title: Ref-2_S22_L003

city: Houston

first: Weiyi

last: Peng

address: 3455 Cullen Blvd., Suite 342

department: Department of Biology and Biochemistry

institute: University of Houston

description:
In vivo screen Sample Ref-2-lane3
220106_WP_PM1608.count.txt

data_processing:
Genome-wide in vitro immune screen analysis: The MAGeCK (v0.5.9.4) count module was used to calculate the read count of individual gRNAs in different samples with the following parameters: “-l Mouse_v2_CRISPR.library --norm-method total --sample-label Ctrl,ET02,ET1 -n Mouse_v2_CRISPR_191205.count.version2.txt --fastq files.fq”. MAGeCK test module was then applied with parameters “-k Mouse_v2_CRISPR_191205.count.version2.txt -c Ctrl,ET02,ET1 --norm-method total --keep-tmp -n Mouse_v2_CRISPR_191205 _ET_Ctrl --gene-lfc-method secondbest”, to identify the genes whose gRNAs were significant differentially presented between the control and T cell treatment groups at the cutoff using |log2(fold-change)| ≥ 0.25 and p< 0.05.
In vivo screen analysis: For the results from the in vivo immune screen, the sequencing reads were mapped to the ICB sub-library using bowtie (1.2.2) with parameters “--best --strata -a --norc -m 1 -5 6 –S”. Samtools (1.9) was used to calculate the read count of each gRNA. The fold change and statistical significance of genes among the between non-responder and IgG control or responder and IgG control groups were calculated as using a modification of the DrugZ algorithm
Assembly: mm10
Supplementary files format and content: gene_summary.txt, sgrna_summary.txt, count.txt

source_name: Cell line

growth_protocol: ID8 and related derived cell lines were obtained from the American Type Culture Collection (ATCC, Bethesda, MD). All cell lines and their genetically modified cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% heated-inactivated fetal bovine serum (FBS; #S11150, R&D System, Minneapolis, MN), 5 ug/mL of insulin, transferrin and sodium selenite and 100μg/ml of Normocin (ant-nr-1, InvivoGen, San Diego, CA). Cells were grown at 37 °C with 5% CO2. All cell lines were authenticated by short tandem repeat fingerprinting or the expression of tagged markers used for genetic modification. The mycoplasma detection kit (#13100-01, SouthernBiotech, Birmingham, AL) was used to routinely monitor for mycoplasma contamination of cultured cells. The maximum length of time of in vitro cell culture between thawing and use in the described experiments was two weeks.

extract_protocol:
Genomic DNA from all cell samples was extracted by using TRIzol (#15596026; ThermoFisher) according to the manufacturer’s protocol.
DNA fragments containing gRNA sequences were amplified and barcoded with adaptation by nested polymerase chain reaction (PCR) as previously described. The quality and concentration of all PCR products were determined by the Qubit ssDNA high sensitivity assay kit (#Q10212; ThermoFisher) and the bioanalyzer High Sensitivity DNA Kit (#5067-4626 2100; Agilent, Santa Clara, CA) respectively. Samples were then sequenced by Illumina Next-Generation Sequencing (NSG) at the MD Anderson Cancer Center Advanced Technology Genomics Core.
PCR amplicon of gRNA fragments

