title: CD4i_R2L01_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L01_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

tag: donor height

tag: donor smoker

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

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

tag: suspension enriched_cell_types

tag: suspension depletion_factors

tag: library protocol

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: db_REG3B, rep1

status: Public on Feb 06 2026

type: SRA

city: Hangzhou

first: Zhuoying

last: Yang

address: Yuhangtang Road

country: China

institute: Zhejiang University

description:
Library name: Sample 24
core_table4.csv

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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.

tag: tissue

value: islet

tag: sample group


title: PerturbFate pooled screen Dual-omics-41

city: New York

first: Zihan

last: Xu

state: NY

address: 1230 York Ave

country: USA

institute: The Rockefeller University

description:
Library name: PerturbFate pooled screen Dual-omics-41
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

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

organism: Homo sapiens

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.

tag: cell line

value: A375 cell line

tag: cell type

value: Melanoma

tag: genotype

value: BRAF V600E

tag: treatment

value: DMSO or Vemurafenib


title: Tor-RNAi, Chol. Starved, Sample 4

city: København Ø

first: Kim

last: Rewitz

state: Capital region

address: Universitetsparken 15, Building 3.3.401

country: Denmark

institute: University of Copenhagen

data_processing:
Base calling by CASAVA
Alignment with HISAT2
Assembly with Stringtie
Quantification with featureCounts
DESeq2, edgeR
Assembly: ensembl_drosophila_melanogaster_bdgp6_gca_000001215_4
Supplementary files format and content: Tab-delimited text file containing raw count data for each sample
Supplementary files format and content: Tab-delimited text file containing FPKM data for each sample

organism: Drosophila melanogaster

source_name: Whole third-instar larvae

growth_protocol: 8-hour egg lay at 18 deg; 2 days at 18 deg until hatching; 1st-instar larvae picked into normal food. At 111 hours after egg collection, larvae were transferred to 29 degrees to induce transgene expression.

extract_protocol:
Qiagen RNeasy Mini Kit (Qiagen, 74104) with DNase from Machery-Nagel #740955.250
Library construction and analysis were performed by NovoGene

treatment_protocol: At 120 hours, animals were transferred to low-cholesterol food (1.2 µg/mL). After ten further hours, animals were transferred onto fresh low-cholesterol medium or onto high-cholesterol (80 µg/mL) medium. Animals were collected and flash-frozen after 10 hours on these diets.

value: Whole third-instar larvae

value: all

value: Tub-GAL80TS/+ Tub-GAL4 /+ UAS-Tor-RNAi/+

value: Maintained on low-cholesterol food


title: CD4i_R2L03_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 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_R2L03_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

molecule: polyA RNA

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: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

tag: donor height

tag: donor smoker

value: no, no

tag: donor blood_type

tag: anticoagulant

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

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: PerturbFate pooled screen Dual-omics-40

description:
Library name: PerturbFate pooled screen Dual-omics-40
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: Tor-RNAi, Chol. Starved, Sample 3

tag: tissue

value: Whole third-instar larvae

tag: cell type

value: all

value: Tub-GAL80TS/+ Tub-GAL4 /+ UAS-Tor-RNAi/+

value: Maintained on low-cholesterol food


title: CD4i_R1L23_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L23_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:D1 - 29 years, D2 - 22 years

tag: source

tag: description donor_sex

value: pooled:D1 - female, D2 - female

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: normal

value: formaldehyde fixed -80C

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

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-42

description:
Library name: PerturbFate pooled screen Dual-omics-42
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: db_GFP, rep2

description:
Library name: Sample 23
core_table4.csv

value: islet

tag: sample group


title: CD4i_R2L02_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R2L02_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

tag: donor ids

tag: donor age

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

tag: donor weight

tag: donor height

tag: donor smoker

value: no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

value: pooled:D3 - female, D4 - male

value: adult

tag: donor disease

tag: sample preservation_method

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: Tor-RNAi, Chol. Starved, Sample 5

tag: tissue

value: Whole third-instar larvae

tag: cell type

value: all

value: Tub-GAL80TS/+ Tub-GAL4 /+ UAS-Tor-RNAi/+

tag: treatment

value: Maintained on low-cholesterol food


title: PerturbFate pooled screen Dual-omics-39

description:
Library name: PerturbFate pooled screen Dual-omics-39
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

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


title: PerturbFate pooled screen Dual-omics-38

description:
Library name: PerturbFate pooled screen Dual-omics-38
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-37

description:
Library name: PerturbFate pooled screen Dual-omics-37
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_R1L22_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L22_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

value: pooled:D1 - 29 years, D2 - 22 years

value: no, no

value: ACDA

tag: source

tag: description donor_sex

value: pooled:D1 - female, D2 - female

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: normal

value: formaldehyde fixed -80C

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

tag: suspension enriched_cell_types

tag: suspension depletion_factors

tag: library protocol

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: KO_REG3B-Fc, rep2

description:
Library name: Sample 21
core_table3.csv

tag: tissue

value: islet

tag: sample group


title: CD4i_R1L20_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L20_GEX_lib

tag: cell type

tag: treatment

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: STEMCELL technologies

tag: donor disease

tag: sample preservation_method

tag: donor ethnicity

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: CD4i_R1L21_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L21_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

value: pooled:D1 - 29 years, D2 - 22 years

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: suspension enriched_cell_types

tag: suspension depletion_factors

tag: library protocol


title: db_GFP, rep1

description:
Library name: Sample 22
core_table4.csv

tag: tissue

tag: sample group


title: Tor-RNAi, Chol. Starved, Sample 2

value: Whole third-instar larvae

tag: cell type

value: all

tag: genotype

value: Tub-GAL80TS/+ Tub-GAL4 /+ UAS-Tor-RNAi/+

tag: treatment

value: Maintained on low-cholesterol food


title: Tor-RNAi, Chol. Fed, Sample 5

value: Switched from low-cholesterol food to normal-cholesterol food


title: Tor-RNAi, Chol. Starved, Sample 1


title: KO_REG3B-Fc, rep1

description:
Library name: Sample 20
core_table3.csv


title: CD4i_R1L19_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L19_GEX_lib

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

value: pooled:D1 - female, D2 - female

value: cell

value: adult stage

value: TRUE

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

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

tag: genetic perturbation_strategy

tag: crispr system_type

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: KO_PBS, rep2

description:
Library name: Sample 19
core_table3.csv

tag: tissue

value: islet


title: PerturbFate pooled screen Dual-omics-35

description:
Library name: PerturbFate pooled screen Dual-omics-35
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: KO_PBS, rep1

description:
Library name: Sample 18
core_table3.csv

tag: sample group


title: Tor-RNAi, Chol. Fed, Sample 3

value: Whole third-instar larvae

tag: cell type

value: all

tag: genotype

value: Tub-GAL80TS/+ Tub-GAL4 /+ UAS-Tor-RNAi/+


title: CD4i_R1L18_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L18_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: experimental perturbation

value: pooled:resting, 8 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years

value: no, no

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

tag: suspension type

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

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


title: PerturbFate pooled screen Dual-omics-36

description:
Library name: PerturbFate pooled screen Dual-omics-36
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


title: Tor-RNAi, Chol. Fed, Sample 2

tag: tissue

value: Whole third-instar larvae

value: all

value: Switched from low-cholesterol food to normal-cholesterol food


title: CD4i_R1L17_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L17_GEX_lib

