNA-seq, guide_id for CRISPR interference guides, raw_matrix_background_barcodes_included:False
Assembly: GRCh38
Supplementary files format and content: h5, count matrix: scRNA-seq and crispr guide UMI

source_name: blood

extract_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). After isolation (day 0), 30 million naive human CD4+ T cells were seeded at 1 x 106 cells/ml in X-VIVO 15 (Lonza Bioscience, catalog no. 04–418Q) supplemented with 5% fetal calf serum (FCS) (cXVIVO) and 200 IU/ml of recombinant human IL-2 (Amerisource Bergen, catalog no. 10101641). Cells were activated using ImmunoCult human CD3/CD28/CD2 T cell activator (10990, STEMCELL Technologies) at 25 µl/ml. The next morning, cells were transduced with 2% v/v concentrated ZIM3KRAB-dCas9-BlastR lentivirus. In the afternoon, cells were transduced with 0.1% v/v [multiplicity of infection (MOI) ~ 0.2] genome-scale sgRNA library lentivirus. At day 3, cells were centrifuged and resuspended with above medium supplemented with 200 IU/mL IL-2. Blasticidin and puromycin were added to 10 µg/mL and 2 µg/mL final concentrations, respectively. At day 5, cells were counted and diluted to 5 x 105 cells/mL with cXVIVO supplemented with 200 IU/mL IL-2 and 10 µg/mL blasticidin. Recombinant human IL-7 (R&D Systems, catalog no. 207-IL) was also added to a final concentration of 5 ng/mL. At day 7, cells were counted and diluted to 7.5 x 105 cells/mL with cXVIVO supplemented with 200 IU/mL IL-2, 5 ng/mL IL-7 and 10 µg/mL blasticidin. At both day 8 and day 10, cells were centrifuged and resuspended at 5 x 105 cells/mL with cXVIVO supplemented with 200 IU/mL IL-2 and 5 ng/mL IL-7. At day 12 morning, cells were centrifuged and resuspended at 1 x 106 cells/ml with cXVIVO supplemented with 200 IU/mL IL-2 and split into three populations. The first population (Rest) was kept at a resting state without restimulation and harvested in the afternoon after 8 hours. The second population (Stim8hr) was restimulated by adding 12.5 µL/ml ImmunoCult human CD3/CD28/CD2 T cell activator and harvested in the afternoon after 8 hours. The third population (Stim48hr) was restimulated by adding 12.5 µL/ml ImmunoCult human CD3/CD28/CD2 T cell activator and harvested after 48 hours.
GEM-X Flex Sample Preparation v2 Kit (10x genomics, catalog no. 1000781) per the manufacturer’s instructions

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

value: 48 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

tag: donor weight

tag: donor height

tag: donor smoker

value: no, no, no, no

value: ACDA

value: STEMCELL technologies

value: pooled:D1 - female, D2 - female, D3 - female, D4 - male

value: cell

value: adult stage

value: TRUE

value: normal

value: formaldehyde fixed -80C

tag: donor ethnicity

value: pooled:D1 - Hispanic or Latin American, D2 - African American, D3 - African American, D4 - Asian

tag: genetic perturbation_strategy

tag: crispr system_type

tag: suspension enriched_cell_types

tag: suspension depletion_factors

tag: library protocol

tag: sample probe_barcode


title: seCLIP_U2O2MYCtetOn_MYC_IP_R1_EtOH

tag: tissue

value: Bone

tag: cell line

tag: cell type

value: Osteosarcoma cell line

value: MYC-Tet-On

value: EtOH (24 h)


title: CD4i_R2L36_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L36_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

tag: treatment

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: donor blood_type

tag: anticoagulant

tag: source

tag: description donor_sex

tag: suspension type

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

value: CRISPR interference

value: constitutive

value: CD4-positive, alpha-beta T cell

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: 10x Gene Expression Flex


title: Galns m/m, 8 dpf, rep  2

description:
Library name: HOM-2
GalnsHOM.2

value: whole animal

tag: genotype

value: galns m/m

tag: time

value: 8 dpf


title: CD4i_R2L37_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L37_GEX_lib

tag: experimental perturbation

value: 48 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

tag: donor weight

tag: donor height

tag: donor smoker

value: no, no, no, no

value: ACDA

value: STEMCELL technologies

value: pooled:D1 - female, D2 - female, D3 - female, D4 - male

value: cell

value: adult stage

value: TRUE

value: normal

value: formaldehyde fixed -80C

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: crispr system_type

tag: suspension enriched_cell_types

tag: suspension depletion_factors

tag: library protocol

tag: sample probe_barcode


title: Galns m/m, 8 dpf, rep  1

description:
Library name: HOM-1
GalnsHOM.1

tag: tissue


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-12
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

tag: cell line

value: A375 cell line

tag: cell type

value: Melanoma

value: BRAF V600E

tag: treatment

value: DMSO or Vemurafenib


title: seCLIP_U2O2MYCtetOn_IgG_IP_DOX

value: Bone

value: Osteosarcoma cell line

tag: genotype

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h)


title: seCLIP_U2O2MYCtetOn_MYC_IP_R2_EtOH

value: EtOH (24 h)


