title: mig-32(n4275) ChIP-seq, H2AK119ub, replicate 4

description:
Library name: mig-32_n4275_ChIP-seq_H2AK119ub_replicate_4
Not spike-in scaled


title: Muscles of 15 individuals of the species Comephorus baicalensis

status: Public on Oct 30 2025

type: SRA

city: Irkutsk

first: Tuyana

last: Sidorova

address: 3, Ulan-Batorskaya

department: Siberian Branch of the Russian Academy of Sciences

country: Russia

institute: Limnological Institute

description: Library name: Sample 2

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v. 0.36.
The preprocessed reads were subjected to a de novo assembly procedure the Trinity v.2.13.2. software package
4 de-novo assemblies of different types are combined into one
The combined assembly was processed using CD-HIT version 4.8.1 to cluster sequences based on percentage similarity (95%).
Read count extrraction and normalization were perfomed using the R package EdgeR v4.0.3.
Assembly: de novo assembly
Supplementary files format and content: tab-delimited text file includes normalized FPKM values for each sample

molecule: total RNA

organism: Comephorus baikalensis

source_name: muscle

extract_protocol:
Total RNA was isolated from the muscles of 15 individuals of each species using TRIzol reagent
The library was examined using Qubit and real-time PCR for quantification and size distribution detection. Quantified libraries were pooled in equimolar amounts and sequenced on Illumina NovaSeq 6000 High Throughput Sequencer using a NovaSeq 6000 Reagent Kit v1.5 in 150 bp paired-end reads at Novogen company (China).

tag: tissue

value: muscle


title: d10_Con_CD8_2

status: Public on Nov 01 2025

city: Birmingham

first: Mingyong

last: Liu

state: AL

address: SHEL 531, 1825 University Blvd

department: Clinical Immunology and Rheumatology

country: USA

institute: University of Alabama at Birmingham

data_processing:
FASTQ reads were mapped to the mm10 mouse genome using STAR with the default parameters and the UCSC KnownGene transcriptome database.
The coverage at exons for all unique Entrez genes was computed using custom R/Bioconductor scripts and the GenomicRanges package.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated values file that includes raw counts of sequencing reads for each sample

organism: Mus musculus

source_name: breast tumors

growth_protocol: The TS/A murine mammary adenocarcinoma cells were cultured in DMEM supplemented with 10% fetal bovine serum and 2% L-glutamine, penicillin, streptomycin solution. Mice were injected with 1x10^5 TS/A cells in the second mammary pad.

extract_protocol:
Tumors were excised and infiltrating CD8+ T cells were collected directly into Qiagen RLT buffer plus 2-mercaptoethanol (Sigma). Total RNA was purified using the Quick-RNA MicroPrep kit.
Total RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara). The resulting cDNA was then used as input for the NexteraXT kit (Illumina) for tagmentation, PCR amplification and indexing. Final libraries were quantitated by Qubit, pooled at equimolar ratio.

treatment_protocol: Tumor-bearing mice were treated with 20mg/kg ENT or Vehicle daily starting on day 7 after tumor cell injection.

tag: strain

value: BALB/c

value: breast tumors

tag: treatment

value: Vehicle

tag: sorting markers

tag: time point

value: day10 post tumor injection


title: N2 ChIP-seq, H2KA119ub, replicate 3

status: Public on Oct 24 2025

city: Toronto

first: Daniel

last: Fusca

state: ON

address: 25 Willcocks Street

department: Department of Ecology and Evolutionary Biology

country: Canada

institute: University of Toronto

description:
Library name: N2_ChIP-seq_H2AK119ub_replicate_3
Spike-in scaled

library_source: genomic

data_processing:
The raw sequencing reads were trimmed for low-quality base calls, with a phred33 < 22, Illumina adapter sequences using a stringency of 12, and poly-G sequences (defined as 13 Gs in a row) using a stringency of 8 with TrimGalore v0.6.5.
Trimmed reads were aligned to the Caenorhabditis elegans ce11 genome using Bowtie2 v2.3.4.3 with the maximum fragment size parameter set to 2000. Alignments were filtered by removing duplicates and multi-mapping reads with a MAPQ < 42, using Samtools v1.11.
Peaks were called with MACS2 v2.2.7.1 with the  -g option set to ce and the --broad option. Peaks that overlap with blacklisted regions, where there is artificially high signal, were removed.
Replicates with a Drosophila chromatin spike-in were processed as above, except that they were aligned to a concatenated Caenorhabditis elegans ce11 and Drosophila melanogaster dm6 genome, reads mapped to both genomes were discarded and the reads were normalized as described. Briefly, the ce11 reads were randomly subsampled using factors that reflect the total number of dm6 reads in that sample and were corrected for the ratio of dm6/ce11 reads in the corresponding input samples.
Coverage files were prepared with the BedTools v2.29.0 genomecov function using the -bga and -pc options.
Log2 transformed ChIP/Input ratios were calculated per base with deepTools v3.5.0 bigwigCompare with a pseudocount of 1.
Assembly: ce11
Supplementary files format and content: Processed data files include genome coverage levels in bigWig format, as well as peak locations in BED format (except for input samples and replicate 2 of mig-32(n4275) H2AK119ub ChIP-seq)

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Strains were maintained on nematode growth medium (NGM) agar with E. coli OP50-1 as a food source at 21°C unless specified otherwise. The N2 (Bristol) strain was used as wild-type. Embryos were isolated from gravid adults using standard alkaline hypochlorite treatment (“bleaching”). After three washes in M9 buffer supplemented with 0.01% (v/v) Triton X-100 (M9/Tx), embryos were allowed to develop to L1 diapause in M9/Tx buffer overnight with aeration. The arrested L1s were plated on NGM agar or added to liquid culture with OP50-1 to start synchronous growth. Arrested L1s were counted and seeded into 40 mL of S-Complete medium with OP50-1 as a food source, at a final density of ~0.5-1.5 animals per uL. Animals were grown with aeration for 71-77 hours to gravid adulthood, and embryos were isolated again by bleaching. After washes with M9/Tx, embryos were processed for ChIP as described below either immediately or after a further 3-5 hours of growth with aeration.