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

tag: donor weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: pooled:D1 - female, D2 - female

value: cell

value: adult stage

value: TRUE

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

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

tag: genetic perturbation_strategy

tag: crispr system_type

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: Tor-RNAi, Chol. Fed, Sample 4

tag: genotype

value: Tub-GAL80TS/+ Tub-GAL4 /+ UAS-Tor-RNAi/+

tag: treatment


title: CTR_PBS,  rep2

description:
Library name: Sample 17
core_table3.csv

value: islet

tag: sample group


title: CD4i_R1L16_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L16_GEX_lib

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:D1 - 29 years, D2 - 22 years

value: no, no

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

tag: suspension type

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

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


title: CTR_PBS,  rep1

description:
Library name: Sample 16
core_table3.csv

tag: tissue


title: PerturbFate pooled screen Dual-omics-32

description:
Library name: PerturbFate pooled screen Dual-omics-32
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

value: DMSO or Vemurafenib


title: Tor-RNAi, Chol. Fed, Sample 1

value: Whole third-instar larvae

value: all

tag: genotype

tag: treatment

value: Switched from low-cholesterol food to normal-cholesterol food


title: CD4i_R1L15_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L15_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 weight

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: pooled:D1 - female, D2 - female

value: cell

value: adult stage

value: TRUE

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

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

tag: genetic perturbation_strategy

tag: crispr system_type

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: PerturbFate pooled screen Dual-omics-34

description:
Library name: PerturbFate pooled screen Dual-omics-34
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


title: WT, rep5

description:
Library name: Sample 15
core_table2.csv

tag: tissue

value: islet

tag: sample group

value: WT


title: PerturbFate pooled screen Dual-omics-33

description:
Library name: PerturbFate pooled screen Dual-omics-33
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

tag: cell type

value: BRAF V600E

value: DMSO or Vemurafenib


title: Hr3-RNAi, Chol. Starved, Sample 4

value: Whole third-instar larvae

value: all

tag: genotype

value: Tub-GAL80TS/+ Tub-GAL4 /+ UAS-Hr3-RNAi/+

tag: treatment

value: Maintained on low-cholesterol food


title: CD4i_R1L13_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L13_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:D1 - 29 years, D2 - 22 years

tag: donor weight

value: no, no

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

value: pooled:D1 - female, D2 - female

tag: suspension type

value: cell

tag: donor dev_stage

tag: donor living_at_sample_collection

tag: donor body_mass_index

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


title: CD4i_R1L14_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L14_GEX_lib

tag: tissue

tag: donor height

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: adult stage

value: TRUE

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

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

tag: genetic perturbation_strategy

tag: crispr system_type

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: CD4i_R1L12_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L12_GEX_lib

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]

tag: experimental perturbation

value: pooled:resting, 8 hr stimulation

tag: donor ids

tag: donor age

tag: donor weight

tag: source

tag: description donor_sex

tag: suspension type

tag: donor dev_stage


title: WT, rep4

description:
Library name: Sample 14
core_table2.csv

tag: tissue

value: islet

tag: sample group

value: WT


title: Hr3-RNAi, Chol. Starved, Sample 5

value: Whole third-instar larvae

value: all

tag: genotype

value: Tub-GAL80TS/+ Tub-GAL4 /+ UAS-Hr3-RNAi/+

value: Maintained on low-cholesterol food


title: WT, rep3

description:
Library name: Sample 13
core_table2.csv


title: PerturbFate pooled screen Dual-omics-30

description:
Library name: PerturbFate pooled screen Dual-omics-30
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: Hr3-RNAi, Chol. Starved, Sample 2


title: PerturbFate pooled screen Dual-omics-29

description:
Library name: PerturbFate pooled screen Dual-omics-29
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: Hr3-RNAi, Chol. Starved, Sample 1


title: CD4i_R1L10_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L10_GEX_lib

value: pooled:D1 - 29 years, D2 - 22 years

tag: donor height

tag: donor smoker

value: no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

value: pooled:D1 - female, D2 - female

value: cell

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

tag: genetic perturbation_strategy

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


title: PerturbFate pooled screen Dual-omics-27

description:
Library name: PerturbFate pooled screen Dual-omics-27
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

tag: treatment


title: Hr3-RNAi, Chol. Fed, Sample 5

tag: tissue

value: Whole third-instar larvae

value: all

tag: genotype

value: Tub-GAL80TS/+ Tub-GAL4 /+ UAS-Hr3-RNAi/+

value: Switched from low-cholesterol food to normal-cholesterol food


title: CD4i_R1L11_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L11_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:D1 - 29 years, D2 - 22 years

tag: donor weight

tag: donor height

value: no, no

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

tag: suspension type

tag: donor dev_stage

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

tag: crispr system_type

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: BcBKO, HFD, rep2

description:
Library name: Sample 10
core_table1.csv

value: islet

tag: sample group

value: BcBKO, HFD


title: WT, rep2

description:
Library name: Sample 12
core_table2.csv

value: WT


title: PerturbFate pooled screen Dual-omics-26

description:
Library name: PerturbFate pooled screen Dual-omics-26
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: PerturbFate pooled screen Dual-omics-28

description:
Library name: PerturbFate pooled screen Dual-omics-28
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 type


title: CD4i_R1L09_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L09_GEX_lib

value: blood

tag: treatment

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: pooled:D1 - female, D2 - female

value: cell

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

tag: genetic perturbation_strategy

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


title: BcBKO, HFD, rep1

description:
Library name: Sample 9
core_table1.csv

tag: tissue

value: islet

value: BcBKO, HFD


title: CD4i_R1L08_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L08_GEX_lib

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:D1 - 29 years, D2 - 22 years

tag: donor weight

tag: donor height

value: no, no

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

tag: suspension type

tag: donor dev_stage

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

tag: crispr system_type

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: PerturbFate pooled screen Dual-omics-31

description:
Library name: PerturbFate pooled screen Dual-omics-31
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: Hr3-RNAi, Chol. Fed, Sample 4

value: Whole third-instar larvae

value: all

value: Tub-GAL80TS/+ Tub-GAL4 /+ UAS-Hr3-RNAi/+

value: Switched from low-cholesterol food to normal-cholesterol food


title: WT, rep1

description:
Library name: Sample 11
core_table2.csv

value: islet

tag: sample group

value: WT


title: PerturbFate pooled screen Dual-omics-24

description:
Library name: PerturbFate pooled screen Dual-omics-24
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: flox/flox, HFD, rep2

description:
Library name: Sample 8
core_table1.csv

tag: tissue

value: flox/flox, HFD


title: CD4i_R1L07_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L07_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:D1 - 29 years, D2 - 22 years

