title: Wildtype-DCS-treated replicate5

value: DCS-treated


title: CA8098CB-04

status: Public on Jul 09 2026

type: RNA

city: Portland

first: Julie

middle: A

last: Saugstad

state: Oregon

address: 3181 SW Sam Jackson Park Road

department: Anesthesiology & Perioperative Medicine

country: USA

institute: Oregon Health & Science University

scan_protocol: Each card was assayed on a QuantStudio 7K Flex (TFS) by automatic loading of the cards using an Orbitor R2 robot to increase throughput.

data_processing:
For each RT-qPCR well, we examined a variety of quality control (QC) metrics exported by ExpressionSuite software. Cq values for miRNA amplifications were included in statistical analysis if they had an AmpScore ≥1.0 with CqConf ≥0.8. MiRNA amplifications (e.g., let-7b-5p) that showed performance slightly below those thresholds (either AmpScore ≥0.9 with CqConf ≥0.8, or CqConf ≥0.75 with AmpScore ≥1.0) had Cq values accepted for statistical analysis conditional on meeting other criteria for good amplification (strong consistency of Cq values across triplicate wells). For accepted amplifications we examined the appropriateness of the baseline separation from the recorded Cq value and compared our QC assessments with other quality flags exported by QuantStudio, finding nothing unusual. Amplifications with acceptable QC but Cq >35 were considered censored values and given special handling using censoring-aware methods in the analysis. Amplifications that did not meet the QC standards for accepted or censored amplifications were considered missing measurements, regardless of Cq value. Amplifications labeled "Undetermined" by QuantStudio were also considered missing measurements. As a final fidelity check we 1) examined the amplifications for the two negative control miRNAs (miR-1293 and miR-647) to verify that no sample had a Cq value recorded for either of those with acceptable QC, and 2) verified that the spike-in positive control (cel-miR-39-3p) and primary endogenous normalization control (miR-16-5p) were both completely observed with acceptable QC in all replicates for all samples. The other endogenous normalizer control miRNAs (miR-24-3p, miR-92a-3p, miR-204-5p) showed good performance, with expression of miR-24-3p and miR-92a-3p in 100% of samples and miR-204-5p in 77% of samples. Given our built-in redundancy of normalizer control miRNAs and model-based methods of normalization that can handle noninformative missing data, we considered this amount of normalizer measurement dropout acceptable.
For technical calibration, all raw Cq values were adjusted for RNA isolation differences via median-alignment of the cel‑miR‑39‑3p spike‑in control reactions as an exogenous calibration factor. This adjustment represented the largest contribution to the overall normalization, with 57% of the technical variance explained by differences in spike-in control values (Note that we define technical variance as the variance in average Cq values across samples.) After technical calibration, all Cq values for the cel‑miR‑39‑3p spike-in (being exactly aligned by median) were removed from the dataset and did not contribute to later normalization steps. Next, these technical calibrated Cq values were batch calibrated to remove residual artifacts attributed to processing order. We fit a linear mixed-effects regression model including the same 5-knot restricted cubic spline of the RT-qPCR run order as above, plus indicators for known abnormal sample or processing events (e.g., visible hemolysis), with PCR run batches entered as random intercepts. Fitted values from this regression were subtracted from the corresponding Cq values for all miRNAs as the adjustment for batch and order-related effects. Batch calibration adjustments were relatively minor for our dataset, accounting for 10% of the technical variance.
Calibrated Cq values were normalized using a mixed-effects model on the endogenous miRNA normalizer Cq values only. The model included quadratic effects of age (interaction effect of age with itself, to model the effect of age at differing ages rather than assuming the effect is linear for all ages), fully-interacted indicators for sex and diagnosis group to adjust out study factors (because we wish to retain these factors for analysis), and crossed random effects of miRNA and sample to model the miRNA-sample interaction. We used this model to estimate the residual differences between samples as BLUPs (best linear unbiased predictions). The BLUP values were subtracted from the fully calibrated Cq values as endogenous normalizer level effects across samples. The resulting normalized Cq values were recentered to the global median of the input Cq value distribution. This final normalization step accounted for 26% of the technical variance in the data. The remaining 7% of technical variance was unexplained. After normalization, 83% of the total Cq variance (expected between-miRNA variance plus signal and residual technical and noise variance) was attributable to differences in mean expression across miRNAs (expected variance), 9% was attributable to sample-miRNA interactions (the biological signal), and <1% to differences in mean expression across samples (the residual technical variance, meaning the normalization was highly successful); the remainder of ~7% is residual variance (the measurement noise). We verified that the normalized Cq values of the normalizer miRNAs themselves had essentially flat profiles and noted that the normalization achieved substantial variance reduction.
Censored Cq values are quantitatively unreliable because their measurement falls outside the linear range of the assay. These were treated as interval observations, defined as an unobserved value falling between an upper and a lower limit. For the purposes of regression on the Cq values as an outcome predicted by diagnosis status these can be handled as interval observations directly via modeling. However, when the Cq values are used as predictors of diagnosis status the interval observation must be collapsed to a single most-likely value falling within the interval. To accomplish this, we used a Bayesian multilevel interval regression model that considers all replicate wells for the sample jointly and naturally accounts for the different character of censored values in the context of non-censored values for the same miRNA. For the Bayesian prior distribution on the mean level for the miRNA, we used a Student's t distribution with 4 degrees of freedom and a (wide and uninformative) scale of 10, and for the log of the root mean square error we used a (similarly uninformative) half-Cauchy distribution with the same scale of 10. Random effects for individual samples were assigned a zero-centered prior normal distribution with default conjugate inverse-gamma hyperprior (shape and scale parameters both 1/100) for the random-effect variance. The imputed value for a censored observation was taken as the posterior grand mean for the miRNA plus the posterior mean of the random effect, based on 10000 Markov chain Monte Carlo draws from the posterior distribution, following a burn-in run of 2500 draws. Note that the rank correlation between the predictions from this model and the naïve means of the corresponding replicate wells was 0.98, reflecting almost complete preservation of rank ordering among samples, but the model prediction is less biased because it accounts for censoring, which prevents it from overestimating the expression level. (The mean overestimate was 0.95 Cq.)
Prior to imputation the normalized Cq values, both censored and uncensored, are converted to an expression scale using inverted Cq units so that positive values mark higher expression. Non-censored Cq values with acceptable QC were used as exact measurements (both bounds of the interval are the same normalized Cq value). Censored Cq values with acceptable QC were treated as falling between the censoring threshold of 35 (lower bound) and the average (upper bound) of the normalized Cq value and the maximum normalized Cq value across all observations on all miRNAs (the "observed maximum", a value that will be strictly less than the maximum cycle number of 40, specified as a machine setting). Missing Cq values were treated as falling between the observed maximum (lower bound) and the maximum cycle number (upper bound of 40). Non-missing Cq values with unacceptable QC were treated as missing measurements for most purposes, but in this context the recorded Cq (with all normalization adjustments) was used as the lower bound and the maximum cycle number (40) as the upper bound. Finally, all the interval bounds were subtracted from the maximum cycle number of 40 to invert the scale.