treatment_protocol: For in vitro CRISPR screen, the mouse improved genome-wide knockout CRISPR Library version 2 consisting of 90,230 gRNAs targeted 18,424 genes was purchased from Addgene and used to generate lentivirus as described above. 1.5× 108 of ID8/GC cells were transduced with pooled library lentivirus at low multiplicity of infection (MOI; ~0.15-0.2) and cultured with growth medium in present of 2ug/ml puromycin to select gRNA-transduced cells. One week after selection, pooled gRNA-transduced tumor cells were washed and seeded incell culture dishes for overnight. For T cell treated groups, cultured Pmel T cells were added at effector: target (ET) ratio of 0.2:1 and 1:1 for 16 hours. For non-T cell treated groups, equal amount of T cell growth medium was added. After treatment, non-adhesive cells including T cells and dead tumor cells were removed by repeated wash using pre-warmed PBS. Adherent cells were harvested by using 0.25% Trypsin-EDTA and washed three times using PBS. Additionally, tumor cells after 48-hour or 7-day puromycin selection were collected to determine the coverage of the genome-wide library in transduced cells before the functional immune screen. Three replicates were performed for all treatment groups, and each sample includes at least 3×107 of transduced cells for genomic DNA isolation using Blood & Cell Culture DNA MAXI Kit as described by the manufacturer’s protocol.  For in vivo CRISPR screen, After construction of the library, ID8/GC cells were transduced to express the pooled in vivo sub-library. Briefly, to generate lentiviral supernatants, HEK293T cells were seeded 16 hours before transfection and transfected with 9μg of lentiviral vectors encoding gRNAs library, along with lentiviral packaging plasmids (3μg of pCMV-VSV-G and 4.5μg of psPAX2) by the jetPRIME transfection reagent according to the manufacturer’s protocol. Viral supernatants were collected 72 hours post-transfection and filtered by 0.45um Syringe Filter Unit to remove cell debris. 1.2x107 ID8/GC cells were transduced with the pooled lentiviral supernatant at a low MOI (~0.15-0.2) and cultured with completed growth media for 48 hours. Then, transduced ID8/GC cells were under the selection pressure with 2μg/mL of puromycin for seven days. Additionally, 3.0x107 sub-library expressing ID8/GC (ID8/GCSL) cells were collected after 7 days of puromycin selection and served as reference samples (Ref). After 7 days of puromycin selection and expansion, ID8/GCSL cells were collected and subcutaneously inoculated into C57BL/6 and NSG mice at 1.0x107 cells per injection into the posterior-lateral flank of the mice. After 3 days post tumor inoculation, tumor-bearing C57BL/6 mice were randomized into two groups to receive anti-PD-1 treatment (N=10) or control (N=5). Intraperitoneal injection of anti-PD-1 at 100μg/per dose, every other day, were used for the mice in anti-PD-1 group. NSG mice bearing pooled tumor cells served as a control to eliminate the genes with essential role in controlling tumor development independent to endogenous immune responses. Additionally, tumor size of all mice was monitored every other day by recording perpendicular diameters taken by calipers. At the end of the treatment cycle of 12 days, tumors were collected to extract genomic DNA as described above.

value: Cell line

value: Murine ovarian cancer cell line

tag: screen

value: In vivo screen


title: R1_CpG-A+230V3

status: Public on Dec 17 2025

type: SRA

city: Shanghai

first: Haomin

last: Huang

address: 399 Libing Road

country: China

institute: 3SBio Inc.

description:
Library name: r1_sam3
MobiNova-100

library_source: transcriptomic single cell

data_processing:
Mobivision-v3.2 software was used to map reads to a reference genome and quantify gene expression levels.  Data analysis and clustering were performed using the “seurat” R package of R software (version 4.3.3).
Assembly: GRCh38
Supplementary files format and content: filtered_matrix

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

growth_protocol: PBMCs were cultured in RPMI 1640 medium supplemented with 10% FBS