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: pooled:D1 - female, D2 - female

value: cell

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

tag: genetic perturbation_strategy

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


title: PerturbFate pooled screen Dual-omics-25

description:
Library name: PerturbFate pooled screen Dual-omics-25
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

value: DMSO or Vemurafenib


title: CD4i_R1L06_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L06_GEX_lib

tag: tissue

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

tag: donor height

value: no, no

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

tag: suspension type

tag: donor dev_stage

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

tag: crispr system_type

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: Hr3-RNAi, Chol. Fed, Sample 3

value: Whole third-instar larvae

value: all

value: Tub-GAL80TS/+ Tub-GAL4 /+ UAS-Hr3-RNAi/+

value: Switched from low-cholesterol food to normal-cholesterol food


title: PerturbFate pooled screen Dual-omics-23

description:
Library name: PerturbFate pooled screen Dual-omics-23
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: Hr3-RNAi, Chol. Fed, Sample 2


title: CD4i_R1L05_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L05_GEX_lib

tag: experimental perturbation

value: pooled:resting, 8 hr stimulation

value: pooled:D1 - 29 years, D2 - 22 years

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

value: pooled:D1 - female, D2 - female

value: cell

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

tag: genetic perturbation_strategy

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


title: Control, Chol. Starved, Sample 5

tag: tissue

tag: cell type

tag: genotype

value: Tub-GAL80TS/+ Tub-GAL4 /+

tag: treatment

value: Maintained on low-cholesterol food


title: flox/flox, HFD, rep1

description:
Library name: Sample 7
core_table1.csv

value: islet

tag: sample group

value: flox/flox, HFD


title: Hr3-RNAi, Chol. Fed, Sample 1

value: Whole third-instar larvae

value: all

value: Tub-GAL80TS/+ Tub-GAL4 /+ UAS-Hr3-RNAi/+

value: Switched from low-cholesterol food to normal-cholesterol food


title: BcBKO, chow, rep3

description: Library name: Sample 6

value: BcBKO, chow


title: BcBKO, chow, rep2

description: Library name: Sample 5


title: CD4i_R1L04_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L04_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:D1 - 29 years, D2 - 22 years

tag: donor weight

tag: donor height

value: no, no

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

value: pooled:D1 - female, D2 - female

tag: suspension type

value: cell

tag: donor dev_stage

value: adult stage

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

tag: crispr system_type

tag: library protocol

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: PerturbFate pooled screen Dual-omics-20

description:
Library name: PerturbFate pooled screen Dual-omics-20
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: BcBKO, chow, rep1

description: Library name: Sample 4

tag: tissue

value: islet

value: BcBKO, chow


title: CD4i_R1L03_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L03_GEX_lib

value: blood

tag: cell type

value: CD4-positive, alpha-beta T cells

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

tag: donor smoker

tag: donor blood_type

tag: anticoagulant

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

tag: genetic perturbation_strategy

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


title: Control, Chol. Starved, Sample 4

value: Whole third-instar larvae

value: all

tag: genotype

value: Tub-GAL80TS/+ Tub-GAL4 /+

tag: treatment

value: Maintained on low-cholesterol food


title: PerturbFate pooled screen Dual-omics-21

description:
Library name: PerturbFate pooled screen Dual-omics-21
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: PerturbFate pooled screen Dual-omics-22

description:
Library name: PerturbFate pooled screen Dual-omics-22
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: Control, Chol. Starved, Sample 3


title: CD4i_R1L02_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L02_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

tag: experimental perturbation

value: pooled:resting, 8 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years

tag: donor weight

tag: donor height

value: no, no

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

value: pooled:D1 - female, D2 - female

tag: suspension type

value: cell

tag: donor dev_stage

value: adult stage

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

tag: crispr system_type

tag: library protocol

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: PerturbFate pooled screen Dual-omics-18

description:
Library name: PerturbFate pooled screen Dual-omics-18
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

tag: cell type


title: PerturbFate pooled screen Dual-omics-19

description:
Library name: PerturbFate pooled screen Dual-omics-19
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: Control, Chol. Starved, Sample 2

tag: tissue

value: Whole third-instar larvae

value: all

value: Tub-GAL80TS/+ Tub-GAL4 /+

value: Maintained on low-cholesterol food


title: flox/flox, chow, rep2

description: Library name: Sample 2

value: islet

tag: sample group

value: flox/flox, chow


title: flox/flox, chow, rep3

description: Library name: Sample 3


title: flox/flox, chow, rep1

description: Library name: Sample 1


title: CreERTLSD1KO_tissues

type: RNA

city: Philadelphia

first: Brian

last: Capell

state: PA

address: 421 Curie Blvd

department: Dermatology

institute: University of Pennsylvania

hyb_protocol: Tissues were paraffin embedded and sectioned onto a Xenium slide per 10X Genomics protocol. 480 custom panel fluorescent probes were hybridized according to protocol

scan_protocol: Slides were run on XeniumAnalyzer instrument

data_processing: Output files can be taken into Seurat for further processing

label: Xenium probe

source_name: Whole dorsal skin

label_protocol: Xenium probe

extract_protocol: Control (corn oil) or LSD1 Knockout (tamoxifen induced) mice were induced at 7wks of age and harvested 6 weeks post induction. Whole skin was excised and fixed with 4% PFA overnight

tag: genotype

value: K14-CreERT +; LSD1 fl/fl

tag: treatment

value: Tamoxifen


title: Control, Chol. Fed, Sample 5

value: Switched from low-cholesterol food to normal-cholesterol food


title: PerturbFate pooled screen Dual-omics-17

description:
Library name: PerturbFate pooled screen Dual-omics-17
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: CreERTLSD1WT_tissues

value: Corn Oil


title: Control, Chol. Fed, Sample 4


title: Hr3-RNAi, Chol. Starved, Sample 3

value: Tub-GAL80TS/+ Tub-GAL4 /+ UAS-Hr3-RNAi/+


title: PerturbFate pooled screen Dual-omics-16

description:
Library name: PerturbFate pooled screen Dual-omics-16
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: GF_replicate_1_A7802Co

city: Houston

first: Lanlan

last: Shen

state: Texas

address: 1100 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

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

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.

value: colonic stem cell

tag: strain

tag: Sex

value: Female

tag: age

value: 15 wk

value: germ-free (GF)


title: PerturbFate pooled screen Dual-omics-15

description:
Library name: PerturbFate pooled screen Dual-omics-15
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: LSD1i_tumors

source_name: Squamous cell carcinoma of mouse skin

extract_protocol: Krt14-Fyn mice from the Seykora Lab were treated with either DMSO or LSD1i for 15d upon generation of tumors. Tumors and surrounding skin were excised and fixed in 4% PFA overnight


title: Control, Chol. Fed, Sample 3

value: Whole third-instar larvae

value: all

value: Tub-GAL80TS/+ Tub-GAL4 /+


title: GF_replicate_7_A460DCo

source_name: colonic differentiated cell

value: colonic differentiated cell


title: CD4i_R1L01_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 2 pooled donors, resting and 8 hr stim

description: Library name: CD4i_R1L01_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:D1 - 29 years, D2 - 22 years

tag: donor weight

tag: donor height

tag: donor smoker

value: no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

value: STEMCELL technologies

value: pooled:D1 - female, D2 - female

value: cell

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

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

tag: genetic perturbation_strategy

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

value: 10x Gene Expression Flex


title: Control, Chol. Starved, Sample 1

tag: tissue

value: Whole third-instar larvae

tag: cell type

value: all

tag: genotype

value: Tub-GAL80TS/+ Tub-GAL4 /+

tag: treatment

value: Maintained on low-cholesterol food


title: GF_replicate_8_A462DCo

value: colonic differentiated cell

tag: strain

tag: Sex

value: Female

tag: age

value: 15 wk

value: germ-free (GF)


title: PerturbFate pooled screen Dual-omics-14

description:
Library name: PerturbFate pooled screen Dual-omics-14
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: PerturbFate pooled screen Dual-omics-13