extract_protocol:
Embryos were collected by centrifugation (1000g, 3 min.) and washed twice in phosphate-buffered saline (PBS) containing 0.01% (v/v) Triton X-100 (PBS/Tx). To crosslink, PBS/Tx was added to at least 80 times the pellet volume, and 37% formaldehyde (Sigma F8775) was added to a final concentration of 1.8%. Samples were incubated at room temperature with rotation for 25 minutes. Glycine was added to a final concentration of 125 mM followed by incubation for an additional 5 minutes. All subsequent steps were performed on ice using pre-chilled buffers and tubes. Embryos were washed twice with PBS/Tx as above and an equal volume of resuspension buffer (50 mM HEPES-KOH pH7.5, 150 mM NaCl, 1 mM EDTA, 0.01% Triton X-100, protease inhibitors (1 tablet per 5 mL, Roche 4693159001) was added to the embryo pellet. The resuspended embryos were aliquoted, snap-frozen in liquid nitrogen and stored at -80°C. Aliquots of cross-linked embryos were thawed in an ice-water bath, the volume was adjusted to 3-4 pellet volumes (PV) using resuspension buffer, and 100 uL was aliquoted to each polystyrene sonication tube (Evergreen 214-3721-010). An equal volume of resuspension buffer containing 2X detergents was added (50 mM HEPES-KOH pH7.5, 150 mM NaCl, 1 mM EDTA, 0.2% sodium deoxycholate, 0.7% sodium sarkosyl). Samples were sonicated in a Q800R3 water bath sonicator (QSonica Q800R3-110; 50% power, 20s on/20s off) for 4 minutes. Samples were gently mixed by pipetting and sonicated an additional 4 minutes. The lysate was transferred to an Eppendorf tube and an equal volume of resuspension buffer without detergents was added (50 mM HEPES-KOH pH7.5, 150 mM NaCl, 1 mM EDTA). The lysate was centrifuged (13,000g, 15 min. 4°C) and the supernatant was transferred to a new tube. Protein concentration was determined using the Bradford assay (Sigma B6916). For samples including a spike-in control for calibration, sonicated Drosophila chromatin (Active Motif, 53083) was added at a ratio of 1:20 or 1:30. The supernatant was aliquoted to tubes for immunoprecipitation (IP), saving 15-20% of the volume of one IP tube as the ‘input’ control, which was stored at -20°C. Triton X-100 (10%, v/v) was added to a final concentration of 1% (v/v). This step was omitted for anti-H3K27me3 (CST 9733, C36B11), for which this detergent led to increased background. After antibody addition, samples were incubated overnight at 4°C with rotation. Protein G dynabeads (Invitrogen 10003D; 7.5 uL per IP) were pre-washed twice with resuspension buffer and added to IPs, which were then incubated as above for 2 hours. Beads were collected on a magnetic stand (Permagen MSR812) and washed as follows, with each wash incubated for 5 minutes at 4°C with rotation: 2X with FA-150 (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate), 1X with FA-1M (FA-150 with 1 M NaCl), 1X with FA-0.5M (FA-150 with 0.5 M NaCl), 1X with TE-LiCl in a new tube (10 mM Tris-Cl pH 8, 1 mM EDTA, 250 mM LiCl, 1% IGEPAL CA-630, 1% sodium deoxycholate), 2X with TE+ (10 mM Tris-Cl pH 8, 1 mM EDTA, 50 mM NaCl, 0.005% IGEPAL CA-630). Elution was performed in a new tube at 65°C for 15 minutes using 50 uL of ChIP elution buffer (10 mM Tris-Cl pH 8, 1 mM EDTA, 200 mM NaCl, 1% SDS). Elution was repeated and the supernatants were pooled. The ‘Input’ aliquot was thawed and brought to 100 uL with ChIP elution buffer. Input and IP samples were treated with RNase A (16.5 ug, Sigma R4642) for 1 hour at 37°C and proteinase K (40 ug, Bioline BIO-37084) for 2 hours at 55°C. Crosslinks were reversed by incubation overnight at 65°C. DNA was isolated using a QIAquick PCR purification kit (Qiagen 28104).
Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645S) according to the manufacturer’s instructions, using 25-50 ng of input DNA or half of ChIP DNA. Library concentration was quantified using NEBNext Library Quant Kit for Illumina (NEB E7630). Pooled libraries were sequenced using NextSeq500 in 50 bp paired-end mode.

value: whole animal

tag: genotype

value: Wild-type

tag: developmental stage

value: mixed embryo

tag: chip target

tag: chip antibody

value: anti-H2AK119ub rabbit monoclonal D27C4, 8240; Cell Signaling Technology

tag: corresponding input

value: N2 ChIP-seq, input, replicate 3


title: N2 ChIP-seq, H2KA119ub, replicate 4

description:
Library name: N2_ChIP-seq_H2AK119ub_replicate_4
Not spike-in scaled


title: HBECs_pool004_GEX

status: Public on Oct 23 2025

city: Somerville

first: Mauricio

last: Cortes

state: MA

address: 101 South Street

institute: Cellarity

description:
Library name: ILD2-036_SRTP0001192
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.

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

organism: Homo sapiens

source_name: HBEC

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

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

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

tag: cell line

value: HBEC

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

tag: batch


title: HBECs_pool003_GEX

description:
Library name: ILD2-036_SRTP0001191
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: HBECs_pool001_GEX

description:
Library name: ILD2-035_SRTP0001189
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: HBECs_pool002_GEX

description:
Library name: ILD2-035_SRTP0001190
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: PreAdip_pool004_GEX

description:
Library name: ILD2-034_SRTP0001188
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.

source_name: PAD

value: PAD


title: PreAdip_pool002_GEX

description:
Library name: ILD2-033_SRTP0001186
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.


title: PreAdip_pool003_GEX

description:
Library name: ILD2-034_SRTP0001187
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.


title: KD_6_10B

status: Public on Oct 31 2025

city: Guangzhou

first: zixuan

last: chen

state: Guangdong

address: 651 Dongfeng Road East, Yuexiu District, Guangzhou, P.R. China

country: China

institute: Sun Yat-sen University Cancer Center

description:
Library name: sample8
gene_fpkm.2.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perlscripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCh38
Supplementary files format and content: gene_fpkm.1.txt
Supplementary files format and content: gene_fpkm.2.txt

source_name: nasopharyngeal carcinoma

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer®spectrophotometer (IMPLEN, CA, USA) . RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of theBioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperaturein NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA wassynthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequentlyperformed using DNA Polymerase I and RNase H. Remaining overhangs wereconverted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure wereligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: nasopharyngeal carcinoma

tag: cell type

value: nasopharyngeal carcinoma cell

value: UPF1 knockdown (UPF1-KD)


title: NC_6_10B

description:
Library name: sample7
gene_fpkm.2.txt

value: NC


title: NC_5_8F

description:
Library name: sample9
gene_fpkm.2.txt


title: PreAdip_pool001_GEX

description:
Library name: ILD2-033_SRTP0001185
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.


title: ILD2Ar2_HBECs_pool02_GEX

description:
Library name: ILD2-031_SRTP0001340
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: ILD2Ar2_HBECs_pool03_GEX

description:
Library name: ILD2-032_SRTP0001341
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: ILD2Ar2_HBECs_pool04_GEX

description:
Library name: ILD2-032_SRTP0001342
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: ILD2Ar2_HEK293_pool03_GEX

description:
Library name: ILD2-030_SRTP0001337
Perturbational single-cell screen with hashtag oligos. for cell line HEK293T, replicate2.


title: ILD2Ar2_HBECs_pool01_GEX

description:
Library name: ILD2-031_SRTP0001339
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: ILD2Ar2_HEK293_pool02_GEX

description:
Library name: ILD2-029_SRTP0001336
Perturbational single-cell screen with hashtag oligos. for cell line HEK293T, replicate2.


title: ILD2Ar2_CD34_pool01_GEX

description:
Library name: ILD2-027_SRTP0001318
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.