label: FAM

molecule: total RNA

organism: Homo sapiens

source_name: total cell-free biofluid RNA

label_protocol: MiRNA was converted to cDNA as previously described using the TaqMan Advanced miRNA cDNA Synthesis kit (TFS). Briefly, 3 μL of total RNA was 3’ poly-adenylated, followed by a 5’ adaptor ligation step and reverse transcription. The resulting cDNA (5 μL) was added to a 14-cycle universal miR-amplification step. The miR-amplification reaction was diluted 1:10 with nuclease free water, 220 µL of the diluted cDNA was mixed with 220 µL of nuclease free water and 440 µL of TaqMan Fast Advanced master mix (TFS). The RT-qPCR mix (100 µL) was loaded into custom TaqMan Advanced Human miRNA Custom Cards.

extract_protocol: Total RNA was isolated from 100 μL of plasma using the MagMax Mirvana Total RNA Isolation Kit (Thermo Fisher Scientific, TFS) using a KingFisher Apex System (TFS) automated purification instrument following the manufacturer’s protocol. For the RNA isolation, the 289 plasma samples were processed in a total of 4 batches (3 plates x 80 samples = 240, 1 plate x 49 samples). On the first day, plasma samples were mixed with 5 µL of proteinase K and 45 µL of digestion buffer and incubated for 30 minutes at 65°C. 100 µL of lysis buffer containing 1% β-mercaptoethanol was added to each well, mixed and stored at -20°C overnight. The following day, the plate was thawed to room temperature and an exogenous cel-miR-39-3p spike-in control (TFS) was added at a final concentration of 3 pM, followed by the addition of 20 µL of magnetic isolation beads. Samples were mixed for 5 minutes using a plate shaker followed by the addition of 270 µL of isopropanol and brief mix. The sample plate as well as 4 wash plates (each containing 150 µL of wash buffer), a DNase plate containing 45 µL of Turbo DNase buffer and 2 µL of DNase, and an elution plate containing 50 µL of nuclease free water were all processed using the KingFisher Apex instrument. Following the DNase step, 50 µL re-binding buffer and 100 µL of isopropanol was added to each well and automation was resumed for the washing and elution steps. All isolations were completed within two consecutive days. Following the elution step, the miRNA concentration of a subset of samples from each batch (minimum of 30% of samples per batch across each plate) was measured using the Qubit miRNA Assay kit (TFS) and read using a Qubit 4.0 fluorometer (TFS) to ensure the isolation was consistent across the batch. Prior to the eluted RNA being frozen at -80°C until RT-qPCR, each plate of 80 RNA samples was divided into 2 plates of 40 RNA samples, as 40 is the maximum number of miRNA RT-qPCR assays that can be processed in a day, and the plate with 49 RNA samples was divided into 1 plate of 40 samples and 1 plate of 9 samples. Thus, the RT-qPCR was performed with the 289 eluted RNA samples in a total of 8 batches (7 x 40 RNA = 280, 1 x 9 RNA), with one batch being completed per day in unbroken succession to mitigate time drift in measurements.

tag: donor id

tag: tissue

value: Plasma

tag: disease

value: AD

tag: Sex

value: Male

tag: age

tag: mmse

tag: anatomical location

value: Circulating blood

tag: sample collection method

value: Venous

tag: starting amount

tag: holding temperature


title: Wildtype-DCS-treated replicate4

type: SRA

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

library_source: transcriptomic

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.2) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.26.0).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

organism: Mus musculus

source_name: Brain

growth_protocol: All mice were housed and bred at the mouse facility of Korea Advanced Institute of Science and Technology (KAIST) and maintained according to the Animal Research Requirements of KAIST. All animals were fed ad libitum and housed under 12 h light/dark cycle. All procedures were approved by the Committee of Animal Research at KAIST (KAIST; KA2020-90).