description:
Library name: PerturbFate pooled screen Dual-omics-13
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: LSD1eKO_embryos

source_name: Whole skin/whole mount embryos

extract_protocol: Krt14-Cre LSD1 WT or LSD1 KO embryos were harvested at E17.5. Whole skin was taken by excising dorsal back or otherwise whole mount embryos were fixed with 4% PFA overnight

tag: developmental stage

value: embryo

value: Krt14Cre +; Lsd1 fl/fl


title: DMSO_tumors

value: DMSO


title: GF_replicate_6_A458DCo

value: Male


title: Control, Chol. Fed, Sample 1

value: Switched from low-cholesterol food to normal-cholesterol food


title: GF_replicate_5_A457DCo


title: LSD1eWT_embryos

value: Krt14Cre -; Lsd1 fl/fl


title: PerturbFate pooled screen Dual-omics-12

description:
Library name: PerturbFate pooled screen Dual-omics-12
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-11

description:
Library name: PerturbFate pooled screen Dual-omics-11
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: Control, Chol. Fed, Sample 2

value: Whole third-instar larvae

value: all


title: GF_replicate_3_A86712DCo


title: Cumulus-oocyte complex, Nanoplastics, 6

city: Utrecht

first: Jorke

last: Kamstra

state: Non United States Or Canada

address: PO Box 80177

department: Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

description: Library name: UU_32

data_processing:
Raw fastq files were adapter trimmed using trim_galore (v0.4.5, Babraham in-stitute, UK) with standard parameters.
STAR aligner (v2.5.4b) was used to align and map sequences to the bos taurus genome (ARS-UCD 1.3)
Generated BAM files were loaded to SeqMonk sequence analysis tool (v1.41, Babraham institute, UK) and mRNAs were quantified using the built-in mRNA seq pipeline.
Normalization of the read counts and differential expression was conducted using the Deseq2 package in SeqMonk.
Assembly: ARS_UCD 1.3
Supplementary files format and content: The processed data files is an excel file containing raw read counts and log2 normalized data.

organism: Bos taurus

source_name: cumulus-oocyte complexes

growth_protocol: Cumulus-oocyte complexes were in vitro matured in 4-well plates.

extract_protocol:
Total RNA was isolated and purified using the NucleoSpin® RNA extraction kit (Macherey-Nagel, Germany) from groups of 50 cumulus-oocyte complexes per condition.
Library preparation and analysis was performed on the Novaseq using 150bp paired end se-quencing.

treatment_protocol: Cumulus-oocyte complexes were cultured in 1) control medium, or 2) 3 μg/mL 50 nm polystyrene nanoplastics.

value: cumulus-oocyte complexes

value: Nanoplastics


title: PerturbFate pooled screen Dual-omics-10

description:
Library name: PerturbFate pooled screen Dual-omics-10
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: MIBC Non-Responder

first: Stephen

middle: Qi Rong

last: Wong

address: 6670 Bertner Ave

institute: Houston Methodist

hyb_protocol: According to 10x Xenium protocol

scan_protocol: According to 10x Xenium protocol

data_processing: Xenium data was generated by Xenium Analyzer (verison 3.4.1.0).

source_name: FFPE

extract_protocol: According to 10x Xenium protocol

tag: subject status

value: Non-Responder

value: Biopsies in FFPE blocks from MIBC patient


title: GF_replicate_4_A005DCo

value: colonic differentiated cell

value: 15 wk

value: germ-free (GF)


title: db/db_db/dbDAPA_Xenium

city: Duarte

first: Rama

last: Natarajan

state: California

address: 1500 E Duarte Rd

department: Department of Diabetes Complications and Metabolism

institute: Beckman Research Institute, City of Hope

hyb_protocol: The Xenium samples were processed following manufacturer’s recommendation and described in protocol (Xenium: https://www.10xgenomics.com/support/in-situ-gene-expression/documentation/steps/assay/xenium-in-situ-gene-expression-probe-hybridization-ligation-amplification.).

scan_protocol: Xenium In Situ Analyzer

data_processing:
Data processed using Xenium Ranger software
Xenium slide for further processing at the Integrative Genomics (IGC) core at City of Hope according to manufacturer’s recommendations. Slides were scanned using a Xenium Analyzer. Data sets were analyzed using Seurat (5.1.1). Quality control analysis revealed a median of 238 transcripts detected per cell, with more than 10,000 total cells detected across samples. We used Seurat to integrate data from all 8 aortas, followed by UMAP-based clustering to analyze the spatial transcriptomics datasets

label: Xenium

source_name: Aorta

label_protocol: Xenium custom panel mouse Probe Set

extract_protocol: Xenium spatial transcriptomics experiments were performed on aortas from db/db and db/dbDAPA groups (N=4/group). We selected 479 genes based on DEG analysis from our scRNA-seq data and literature documenting cell type markers in the mouse aorta. Aortas were cut (5 µM thickness) and transferred to the Xenium slide for further processing at the Integrative Genomics (IGC) core at City of Hope according to manufacturer’s recommendations.

treatment_protocol: We randomly divided db/db mice into two groups, and treated them daily with either saline (db/db) or DAPA (db/dbDAPA) by oral gavage (n=12 per group). Initially, for four weeks we dosed db/db mice with 1 mg/kg/day DAPA, which is equvalent to the clinicaly recommended starting dose (5 mg/day oral) to reduce hyperglycemia in T2D patients. In the subsequent two weeks of treatment (4-6 weeks), we increased DAPA dose to 3 mg/kg/day for db/db mice to achieve additional glycemic control.

value: Aorta tissue

value: db/db mice

value: either saline or DAPA


title: Cumulus-oocyte complex, Control, 5

description: Library name: UU_25


title: GF_replicate_1_A328329DCo


title: PerturbFate pooled screen Dual-omics-08

description:
Library name: PerturbFate pooled screen Dual-omics-08
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: Antibody Capture

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

description: Library name: BRI-2659

data_processing:
The raw sequencing data was aligned to the mouse genome mm10 using cell ranger count (v 8.0.0) (default parameters) with the antibody sequences of each hashtag (sample). Ambient RNA was quantified and deducted with SoupX (V1.6.2)
Assembly: mm10
Supplementary files format and content: RawCounts_ambientRNA_removed.rds: raw RNA counts with ambient RNA quantified and removed
Supplementary files format and content: HTO_counts.rds: counts of HTO oligos of each sample in each cell

source_name: CD3+ T cells

extract_protocol:
RNA extraction was performed per manufacturer’s instructions (Single cell 3’ v2 protocol, 10x genomics). RNA quality was checked using RIN numbers and nanodrop.
Library preparation was performed per manufacturer’s instructions (Single cell 3’ v2 protocol, 10x genomics). Briefly, FACS sorted CD3+T-cells from homogenized single cell suspension of each cardiac allografts (n=3 G1 and 3 G0 chimeric recipients) were treated with hashtagging barcoded antibodies (10x genomics). Cells were resuspended in master mix and loaded together with partitioning oil and gel beads to generate gel bead-in-emulsions. Poly-A RNA from cell lysate was reverse transcribed, bar-coded, amplified and sequenced.