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


title: ILD2Ar2_preAdip_pool04_GEX

description:
Library name: ILD2-026_SRTP0001317
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: ILD2Ar2_preAdip_pool03_GEX

description:
Library name: ILD2-026_SRTP0001316
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: ILD2Ar2_HEK293_pool04_GEX

description:
Library name: ILD2-030_SRTP0001338
Perturbational single-cell screen with hashtag oligos. for cell line HEK293T, replicate2.


title: ILD2Ar2_CD34_pool04_GEX

description:
Library name: ILD2-028_SRTP0001321
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.

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


title: ILD2Ar2_preAdip_pool02_GEX

description:
Library name: ILD2-025_SRTP0001315
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: ILD2Ar2_HA1E_pool04_GEX

description:
Library name: ILD2-024_SRTP0001231
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.

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


title: ILD2Ar2_HA1E_pool03_GEX

description:
Library name: ILD2-024_SRTP0001230
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.


title: ILD2Ar2_HEK293_pool01_GEX

description:
Library name: ILD2-029_SRTP0001335
Perturbational single-cell screen with hashtag oligos. for cell line HEK293T, replicate2.


title: ILD2Ar2_HA1E_pool02_GEX

description:
Library name: ILD2-023_SRTP0001229
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.

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


title: ILD2Ar2_CD34_pool02_GEX

description:
Library name: ILD2-027_SRTP0001319
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: ILD2Ar2_CD34_pool03_GEX

description:
Library name: ILD2-028_SRTP0001320
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: ILD2Ar2_preAdip_pool01_GEX

description:
Library name: ILD2-025_SRTP0001314
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: ILD2Ar2_HepG2_pool01_GEX

description:
Library name: ILD2-021_SRTP0001236
Perturbational single-cell screen with hashtag oligos. for cell line HepG2, replicate2.

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


title: ILD2Ar2_HepG2_pool02_GEX

description:
Library name: ILD2-021_SRTP0001237
Perturbational single-cell screen with hashtag oligos. for cell line HepG2, replicate2.


title: ILD2Ar2_HepG2_pool03_GEX

description:
Library name: ILD2-022_SRTP0001238
Perturbational single-cell screen with hashtag oligos. for cell line HepG2, replicate2.

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


title: ILD2Ar2_A375_pool04_GEX

description:
Library name: ILD2-020_SRTP0001235
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.

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


title: ILD2Ar2_A375_pool03_GEX

description:
Library name: ILD2-020_SRTP0001234
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.


title: ILD2Ar2_A375_pool02_GEX

description:
Library name: ILD2-019_SRTP0001233
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.

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


title: ILD2Ar2_PC3_pool03_GEX

description:
Library name: ILD2-018_SRTP0001250
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: ILD2Ar2_PC3_pool04_GEX

description:
Library name: ILD2-018_SRTP0001251
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: ILD2Ar2_A375_pool01_GEX

description:
Library name: ILD2-019_SRTP0001232
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.


title: ILD2Ar2_A549_pool02_GEX

description:
Library name: ILD2-015_SRTP0001245
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: ILD2Ar2_A549_pool01_GEX

description:
Library name: ILD2-015_SRTP0001244
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: ILD2Ar2_A549_pool03_GEX

description:
Library name: ILD2-016_SRTP0001246
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: HepG2_pool004_GEX

description:
Library name: ILD2-014_SRTP0001156
Perturbational single-cell screen with hashtag oligos. for cell line HepG2, replicate1.


title: HepG2_pool003_GEX

description:
Library name: ILD2-014_SRTP0001155
Perturbational single-cell screen with hashtag oligos. for cell line HepG2, replicate1.


title: ILD2Ar2_PC3_pool01_GEX

description:
Library name: ILD2-017_SRTP0001248
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: HepG2_pool002_GEX

description:
Library name: ILD2-013_SRTP0001154
Perturbational single-cell screen with hashtag oligos. for cell line HepG2, replicate1.


title: ILD2Ar2_A549_pool04_GEX

description:
Library name: ILD2-016_SRTP0001247
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: ILD2Ar2_HepG2_pool04_GEX

description:
Library name: ILD2-022_SRTP0001239
Perturbational single-cell screen with hashtag oligos. for cell line HepG2, replicate2.


title: A549_pool002_GEX

description:
Library name: ILD2-009_SRTP0001146
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.

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


title: ILD2Ar2_HA1E_pool01_GEX

description:
Library name: ILD2-023_SRTP0001228
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.


title: HEK293T_pool004_GEX

description:
Library name: ILD2-012_SRTP0001152
Perturbational single-cell screen with hashtag oligos. for cell line HEK293T, replicate1.


title: HepG2_pool001_GEX

description:
Library name: ILD2-013_SRTP0001153
Perturbational single-cell screen with hashtag oligos. for cell line HepG2, replicate1.


title: HEK293T_pool003_GEX

description:
Library name: ILD2-012_SRTP0001151
Perturbational single-cell screen with hashtag oligos. for cell line HEK293T, replicate1.


title: HEK293T_pool002_GEX

description:
Library name: ILD2-011_SRTP0001150
Perturbational single-cell screen with hashtag oligos. for cell line HEK293T, replicate1.


title: A549_pool003_GEX

description:
Library name: ILD2-010_SRTP0001147
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.

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


title: A549_pool004_GEX

description:
Library name: ILD2-010_SRTP0001148
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.


title: A375_pool004_GEX

description:
Library name: ILD2-008_SRTP0001144
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.

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


title: A375_pool003_GEX

description:
Library name: ILD2-008_SRTP0001143
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.

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


title: PC3_pool003_GEX

description:
Library name: ILD2-006_SRTP0001139
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: PC3_pool004_GEX

description:
Library name: ILD2-006_SRTP0001140
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: PC3_pool002_GEX

description:
Library name: ILD2-005_SRTP0001138
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: PC3_pool001_GEX

description:
Library name: ILD2-005_SRTP0001137
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: HA1E_pool003_GEX

description:
Library name: ILD2-004_SRTP0001135
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: A375_pool001_GEX

description:
Library name: ILD2-007_SRTP0001141
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.