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-11
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: Galns m/m, 8 dpf, rep  3

description:
Library name: HOM-3
GalnsHOM.3

value: whole animal

value: galns m/m

tag: time

value: 8 dpf


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-14
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: CD4i_R2L35_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L35_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

value: 48 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

value: no, no, no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

value: pooled:D1 - female, D2 - female, D3 - female, D4 - male

tag: suspension type

value: cell

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

tag: sample preservation_method

value: pooled:D1 - Hispanic or Latin American, D2 - African American, D3 - African American, D4 - Asian

value: CRISPR interference

value: constitutive

value: CD4-positive, alpha-beta T cell

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: 10x Gene Expression Flex


title: seCLIP_U2O2MYCtetOn_IgG_IP_EtOH

tag: tissue

value: Bone

tag: cell line

tag: cell type

value: Osteosarcoma cell line

value: MYC-Tet-On

value: EtOH (24 h)


title: CD4i_R2L34_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L34_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

tag: treatment

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

value: 48 hr stimulation

tag: donor weight

tag: donor height

tag: donor smoker

value: adult stage

value: TRUE

value: normal

value: formaldehyde fixed -80C

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: crispr system_type

tag: suspension enriched_cell_types

tag: suspension depletion_factors

tag: library protocol

tag: sample probe_barcode


title: seCLIP_K562_IgG_IP_R2

source_name: hematopoietic

value: hematopoietic

value: chronic myeloid leukemia cells


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-09
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


title: CD4i_R2L31_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L31_GEX_lib

tag: experimental perturbation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

value: no, no, no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

value: pooled:D1 - female, D2 - female, D3 - female, D4 - male

tag: suspension type

value: cell

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: pooled:D1 - Hispanic or Latin American, D2 - African American, D3 - African American, D4 - Asian

value: CRISPR interference

value: constitutive

value: CD4-positive, alpha-beta T cell

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: 10x Gene Expression Flex


title: B2-1_mCheHI_CitHI

city: Houston

first: Isaac

middle: B

last: Hilton

state: Texas

address: 6500 Main St., BRC Rm 660

institute: Rice University

description: Library name: Library2

library_source: genomic

data_processing:
Sequencing reads were processed as described previously using the HT-recruit pipeline. Briefly, reads from each quadrant were grouped by fluorophore expression level, mCherryhi/lo and Citrinehi/lo. A custom reference was generated using Bowtie from the designed p300 library using the script ‘makeIndices.py’ and reads were aligned with a mismatch allowance of 3 using the script ‘makeCounts.py’. The enrichments for each domain between HI and LO samples were determined using the script ‘makeRhos.py’. Domains with < 5 reads were adjusted to 5 to avoid inflation of enrichment values due to low sequencing depth.
Assembly: Custom reference
Supplementary files format and content: individual CSV files corresponding to each sample counting reads for reporter expression and gene activation levels
Library strategy: Targeted Amplicon Sequencing

molecule: genomic DNA

growth_protocol: HEK293T (ATCC, CRL-11268) were cultured in  ATCC-recommended DMEM media supplemented with 10% FBS (Sigma-Aldrich) and 1% pen/strep (100units/ mL penicillin, 100µg/ mL streptomycin; Gibco) at 37° C and 5% CO2.

extract_protocol:
Genomic DNA was extracted with a DNEasy Blood and Tissue Kit (QIAgen) following manufacturer’s protocol for each bin extracted from the sorting experiment (at 1e5 cells). DNA was eluted in EB and sequences were amplified by PCR.
A two-step PCR process was used to append Illumina adapters as overhangs. 6x reactions were prepared with 1ug of genomic DNA, 5uL of each 10uM primer, and 25uL of NEBnext 2x Master Mix (NEB) was used for the first reaction. PCR amplification parameters were as follows: 3 minutes at 98˚C, then 21x cycles of 98˚C for 10 sec, 68˚C for 30 sec, 72˚C for 30 sec, and a final step of 72˚C for 2 minutes. Resulting DNA was gel extracted using a QIAgen Gel Extraction Kit (QIAgen). A second PCR was performed with the Illumina indexed primers with the following PCR amplification parameters: 3 minutes at 98˚C, then 11x cycles of 98˚C for 10 sec, 68˚C for 30 sec, 72˚C for 30 sec, and a final step of 72˚C for 2 minutes. Resulting DNA was again gel extracted using a QIAgen Gel Extraction Kit (QIAgen). Libraries were then quantified with a Qubit HS dsDNA High Sensitivity Kit (Thermo Fisher), pooled with 15% PhiX control (Illumina), and sequenced on an Illumina HiSeq 3000.

treatment_protocol: 5e6 reporter HEK293T cells expressing 9xTetO-SV40core were transduced with the lentiviral library containing the library of p300 variants on Day 0 by reverse transduction with 10ug/mL polybrene. On Day 2, transduced cells were selected with 10ug/mL blasticidin. Cells were maintained in 3 15cm2 tissue culture plates. On Day 7, cells were treated with 1ug/mL doxycycline for 2 days. On Day 9, cells were collected for cell sorting. Citrine and mCherry levels were measured on a Sony MA900 cell sorter and ~100k cells were collected per bin corresponding to mChelo/Citlo, mChelo/Cithi, mChehi/Citlo, mChehi/Cithi.

tag: cell line

tag: cell type

value: Human embryonic kidney cells

tag: treatment

value: AAVS1 reporter and transduced at MOI ~0.3 with rTetR-p300var library


title: CD4i_R2L28_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L28_GEX_lib