value: CD3+ T cells


title: Gene Expression

description: Library name: BRI-2658


title: PerturbFate pooled screen Dual-omics-09

description:
Library name: PerturbFate pooled screen Dual-omics-09
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: Cumulus-oocyte complex, Nanoplastics, 4

description: Library name: UU_20


title: Cumulus-oocyte complex, Control, 6

description: Library name: UU_31


title: PerturbFate pooled screen Dual-omics-06

description:
Library name: PerturbFate pooled screen Dual-omics-06
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: SPF_replicate_6_LDf8595DCo

value: Female

value: specific-pathogen-free (SPF)


title: SPF_replicate_1_LDf42Co

value: colonic stem cell


title: PerturbFate pooled screen Dual-omics-07

description:
Library name: PerturbFate pooled screen Dual-omics-07
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: Cumulus-oocyte complex, Control, 4

description: Library name: UU_19

value: cumulus-oocyte complexes


title: PerturbFate pooled screen Dual-omics-05

description:
Library name: PerturbFate pooled screen Dual-omics-05
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: G1_2

description: Library name: G1-345

data_processing:
The quality control of the raw sequencing data was conducted with FastQC v0.11.8 and the adapter sequences were trimmed by cutadapt (V4.1) with parameters as “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT”. The cleaned sequences were aligned to the mouse genome (Ensembl mm39) using STAR v2.7.5.b with default parameters. The expression was quantified as the read counts within each gene region using htseq-count with parameters, “-m union --nonunique none”. The differentially expressed gene (DEG) analysis was conducted by limma-voom (V3.46.0) with read count matrix, adjusting for experiment batches.
Assembly: mm39
Supplementary files format and content: Expression profiles corrected by batch effects using limma voom

source_name: CD8+ T cells

extract_protocol:
RNA extraction was performed using the Qiagen RNAesy spin column method according to manufacturer’s protocol. RNA quality was checked using RIN numbers and nanodrop.
Library preparation of quality affirmed RNA from each sample was done using poly-A selection at Yale center for genome analyses (YCGA).

value: CD8+ T cells

value: APOL1 G1/G1


title: G1_3

description: Library name: G1-CD8


title: GF_replicate_2_A332333DCo

value: colonic differentiated cell

value: Male


title: Cumulus-oocyte complex, Nanoplastics, 3

description: Library name: UU_14

value: Nanoplastics


title: MIBC Responder

value: Responder

value: Biopsies in FFPE blocks from MIBC patient


title: Cumulus-oocyte complex, Nanoplastics, 5

description: Library name: UU_26


title: SPF_replicate_5_LDf21708DCo

value: 15 wk


title: G1_1

description: Library name: G1-2


title: PerturbFate pooled screen Dual-omics-04

description:
Library name: PerturbFate pooled screen Dual-omics-04
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


title: Cumulus-oocyte complex, Nanoplastics, 2

description: Library name: UU_08


title: G0_4

description: Library name: G0-CD8

value: APOL1 G0/G0


title: PerturbFate pooled screen Dual-omics-03

description:
Library name: PerturbFate pooled screen Dual-omics-03
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: Melanoma

value: BRAF V600E


title: SPF_replicate_4_LDf179DCo


title: Cumulus-oocyte complex, Control, 2

description: Library name: UU_07


title: SPF_replicate_2_LDf1021Co


title: SPF_replicate_3_LDf178DCo


title: Cumulus-oocyte complex, Control, 3

description: Library name: UU_13


title: G0_3

description: Library name: G0-365


title: Cumulus-oocyte complex, Nanoplastics, 1

description: Library name: UU_02


title: PerturbFate pooled screen Dual-omics-02

description:
Library name: PerturbFate pooled screen Dual-omics-02
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: DMSO or Vemurafenib


title: SPF_replicate_2_LDf168DCo


title: PerturbFate pooled screen Dual-omics-01

description:
Library name: PerturbFate pooled screen Dual-omics-01
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: Cumulus-oocyte complex, Control, 1

description: Library name: UU_01


title: SPF_replicate_1_LDf170DCo


title: HC_064, DSD

status: Public on Feb 05 2026

city: Barcelona

first: René

middle: Albert Johan

last: Crans

state: Catalonia

address: Carrer del Dr. Aiguader, 88

department: Systems and Synthetic Biology

country: Spain

institute: Centre for Genomic Regulation

description:
Library name: Sample 18
Colum name in raw_counts_matrix.txt:  HC_064

data_processing:
Raw sequencing reads in the FASTQ les were mapped with STAR (version 2.7.8a) against the Gencode v41 transcriptome, which was based on the GRCh38.p13 reference genome. BAM les were deduplicated with UMI-Tools dedup (version 1.1.2) using the --method = unique to retain one representative read per unique UMI. The generation of a table of counts with the subread R package (version 2.0.3). The options applied to quantify the abundance at gene level were -p to count read pairs, -t "exon" as features to be quantied, --largestOverlap to assign reads to the feature with the largest overlap and -g "gene_name" to collapse transcript-level quantication into gene-level counts.
Assembly: GRCh38.p13
Supplementary files format and content: tab-limited text file includes raw counts for each sample.

source_name: Hippocampus

extract_protocol:
Dissected hippocampi were weighted to calculate the homogenization volume of the buffer for obtaining a 20% concentrated suspension (weight/volume). The tissue was homogenized in ice-cold 50 mM Tris–HCl (pH 7.4) supplemented with Halt™ Protease and Phosphatase Inhibitor Cocktail (#78438, Thermo Fisher Scientic, Pittsburgh, PA, United States) by using the Bio-Gen PRO200 Homogenizer (#01-01200, PRO Scientic Inc., Oxford, CT, United States) at setting three for 30 seconds and then at full speed for one minute. Subsequently, the suspension was centrifuged at 3000 x g for 10 minutes (4°C). Then, the supernatant was used for RNA extraction. Total RNA was isolated with RNeasy Mini Kit (#74104, Qiagen, Hilden, Germany), according to manufacturer's instructions to achieve maximum yields of RNA. Next, the samples were treated with the Heat&Run® gDNA Removal Kit (#80200, ArticZymes, Tromsø, Norway) to avoid amplication of genomic DNA during further processing steps.
The SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (#634485, Takara Bio, Kusatsu, Japan) was used for library preparation, which was followed by a purication with AMPure XP beads (#A63880, Beckman Coulter Inc., Brea, CA, United States). Then, library fragments originating from rRNA (18S and 28S) and mitochondrial rRNA (m12S and m16S) were cleaved by ZapR v3 in the presence of mammalian specic R-Probes v3 (Takara Bio, Kusatsu, Japan). Paired-end sequencing for 50 bp each was performed on the NovaSeq 6000 platform (Illumina Inc., San Diego, CA, United States) to a depth of around 50 million reads (i.e., 25 million reads paired-end fragments).