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


title: HA1E_pool004_GEX

description:
Library name: ILD2-004_SRTP0001136
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: ILD2Ar2_PC3_pool02_GEX

description:
Library name: ILD2-017_SRTP0001249
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: A375_pool002_GEX

description:
Library name: ILD2-007_SRTP0001142
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.


title: HA1E_pool001_GEX

description:
Library name: ILD2-003_SRTP0001133
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: CD34_pool002_GEX

description:
Library name: ILD2-001_SRTP0001158
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: HA1E_pool002_GEX

description:
Library name: ILD2-003_SRTP0001134
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: HEK293T_pool001_GEX

description:
Library name: ILD2-011_SRTP0001149
Perturbational single-cell screen with hashtag oligos. for cell line HEK293T, replicate1.


title: DrugSeq09_24well_hPreadipocytes_rep1_row6_GEX

description:
Library name: ILD1-022_SRTP0000705
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.

value: PAD

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


title: CD34_pool001_GEX

description:
Library name: ILD2-001_SRTP0001157
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: DrugSeq09_24well_hPreadipocytes_rep1_row7_GEX

description:
Library name: ILD1-022_SRTP0000706
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.


title: DrugSeq11_96well_hCD34_v1_row5_GEX

description:
Library name: ILD1-020_SRTP0000666
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: DrugSeq11_96well_hCD34_v1_row7_GEX

description:
Library name: ILD1-020_SRTP0000668
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: DrugSeq15_24well_Preadipocytes_v2_Row7_GEX

description:
Library name: ILD1-019_SRTP0000763
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: DrugSeq09_24well_hPreadipocytes_rep1_row5_GEX

description:
Library name: ILD1-022_SRTP0000704
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.


title: DrugSeq13_96well_hCD8_v2_row7_GEX

description:
Library name: ILD1-018_SRTP0000728
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate2.


title: A549_pool001_GEX

description:
Library name: ILD2-009_SRTP0001145
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.


title: DrugSeq15_24well_Preadipocytes_v2_Row5_GEX

description:
Library name: ILD1-019_SRTP0000761
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: DrugSeq13_96well_hCD8_v2_row5_GEX

description:
Library name: ILD1-018_SRTP0000726
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate2.


title: DrugSeq12_96well_hCD8_v1_row6_GEX

description:
Library name: ILD1-021_SRTP0000698
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate1.

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


title: DrugSeq12_96well_hCD8_v1_row5_GEX

description:
Library name: ILD1-021_SRTP0000697
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate1.


title: DrugSeq15_24well_Preadipocytes_v2_Row6_GEX

description:
Library name: ILD1-019_SRTP0000762
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: DrugSeq11_96well_hCD34_v1_row6_GEX

description:
Library name: ILD1-020_SRTP0000667
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: DrugSeq12_96well_hCD8_v1_row7_GEX

description:
Library name: ILD1-021_SRTP0000699
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate1.


title: DrugSeq13_96well_hCD8_v2_row6_GEX

description:
Library name: ILD1-018_SRTP0000727
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate2.


title: CD34_pool004_GEX

description:
Library name: ILD2-002_SRTP0001160
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: DrugSeq14_96well_hCD34_v2_row5_GEX

description:
Library name: ILD1-017_SRTP0000737
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: DrugSeq15_24well_Preadipocytes_v2_Row3_GEX

description:
Library name: ILD1-016_SRTP0000759
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: DrugSeq15_24well_Preadipocytes_v2_Row4_GEX

description:
Library name: ILD1-016_SRTP0000760
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: DrugSeq14_96well_hCD34_v2_row7_GEX

description:
Library name: ILD1-017_SRTP0000739
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: CD34_pool003_GEX

description:
Library name: ILD2-002_SRTP0001159
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: DrugSeq15_24well_Preadipocytes_v2_Row1_GEX

description:
Library name: ILD1-016_SRTP0000757
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: DrugSeq14_96well_hCD34_v2_row6_GEX

description:
Library name: ILD1-017_SRTP0000738
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: DrugSeq09_24well_hPreadipocytes_rep1_row2_GEX

description:
Library name: ILD1-015_SRTP0000701
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.

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


title: DrugSeq09_24well_hPreadipocytes_rep1_row4_GEX

description:
Library name: ILD1-015_SRTP0000703
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.


title: DrugSeq13_96well_hCD8_v2_row3_GEX

description:
Library name: ILD1-014_SRTP0000724
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate2.


title: DrugSeq09_24well_hPreadipocytes_rep1_row3_GEX

description:
Library name: ILD1-015_SRTP0000702
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.


title: DrugSeq15_24well_Preadipocytes_v2_Row2_GEX

description:
Library name: ILD1-016_SRTP0000758
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate2.


title: DrugSeq13_96well_hCD8_v2_row4_GEX

description:
Library name: ILD1-014_SRTP0000725
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate2.


title: DrugSeq13_96well_hCD8_v2_row2_GEX

description:
Library name: ILD1-014_SRTP0000723
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate2.


title: DrugSeq09_24well_hPreadipocytes_rep1_row1_GEX

description:
Library name: ILD1-015_SRTP0000700
Perturbational single-cell screen with hashtag oligos. for cell line PAD, replicate1.


title: DrugSeq12_96well_hCD8_v1_row4_GEX

description:
Library name: ILD1-013_SRTP0000696
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate1.

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


title: DrugSeq13_96well_hCD8_v2_row1_GEX

description:
Library name: ILD1-014_SRTP0000722
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate2.


title: DrugSeq12_96well_hCD8_v1_row2_GEX

description:
Library name: ILD1-013_SRTP0000694
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate1.


title: DrugSeq12_96well_hCD8_v1_row1_GEX

description:
Library name: ILD1-013_SRTP0000693
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate1.


title: DrugSeq12_96well_hCD8_v1_row3_GEX

description:
Library name: ILD1-013_SRTP0000695
Perturbational single-cell screen with hashtag oligos. for cell line CD8+, replicate1.


title: DrugSeq14_96well_hCD34_v2_row4_GEX

description:
Library name: ILD1-012_SRTP0000736
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: DrugSeq14_96well_hCD34_v2_row3_GEX

description:
Library name: ILD1-012_SRTP0000735
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: DrugSeq14_96well_hCD34_v2_row1_GEX

description:
Library name: ILD1-012_SRTP0000733
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: DrugSeq11_96well_hCD34_v1_row4_GEX

description:
Library name: ILD1-011_SRTP0000665
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: DrugSeq11_96well_hCD34_v1_row3_GEX

description:
Library name: ILD1-011_SRTP0000664
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: DrugSeq16_24well_BronchialEpithelium_v2_row2_GEX

description:
Library name: ILD1-010_SRTP0000746
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.

value: HBEC


title: DrugSeq11_96well_hCD34_v1_row1_GEX

description:
Library name: ILD1-011_SRTP0000662
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: DrugSeq11_96well_hCD34_v1_row2_GEX

description:
Library name: ILD1-011_SRTP0000663
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate1.


title: DrugSeq10_24well_hBronchialEpithelium_v1_row5_GEX

description:
Library name: ILD1-009_SRTP0000660
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: DrugSeq10_24well_hBronchialEpithelium_v1_row4_GEX

description:
Library name: ILD1-009_SRTP0000659
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: DrugSeq10_24well_hBronchialEpithelium_v1_row6_GEX

description:
Library name: ILD1-009_SRTP0000661
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: DrugSeq14_96well_hCD34_v2_row2_GEX

description:
Library name: ILD1-012_SRTP0000734
Perturbational single-cell screen with hashtag oligos. for cell line CD34+, replicate2.