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

value: 48 hr stimulation

tag: donor weight

tag: donor height

tag: donor smoker

value: adult stage

value: TRUE

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: crispr system_type

tag: suspension enriched_cell_types

tag: suspension depletion_factors

tag: library protocol

tag: sample probe_barcode


title: seCLIP_U2O2MYCtetOn_Input_DOX

value: Bone

value: Osteosarcoma cell line

tag: genotype

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h)


title: B4-2_mCheLO_CitLO

description: Library name: Library8


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-05
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line

value: Melanoma

value: BRAF V600E

value: DMSO or Vemurafenib


title: CD4i_R2L32_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L32_GEX_lib

tag: experimental perturbation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

value: no, no, no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

value: pooled:D1 - female, D2 - female, D3 - female, D4 - male

tag: suspension type

value: cell

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: pooled:D1 - Hispanic or Latin American, D2 - African American, D3 - African American, D4 - Asian

value: CRISPR interference

value: constitutive

value: CD4-positive, alpha-beta T cell

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: 10x Gene Expression Flex


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-10
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

tag: cell line

tag: cell type

tag: treatment


title: seCLIP_U2O2MYCtetOn_Input_EtOH

tag: tissue

value: Bone

value: Osteosarcoma cell line

value: MYC-Tet-On

value: EtOH (24 h)


title: B3-2_mCheHI_CitLO

description: Library name: Library7

value: Human embryonic kidney cells

value: AAVS1 reporter and transduced at MOI ~0.3 with rTetR-p300var library


title: seCLIP_K562_MYC_IP_R1

value: hematopoietic

value: chronic myeloid leukemia cells


title: CD4i_R2L30_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L30_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

value: 48 hr stimulation

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

tag: donor weight

tag: donor height

tag: donor smoker

value: no, no, no, no

value: ACDA

value: STEMCELL technologies

value: adult stage

value: TRUE

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: crispr system_type

tag: suspension enriched_cell_types

tag: suspension depletion_factors

tag: library protocol

tag: sample probe_barcode


title: seCLIP_K562_IgG_IP_R1


title: B1-2_mCheLO_CitHI

description: Library name: Library5


title: CD4i_R2L33_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L33_GEX_lib

tag: experimental perturbation

tag: donor ids

tag: donor age

tag: donor blood_type

tag: anticoagulant

tag: source

tag: description donor_sex

value: pooled:D1 - female, D2 - female, D3 - female, D4 - male

tag: suspension type

value: cell

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

value: pooled:D1 - Hispanic or Latin American, D2 - African American, D3 - African American, D4 - Asian

value: CRISPR interference

value: constitutive

value: CD4-positive, alpha-beta T cell

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: 10x Gene Expression Flex


title: B2-2_mCheHI_CitHI

description: Library name: Library6

tag: cell line

tag: cell type

value: Human embryonic kidney cells

tag: treatment

value: AAVS1 reporter and transduced at MOI ~0.3 with rTetR-p300var library


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-06
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


title: seCLIP_K562_MYC_IP_R2

tag: tissue

value: hematopoietic

value: chronic myeloid leukemia cells


title: B4-1_mCheLO_CitLO

description: Library name: Library4


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-08
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-07
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: B1-1_mCheLO_CitHI

description: Library name: Library1


title: B3-1_mCheHI_CitLO

description: Library name: Library3


title: CD4i_R2L29_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L29_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

value: 48 hr stimulation

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

tag: donor weight

tag: donor height

tag: donor smoker

value: no, no, no, no

value: ACDA

value: STEMCELL technologies

value: adult stage

value: TRUE

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: crispr system_type

tag: suspension enriched_cell_types

tag: suspension depletion_factors

tag: library protocol

tag: sample probe_barcode


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-04
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

tag: cell line

value: A375 cell line

value: Melanoma


title: seCLIP_K562_Input_MYC

tag: cell type


title: seCLIP_K562_Input_IgG


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-03
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: BRAF V600E

tag: treatment

value: DMSO or Vemurafenib


title: dCas9-p300 I1417N_rep2[RNA-Seq, 2]

description: Library name: Library8

data_processing:
Sequencing reads were aligned to the human genome (GRCh38.p13) using the STAR (Spliced Transcripts Alignment to a Reference, version 2.7.9a) against the Gencode Release 36 primary assembly annotation. Sequence alignment was conducted on an Amazon Web Services Elastic Compute Cloud Instance (EC2) with 64 GB of memory and 256 GB of storage. Read quantification and differential expression analysis were conducted on R (version 4.2.2). Read quantification was carried out with featureCounts. Differential expression analysis was performed using DESeq2. Volcano plots, PCA plots, and heat maps were created on DESeq2 using the analyzed data.
Assembly: GRCh38.p13
Supplementary files format and content: individual tab-delimited text files corresponding to each sample includes log2rpm values

extract_protocol:
72 hours post-transfection RNA was isolated using the RNeasy Plus mini kit (Qiagen). RNA integrity was first assessed using a Bioanalyzer 2200 (Agilent)
RNA-seq libraries were constructed using the TruSeq Stranded Total RNA Gold (Illumina, RS-122-2303).The qualities of RNA-seq libraries were verified using the Tape Station D1000 assay (Tape Station 2200, Agilent Technologies) and the concentration of RNA-seq libraries were checked again using real time PCR (QuantStudio 6 Flex Real time PCR System, Applied Biosystem).RNA sequencing libraries were prepared with ERCC92 spike-in controls. Libraries were normalized and pooled prior to sequencing. Sequencing was performed using an Illumina Hiseq 3000 with paired end 75 base pair reads.

treatment_protocol: Approximately 150000 HEK293T cells were plated the day before transfection and then transfected using Lipofectamine 3000 (Invitrogen, USA) as per manufacturer’s instruction in 24-well plates using 375ng of dCas9 (or dCas9-p300 variant) expression plasmid and 125ng of equimolar pooled gRNAs for HS2.