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain

tag: strain

value: male

tag: genotype

value: wildtype

tag: treatment


title: DLBC-03-019

value: DLB

value: Female


title: Wildtype-DCS-treated replicate3


title: Wildtype-DCS-treated replicate2


title: PWA12-0483

value: PD


title: JA8080XH-03

value: NC


title: HA807726-04


title: PWA20-0783


title: Wildtype-DCS-treated replicate1


title: PWA19-0760


title: Heterotype-DCS-vehicle replicate3

value: Grin2b heterozygous

value: vehicle


title: PWA11-0314


title: PWA11-0214


title: BA80CRSJ-03


title: Heterotype-DCS-vehicle replicate2


title: JA808Q9V-04


title: Heterotype-DCS-treated replicate6


title: DLBC-03-006


title: Heterotype-DCS-vehicle replicate1


title: Heterotype-DCS-treated replicate5


title: Heterotype-DCS-treated replicate4


title: PWA10-0098


title: EA80741Q-11


title: Heterotype-DCS-treated replicate3


title: Heterotype-DCS-treated replicate2


title: HA807M9C-03


title: Heterotype-DCS-treated replicate1


title: PWA11-0428


title: RSL3+M-3.R2

city: Bengbu City, Anhui Province

first: Bohan

last: Li

address: 安徽省蚌埠市东海大道2600号

department: School of Pharmacy

country: China

institute: Bengbu Medical University

description: Library name: SAMPLES 6

data_processing:
Raw reads were filtered to remove adapter sequences and low‑quality reads using Trimmomatic (v0.39).
Clean reads were aligned to the human reference genome (GRCh38) using HISAT2 (v2.2.1).
Gene expression levels were quantified as fragments per kilobase of transcript per million mapped reads (FPKM) using StringTie (v2.1.5).
Differentially expressed genes (DEGs) were identified using DESeq2 (v1.30.0) with
KEGG and GO pathway enrichment analyses were performed using clusterProfiler (v4.0.5) in R.
Assembly: hg38
Supplementary files format and content: Processed data files include a gene expression matrix (FPKM values) for all samples.
Supplementary files format and content: Raw count matrix and differential expression results are also provided.

source_name: lung

growth_protocol: BEAS‑2B human bronchial epithelial cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco), 100 U/mL penicillin and 100 μg/mL streptomycin (Gibco) in a humidified incubator with 5% CO₂ at 37°C.

extract_protocol:
Total RNA was extracted from cells using TRIzol® reagent (Invitrogen, USA) according to the manufacturer’s instructions. RNA purity and integrity were assessed using a NanoDrop™ spectrophotometer and an Agilent 2100 Bioanalyzer.
RNA‑seq libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA) following the manufacturer’s protocol

treatment_protocol: Cells were treated with RSL3 (2 μM), indirubin (7.5–30 μM), or ferrostatin‑1 (Fer‑1, 30 μM) for 24 h. For combination treatments, cells were pretreated with indirubin or Fer‑1 for 2 h prior to RSL3 exposure.

value: lung

tag: cell line

tag: cell type

value: pulmonary epithelial cells


title: RSL3+M-2.R2

address: 安徽省蚌埠市东海大道2600号

description: Library name: SAMPLES 4


title: JA8095VZ-02


title: PWA11-0425


title: RSL3+M-2.R1

address: 安徽省蚌埠市东海大道2600号

description: Library name: SAMPLES 3


title: PWA19-0758


title: RSL3+M-1.R2

address: 安徽省蚌埠市东海大道2600号

description: Library name: SAMPLES 2


title: HA807TKK-03


title: RSL3+M-1.R1

address: 安徽省蚌埠市东海大道2600号

description: Library name: SAMPLES 1


title: PWA18-0734


title: PWA19-0747


title: F ELF1 KO BMDM M1-1

city: Beijing

first: Zhaoqi

last: Zhang

state: Beijing

address: Peking University People’s Hospital

institute: Peking University People’s Hospital

description: Library name: ELF1 KO BMDM M1-1

data_processing:
Raw sequencing reads were filtered to remove low-quality sequences, ensuring high-quality data for subsequent analyses. Differentially expressed genes (DEGs) were identified using the DESeq2 package with thresholds of P < 0.05 and |log₂(fold change)| > 0.5. Functional enrichment analyses, including KEGG and GSEA, were conducted to explore the biological pathways and processes associated with ELF-1-regulated genes.
Assembly: mm10
Supplementary files format and content: XLSX

source_name: bone marrow

extract_protocol:
For RNA-seq analysis, 1 × 10⁶ cells per sample were harvested in 1 mL of TRIzol reagent (Thermo Fisher Scientific), and total RNA was extracted following the manufacturer's protocol. RNA samples were immediately frozen on dry ice and transported for downstream processing.
Library construction and sequencing were performed by Novogene (Tianjin, China).