title: DrugSeq10_24well_hBronchialEpithelium_v1_row3_GEX

description:
Library name: ILD1-009_SRTP0000658
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: DrugSeq16_24well_BronchialEpithelium_v2_row1_GEX

description:
Library name: ILD1-010_SRTP0000747
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: DrugSeq16_24well_BronchialEpithelium_v2_row3_GEX

description:
Library name: ILD1-010_SRTP0000745
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: DrugSeq16_24well_BronchialEpithelium_v2_row4_GEX

description:
Library name: ILD1-010_SRTP0000744
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: DrugSeq10_24well_hBronchialEpithelium_v1_row2_GEX

description:
Library name: ILD1-009_SRTP0000657
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: DrugSeq16_24well_BronchialEpithelium_v2_row5_GEX

description:
Library name: ILD1-010_SRTP0000743
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: DrugSeq10_24well_hBronchialEpithelium_v1_row1_GEX

description:
Library name: ILD1-009_SRTP0000656
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate1.


title: DrugSeq16_24well_BronchialEpithelium_v2_row6_GEX

description:
Library name: ILD1-010_SRTP0000742
Perturbational single-cell screen with hashtag oligos. for cell line HBEC, replicate2.


title: DrugSEQ06_24well_PC3_Replicate2_row6_GEX

description:
Library name: ILD1-008_SRTP0000610
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: DrugSEQ06_24well_PC3_Replicate2_row4_GEX

description:
Library name: ILD1-008_SRTP0000608
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: DrugSEQ07_24well_HA1E_replicate2_row6_GEX

description:
Library name: ILD1-007_SRTP0000616
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.


title: DrugSEQ06_24well_PC3_Replicate2_row3_GEX

description:
Library name: ILD1-008_SRTP0000607
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: DrugSEQ06_24well_PC3_Replicate2_row1_GEX

description:
Library name: ILD1-008_SRTP0000605
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: DrugSEQ06_24well_PC3_Replicate2_row2_GEX

description:
Library name: ILD1-008_SRTP0000606
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: DrugSEQ06_24well_PC3_Replicate2_row5_GEX

description:
Library name: ILD1-008_SRTP0000609
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate2.


title: DrugSEQ07_24well_HA1E_replicate2_row5_GEX

description:
Library name: ILD1-007_SRTP0000615
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.


title: DrugSEQ07_24well_HA1E_replicate2_row4_GEX

description:
Library name: ILD1-007_SRTP0000614
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.


title: DrugSEQ07_24well_HA1E_replicate2_row1_GEX

description:
Library name: ILD1-007_SRTP0000611
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.


title: DrugSEQ07_24well_HA1E_replicate2_row2_GEX

description:
Library name: ILD1-007_SRTP0000612
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.


title: DrugSEQ08_24well_A549_Replicate2_repeat_row6_GEX

description:
Library name: ILD1-006_SRTP0000637
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: DrugSEQ08_24well_A549_Replicate2_repeat_row5_GEX

description:
Library name: ILD1-006_SRTP0000636
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: DrugSEQ08_24well_A549_Replicate2_repeat_row4_GEX

description:
Library name: ILD1-006_SRTP0000635
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: DrugSEQ08_24well_A549_Replicate2_repeat_row2_GEX

description:
Library name: ILD1-006_SRTP0000633
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: DrugSEQ08_24well_A549_Replicate2_repeat_row1_GEX

description:
Library name: ILD1-006_SRTP0000632
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: DrugSEQ08_24well_A549_Replicate2_repeat_row3_GEX

description:
Library name: ILD1-006_SRTP0000634
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate2.


title: DrugSEQ05_24well_A375_replicate2_row6_GEX

description:
Library name: ILD1-005_SRTP0000604
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.


title: DrugSEQ05_24well_A375_replicate2_row5_GEX

description:
Library name: ILD1-005_SRTP0000603
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.


title: DrugSEQ01_24well_PC3_row4_GEX

description:
Library name: ILD1-004_SRTP0000496
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.

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


title: DrugSEQ01_24well_PC3_row5_GEX

description:
Library name: ILD1-004_SRTP0000497
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: DrugSEQ05_24well_A375_replicate2_row2_GEX

description:
Library name: ILD1-005_SRTP0000600
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.


title: DrugSEQ05_24well_A375_replicate2_row3_GEX

description:
Library name: ILD1-005_SRTP0000601
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.


title: DrugSEQ01_24well_PC3_row1_GEX

description:
Library name: ILD1-004_SRTP0000493
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: DrugSEQ05_24well_A375_replicate2_row4_GEX

description:
Library name: ILD1-005_SRTP0000602
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.


title: DrugSEQ01_24well_PC3_row3_GEX

description:
Library name: ILD1-004_SRTP0000495
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: DrugSEQ01_24well_PC3_row6_GEX

description:
Library name: ILD1-004_SRTP0000498
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: DrugSEQ01_24well_PC3_row2_GEX

description:
Library name: ILD1-004_SRTP0000494
Perturbational single-cell screen with hashtag oligos. for cell line PC3, replicate1.


title: drugSEQ04_24well_HA1Ev2_row3_GEX

description:
Library name: ILD1-003_SRTP0000562
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: drugSEQ04_24well_HA1Ev2_row5_GEX

description:
Library name: ILD1-003_SRTP0000564
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: drugSEQ04_24well_HA1Ev2_row4_GEX

description:
Library name: ILD1-003_SRTP0000563
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: DrugSEQ02_24well_A549_row6_GEX

description:
Library name: ILD1-002_SRTP0000504
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.


title: drugSEQ04_24well_HA1Ev2_row1_GEX

description:
Library name: ILD1-003_SRTP0000560
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: DrugSEQ02_24well_A549_row4_GEX

description:
Library name: ILD1-002_SRTP0000502
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.


title: DrugSEQ02_24well_A549_row5_GEX

description:
Library name: ILD1-002_SRTP0000503
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.


title: DrugSEQ07_24well_HA1E_replicate2_row3_GEX

description:
Library name: ILD1-007_SRTP0000613
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate2.


title: DrugSEQ02_24well_A549_row3_GEX

description:
Library name: ILD1-002_SRTP0000501
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.


title: DrugSEQ02_24well_A549_row1_GEX

description:
Library name: ILD1-002_SRTP0000499
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.


title: DrugSEQ05_24well_A375_replicate2_row1_GEX

description:
Library name: ILD1-005_SRTP0000599
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate2.


title: DrugSEQ02_24well_A549_row2_GEX

description:
Library name: ILD1-002_SRTP0000500
Perturbational single-cell screen with hashtag oligos. for cell line A549, replicate1.