extract_protocol:
Cells were loaded onto a Chip A Single-Cell Kit v2.1 (MobiDrop (Zhejiang) Co., Ltd., Cat. No. S050100301, Zhejiang, China) to generate droplets with MobiNova-100 (MobiDrop (Zhejiang) Co., Ltd., Cat. No. A1A40001). Each cell was prepared in a droplet that contained a gel bead linked with up to millions of oligos (cell unique barcodes). After encapsulation, the droplets are cut by light with a MobiNovaSP-100 (MobiDrop (Zhejiang) Co., Ltd., Cat. No. A2A40001), while the oligos diffused into the reaction mixture. The mRNAs were captured by cell barcodes with cDNA amplification in droplets. Following reverse transcription, cDNAs with barcodes were amplified, and a library was constructed using the High Throughput Single-Cell 3' Transcriptome Kit v2.1 (MobiDrop (Zhejiang) Co., Ltd., Cat. No. S050200301) and the 3' Dual Index Kit (MobiDrop (Zhejiang) Co., Ltd., Cat. No. S050300301). The resulting libraries were subsequently sequenced on an Illumina NovaSeq Xplus System.
Generating the “water in oil” droplets based on the microflu-idics technology, by identifying the fluorescence signal in the droplets, and deflecting droplets to different channels using dielectrophoresis, thereby fulfilling highly efficient cell sorting.MobiNova-100 Single Cell System utilizes patented barcoding and microfluidic technologies to achieve reliable single cell partitioning and effective cell capture in minutes.

treatment_protocol: Aliquots of 5×10⁶ cells were transferred to 96-well culture plates, after which 50 μL of 230 variants that were diluted in culture medium to achieve a final concentration of 4 nM were added to each well, and the cells were preincubated at 37 °C with 5% CO₂ for 1 hour. Afterward, 50 μL of CpG2216 was added to each well to achieve a final concentration of 2 μg/mL. The cultures were maintained at 37 °C with 5% CO₂ for 18 hours prior to harvesting the cells by centrifugation. The pellets were subsequently washed twice with PBS and processed for the sequencing analysis

tag: cell type

value: PBMC

tag: treatment

tag: batch


title: 07L_Ctl

city: Madison

first: Cara

middle: L

last: Green

state: WI

address: 2500 Overlook Terrace

country: USA

institute: University of Wisconsin-Madison

description: Library name: 07L

library_source: transcriptomic

data_processing:
Analysis of significantly differentially expressed genes (DEGs) was completed in R version 4.3.0. using edgeR and limma. Gene names were converted to gene symbol and Entrez ID formats using the mygene package. Genes with too many missing values were removed, if genes were present in less than one diet/age group they were removed. To reduce the impact of external factors not of biological interest that may affect expression, data was normalized to ensure the expression distributions of each sample are within a similar range. We normalized using the trimmed mean of M-values (TMM), which scales to library size. Heteroscedasticity was accounted for using the voom function, DEGs were identified using an empirical Bayes moderated linear model, and log coefficients and Benjamini-Hochberg (BH) adjusted p-values were generated for each comparison of interest.
Assembly: Reads were aligned to the mouse (Mus musculus) with genome-build GRCm38.p5 of accession NCBI:GCA_000001635.7[DL9]  and expected counts were generated with ensembl gene IDs.
Supplementary files format and content: Processed data file containing log2 fold-changes, gene IDs and unadjusted and Benjamini-Hochberg adjusted p-values. Haws2025_JBC_TableS2_Liver_RNAseqSummary.xlsx

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was extracted from liver with TRI Reagent (Thermo Fisher, AM9738), then treated with DNase (Invitrogen, 12185010) and purified with RNA purification kit (Ambion, 12183025). The concentration and purity of RNA was determined using a NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and RNA was diluted to 100-400 ng/µl for sequencing. The RNA was then submitted to the University of Wisconsin-Madison Biotechnology Center Gene Expression Center & DNA Sequencing Facility, and RNA quality was assayed using an Agilent RNA NanoChip.
RNA libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation protocol (Illumina, San Diego, CA) with 250ng of mRNA, and cleanup was done using RNA Clean beads (lot #17225200).

tag: tissue

value: Liver


title: Ref-2_S22_L002

state: TX

description:
In vivo screen Sample Ref-2-lane2
220106_WP_PM1608.count.txt

library_source: genomic

molecule: genomic DNA

tag: cell line


title: 07R_Ctl

description: Library name: 07R


title: 11N_Ctl

description: Library name: 11N


title: Ref-2_S22_L001

description:
In vivo screen Sample Ref-2-lane1
220106_WP_PM1608.count.txt


title: 82_TNYAKK1

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description: Library name: lib32938