value: Hippocampus

tag: disease state

value: Down syndrome dementia

tag: brain bank

value: Cambridge Brain Bank

tag: pmi


title: HC_066, DSD

description:
Library name: Sample 19
Colum name in raw_counts_matrix.txt:  HC_066


title: HC_069, DSD

description:
Library name: Sample 17
Colum name in raw_counts_matrix.txt:  HC_069

value: Female


title: HC_130, AD

description:
Library name: Sample 14
Colum name in raw_counts_matrix.txt:  HC_130

value: Alzheimer's disease

value: Institute Born-Bunge


title: HC_020, AD

description:
Library name: Sample 15
Colum name in raw_counts_matrix.txt:  HC_020

value: Neuro-CEB


title: G0_1

description: Library name: G0-1

value: CD8+ T cells


title: G0_2

description: Library name: G0-2


title: HC_132, AD

description:
Library name: Sample 13
Colum name in raw_counts_matrix.txt:  HC_132

value: Male


title: HC_128, AD

description:
Library name: Sample 11
Colum name in raw_counts_matrix.txt:  HC_128


title: HC_131, AD

description:
Library name: Sample 10
Colum name in raw_counts_matrix.txt:  HC_131


title: HC_148, AD

description:
Library name: Sample 12
Colum name in raw_counts_matrix.txt:  HC_148


title: HC_025, PDD

description:
Library name: Sample 6
Colum name in raw_counts_matrix.txt:  HC_025

value: Parkinson's disease dementia


title: HC_176, PDD

description:
Library name: Sample 9
Colum name in raw_counts_matrix.txt:  HC_176


title: HC_111, Control

description:
Library name: Sample 5
Colum name in raw_counts_matrix.txt:  HC_111

value: Non-demented


title: HC_063, DSD

description:
Library name: Sample 20
Colum name in raw_counts_matrix.txt:  HC_063


title: HC_110, Control

description:
Library name: Sample 3
Colum name in raw_counts_matrix.txt:  HC_110


title: HC_109, Control

description:
Library name: Sample 4
Colum name in raw_counts_matrix.txt:  HC_109


title: HC_108, Control

description:
Library name: Sample 2
Colum name in raw_counts_matrix.txt:  HC_108


title: HC_027, PDD

description:
Library name: Sample 7
Colum name in raw_counts_matrix.txt:  HC_027


title: HC_105, Control

description:
Library name: Sample 1
Colum name in raw_counts_matrix.txt:  HC_105


title: c2_mock_2

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

description:
Library name: c2_mock_2
c2.mock.2

data_processing:
kallisto tpm estimation, splicing analyses using rMATSv4.1.2 , DESeq2v1.44.0 in Rv4.4.0
Assembly: GENCODE Release 49 (GRCh38.p14)
Supplementary files format and content: kallisto tpm estimation

growth_protocol: High-glucose DMEM media (Gibco, 11995-065) supplemented with 10% Fetal Bovine Serum (Gibco, A52567-01) and 100 units/ml Pen/Strep antibiotics (Sigma-Aldrich, A5955) at 37°C with 5% CO2.

extract_protocol:
RNA was harvested using Trizol (Invitrogen, #15596026).
Total RNA extracts assessed by Bioanalyzer with a RIN value > 6.0 and were sent to Azenta for Illumina library preparation with PolyA selection for paired-end, 150bp sequencing at a minimum of 100 million reads per sample.

treatment_protocol: An OnTarget Plus SMARTpool (Dharmacon, #SO-3019437G) siRNA targeting TAOK2 (9344) was used for TAOK2 knockdown. A549 cells raised in media were reverse transfected in triplicate with siRNAs using Lipofectamine RNAiMAX transfection reagent (Invitrogen, 13778150) according to the manufacturer’s instructions. siCON control pool #2 (Dharmacon, #D-001206-14-20) was used in parallel for control samples. siRNAs were used at a final concentration of 30 nM.

value: Lung epithelial

value: WT

value: compound2 (taok2 kinase inhibitor)

tag: batch

value: B


title: dmso_mock_2

description:
Library name: dmso_mock_2
dmso.mock.2

value: DMSO


title: HC_061, DSD

description:
Library name: Sample 16
Colum name in raw_counts_matrix.txt:  HC_061

value: Kings College Brain Bank


title: dmso_mock_3

description:
Library name: dmso_mock_3
dmso.mock.3

value: C


title: c2_mock_1

description:
Library name: c2_mock_1
c2.mock.1

value: A


title: HC_178, PDD

description:
Library name: Sample 8
Colum name in raw_counts_matrix.txt:  HC_178

value: Hippocampus


title: dmso_mock_1

description:
Library name: dmso_mock_1
dmso.mock.1


title: c2_mock_3

description:
Library name: c2_mock_3
c2.mock.3


title: taok2_mock_3

description:
Library name: taok2_mock_3
taok2.mock.3

value: TAOK2 siRNA


title: taok2_mock_2

description:
Library name: taok2_mock_2
taok2.mock.2


title: con_mock_1

description:
Library name: con_mock_1
con.mock.1

value: non-targeting pool siRNA


title: taok2_mock_1

description:
Library name: taok2_mock_1
taok2.mock.1


title: con_mock_2

description:
Library name: con_mock_2
con.mock.2


title: con_mock_3

description:
Library name: con_mock_3
con.mock.3


title: XIII-SGF29sgC-Rep1_H3K4me3

first: Jamie

middle: N.

last: Anastas

state: TX

address: 1 Baylor Plaza

department: Neurosurgery

description: Library name: XIII_SGF29KO_C_R_H3K4me3_rep1

library_source: genomic

data_processing:
Reads were processed with trimgalore
Reads were aligned to the genome with bowtie2
Peaks were called with MACS2
D
Assembly: hg38
Supplementary files format and content: bigwig files for each sample
Supplementary files format and content: narrowpeak files for each sample
Library strategy: CUT&Run

molecule: genomic DNA

source_name: diffuse midline glioma

growth_protocol: SU-DIPGXIII cells were maintained as gliomaspheres in DMG media (50:50 DMEM/F12 and Neurobasal A, supplements with B27 minus Vitamin A, heparin, sodium pyruvate, GlutaMAX, MEM non-essential amino acids,  HEPES, Antibiotic-Antimyotic, Heparin, hPDGF-AA, hPDGF-BB, hFGF154, and hEGF) in a humidified chamber with 5% CO2 at 37C

extract_protocol:
SU-DIPGXIII+Cas9 cells were immobilized on ConA beads, permeabilized with 0.01% Digitonin, incubated with primary antibodies, and then cut with pAG-MNase to release DNA fragments as previously described.
Libraries were prepared from 3 ng of enriched DNA using the SMARTer ThruPLEX Plasma-seq kit (Takara Bio, Cat. No. R400681) with dual indexes (Takara Bio, Cat. No. DX34752) according to the manufacturer’s protocol. Adapter-ligated libraries were amplified for 11 PCR cycles, purified using AMPure XP beads (Beckman Coulter), and evaluated for fragment size distribution on an Agilent 2100 Bioanalyzer. Library molar concentrations were determined by quantitative PCR with the KAPA Library Quantification Kit (Roche) before pooling for sequencing on an Illumina NovaSeq 6000 to generate 150-bp paired-end reads.