title: DrugSEQ03_24well_A375v2_row6_GEX

description:
Library name: ILD1-001_SRTP0000511
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.


title: drugSEQ04_24well_HA1Ev2_row6_GEX

description:
Library name: ILD1-003_SRTP0000565
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: DrugSEQ03_24well_A375v2_row4_GEX

description:
Library name: ILD1-001_SRTP0000509
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.


title: DrugSEQ03_24well_A375v2_row3_GEX

description:
Library name: ILD1-001_SRTP0000508
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.


title: DrugSEQ03_24well_A375v2_row2_GEX

description:
Library name: ILD1-001_SRTP0000507
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.


title: DrugSEQ03_24well_A375v2_row1_GEX

description:
Library name: ILD1-001_SRTP0000506
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.


title: Small RNA_swi6∆Cryptic SS mut_Rep2

status: Public on Oct 15 2025

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

description: Small RNA_swi6∆Cryptic SS mut_Rep2

data_processing:
Single ended fastq format sequences derived from small RNA-seq data were quality-trimmed using fastp (Chen et al. 2018). Trimmed fastqs were aligned to the S. pombe reference (Wood et al. 2002) using the Novoalign aligner (http:// www.novocraft.com/products/novoalign).  SGR format files were created from the resulting BAM files using an inhouse script (available upon request).
Assembly: Schizosaccharomyces pombe V2 reference sequence.
Supplementary files format and content: SGR of normalized small RNAseq signal

organism: Schizosaccharomyces pombe

source_name: Yeast Whole Cells

growth_protocol: For RNA Seq-YEA, 30°C and 18°C, 2hrs, For Small RNA Seq-YEA, 30°C then shifted to 36°C, 5hrs

extract_protocol:
For RNA Seq Hot-phenol method, For small RNA Seq
For RNA Seq-Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E swi6delta::NatMX6 Cryptic SS mut

value: Yeast Whole Cells

tag: growth

value: Growth in YEA 30°C


title: Small RNA_swi6∆Cryptic SS mut_Rep1

description: Small RNA_swi6∆Cryptic SS mut_Rep1


title: Small RNA_Cryptic SS mut_Rep2

description: Small RNA_Cryptic SS mut_Rep2

value: mat1Msmt0 ade6-216 his2 ura4D18 Cryptic SS mut


title: drugSEQ04_24well_HA1Ev2_row2_GEX

description:
Library name: ILD1-003_SRTP0000561
Perturbational single-cell screen with hashtag oligos. for cell line HA1E, replicate1.


title: Small RNA_swi6∆cwf10-1_Rep2

description: Small RNA_swi6∆cwf10-1_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E swi6delta::NatMX6 cwf10-1, Otr1R (Sph1)::ura4+

value: Growth in YEA 30°C, shifted to 36°C for 5hrs


title: Small RNA_swi6∆ cenH CCAATATGAC_Rep2

description: Small RNA_swi6∆CCAATATGAC_Rep2

value: mat1Msmt0 ade6-210 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+ cenH CCAATATGAC swi6delta::NatMX6


title: Small RNA_swi6∆_Rep4

description: Small RNA_swi6∆_Rep4

value: mat1Msmt0 ade6-216 his2 ura4D18 swi6delta::NatMX6


title: Small RNA_WT_Rep3

description: Small RNA_WT_Rep3

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E


title: Small RNA_moc3∆_Rep2

description: Small RNA_moc3∆_Rep2

value: mat1Msmt0 ade6-216 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+ moc3delta::KanMX6


title: Small RNA_cenH CCAATATGAC_Rep2

description: Small RNA_cenH CCAATATGAC_Rep2

value: mat1Msmt0 ade6-210 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+ cenH CCAATATGAC


title: Small RNA_Cryptic SS mut_Rep1

description: Small RNA_Cryptic SS mut_Rep1


title: RNA_clr4∆_Rep2

data_processing:
Single ended fastq format sequences derived from RNA-seq data were quality-trimmed using fastp (Chen et al. 2018). Trimmed fastqs were aligned to the S. pombe reference (Wood et al. 2002) using the STAR aligner (Dobin et al. 2013) and bedgraphs generated by STAR, normalized to library size, were converted to a uniformly binned (10bp bins) format using an inhouse script (available upon request).?
Assembly: Schizosaccharomyces pombe V2 reference sequence.
Supplementary files format and content: Bedgraph of normalized RNAseq signal.

value: mat1Msmt0 leu1-32 ade6-216 ura4 clr4delta::KanMX6 otr1R(Spn1)::ura4

value: Growth in YEA 30°C and 18°C/2hrs


title: RNA_php2∆_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E php2delta::NatMX6 otr1R(Spn1)::ura4


title: Small RNA_swi6∆moc3∆_Rep2

description: Small RNA_swi6∆moc3∆_Rep2

value: mat1Msmt0 ade6-216 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+ moc3delta::KanMX6 swi6delta::NatMX6


title: Small RNA_php3∆_Rep2

description: Small RNA_php3∆_Rep2

value: mat1Msmt0 ade6-210 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+ php3delta::KanMX6


title: RNA_WT_Rep2


title: DrugSEQ03_24well_A375v2_row5_GEX

description:
Library name: ILD1-001_SRTP0000510
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.

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


title: Untag-IP_Rep3

data_processing:
Single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (Chen et al. 2018).
Trimmed fastqs were aligned to the S. pombe reference (Wood et al. 2002) using the BWA aligner (Li H. and Durbin R. 2009) and fold enrichment bedgraphs were generated using Macs2 (Zhang Y et al, 2008).
Assembly: Schizosaccharomyces pombe V2 reference sequence.
Supplementary files format and content: Bedgraph of normalized ChIP signal.

growth_protocol: YEA, 30°C and 18°C, 2hrs

extract_protocol:
Cells were crosslinked using 3% PFA at 18°C for 30 min and cells were spun at 2,000g for 5 min, washed with PBS and treated with DMA at room temperature for 45min. Cells pellets were lysed using glass beads and lysis buffer (50mM Hepes/KOH, 140mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% DOC plus protease inhibitors). Cell lysates were sheared using a Bioruptor-300 (Diagenode) to an approximate size of 300–600 bp.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).