value: bone marrow


title: PWA11-0213

value: Plasma


title: E WT BMDM M1-2

description: Library name: WT BMDM M1-2


title: E WT BMDM M1-1

description: Library name: WT BMDM M1-1


title: EA8099MG-10


title: C ELF1 KO BMDM con2

description: Library name: ELF1 KO BMDM con2


title: AD_Quinn_3

value: AD


title: EA807NX8-07


title: A WT BMDM con2

description: Library name: WT BMDM con2


title: HA80BRX9-03


title: A WT BMDM con1

description: Library name: WT BMDM con1


title: GA80B4GC-02


title: Trim28/Setdb1 Perturb-seq: lane 16, second harvest: CRISPR guide capture

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 415 Main Street, Room 6032

department: Cell Circuits Program / Center for Cell Circuits

institute: Broad Institute

description:
Library name: Tcf7_trim28_setdb1_lane16_grna
CRISPR guide capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 16; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 16 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.

library_source: genomic

data_processing:
Single-cell gene-expression and hashtag data were processed with Cell Ranger and Scanpy. For guide/construct libraries, Pycashier extracted guide sequences and clonal barcodes from paired-end reads using adapter context. Guide read sequences were aligned to the Trim28/Setdb1 Perturb-seq guide set with STAR, and reads were deduplicated by molecular UMI, cell barcode, clonal barcode, and guide identity. Each construct was defined as a unique guide-clonal-barcode pair. Cell-construct entries with more than 3 construct UMIs were retained, cells were encoded by retained construct sets, and construct-sharing patterns consistent with doublets were removed with a linear-program filter. Retained cells are included in the processed AnnData object with expression layers, guide labels, hashtag labels, clonal labels, embeddings, and clustering results.
Assembly: GRCm38/mm10 mouse reference for gene-expression features; sgRNA feature references are provided as supplementary files.
Supplementary files format and content: H5AD AnnData archive containing cell-level gene-expression values, guide labels, clonal metadata, and processed analysis layers for all retained cells.
Library strategy: CRISPR Screen

molecule: genomic DNA

source_name: B16-OVA tumor

growth_protocol: Naive CD8 T cells were isolated from 18 Cas9 x OT-I donor mice, transduced with the Trim28/Setdb1 Perturb-seq library on RetroNectin-coated plates, and cultured to day 5 after transduction before Thy1.1 enrichment. Recipient Cas9 x CD45.1 or Cas9 x CD45.1/CD45.2 mice were implanted bilaterally with 4 x 10^5 B16-OVA cells per flank. Transduced donor T cells were transferred 1 day after tumor implantation, with a target dose of 2 x 10^5 Thy1.1+ cells per mouse; approximately 1.7 x 10^5 Thy1.1+ cells were transferred per mouse for most mice.

extract_protocol:
Tumors were dissociated to single-cell suspensions and enriched for donor T cells before sorting. Draining lymph nodes were mechanically dissociated and processed separately. Depending on experiment and sample quality, lymphocytes were enriched by Lympholyte-M density-gradient separation and/or magnetic enrichment before flow sorting. Single-cell suspensions were stained with viability dye, Fc block, and surface antibodies to identify live CD8 T cells, donor-derived transferred cells, and transduced Thy1.1+ cells, using congenic CD45.1 and CD45.2 markers together with Thy1.1 and OT-I/TCR markers where used. Purified or enriched cell suspensions from individual mice were stained with BioLegend TotalSeq-C mouse hashtag antibodies according to the manufacturer's protocol, including repeated washes to reduce ambient hashtag oligonucleotide background. Each hashtag corresponded to one mouse. Hashtag-labeled cells were pooled by tissue and harvest batch and sorted before 10x loading to maximize cell viability.
Hashtag-labeled donor-cell pools were loaded onto the 10x Genomics Chromium platform, and single-cell gene-expression, CRISPR guide-capture, and feature-barcode libraries were prepared using the Chromium 5-prime workflow. The CRISPR guide/construct libraries captured sgRNA and clonal-barcode information. Guide/construct libraries were sequenced as paired-end FASTQs in which the forward read carried the cell barcode and molecular UMI and the reverse read carried the sgRNA sequence and clonal barcode flanked by known adapter sequence. Gene-expression, feature-barcode, and guide/construct libraries were sequenced on Illumina instruments.

treatment_protocol: The Trim28/Setdb1 Perturb-seq library contained ten sgRNAs targeting Trim28, ten sgRNAs targeting Setdb1, and six NO_SITE control sgRNAs. Mice received anti-PD-1 or isotype control after tumors reached approximately 50 mm3, 11 days after tumor implantation. Anti-PD-1 treatment used Bio X Cell anti-mouse PD-1 clone RMP1-14, and control treatment used Bio X Cell rat IgG2a isotype control clone 2A3, dosed by intraperitoneal injection at 200 ug per mouse per dose. Mice were harvested in two batches 6 and 11 days after treatment initiation. Treatment condition was assigned from the mouse hashtag key. At harvest, tumors and draining lymph nodes were collected; tumor and lymph-node samples were processed separately.

value: B16-OVA tumor

value: CD8 T cells

value: anti-PD-1 or isotype control antibody; mouse-level condition encoded by hashtag

tag: library type

value: gRNA


title: EA808TV0-03

value: Circulating blood

value: Venous


title: HA807YGP-03

value: Male


title: Trim28/Setdb1 Perturb-seq: lane 16, second harvest: GEX

description:
Library name: Tcf7_trim28_setdb1_lane16_gex
GEX FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 16; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 16 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.