value: Human embryonic kidney cells

value: Transfected with dCas9-p300 I1417N in presence of HS2 gRNA


title: CD4i_R2L26_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L26_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

tag: donor ids

tag: donor age

tag: donor blood_type

tag: anticoagulant

tag: source

tag: description donor_sex

value: pooled:D1 - female, D2 - female, D3 - female, D4 - male

tag: suspension type

value: cell

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

value: pooled:D1 - Hispanic or Latin American, D2 - African American, D3 - African American, D4 - Asian

value: CRISPR interference

value: constitutive

value: CD4-positive, alpha-beta T cell

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: 10x Gene Expression Flex


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-02
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

tag: genotype


title: DRIPc_Rx_U2OSMYCtetOn_DMSO_RNaseH_r1

data_processing:
Fastq files of DRIPc-Rx samples were mapped separately to murine GRCm39 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 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).
Assembly: GRCh38
Supplementary files format and content: bedgraph files

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.

tag: tissue

value: Bone

value: Osteosarcoma cell line

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h); DMSO; 60 U RNase H1 during sample preparation


title: CD4i_R2L27_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L27_GEX_lib

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

value: 48 hr stimulation

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

tag: donor weight

tag: donor height

tag: donor smoker

value: no, no, no, no

value: ACDA

value: STEMCELL technologies

value: adult stage

value: TRUE

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: crispr system_type

tag: suspension enriched_cell_types

tag: suspension depletion_factors

tag: library protocol

tag: sample probe_barcode


title: PerturbFate pooled screen Dual-omics-64

description:
Library name: PerturbFate pooled screen Dual-omics-64
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad

tag: cell line

value: A375 cell line

tag: cell type

value: Melanoma

value: BRAF V600E

tag: treatment

value: DMSO or Vemurafenib


title: dCas9-p300 D1399Y_rep2[RNA-Seq, 2]

description: Library name: Library6

value: Human embryonic kidney cells

value: Transfected with dCas9-p300 D1399Y in presence of HS2 gRNA


title: DRIPc_Rx_U2OSMYCtetOn_Input_DMSO_r1

value: Bone

value: Osteosarcoma cell line

tag: genotype

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h); DMSO


title: DRIPc_Rx_U2OSMYCtetOn_DMSO_r1

tag: tissue


title: dCas9-p300 D1399Y_rep1[RNA-Seq, 2]

description: Library name: Library5


title: dCas9-p300 WT_rep2[RNA-Seq, 2]

description: Library name: Library4

value: Transfected with dCas9-p300 WT in presence of HS2 gRNA


title: PerturbFate pooled screen Dual-omics-62

description:
Library name: PerturbFate pooled screen Dual-omics-62
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-01
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: dCas9-p300 I1417N_rep1[RNA-Seq, 2]

description: Library name: Library7

value: Transfected with dCas9-p300 I1417N in presence of HS2 gRNA


title: dCas9_rep2[RNA-Seq, 2]

description: Library name: Library2

value: Transfected with dCas9 in presence of HS2 gRNA


title: PerturbFate pooled screen Dual-omics-63

description:
Library name: PerturbFate pooled screen Dual-omics-63
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad


title: DRIPc_Rx_U2OSMYCtetOn_Input_CBL0137_r1

value: doxycycline (1 µg/ml, 24 h); CBL0137 (5 µM, 2 h)


title: dCas9-p300 WT_rep1[RNA-Seq, 2]

description: Library name: Library3


title: PerturbFate pooled screen Dual-omics-61

description:
Library name: PerturbFate pooled screen Dual-omics-61
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad


title: CD4i_R2L25_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L25_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

value: 48 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

tag: donor weight

value: no, no, no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

value: pooled:D1 - female, D2 - female, D3 - female, D4 - male

tag: suspension type

value: cell

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: pooled:D1 - Hispanic or Latin American, D2 - African American, D3 - African American, D4 - Asian

value: CRISPR interference

value: constitutive

value: CD4-positive, alpha-beta T cell

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: 10x Gene Expression Flex


title: CD4i_R2L22_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L22_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:na, [ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

value: pooled:resting, 8 hr stimulation

value: pooled:D3 - 23 years, D4 - 34 years

tag: donor height

tag: donor smoker

value: no, no

value: pooled:D3 - female, D4 - male

value: adult

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

value: pooled:D3 - African American, D4 - Asian

tag: genetic perturbation_strategy

tag: crispr system_type

tag: suspension enriched_cell_types

tag: suspension depletion_factors

tag: library protocol

tag: sample probe_barcode


title: DRIPc_Rx_U2OSMYCtetOn_CBL0137_r1

tag: tissue

value: Bone

tag: cell line

tag: cell type

value: Osteosarcoma cell line

tag: genotype

value: MYC-Tet-On

tag: treatment

value: doxycycline (1 µg/ml, 24 h); CBL0137 (5 µM, 2 h)


title: CD4i_R2L20_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L20_GEX_lib

tag: experimental perturbation

tag: donor ids

tag: donor age

tag: donor weight

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

tag: suspension type

value: cell

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: CRISPR interference

value: constitutive

value: CD4-positive, alpha-beta T cell

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: CD4i_R2L23_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L23_GEX_lib