value: mat1Msmt0 leu1-32 ade6-216 ura4D18

value: Abcam anti-GFP (cat# ab290)

tag: fixation

value: 3% PFA and DMA


title: Php3L12R-GFP _Input_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E Php3L12R-GFP::KanMX6


title: Untag_Input_Rep3


title: Moc3-GFP_php2∆_FE_Rep2

value: mat1Msmt0 leu1-32 ade6-216 ura4DS/E Moc3-GFP::KanMX6 php2delta::KanMX6


title: Php3-GFP_moc3∆_FE_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E Php3-GFP::KanMX6 moc3delta::KanMX6


title: Php3-GFP_FE_Rep3

value: mat1Msmt0 leu1-32 ade6-216 ura4DS/E Php3-GFP::KanMX6 php2delta::KanMX6


title: Php3L12R-GFP_FE_Rep1


title: Php3-GFP_php2∆_FE_Rep2


title: D7 macaque perturb-seq targeting 5 TFs coupled with lineage tracing , 10X lane2,  STICR

status: Public on Oct 13 2025

city: San Francisco

first: Alex

last: Pollen

institute: UCSF

description:
Library name: HM2D_L2_STICR
Raw data for macaque specimens are deposited
clones.h5ad

library_source: other

data_processing:
10X gene expression libraries together with sgRNA and STICR libraries were aligned to the hg38 genome obtained from CellRanger (refdata-gex-GRCh38-2024-A) with feature barcode reference using CellRanger-7.2.0. Aligned counts were then processed with Cellbender(Fleming et al. 2023, PMID: 37550580) for ambient removal. The resulting counts were processed by Scanpy (Wolf et al. 2018, PMID: 29409532) to remove low quality cells containing fewer than 1000 genes, a high abundance of mitochondrial reads (greater than 15% of total transcripts), or a high abundance of ribosomal reads (greater than 40% of total transcripts). Illumina Single Cell CRISPR libraries were aligned using DRAGEN Single Cell RNA v4.4.5 with additional arguments --single-cell-barcode-tag and --single-cell-umi-tag to support downstream individual demultiplexing. Low quality cells that had fewer than 500 genes or high abundance of mitochondrial or ribosomal reads were removed.
To align 10X runs with pooled human and rhesus macaque individuals, we made a composite genome using CellRanger mkref function with (1) hg38 (CellRanger refdata-gex-GRCh38-2024-A) and (2) a version of rheMac10 included in a hierarchical alignment and annotated with the Comparative Annotation Toolkit as part of Mao et al. (PMID: 33953399), then filtered with litterbox(https://github.com/nkschaefer/litterbox). Cells identified as cross-species multiplets were removed from downstream analyses. STICR barcodes for lineage tracing experiments were aligned and assigned using the NextClone (Putri et al. 2023) workflow. Individual barcodes were filtered by at least 3 reads supporting a single UMI and at least 2 UMI to call cells with a barcode.
Assembly: GRCh38, RheMac10
Supplementary files format and content: Merged anndata object of cells with assigned sgRNA and lineage barcode, including gene count matrix and metadata including individulal, developmental stages, cellt ype annotation, sgRNA assignment and clonal barcode assignment for experiments containing lineage tracing. For lineage tracing experiments, merged anndata objecta at the clone level at the clonexcell type format.
Supplementary files format and content: Csv files contain sgRNA sequences and target gene information used for sgRNA alignment.

molecule: other

organism:
Macaca mulatta
Homo sapiens

source_name: Cortical neural Progenitors

extract_protocol:
Culture of primary human and macaque neural progenitors were dissociated for 20 min in papain, spun down and resuspended in 0.5% BSA, 5% Trehalose in PBS and sorted with FACSAria Fusion cell sorter (BD) based on GFP (and mCherry) expression. Collected cells were resuspended in 0.02%BSA in PBS and captured following manufacture's protocol.
Gene expression library was constructed according to manufacturer's instructions. sgRNA libraries were separately amplified from each cDNA library. To generate STICR barcode libraries, cDNA library was used as template following protocol described in Delgado et al. 2021, PMID: 34912114.

value: Cortical neural Progenitors


title: Small RNA_swi6∆_Rep3

description: Small RNA_swi6∆_Rep3

value: mat1Msmt0 ade6-216 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+ swi6delta::NatMX6

value: Yeast Whole Cells

value: Growth in YEA 30°C


title: Small RNA_swi6∆php3∆_Rep2

description: Small RNA_swi6∆php3∆_Rep2

value: mat1Msmt0 ade6-216 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+ php3delta::KanMX6 swi6delta::NatMX6


title: D7 macaque perturb-seq targeting 5 TFs coupled with lineage tracing,10X lane3 , GEX

description:
Library name: HM2D_L3_GEX
Raw data for macaque specimens are deposited
merged.h5ad

library_source: transcriptomic single cell

molecule: polyA RNA


title: D7 macaque perturb-seq targeting 5 TFs coupled with lineage tracing , 10X lane3,  STICR

description:
Library name: HM2D_L3_STICR
Raw data for macaque specimens are deposited
clones.h5ad


title: RNA_clr4∆php2∆_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E php2delta::NatMX6 clr4delta::KanMX6

value: Growth in YEA 30°C and 18°C/2hrs


title: D7 macaque perturb-seq targeting 5 TFs coupled with lineage tracing , 10X lane1,  STICR

description:
Library name: HM2D_L1_STICR
Raw data for macaque specimens are deposited
clones.h5ad


title: D7 macaque perturb-seq targeting 5 TFs coupled with lineage tracing, 10X lane3,  sgRNA

description:
Library name: HM2D_L3_sgRNA
Raw data for macaque specimens are deposited
feature_ref.csv


title: D7 macaque perturb-seq targeting 5 TFs coupled with lineage tracing, 10X lane2,  sgRNA

description:
Library name: HM2D_L2_sgRNA
Raw data for macaque specimens are deposited
feature_ref.csv


title: D7 macaque perturb-seq targeting 5 TFs coupled with lineage tracing, 10X lane2 , GEX

description:
Library name: HM2D_L2_GEX
Raw data for macaque specimens are deposited
merged.h5ad


title: Small RNA_cwf10-1_Rep2

description: Small RNA_cwf10-1_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4D18 cwf10-1 Otr1R (Sph1)::ura4+

value: Growth in YEA 30°C, shifted to 36°C for 5hrs


title: D7 macaque perturb-seq targeting 5 TFs coupled with lineage tracing, 10X lane1 , GEX

description:
Library name: HM2D_L1_GEX
Raw data for macaque specimens are deposited
merged.h5ad


title: Primary CD4 T cells, sgHOIP, CD3_CD28, Donor1

status: Public on Oct 11 2025

city: Parkville

first: Göksu

last: Avar

state: Victoria

address: 30 Flemington Road

department: Biochemistry and Pharmacology

country: Australia

institute: University of Melbourne

description:
Library name: Sample_24L018215
S15

data_processing:
100-bp paired-end reads were aligned to the human genome (GRCh38.p14) using STAR v2.7.11b. Gene-level quantification was performed using Rsubread in R v4.4.3.
Assembly: GRCh38.p14
Supplementary files format and content: "rcounts.csv" contains the raw, gene-level count table.