library_source: transcriptomic single cell

data_processing:
Single-cell gene-expression and hashtag data were processed with Cell Ranger and Scanpy. For guide/construct libraries, Pycashier extracted guide sequences and clonal barcodes from paired-end reads using adapter context. Guide read sequences were aligned to the Trim28/Setdb1 Perturb-seq guide set with STAR, and reads were deduplicated by molecular UMI, cell barcode, clonal barcode, and guide identity. Each construct was defined as a unique guide-clonal-barcode pair. Cell-construct entries with more than 3 construct UMIs were retained, cells were encoded by retained construct sets, and construct-sharing patterns consistent with doublets were removed with a linear-program filter. Retained cells are included in the processed AnnData object with expression layers, guide labels, hashtag labels, clonal labels, embeddings, and clustering results.
Assembly: GRCm38/mm10 mouse reference for gene-expression features; sgRNA feature references are provided as supplementary files.
Supplementary files format and content: H5AD AnnData archive containing cell-level gene-expression values, guide labels, clonal metadata, and processed analysis layers for all retained cells.

molecule: polyA RNA

value: mRNA


title: Heterotype-DCS-vehicle replicate5

value: Brain

value: male


title: Heterotype-DCS-vehicle replicate6

value: Grin2b heterozygous


title: FA807TPX-04


title: Heterotype-DCS-vehicle replicate4

value: vehicle


title: PWA17-0659

value: PD

value: Female


title: Trim28/Setdb1 Perturb-seq: lane 16, second harvest: feature-barcode capture

description:
Library name: Tcf7_trim28_setdb1_lane16_fb
feature-barcode capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 16; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 16 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.

library_source: other

data_processing:
Single-cell gene-expression and hashtag data were processed with Cell Ranger and Scanpy. For guide/construct libraries, Pycashier extracted guide sequences and clonal barcodes from paired-end reads using adapter context. Guide read sequences were aligned to the Trim28/Setdb1 Perturb-seq guide set with STAR, and reads were deduplicated by molecular UMI, cell barcode, clonal barcode, and guide identity. Each construct was defined as a unique guide-clonal-barcode pair. Cell-construct entries with more than 3 construct UMIs were retained, cells were encoded by retained construct sets, and construct-sharing patterns consistent with doublets were removed with a linear-program filter. Retained cells are included in the processed AnnData object with expression layers, guide labels, hashtag labels, clonal labels, embeddings, and clustering results.
Assembly: GRCm38/mm10 mouse reference for gene-expression features; sgRNA feature references are provided as supplementary files.
Supplementary files format and content: H5AD AnnData archive containing cell-level gene-expression values, guide labels, clonal metadata, and processed analysis layers for all retained cells.
Library strategy: CITE-seq

molecule: protein

value: HTO


title: Trim28/Setdb1 Perturb-seq: lane 15, second harvest: CRISPR guide capture

description:
Library name: Tcf7_trim28_setdb1_lane15_grna
CRISPR guide capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 15; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 15 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: PWA10-0033

value: Plasma


title: EA808FRW-03

value: NC


title: Trim28/Setdb1 Perturb-seq: lane 15, second harvest: GEX

description:
Library name: Tcf7_trim28_setdb1_lane15_gex
GEX FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 15; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 15 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.

value: B16-OVA tumor


title: Trim28/Setdb1 Perturb-seq: lane 15, second harvest: feature-barcode capture

description:
Library name: Tcf7_trim28_setdb1_lane15_fb
feature-barcode capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 15; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 15 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.

value: CD8 T cells


title: GA8095LS-03

value: AD


title: Trim28/Setdb1 Perturb-seq: lane 14, second harvest: CRISPR guide capture

description:
Library name: Tcf7_trim28_setdb1_lane14_grna
CRISPR guide capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 14; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 14 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.

value: anti-PD-1 or isotype control antibody; mouse-level condition encoded by hashtag

value: gRNA


title: Trim28/Setdb1 Perturb-seq: lane 14, second harvest: GEX

description:
Library name: Tcf7_trim28_setdb1_lane14_gex
GEX FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 14; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 14 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: DLBC-03-020

value: DLB

value: Circulating blood

value: Venous


title: Trim28/Setdb1 Perturb-seq: lane 14, second harvest: feature-barcode capture

description:
Library name: Tcf7_trim28_setdb1_lane14_fb
feature-barcode capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 14; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 14 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: BA807MG3-07

value: Male


title: PWA10-0002


title: GA809WFJ-02


title: Trim28/Setdb1 Perturb-seq: lane 13, second harvest: CRISPR guide capture

description:
Library name: Tcf7_trim28_setdb1_lane13_grna
CRISPR guide capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 13; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 13 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: EA807ZRJ-01


title: DA807N7W-03


title: Trim28/Setdb1 Perturb-seq: lane 13, second harvest: GEX

description:
Library name: Tcf7_trim28_setdb1_lane13_gex
GEX FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 13; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 13 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.