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:na, [ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

value: pooled:resting, 8 hr stimulation

value: pooled:D3 - 23 years, D4 - 34 years

tag: donor height

tag: donor smoker

value: no, no

value: pooled:D3 - female, D4 - male

tag: donor disease

tag: sample preservation_method

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: crispr system_type

tag: suspension enriched_cell_types

tag: suspension depletion_factors

tag: library protocol

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: PerturbFate pooled screen Dual-omics-60

description:
Library name: PerturbFate pooled screen Dual-omics-60
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad

tag: cell line

value: A375 cell line

tag: cell type

value: Melanoma

tag: genotype

value: BRAF V600E

tag: treatment

value: DMSO or Vemurafenib


title: CD4i_R2L21_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L21_GEX_lib

tag: experimental perturbation

tag: donor ids

tag: donor age

tag: donor weight

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

tag: suspension type

value: cell

tag: donor dev_stage

value: adult

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: normal

value: formaldehyde fixed -80C

value: pooled:D3 - African American, D4 - Asian


title: DRIPc_Rx_U2OSMYCtetOn_CBL0137_RNaseH_r1

tag: tissue

value: Bone

value: Osteosarcoma cell line

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h); CBL0137 (5 µM, 2 h); 60 U RNase H1 during sample preparation


title: ChIP_Rx_U2OSMYCtetOn_MYC_IP_PlaB_R2

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.
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.

tag: cell line

value: doxycycline (1 µg/ml, 24 h); PlaB (1 µM, 4 h)


title: dCas9_rep1[RNA-Seq, 2]

description: Library name: Library1

tag: cell type

value: Human embryonic kidney cells

value: Transfected with dCas9 in presence of HS2 gRNA


title: PerturbFate pooled screen Dual-omics-59

description:
Library name: PerturbFate pooled screen Dual-omics-59
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E


title: CD4i_R2L19_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L19_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

tag: treatment

value: pooled:na, [ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

value: pooled:resting, 8 hr stimulation

value: pooled:D3 - 23 years, D4 - 34 years

tag: donor height

tag: donor smoker

value: no, no

value: ACDA

value: STEMCELL technologies

value: pooled:D3 - female, D4 - male

tag: donor disease

tag: sample preservation_method

tag: donor ethnicity

tag: genetic perturbation_strategy

value: CRISPR interference

tag: crispr system_type

value: constitutive

tag: suspension enriched_cell_types

value: CD4-positive, alpha-beta T cell

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: library protocol

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: CD4i_R2L24_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L24_GEX_lib

tag: experimental perturbation

tag: donor ids

tag: donor age

tag: donor weight

tag: donor blood_type

tag: anticoagulant

tag: source

tag: description donor_sex

tag: suspension type

value: cell

tag: donor dev_stage

value: adult

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

value: normal

value: formaldehyde fixed -80C

value: pooled:D3 - African American, D4 - Asian


title: CD4i_R2L18_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L18_GEX_lib

tag: tissue

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: treatment

value: pooled:na, [ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

value: pooled:resting, 8 hr stimulation

tag: donor height

tag: donor smoker

tag: donor disease

tag: sample preservation_method

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: crispr system_type


title: ChIP_Rx_U2OSMYCtetOn_MYC_IP_CBL0137_R2

value: Bone

tag: cell line

value: Osteosarcoma cell line

tag: genotype

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h); CBL0137 (5 µM, 2 h)


title: PerturbFate pooled screen Dual-omics-58

description:
Library name: PerturbFate pooled screen Dual-omics-58
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line

value: Melanoma

value: BRAF V600E

value: DMSO or Vemurafenib


title: dCas9-p300 I1417N_rep2

extract_protocol:
72 hours post-transfection RNA was isolated using the RNeasy Plus mini kit (Qiagen). RNA integrity was first assessed using a Bioanalyzer 2200 (Agilent)
RNA-seq libraries were constructed using the TruSeq Stranded Total RNA Gold (Illumina, RS-122-2303).The qualities of RNA-seq libraries were verified using the Tape Station D1000 assay (Tape Station 2200, Agilent Technologies) and the concentration of RNA-seq libraries were checked again using real time PCR (QuantStudio 6 Flex Real time PCR System, Applied Biosystem). Libraries were normalized and pooled prior to sequencing. Sequencing was performed using an Illumina Hiseq 3000 with paired end 75 base pair reads.

value: Human embryonic kidney cells

value: Transfected with dCas9-p300 I1417N in presence of HS2 gRNA


title: PerturbFate pooled screen Dual-omics-57

description:
Library name: PerturbFate pooled screen Dual-omics-57
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad


title: CD4i_R2L17_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L17_GEX_lib

tag: experimental perturbation

tag: donor ids

tag: donor age

value: pooled:D3 - 23 years, D4 - 34 years

tag: donor weight

value: no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

value: pooled:D3 - female, D4 - male

value: cell

value: adult

value: TRUE

value: normal

value: CRISPR interference

value: constitutive

tag: suspension enriched_cell_types

value: CD4-positive, alpha-beta T cell

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: library protocol

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: PerturbFate pooled screen Dual-omics-56

description:
Library name: PerturbFate pooled screen Dual-omics-56
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line

tag: cell type

value: Melanoma

value: BRAF V600E

tag: treatment

value: DMSO or Vemurafenib


title: ChIP_Rx_U2OSMYCtetOn_MYC_IP_DMSO_R2

tag: tissue

value: Bone

value: Osteosarcoma cell line

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h); DMSO


title: dCas9-p300 I1417N_rep1

tag: cell line

value: Human embryonic kidney cells

value: Transfected with dCas9-p300 I1417N in presence of HS2 gRNA


title: ChIP_Rx_U2OSMYCtetOn_Input_PlaB_R2

tag: genotype

value: doxycycline (1 µg/ml, 24 h); PlaB (1 µM, 4 h)


title: dCas9-p300 D1399Y_rep3

value: Transfected with dCas9-p300 D1399Y in presence of HS2 gRNA


title: ChIP_Rx_U2OSMYCtetOn_Input_CBL0137_R2

value: doxycycline (1 µg/ml, 24 h); CBL0137 (5 µM, 2 h)