source_name: Primary CD4 T cell

extract_protocol:
RNA isolation was performed using the Qiagen QiaCube instrument and quantified using Aligent TapeStation. RIN and Qubit-measurement was performed for quality control.
Illumina Stranded mRNA Ligation

value: Primary CD4 T cell

value: sgHOIP


title: Primary CD4 T cells, sgHOIP, CD3_CD28, Donor 3

description:
Library name: Sample_24L018239
S39


title: Primary CD4 T cells, sgHOIP, CD3_CD28, Donor 4

description:
Library name: Sample_24L018251
S51


title: Primary CD4 T cells, sgHOIP, CD3_CD28, Donor 2

description:
Library name: Sample_24L018227
S27


title: D7 macaque perturb-seq targeting 5 TFs coupled with lineage tracing , 10X lane1,  sgRNA

description:
Library name: HM2D_L1_sgRNA
Raw data for macaque specimens are deposited
feature_ref.csv


title: Primary CD4 T cells, sgTRAF6, CD3_CD28, Donor 3

description:
Library name: Sample_24L018235
S35


title: Primary CD4 T cells, sgTRAF6, CD3_CD28, Donor 2

description:
Library name: Sample_24L018223
S23


title: Php3L12R-GFP_FE_Rep2

value: Abcam anti-GFP (cat# ab290)


title: Primary CD4 T cells, sgTRAF6, CD3_CD28, Donor 4

description:
Library name: Sample_24L018247
S47


title: Primary CD4 T cells, sgTRAF6, CD3_CD28, Donor1

description:
Library name: Sample_24L018211
S11


title: Primary CD4 T cells, Non-Targeting Control, CD3_CD28, Donor 4

description:
Library name: Sample_24L018243
S43

value: NTC


title: Primary CD4 T cells, Non-Targeting Control, CD3_CD28, Donor 3

description:
Library name: Sample_24L018231
S31


title: Primary CD4 T cells, Non-Targeting Control, CD3_CD28, Donor 2

description:
Library name: Sample_24L018219
S19


title: Primary CD4 T cells, sgHOIP, Untreated, Donor 3

description:
Library name: Sample_24L018236
S36

value: Untreated


title: Primary CD4 T cells, sgHOIP, Untreated, Donor 4

description:
Library name: Sample_24L018248
S48


title: Primary CD4 T cells, sgHOIP, Untreated, Donor 2

description:
Library name: Sample_24L018224
S24


title: Primary CD4 T cells, Non-Targeting Control, CD3_CD28, Donor1

description:
Library name: Sample_24L018207
S07


title: Primary CD4 T cells, sgTRAF6, Untreated, Donor 4

description:
Library name: Sample_24L018244
S44


title: Primary CD4 T cells, sgTRAF6, Untreated, Donor 3

description:
Library name: Sample_24L018232
S32


title: Primary CD4 T cells, sgHOIP, Untreated, Donor1

description:
Library name: Sample_24L018212
S12


title: Primary CD4 T cells, sgTRAF6, Untreated, Donor 2

description:
Library name: Sample_24L018220
S20


title: Primary CD4 T cells, Non-Targeting Control, Untreated, Donor 2

description:
Library name: Sample_24L018216
S16


title: Primary CD4 T cells, Non-Targeting Control, Untreated, Donor 3

description:
Library name: Sample_24L018228
S28


title: Primary CD4 T cells, Non-Targeting Control, Untreated, Donor1

description:
Library name: Sample_24L018204
S04


title: Slide 10 ( SU20-28006 M3) | 011 | PanCK

status: Public on Oct 07 2025

city: Dallas

first: Fabiana

last: Napolitano

state: TX

address: 6000 Harry Hines Blvd.

institute: Simmons Comprehensive Cancer Center

description: Library name: DSP-1001660012370-F-C02

data_processing:
FASTQ files were processed into digital count conversion files using Nanostring’s GeoMx NGS Pipeline software.
Assembly: hg38
Supplementary files format and content: Normalized count file in csv format
Library strategy: Spatial Transcriptomics

source_name: breast cancer

extract_protocol:
FFPE tumor sections (5-µm) were mounted on charged slides
GeoMx NGS libraries were prepared following the manufacturer's protocol.

value: breast cancer

value: ED-resistant

value: letrozole


title: Slide 10 ( SU20-28006 M3) | 010 | CD45

description: Library name: DSP-1001660012370-F-B12


title: Slide 10 ( SU20-28006 M3) | 011 | CD45

description: Library name: DSP-1001660012370-F-C03


title: Slide 10 ( SU20-28006 M3) | 011 | REST

description: Library name: DSP-1001660012370-F-C04


title: Slide 10 ( SU20-28006 M3) | 007 | REST

description: Library name: DSP-1001660012370-F-B05


title: Slide 10 ( SU20-28006 M3) | 009 | REST

description: Library name: DSP-1001660012370-F-B10


title: Slide 10 ( SU20-28006 M3) | 008 | CD45

description: Library name: DSP-1001660012370-F-B07


title: Slide 10 ( SU20-28006 M3) | 007 | PanCK

description: Library name: DSP-1001660012370-F-B03


title: Slide 10 ( SU20-28006 M3) | 008 | REST

description: Library name: DSP-1001660012370-F-B08


title: Slide 10 ( SU20-28006 M3) | 007 | CD45

description: Library name: DSP-1001660012370-F-B04


title: Slide 10 ( SU20-28006 M3) | 009 | CD45

description: Library name: DSP-1001660012370-F-B09


title: Slide 10 ( SU20-28006 M3) | 006 | REST

description: Library name: DSP-1001660012370-F-B02


title: Slide 10 ( SU20-28006 M3) | 006 | CD45

description: Library name: DSP-1001660012370-F-B01


title: Slide 10 ( SU20-28006 M3) | 006 | PanCK

description: Library name: DSP-1001660012370-F-A12


title: Primary CD4 T cells, Non-Targeting Control, Untreated, Donor 4

description:
Library name: Sample_24L018240
S40


title: Slide 10 ( SU20-28006 M3) | 005 | PanCK

description: Library name: DSP-1001660012370-F-A10


title: Primary CD4 T cells, sgTRAF6, Untreated, Donor1

description:
Library name: Sample_24L018208
S08


title: Slide 10 ( SU20-28006 M3) | 005 | REST

description: Library name: DSP-1001660012370-F-A11


title: Slide 10 ( SU20-28006 M3) | 003 | PanCK

description: Library name: DSP-1001660012370-F-A06


title: Slide 10 ( SU20-28006 M3) | 004 | REST

description: Library name: DSP-1001660012370-F-A09


title: Slide 10 ( SU20-28006 M3) | 002 | PanCK

description: Library name: DSP-1001660012370-F-A04


title: Slide 10 ( SU20-28006 M3) | 010 | REST

description: Library name: DSP-1001660012370-F-C01


title: Slide 10 ( SU20-28006 M3) | 001 | REST

description: Library name: DSP-1001660012370-F-A03


title: Slide 10 ( SU20-28006 M3) | 003 | REST

description: Library name: DSP-1001660012370-F-A07


title: Slide 10 ( SU20-28006 M3) | 001 | PanCK

description: Library name: DSP-1001660012370-F-A02


title: Slide 10 ( SU20-28006 M3) | 010 | PanCK

description: Library name: DSP-1001660012370-F-B11


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