value: mRNA


title: PWA11-0255


title: RSL3+M-3.R1

address: 安徽省蚌埠市东海大道2600号

description: Library name: SAMPLES 5

value: lung

value: pulmonary epithelial cells


title: Trim28/Setdb1 Perturb-seq: lane 13, second harvest: feature-barcode capture

description:
Library name: Tcf7_trim28_setdb1_lane13_fb
feature-barcode capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 13; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 13 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: PWA13-0565

value: PD


title: Trim28/Setdb1 Perturb-seq: lane 12, second harvest: CRISPR guide capture

description:
Library name: Tcf7_trim28_setdb1_lane12_grna
CRISPR guide capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 12; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 12 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: PWA11-0390


title: Trim28/Setdb1 Perturb-seq: lane 12, second harvest: GEX

description:
Library name: Tcf7_trim28_setdb1_lane12_gex
GEX FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 12; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 12 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: Trim28/Setdb1 Perturb-seq: lane 12, second harvest: feature-barcode capture

description:
Library name: Tcf7_trim28_setdb1_lane12_fb
feature-barcode capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 12; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 12 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: PWA13-0586


title: FA8099ZS-10


title: Trim28/Setdb1 Perturb-seq: lane 11, second harvest: CRISPR guide capture

description:
Library name: Tcf7_trim28_setdb1_lane11_grna
CRISPR guide capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 11; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 11 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: PWA10-0139


title: Trim28/Setdb1 Perturb-seq: lane 11, second harvest: GEX

description:
Library name: Tcf7_trim28_setdb1_lane11_gex
GEX FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 11; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 11 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: PWA19-0763


title: F ELF1 KO BMDM M1-2

description: Library name: ELF1 KO BMDM M1-2

value: bone marrow


title: DA807MF1-07


title: Trim28/Setdb1 Perturb-seq: lane 11, second harvest: feature-barcode capture

description:
Library name: Tcf7_trim28_setdb1_lane11_fb
feature-barcode capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 11; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 11 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.

value: HTO


title: FA807T0C-06

value: Plasma


title: Trim28/Setdb1 Perturb-seq: lane 10, second harvest: CRISPR guide capture

description:
Library name: Tcf7_trim28_setdb1_lane10_grna
CRISPR guide capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 10; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 10 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: EA807ZPB-12

value: NC


title: Trim28/Setdb1 Perturb-seq: lane 10, second harvest: GEX

description:
Library name: Tcf7_trim28_setdb1_lane10_gex
GEX FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 10; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 10 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.

value: B16-OVA tumor


title: Trim28/Setdb1 Perturb-seq: lane 10, second harvest: feature-barcode capture

description:
Library name: Tcf7_trim28_setdb1_lane10_fb
feature-barcode capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 10; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 10 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.

value: CD8 T cells


title: PWA19-0770


title: PWA10-0027


title: Trim28/Setdb1 Perturb-seq: lane 9, second harvest: CRISPR guide capture

description:
Library name: Tcf7_trim28_setdb1_lane9_grna
CRISPR guide capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from draining lymph node profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 9; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from draining lymph node. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 9 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.

source_name: draining lymph node

value: draining lymph node


title: BA80860F-08


title: PWA10-0106


title: Trim28/Setdb1 Perturb-seq: lane 9, second harvest: GEX

description:
Library name: Tcf7_trim28_setdb1_lane9_gex
GEX FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from draining lymph node profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 9; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from draining lymph node. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 9 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.

value: anti-PD-1 or isotype control antibody; mouse-level condition encoded by hashtag


title: C ELF1 KO BMDM con1

description: Library name: ELF1 KO BMDM con1


title: Trim28/Setdb1 Perturb-seq: lane 8, first harvest: CRISPR guide capture

description:
Library name: Tcf7_trim28_setdb1_lane8_grna
CRISPR guide capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 8; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 8 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.

value: gRNA


title: Trim28/Setdb1 Perturb-seq: lane 9, second harvest: feature-barcode capture

description:
Library name: Tcf7_trim28_setdb1_lane9_fb
feature-barcode capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from draining lymph node profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 9; harvest batch: second harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from draining lymph node. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 9 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: DA8083YH-03


title: BA80BNCB-02

value: AD


title: Trim28/Setdb1 Perturb-seq: lane 8, first harvest: GEX

description:
Library name: Tcf7_trim28_setdb1_lane8_gex
GEX FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 8; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 8 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: DLBC-03-025

value: DLB

value: Circulating blood


title: FA80BYR6-02

value: Female

value: Venous


title: Trim28/Setdb1 Perturb-seq: lane 8, first harvest: feature-barcode capture

description:
Library name: Tcf7_trim28_setdb1_lane8_fb
feature-barcode capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 8; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 8 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: Trim28/Setdb1 Perturb-seq: lane 7, first harvest: CRISPR guide capture

description:
Library name: Tcf7_trim28_setdb1_lane7_grna
CRISPR guide capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 7; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 7 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: PWA19-0751

value: Male


title: Trim28/Setdb1 Perturb-seq: lane 7, first harvest: GEX

description:
Library name: Tcf7_trim28_setdb1_lane7_gex
GEX FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 7; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 7 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.