title: CD4i_R2L16_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L16_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:na, [ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

value: pooled:resting, 8 hr stimulation

value: pooled:D3 - 23 years, D4 - 34 years

tag: donor height

tag: donor smoker

value: no, no

value: ACDA

value: STEMCELL technologies

value: pooled:D3 - female, D4 - male

tag: suspension type

value: cell

tag: donor dev_stage

value: adult

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

value: pooled:D3 - African American, D4 - Asian

tag: genetic perturbation_strategy

value: CRISPR interference

tag: crispr system_type

value: constitutive


title: CD4i_R2L15_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L15_GEX_lib

value: blood

tag: cell type

tag: donor ids

tag: donor age

tag: donor weight

tag: donor blood_type

tag: anticoagulant

tag: source

tag: description donor_sex

tag: suspension enriched_cell_types

value: CD4-positive, alpha-beta T cell

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: library protocol

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: dCas9-p300 D1399Y_rep2

tag: cell line

value: Human embryonic kidney cells

tag: treatment

value: Transfected with dCas9-p300 D1399Y in presence of HS2 gRNA


title: ChIP_Rx_U2OSMYCtetOn_Input_DMSO_R2

tag: tissue

value: Bone

value: Osteosarcoma cell line

tag: genotype

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h); DMSO


title: PerturbFate pooled screen Dual-omics-53

description:
Library name: PerturbFate pooled screen Dual-omics-53
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line

value: Melanoma

value: BRAF V600E

value: DMSO or Vemurafenib


title: dCas9-p300 I1417N_rep3

value: Transfected with dCas9-p300 I1417N in presence of HS2 gRNA


title: PerturbFate pooled screen Dual-omics-55

description:
Library name: PerturbFate pooled screen Dual-omics-55
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad


title: ChIP_Rx_U2OSMYCtetOn_MYC_IP_PlaB_R1

value: doxycycline (1 µg/ml, 24 h); PlaB (1 µM, 4 h)


title: PerturbFate pooled screen Dual-omics-54

description:
Library name: PerturbFate pooled screen Dual-omics-54
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad


title: dCas9-p300 WT_rep3

value: Transfected with dCas9-p300 WT in presence of HS2 gRNA


title: CD4i_R2L13_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L13_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:na, [ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

value: pooled:resting, 8 hr stimulation

value: pooled:D3 - 23 years, D4 - 34 years

tag: donor height

tag: donor smoker

value: no, no

value: ACDA

value: STEMCELL technologies

value: pooled:D3 - female, D4 - male

tag: suspension type

value: cell

tag: donor dev_stage

value: adult

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

value: pooled:D3 - African American, D4 - Asian

tag: genetic perturbation_strategy

value: CRISPR interference

tag: crispr system_type

value: constitutive


title: ChIP_Rx_U2OSMYCtetOn_MYC_IP_CBL0137_R1

value: Bone

tag: cell type

value: Osteosarcoma cell line

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h); CBL0137 (5 µM, 2 h)


title: PerturbFate pooled screen Dual-omics-52

description:
Library name: PerturbFate pooled screen Dual-omics-52
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad

tag: cell line

value: A375 cell line

value: Melanoma

value: BRAF V600E

value: DMSO or Vemurafenib


title: dCas9-p300 WT_rep2

value: Human embryonic kidney cells

tag: treatment

value: Transfected with dCas9-p300 WT in presence of HS2 gRNA


title: ChIP_Rx_U2OSMYCtetOn_MYC_IP_DMSO_R1

tag: tissue

value: doxycycline (1 µg/ml, 24 h); DMSO


title: PerturbFate pooled screen Dual-omics-51

description:
Library name: PerturbFate pooled screen Dual-omics-51
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad

tag: genotype


title: CD4i_R2L14_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L14_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:na, [ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

value: pooled:resting, 8 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D3 - 23 years, D4 - 34 years

tag: donor weight

value: no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

value: pooled:D3 - female, D4 - male

value: cell

value: adult

value: TRUE

tag: suspension enriched_cell_types

value: CD4-positive, alpha-beta T cell

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: library protocol

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: CD4i_R2L12_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L12_GEX_lib

tag: cell type

tag: donor height

tag: donor smoker

tag: suspension type

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

value: pooled:D3 - African American, D4 - Asian

tag: genetic perturbation_strategy

value: CRISPR interference

tag: crispr system_type

value: constitutive


title: dCas9-p300 D1399Y_rep1

tag: cell line

value: Human embryonic kidney cells

tag: treatment

value: Transfected with dCas9-p300 D1399Y in presence of HS2 gRNA


title: ChIP_Rx_U2OSMYCtetOn_Input_PlaB_R1

tag: tissue

value: Bone

value: Osteosarcoma cell line

tag: genotype

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h); PlaB (1 µM, 4 h)


title: PerturbFate pooled screen Dual-omics-49

description:
Library name: PerturbFate pooled screen Dual-omics-49
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line

value: Melanoma

value: BRAF V600E

value: DMSO or Vemurafenib


title: CD4i_R2L10_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L10_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:na, [ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

value: pooled:resting, 8 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D3 - 23 years, D4 - 34 years

tag: donor weight

value: no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

value: pooled:D3 - female, D4 - male

value: cell

value: adult

value: TRUE

tag: suspension enriched_cell_types

value: CD4-positive, alpha-beta T cell

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: library protocol

tag: sample probe_barcode


title: dCas9-p300 WT_rep1

tag: cell type

value: Human embryonic kidney cells

value: Transfected with dCas9-p300 WT in presence of HS2 gRNA


title: dCas9_rep3

tag: cell line

value: Transfected with dCas9 in presence of HS2 gRNA


title: ChIP_Rx_U2OSMYCtetOn_Input_DMSO_R1

value: Bone

value: Osteosarcoma cell line

value: MYC-Tet-On

tag: treatment

value: doxycycline (1 µg/ml, 24 h); DMSO


title: CD4i_R2L09_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L09_GEX_lib