treatment_protocol: Cells were not treated for this study

value: diffuse midline glioma

value: SU-DIPGXIII

value: patient-derived tumor cell line


title: XIII-SGF29sgC-Rep2_H3K9ac

description: Library name: XIII_SGF29KO_C_R_H3K9ac_rep2


title: DIPGXIII-SGF29sgC_Rep1_IgG

description: Library name: XIII_SGF29KO_C_R_IgG


title: XIII-SGF29sgC-Rep1_H3K9ac

description: Library name: XIII_SGF29KO_C_R_H3K9ac_rep1


title: DIPGXIII-CTLsg-Rep2_H3K4me3

description: Library name: XIII_CTL_C_R_H3K4me3_rep2


title: DIPGXIII-CTLsg-Rep2_H3K9ac

description: Library name: XIII_CTL_C_R_H3K9ac_rep2


title: DIPGXIII-CTLsg-Rep1_H3K9ac

description: Library name: XIII_CTL_C_R_H3K9ac_rep1


title: DIPGXIII-CTLsg-Rep1_H3K4me3

description: Library name: XIII_CTL_C_R_H3K4me3_rep1


title: DIPGXIII-CTLsg_Rep1_IgG

description: Library name: XIII_CTL_C_R_IgG


title: Huh7 cells, Hypoxia, 24 h, rep1

city: Hefei

first: Kejia

last: Liu

address: No. 96 Jinzhai Road

institute: University of Science and Technology of China

description:
Library name: Huh7_Hypoxia_24h_rep1
Biological replicate of Huh7 cells cultured under hypoxia for 24 h

data_processing:
Adapter sequences were removed from raw sequencing reads using Cutadapt.
Low-quality reads and bases were filtered based on default parameters to obtain clean reads.
Clean reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2.
Gene expression levels were quantified at the gene level as raw read counts and FPKM values using RSEM.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text files containing raw read counts for each sample.
Supplementary files format and content: Tab-delimited text files containing FPKM values for each sample.

source_name: liver

growth_protocol: Huh7 human hepatocellular carcinoma cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA quality and concentration were assessed by NanoDrop and Agilent Bioanalyzer.
RNA-seq libraries were prepared using a strand-specific rRNA-depleted library preparation protocol following the manufacturer’s instructions and sequenced on an Illumina platform to generate paired-end reads.

treatment_protocol: For hypoxia treatment, cells were cultured in a hypoxic chamber with 1% O2, 5% CO2, and 94% N2 for 24 h. Normoxia control cells were maintained under standard culture conditions (21% O2).

value: liver

value: hepatocellular carcinoma cells

value: hypoxia

tag: time


title: Huh7 cells, Hypoxia, 24 h, rep3

description:
Library name: Huh7_Hypoxia_24h_rep3
Biological replicate of Huh7 cells cultured under hypoxia for 24 h


title: Huh7 cells, Normoxia, 24 h, rep2

description:
Library name: Huh7_Normoxia_rep2
Biological replicate of Huh7 cells cultured under normoxia for 24 h

value: normoxia


title: Huh7 cells, Normoxia, 24 h, rep3

description:
Library name: Huh7_Normoxia_rep3
Biological replicate of Huh7 cells cultured under normoxia for 24 h

value: WT


title: SK-Hep1 SR siCOL6A3 + rhETP replicate 2

city: Ulsan

first: Jiyoung

last: Park

state: Ulsan

address: Building No. 110, Room 501-7

department: Department of Biological Sciences

country: South Korea

institute: Ulsan National Institute of Science and Technology (UNIST)

description:
Library name: SKHcpI_SR_siccl6A3_ETP_2
Sorafenib-resistant SK-Hep1 cells treated with COL6A3 siRNA and recombinant endotrophin (biological replicate 2)

data_processing:
Raw sequencing reads were processed using standard RNA-seq pipelines. Gene expression levels were quantified and normalized as fragments per kilobase of transcript per million mapped reads (FPKM). Downstream analyses, including clustering and visualization, were performed in R.
Assembly: GRCh38
Supplementary files format and content: Processed data files consist of gene-level expression matrices containing normalized FPKM values for all samples.

growth_protocol: SK-Hep1 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent followed by chloroform phase separation. After centrifugation, the aqueous phase was collected and RNA was purified according to the manufacturer’s instructions.
mRNA libraries were prepared using poly(A) enrichment. Library construction was performed according to the standard protocol provided by the sequencing service provider.

treatment_protocol: Cells were classified as sorafenib-sensitive or sorafenib-resistant. Cells were transfected with control siRNA or COL6A3-targeting siRNA, with or without supplementation of recombinant endotrophin, as indicated for each experimental condition.

value: cancer cell line

value: siCOL6A3 + recombinant endotrophin (sorafenib-resistant)


title: Huh7 cells, Hypoxia, 24 h, rep2

description:
Library name: Huh7_Hypoxia_24h_rep2
Biological replicate of Huh7 cells cultured under hypoxia for 24 h


title: Huh7 cells, Normoxia, 24 h, rep1

description:
Library name: Huh7_Normoxia_rep1
Biological replicate of Huh7 cells cultured under normoxia for 24 h


title: SK-Hep1 SR siCtrl replicate 2

description:
Library name: SKHcpI_SR_sictr1_2
Sorafenib-resistant SK-Hep1 cells treated with control siRNA (biological replicate 2)

value: siCtrl (sorafenib-resistant)


title: SK-Hep1 SS siCtrl replicate 1

description:
Library name: SKHcpI_SS_sictr1_1
Sorafenib-sensitive SK-Hep1 cells treated with control siRNA (biological replicate 1)

value: siCtrl (sorafenib-sensitive)


title: SK-Hep1 SS siCtrl replicate 2

description:
Library name: SKHcpI_SS_sictr1_2
Sorafenib-sensitive SK-Hep1 cells treated with control siRNA (biological replicate 2)


title: SK-Hep1 SR siCOL6A3 replicate 1

description:
Library name: SKHcpI_SR_siccl6A3_1
Sorafenib-resistant SK-Hep1 cells treated with COL6A3 siRNA (biological replicate 1)

value: siCOL6A3 (sorafenib-resistant)


title: SK-Hep1 SR siCOL6A3 replicate 2

description:
Library name: SKHcpI_SR_siccl6A3_2
Sorafenib-resistant SK-Hep1 cells treated with COL6A3 siRNA (biological replicate 2)


title: XIII-SGF29sgC-Rep2_H3K4me3

description: Library name: XIII_SGF29KO_C_R_H3K4me3_rep2


title: SK-Hep1 SR siCtrl replicate 1

description:
Library name: SKHcpI_SR_sictr1_1
Sorafenib-resistant SK-Hep1 cells treated with control siRNA (biological replicate 1)


title: SK-Hep1 SR siCOL6A3 + rhETP replicate 1

description:
Library name: SKHcpI_SR_siccl6A3_ETP_1
Sorafenib-resistant SK-Hep1 cells treated with COL6A3 siRNA and recombinant endotrophin (biological replicate 1)


title: RE55, PBMC before treatment, Feature Barcoding(ADT)

city: Hidaka-City, Saitama

first: Satoshi

last: Yamasaki

department: Department of Respiratory Medicine

country: Japan

institute: Saitama Medical University

description:
Library name: RE55_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

data_processing:
The demultiplexing, barcoded processing, gene counting and TCR repertoire analysis were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files and comma-separated values files
Library strategy: CITE-seq

molecule: protein

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Manufactured protocol of Chromium system (10x genomics)
Library construction was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 5' Reagent Kits v1.1 or v2 (Dual Index) protocol (CG000208 or CG000331), 10x Genomics).

value: Peripheral Blood Mononuclear Cells

value: CD3+ T cell

tag: disease

value: Lung cancer

tag: adt

value: Anti-CD4/TotalSeq-C0072 ; Anti-CD8A/TotalSeq-C0080 ; Anti CD62L/TotalSeq-C0147 ; Anti CD45RA/TotalSeq-C0063 ; Anti CD183/TotalSeq-C0140 ; Anti CD194/TotalSeq-C0071 ; Anti CD196/TotalSeq-C0143 ; Anti IgG1/TotalSeq-C090


title: RE55, PBMC before treatment, scTCR-seq

description:
Library name: RE55_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.