value: mRNA


title: DA80B3X3-02


title: Trim28/Setdb1 Perturb-seq: lane 7, first harvest: feature-barcode capture

description:
Library name: Tcf7_trim28_setdb1_lane7_fb
feature-barcode capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 7; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 7 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: Trim28/Setdb1 Perturb-seq: lane 6, first harvest: CRISPR guide capture

description:
Library name: Tcf7_trim28_setdb1_lane6_grna
CRISPR guide capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 6; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 6 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: EA80B3RT-02


title: DA80C5SK-03


title: Trim28/Setdb1 Perturb-seq: lane 6, first harvest: GEX

description:
Library name: Tcf7_trim28_setdb1_lane6_gex
GEX FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 6; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 6 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: GA8090T6-03


title: Trim28/Setdb1 Perturb-seq: lane 6, first harvest: feature-barcode capture

description:
Library name: Tcf7_trim28_setdb1_lane6_fb
feature-barcode capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 6; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 6 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: EA808LNC-12


title: BA80B46S-02


title: PWA11-0211

value: PD


title: Trim28/Setdb1 Perturb-seq: lane 5, first harvest: feature-barcode capture

description:
Library name: Tcf7_trim28_setdb1_lane5_fb
feature-barcode capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 5; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 5 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: Trim28/Setdb1 Perturb-seq: lane 5, first harvest: GEX

description:
Library name: Tcf7_trim28_setdb1_lane5_gex
GEX FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 5; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 5 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: Trim28/Setdb1 Perturb-seq: lane 5, first harvest: CRISPR guide capture

description:
Library name: Tcf7_trim28_setdb1_lane5_grna
CRISPR guide capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 5; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 5 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: DA808Q3Z-10


title: PWA12-0499


title: Trim28/Setdb1 Perturb-seq: lane 4, first harvest: CRISPR guide capture

description:
Library name: Tcf7_trim28_setdb1_lane4_grna
CRISPR guide capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 4; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 4 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: Trim28/Setdb1 Perturb-seq: lane 4, first harvest: GEX

description:
Library name: Tcf7_trim28_setdb1_lane4_gex
GEX FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 4; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 4 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: PWA10-0140


title: Trim28/Setdb1 Perturb-seq: lane 4, first harvest: feature-barcode capture

description:
Library name: Tcf7_trim28_setdb1_lane4_fb
feature-barcode capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 4; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 4 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: PWA11-0342


title: Trim28/Setdb1 Perturb-seq: lane 3, first harvest: CRISPR guide capture

description:
Library name: Tcf7_trim28_setdb1_lane3_grna
CRISPR guide capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 3; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 3 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: DLBC-03-026


title: DLBC-03-005


title: AD_Quinn_7


title: Trim28/Setdb1 Perturb-seq: lane 3, first harvest: feature-barcode capture

description:
Library name: Tcf7_trim28_setdb1_lane3_fb
feature-barcode capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 3; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 3 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: Trim28/Setdb1 Perturb-seq: lane 3, first harvest: GEX

description:
Library name: Tcf7_trim28_setdb1_lane3_gex
GEX FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 3; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 3 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: DLBC-03-013


title: BA80BN7F-03


title: Trim28/Setdb1 Perturb-seq: lane 2, first harvest: GEX

description:
Library name: Tcf7_trim28_setdb1_lane2_gex
GEX FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 2; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 2 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: Trim28/Setdb1 Perturb-seq: lane 2, first harvest: feature-barcode capture

description:
Library name: Tcf7_trim28_setdb1_lane2_fb
feature-barcode capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 2; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 2 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: DA807837-07


title: Trim28/Setdb1 Perturb-seq: lane 1, first harvest: CRISPR guide capture

description:
Library name: Tcf7_trim28_setdb1_lane1_grna
CRISPR guide capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from draining lymph node profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 1; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from draining lymph node. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 1 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: PWA19-0741


title: Trim28/Setdb1 Perturb-seq: lane 1, first harvest: GEX

description:
Library name: Tcf7_trim28_setdb1_lane1_gex
GEX FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from draining lymph node profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 1; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from draining lymph node. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 1 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: PWA11-0366


title: Trim28/Setdb1 Perturb-seq: lane 2, first harvest: CRISPR guide capture

description:
Library name: Tcf7_trim28_setdb1_lane2_grna
CRISPR guide capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from B16-OVA tumor profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 2; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from B16-OVA tumor. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 2 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: Trim28/Setdb1 Perturb-seq: lane 1, first harvest: feature-barcode capture

description:
Library name: Tcf7_trim28_setdb1_lane1_fb
feature-barcode capture FASTQ files from mouse donor Thy1.1-positive OT-I CD8 T cell sample from draining lymph node profiled in the Trim28/Setdb1 Perturb-seq experiment. The sgRNA library contained ten Trim28-targeting sgRNAs, ten Setdb1-targeting sgRNAs, and six NO_SITE control sgRNAs. Cells from each mouse were hashtagged, pooled by tissue and harvest batch, and loaded using the 10x Genomics Chromium 5' workflow. Original sample/lane ID: lane 1; harvest batch: first harvest. All sequencing-lane files for this library are listed in the same run row. Sample description: Trim28/Setdb1 Perturb-seq single-cell sample from donor Thy1.1-positive OT-I CD8 T cells recovered from draining lymph node. Naive Cas9 x OT-I CD8 T cells were transduced with a construct library containing ten Trim28 guides, ten Setdb1 guides, and six NO_SITE controls; Trim28-1/Trim28-2 and Setdb1-1/Setdb1-2 matched the 10-gene Perturb-seq screen. Cells were transferred into B16-OVA-bearing mice that received isotype or anti-PD-1 therapy. Donor cells were harvested, mouse-hashtagged, pooled by tissue, and loaded in 10x lane 1 to profile each cell's transcriptome, guide assignment, mouse hashtag, tissue/lane origin, and clonal barcode.