tag: tissue

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:na, [ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

value: pooled:resting, 8 hr stimulation

value: pooled:D3 - 23 years, D4 - 34 years

tag: donor height

tag: donor smoker

tag: suspension type

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

value: pooled:D3 - African American, D4 - Asian

tag: genetic perturbation_strategy

value: CRISPR interference

tag: crispr system_type

value: constitutive

value: 10x Gene Expression Flex


title: PerturbFate pooled screen Dual-omics-50

description:
Library name: PerturbFate pooled screen Dual-omics-50
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


title: ChIP_Rx_U2OSMYCtetOn_Input_CBL0137_R1

value: Bone

value: Osteosarcoma cell line

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h); CBL0137 (5 µM, 2 h)


title: CD4i_R2L11_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L11_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:na, [ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

tag: donor ids

tag: donor age

tag: donor weight

value: no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

value: pooled:D3 - female, D4 - male

value: cell

value: adult

value: TRUE

tag: suspension enriched_cell_types

value: CD4-positive, alpha-beta T cell

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: library protocol

tag: sample probe_barcode


title: dCas9_rep2

tag: cell line

tag: cell type

value: Human embryonic kidney cells

tag: treatment

value: Transfected with dCas9 in presence of HS2 gRNA


title: dCas9-p300 I1417N_rep2

data_processing:
Sequencing reads were aligned to Human hg38 using Bowtie2, with multi-aligned, duplicate, and blacklist region reads removed. RPKM-normalized bigWigs were generated using deepTools with –binsize set to 20. Smoothed Bigwigs were generated for visualization in the Integrative Genomics Viewer (IGV), using the –smoothLength option set to 100.
Assembly: hg38
Supplementary files format and content: individual bigwig files corresponding to each sample include merged biological replicate data
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN was performed using the Epicypher CUTANA ChIC/CUT&RUN Kit (Epicypher, #14-1048). Briefly, 48 hours post-transfection, 500k HEK293T cells were detached and harvested using 0.5mM EDTA (Fisher, #BP2482-500), washed once with 1X PBS and then resuspended in 300ul of wash buffer. 100ul aliquots (~1/3 of each 24 well) of cells were processed for H3K27ac antibody (Epicypher, #13-0045). Cells were first immobilized on concanavalin A beads, and then incubated with respective antibody (0.5ug/sample) overnight at 4°C in antibody dilution buffer (cell permeabilization buffer + EDTA). On the following day, cells were washed twice with cell permeabilization buffer. After washing the beads, pAG-MNase was added to the immobilized cells and then incubated for 2 hours at 4°C to digest and release DNA.
Libraries were prepared using the CUT&RUN Library Prep Kit (Epicypher, #14-1001) and DNA was quantified using the Qubit HS dsDNA High Sensitivity Kit (Thermo Fisher) and sequenced at a depth of 15M paired end reads per sample on a NextSeq 2000 (High Output 2x100). Samples were normalized using an E. Coli spike-in DNA (Epicypher, #18-1401).

treatment_protocol: Approximately 150000 HEK293T cells were plated the day before transfection and then transfected using Lipofectamine 3000 (Invitrogen, USA) as per manufacturer’s instruction in 24-well plates using 375ng of dCas9-p300 variant expression plasmid and 125ng of equimolar pooled gRNAs for HS2.

tag: chip antibody

value: Transfected with dCas9-p300 I1417N in presence of HBG1 gRNA


title: CD4i_R2L07_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L07_GEX_lib

tag: tissue

value: pooled:resting, 8 hr stimulation

value: pooled:D3 - 23 years, D4 - 34 years

tag: donor height

tag: donor smoker

tag: suspension type

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

value: pooled:D3 - African American, D4 - Asian

tag: genetic perturbation_strategy

value: CRISPR interference

tag: crispr system_type

value: constitutive

value: 10x Gene Expression Flex


title: Q4_mCheLO_CitLO

data_processing:
Sequencing reads were processed as described previously using the HT-recruit pipeline. Briefly, reads from each quadrant were grouped by fluorophore expression level, mCherryhi/lo and Citrinehi/lo. A custom reference was generated using Bowtie from the designed p300 library using the script ‘makeIndices.py’ and reads were aligned with a mismatch allowance of 3 using the script ‘makeCounts.py’. The enrichments for each domain between HI and LO samples were determined using the script ‘makeRhos.py’. Domains with < 5 reads were adjusted to 5 to avoid inflation of enrichment values due to low sequencing depth.
Assembly: Custom reference
Supplementary files format and content: individual comma-delimited text files corresponding to the counts of each variant and calculated -log2(ON/OFF)
Library strategy: Targeted Amplicon Sequencing

value: AAVS1 reporter and transduced at MOI ~0.3 with rTetR-p300var library


title: Q3_mCheHI_CitLO


title: dCas9_rep1


title: CD4i_R2L06_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L06_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:na, [ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

tag: donor ids

tag: donor age

tag: donor weight

value: no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

value: pooled:D3 - female, D4 - male

value: cell

tag: suspension enriched_cell_types

tag: suspension depletion_factors

tag: library protocol

tag: sample probe_barcode


title: PerturbFate pooled screen Dual-omics-46

description:
Library name: PerturbFate pooled screen Dual-omics-46
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad

tag: cell line

value: A375 cell line

tag: cell type

value: Melanoma

tag: genotype

value: BRAF V600E

tag: treatment

value: DMSO or Vemurafenib


title: PerturbFate pooled screen Dual-omics-48

description:
Library name: PerturbFate pooled screen Dual-omics-48
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad


title: dCas9-p300 D1399Y_rep2

value: Human embryonic kidney cells

tag: chip antibody

value: Transfected with dCas9-p300 D1399Y in presence of HBG1 gRNA


title: CD4i_R2L05_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L05_GEX_lib

tag: tissue

tag: experimental perturbation

value: pooled:resting, 8 hr stimulation

value: pooled:D3 - 23 years, D4 - 34 years

tag: donor height

tag: donor smoker

tag: suspension type

tag: donor dev_stage

value: adult

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

value: pooled:D3 - African American, D4 - Asian

tag: genetic perturbation_strategy

value: CRISPR interference

tag: crispr system_type

value: constitutive

value: CD4-positive, alpha-beta T cell

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: Q2_mCheHI_CitHI

tag: cell line

tag: cell type

value: AAVS1 reporter and transduced at MOI ~0.3 with rTetR-p300var library


title: CD4i_R2L08_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L08_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

tag: treatment

value: pooled:na, [ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: donor ids

tag: donor age

tag: donor weight

value: no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

value: pooled:D3 - female, D4 - male

value: cell

tag: suspension enriched_cell_types

tag: suspension depletion_factors

tag: library protocol

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: PerturbFate pooled screen Dual-omics-47

description:
Library name: PerturbFate pooled screen Dual-omics-47
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


title: dCas9-p300 D1399Y_rep1

value: Human embryonic kidney cells

tag: chip antibody

value: Transfected with dCas9-p300 D1399Y in presence of HBG1 gRNA


title: PerturbFate pooled screen Dual-omics-44

description:
Library name: PerturbFate pooled screen Dual-omics-44
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad


title: PerturbFate pooled screen Dual-omics-45

description:
Library name: PerturbFate pooled screen Dual-omics-45
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad


title: dCas9-p300 I1417N_rep1

value: Transfected with dCas9-p300 I1417N in presence of HBG1 gRNA


title: dCas9-p300 WT_rep2

value: Transfected with dCas9-p300 WT in presence of HBG1 gRNA


title: CD4i_R2L04_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L04_GEX_lib

tag: tissue

value: blood

tag: experimental perturbation

value: pooled:resting, 8 hr stimulation

value: pooled:D3 - 23 years, D4 - 34 years

tag: donor height

tag: donor smoker

tag: suspension type

tag: donor dev_stage

value: adult

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

value: pooled:D3 - African American, D4 - Asian

tag: genetic perturbation_strategy

value: CRISPR interference

tag: crispr system_type

value: constitutive

value: CD4-positive, alpha-beta T cell

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: Q1_mCheLO_CitHI

tag: cell line

tag: cell type

tag: treatment

value: AAVS1 reporter and transduced at MOI ~0.3 with rTetR-p300var library


title: PerturbFate pooled screen Dual-omics-43

description:
Library name: PerturbFate pooled screen Dual-omics-43
PerturbFate Dual-omics single-cell library containing RNA and ATAC modalities
Dual_omics_RNA_cell_metadata.csv
Dual_omics_RNA_gene_count_matrix.RDS
Dual_omics_sgRNA_count_matrix.RDS
Dual_omics_ATAC_cell_metadata.csv
Dual_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


title: dCas9-p300 WT_rep1

value: Human embryonic kidney cells

tag: chip antibody

value: Transfected with dCas9-p300 WT in presence of HBG1 gRNA


title: GF_replicate_2_GFP100_CO_S

first: Lanlan

last: Shen

address: 1100 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

description:
Library name: GF_replicate_2_GFP100_CO_S
GF_replicate_2_GFP100_CO_S

data_processing:
BOWTIE2 software was used for efficient realignment of RNA sequences, and gene expression levels for each sample were calculated with RSEM. For DEG analysis, DEseq265 was used to rank genes by fold change and adjusted the P-values based on multiple testing corrections (Bonferroni).
Assembly: mm10
Supplementary files format and content: DESeq_RNAseqSPF_VS_GF.txt

organism: Mus musculus

source_name: colonic stem cell

extract_protocol:
RNA was extracted using AllPrep DNA/RNA Mini Kit (QIAGEN). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using standard Novogene protocols.

tag: tissue

value: colonic stem cell

tag: strain

tag: Sex

value: Female

tag: age

value: 15 wk

value: germ-free (GF)

tag: batch


title: db_REG3B, rep2

city: Hangzhou

first: Zhuoying

last: Yang

address: Yuhangtang Road

country: China

institute: Zhejiang University

description:
Library name: Sample 25
core_table4.csv

data_processing:
Data were processed using the standard BGI mRNA analysis pipeline.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: csv files include FPKM for indicated samples
Supplementary files format and content: bigwig files for indicated samples

source_name: islet

extract_protocol:
In this research,  each islet sample was isolated and pooled from at least three mice.
Samples of islet RNA were dispatched to the BGI group (Wuhan, China) for library preparation and the sequencing process. Initially, mRNAs were extracted from the total RNA pool and subsequently fragmented. The fragmented mRNAs were used for reverse transcription and second-strand cDNA synthesis. Following this, adenine tailing and adaptor ligation procedures were employed to prepare the cDNAs for PCR amplification and subsequent sequencing. The sequencing itself was executed in the paired-end mode on the BGISEQ-500 system.

value: islet

tag: sample group