data_processing:
The demultiplexing, barcoded processing, gene counting and TCR repertoire analysis were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files and comma-separated values files
Library strategy: TCR-Seq

tag: tissue


title: RE52, PBMC before treatment, scRNA-seq

description:
Library name: RE52_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.

data_processing:
The demultiplexing, barcoded processing, gene counting and TCR repertoire analysis were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files and comma-separated values files

tag: cell type


title: RE52, PBMC before treatment, scTCR-seq

description:
Library name: RE52_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.


title: RE55, PBMC before treatment, scRNA-seq

description:
Library name: RE55_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.


title: mRNA from uninfected clones from donor 603

first: Alberto

last: Herrera

state: New York

department: Medicine

institute: Weill Cornell Medicine

description:
Library name: BJ-Clones-6-pool-2_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
FASTQ files from the 10x gene expression, surface protein, and TCR α/β libraries were processed using Cell Ranger v7.0.1 or v9.0.1 (10x Genomics), using either the count or the multi pipeline (when TCR libraries were available) with default parameters.
RNA transcripts from ECCITE-seq were mapped to a modified version of Cell Ranger’s GRCh38-2020-A reference package (GRCh38 / GENCODE v32 annotations), with the addition of the HIV-1 HXB2 reference sequence. TCR α/β libraries were mapped to Cell Ranger’s cellranger-vdj-GRCh38-alts-ensembl-7.1.0 reference package.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: *.h5 (feature barcode matrices in HDF5 format)
Supplementary files format and content: CellRanger output files: *.filtered_contig_annotations.csv (high-level annotations of each high-confidence contigs from cell-associated barcodes)
Supplementary files format and content: CellRanger output files: *.feature_reference.csv
Library strategy: CITE-seq

source_name: peripheral blood

growth_protocol: Memory CD4+ T-cells (mCD4) were isolated from the PBMCs  of people with HIV (PWH) by negative selection using EasySep™ Human Memory CD4+ T Cell Enrichment Kit (STEMCELL Technologies), plated (10 cells/well, 96-well plates), and stimulated with irradiated allogeneic HIV-negative PBMCs (1x106/mL) in R10-100 with ARVs (RPMI 1640 supplemented with 10% FBS and 1% penicillin/streptomycin, 1% HEPES buffer, 1% L-Glutamine supplemented with 100 Units/mL of IL-2, 1 µM Nevirapine, 1 µM Emtricitabine, 1 µM Tenofovir, 10 µM Enfuvirtide, and 10 µg/mL 10-1074 bNAb) with CD3 and CD28 antibodies for 21 days. Feeder PBMCs were depleted of CD8+ T-cells and NK cells using EasySep™ Human CD8 Positive Selection Kit II and EasySep™ Human CD56 Positive Selection Kit II (STEMCELL Technologies) before being co-cultured with mCD4 T-cells from PWH. At the end of stimulation cycle, p24 ELISA was performed on all plates. Cells from p24 ELISA-positive wells were plated in serial 3-fold dilution (96-well plates), stimulated at the same condition as aforementioned, and subjected to p24 ELISA after 21 days. After the second round of plating and ELISA, cells from p24 ELISA-positive wells were expanded under the same stimulation condition. Clonal purity of isolated infected populations was determined using IPDA and further serial dilution subs were performed as needed.

extract_protocol:
Following 2 weeks of rest from stimulation with  CD3 and CD28 antibodies and feeders in R10-100 with ARVs, cells were stained with DNA oligo-barcoded antibodies and loaded onto the 10x Chromium single-cell workflow (10X Genomics) as previously described61 with a few modifications. Approximately 0.05-0.3 x 106 cells per sample were resuspended in R10 media and incubated with the TotalSeq™-C Human Universal Cocktail (Biolegend) for 30 minutes at 4°C. In some cases, TotalSeq™-C hashing antibodies #1, #3 and #4 (Biolegend) were spiked into individual samples, which allowed for multiplexing of ARCs and uninfected clone combinations into the same 10X lane. After staining, cells were washed 3 times in R10 media, followed by centrifugation (400 × g for 5 minutes at 4°C) and supernatant aspiration. After the final wash, cells were resuspended in PBS and filtered through 70-µm cell strainers
All experiments were performed using the 10x genomics V(D)J solution which incorporates scRNA-seq with additional profiling of protein surface markers . Antibody oligo counts are listed in the ADT and HTO tables. Stained cells from each sample were pooled and loaded into the 10X Chromium Single Cell Immune Profiling workflow according to the manufacturer’s instructions (CG000330, revision G)

value: peripheral blood

value: CD4+ T cells


title: mRNA from ARC ZNF486 and uninfected clone from donor 603

description:
Library name: BJ-Clones-6-pool-1_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: ADT and HTO from uninfected clones from donor 603

description:
Library name: BJ-Clones-6-pool-2_ADT_HTO
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: TotalSeq-C Human Universal Cocktail, V1.0 (BioLegend Cat. No. 399905)

tag: hto

value: TotalSeq-C Hashtag 3 TTCCGCCTCTCTTTG (uninfected clone 3), TotalSeq-C Hashtag 1 GTCAACTCTTTAGCG (Uninfected clone 2)


title: RE52, PBMC before treatment, Feature Barcoding(ADT)

description:
Library name: RE52_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.


title: mRNA from ARC ZNF721 and uninfected clone from donor OM5334

description:
Library name: BJ-Clones-5_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: ADT and HTO from ARC ZNF721 and uninfected clone from donor OM5334

description:
Library name: BJ-Clones-5_ADT_HTO
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads, HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Oligo reads

value: TotalSeq-C Hashtag 3 TTCCGCCTCTCTTTG (ARC ZNF721), TotalSeq-C Hashtag 1 GTCAACTCTTTAGCG (ARC ZNF721), TotalSeq-C Hashtag 4 AGTAAGTTCAGCGTA (Uninfected clones)


title: ADT and HTO from ARC ZNF486 and uninfected clone from donor 603

description:
Library name: BJ-Clones-6-pool-1_ADT_HTO
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: TotalSeq-C Hashtag 3 TTCCGCCTCTCTTTG (Uninfected clone 1), TotalSeq-C Hashtag 1 GTCAACTCTTTAGCG (ARC ZNF486)


title: ADT and HTO from uninfected clones from donor 5104

description:
Library name: BJ-Clones-2_ADT_HTO
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads, HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Oligo reads

value: TotalSeq-C Hashtag 3 TTCCGCCTCTCTTTG (Uninfected clone 2), TotalSeq-C Hashtag 1 GTCAACTCTTTAGCG (Uninfected clone 1)


title: mRNA from ARC Chr22 and uninfected clone from donor 5104

description:
Library name: BJ-Clones-1_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: ADT and HTO from ARC Chr22 and uninfected clone from donor 5104

description:
Library name: BJ-Clones-1_ADT_HTO
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads, , HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Oligo reads

value: TotalSeq-C Hashtag 3 TTCCGCCTCTCTTTG (Uninfected clone 0), TotalSeq-C Hashtag 1 GTCAACTCTTTAGCG (ARC Chr22)