title: HA808P75-06


title: TM_cKO3

city: Hangzhou

first: Fan

last: Zhao

state: Zhejiang Province

address: 866 Yuhangtang Road, Xihu District

institute: Zhejiang University

description:
Library name: Sample 18
Hspa9 cKO memory CD8+ T cell

data_processing:
Raw sequencing reads were quality-controlled and adapter-trimmed using fastp to generate clean data. These clean reads were aligned to the mouse referenceG genome (GRCm39) using HISAT2 (v2.2.1), and gene expression levels were quantified using featureCounts (v2.0.6). Differential expression analysis was performed with DESeq2 (v1.42.0), applying a significance threshold of adjusted p-value < 0.05 and |log2(fold change)| > 1.
Assembly: GRCm39
Supplementary files format and content: excel file includes RPKM values for each Sample

source_name: lymph nodes and spleen

extract_protocol:
WT and cKO naive CD8⁺ T cells, along with their in-vitro-differentiated effector and memory subsets, were lysed in TRIzol reagent (Invitrogen). Total RNA was extracted from the lysates using the Direct-zol RNA MiniPrep kit (Zymo Research) according to the manufacturer's protocol.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: lymph nodes and spleen

value: memory CD8+ T cell

value: cKO

value: no treatment


title: HA807YXW-07

value: Plasma

value: NC


title: TM_cKO2

description:
Library name: Sample 17
Hspa9 cKO memory CD8+ T cell


title: CA80C2NF-02


title: TM_WT3

description:
Library name: Sample 15
WT memory CD8+ T cell

value: WT


title: KA807L88-11


title: TM_cKO1

description:
Library name: Sample 16
Hspa9 cKO memory CD8+ T cell


title: TM_WT2

description:
Library name: Sample 14
WT memory CD8+ T cell


title: JA808WYQ-03


title: EA808744-02


title: PWA12-0445


title: TM_WT1

description:
Library name: Sample 13
WT memory CD8+ T cell


title: TE_cKO3

description:
Library name: Sample 12
Hspa9 cKO effector CD8+ T cell

value: effector CD8+ T cell


title: PWA17-0653


title: TE_cKO2

description:
Library name: Sample 11
Hspa9 cKO effector CD8+ T cell


title: CA8071QS-11


title: TE_cKO1

description:
Library name: Sample 10
Hspa9 cKO effector CD8+ T cell


title: DLBC-03-004


title: Sample 6; Knockout Group, Replicate 3

city: Huntington

first: Yen On

last: Chan

state: WV

address: Arthur Weisberg Family Applied Engineering Complex, Suite # 4103, 1676 Third Avenue

department: Department of Biomedical Sciences

institute: Marshall University

description: Library name: T3_Pos

data_processing:
The snRNA-seq bioinformatics analysis was performed on six datasets corresponding to three KO and three CO conditions. The reads were then aligned to the mouse reference genome (GRCm38) and quantified using Cell Ranger v3.0.2 to generate six filtered feature-barcode matrices suitable for analysis with the Seurat v5.2.1 package in the R programming language. The Read10X function in the Seurat package was employed to import the matrices, followed by the Seurat CreateSeuratObject function to generate individual Seurat objects for each sample. The Seurat objects were then normalized and variance-stabilized using the SCTransform function and subsequently integrated across all samples using the Harmony algorithm to correct for batch effects and inter-sample variability. Following integration, a shared nearest neighbor (SNN) graph was constructed using the FindNeighbors function, and clusters were identified with the FindClusters function to facilitate unsupervised cell-type identification. Dimensionality reduction was performed using both the RunTSNE and RunUMAP functions to enable visualization of cellular heterogeneity and clustering in two-dimensional space.
Assembly: Mus Musculus GRCm38
Supplementary files format and content: Feature Barcode Matrices

source_name: Lung

extract_protocol:
Frozen mouse tumor tissues were processed for nuclei isolation. Approximately 200 mg tissue per sample was homogenized on ice using a Dounce homogenizer in RNase-free lysis buffer, lysed at 4°C for 5 min, filtered through a 40 μm nylon filter, rinsed with wash buffer ± RNase inhibitor, and centrifuged at 500g for 5 min at 4°C. Nuclear pellets were resuspended in PBS with 0.02% BSA ± RNase inhibitor. Selected samples received 1–3 additional PBS/BSA washes to reduce ambient RNA contamination. Nuclei were counted using a Countess II Automated Cell Counter.
Single-nucleus libraries were generated using the Chromium Next GEM Single Cell 3′ Kit v3.1 with Chip G. Approximately 4,000 nuclei per sample were loaded into the Chromium Controller to generate GEMs. cDNA synthesis and library construction followed the manufacturer’s 10x Genomics protocol. Final libraries were sequenced on an Illumina NextSeq platform targeting approximately 25,000 reads per cell.

value: Lung

value: MCT2 Knockout


title: TE_WT3

description:
Library name: Sample 9
WT effector CD8+ T cell


title: Sample 5; Control Group, Replicate 3

description: Library name: T3_NG

value: MCT2 Control


title: FA809FHM-02

value: AD

value: Circulating blood


title: TE_WT2

description:
Library name: Sample 8
WT effector CD8+ T cell


title: CA80975P-01

value: Female

value: Venous


title: Sample 4; Knockout Group, Replicate 2

description: Library name: T2_Pos


title: Sample 3; Control Group, Replicate 2

description: Library name: T2_NG