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads.
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned by STAR1 2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: Raw counts are provided in .csv format. Each row is a gene, each column is a sample.

source_name: whole blood

extract_protocol:
Whole blood was collected in Tempus Blood RNA Tubes (Thermo Fisher Scientific), RNA was extracted using MagMax for Stabilized Blood Tubes RNA Isolation Kit (Thermo Fisher Scientific), followed by globin reduction using GlobinClear Human (Thermo Fisher Scientific).
To generate sequencing libraries, total RNA (0.5 ng) was added to reaction buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), and reverse transcription was performed followed by PCR amplification to generate full-length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit Fluorometer (Life Technologies). Dual-index, single-read sequencing of pooled libraries was carried out on a HiSeq 2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 5 million reads per sample.

value: whole blood

tag: donor id

tag: age

tag: gender

value: female

tag: visit

tag: group

value: Placebo


title: 81_TNYA7A9

description: Library name: lib32937

value: male


title: bulk, stimulated, E9, RNA

city: Iowa City

first: Muhammad

last: Elsadany

state: IA

address: 25 S Grand Ave

department: Psychiatry

institute: University of Iowa

description: Library name: bulk_E9B_RNA

data_processing:
Bulk RNA-seq raw files were processed with bcbio-nextgen-1.2.9. Multiomic raw files were processed with cellranger-arc-2.0.2 and used as input to build a Seurat object in R. Cell type labeling was done by integration with the Allen Institute dataset. pseudo-bulk was done by sampling random cells and aggregating them per cell type.
Assembly: hg38 for human samples and mm10 for mouse data
Supplementary files format and content: RDS file for the Seurat object of each sample. the object contains RNA gene expression, Gene activity from ATAC, and metadata containing cell type labeling and other meta information. no filtering was done for this file and it contains the output from CellRanger arc: E1A.rds, E1B.rds, E2A.rds, E2B.rds, E3A.rds, E3B.rds, E4A.rds, E4B.rds, G1A.rds, G1B.rds, G2A.rds, G2B.rds another separate RDS file for each sample is provided for the pseudo-bulk RNA data per cell type. txt files for bulk RNA-Seq data from stimulated and unstimulated paradigms from human and mouse: each column is for a different sample and includes the raw counts per transcript.

source_name: anterior temporal lobe

extract_protocol:
for bulk RNA-Seq, total RNA was extracted using miRNeasy Mini Kite and homogenized in Qiazol using stainless steel beads. Chloroform was then used for phase separation. RNA containing an aqueous layer was further purified using the RNeasy MinElute spin column. RNA was finally eluted in RNase-free water. for sn-multi-omics, nuclei were isolated using the Chromium Nuclei Isolation Kit. Nuclei were directly processed for droplet capture for single cell multiome ATAC + gene expression using a chromium controller.
For bulk RNA-seq, librairies were prepared using Ribo-Zero gold sample preparation kit. Library concentrations were measured using KAPA Illumina Library Quantification Kit. Pooled libraries were sequenced on Illumina NovaSeq6000 sequencer with 150-bp Paired-End chemistry. For sn-multi-omics, Chromium Next GEM Single Cell Multiome ATAC + Gene v1 chemistry was used to create single nuclei ATAC and RNA libraries from the same cell. Libraries were sequenced on an Illumina Novaseq 6000 with a 150 bp paired end read setup.

value: anterior temporal lobe

tag: hemisphere

value: left

tag: condition

value: stimulated

value: neurons/glia

tag: Sex

value: F

tag: diagnosis

value: epilepsy

tag: anesthesia

value: awake

tag: paradigm


title: R1_Ctrl

description:
Library name: r1_sam1
MobiNova-100

value: Ctrl


title: Ref-1_S21_L004

description:
In vivo screen Sample Ref-1-lane4
220106_WP_PM1608.count.txt

value: Cell line

tag: screen


title: 01L_Ctl

description: Library name: 01L


title: bulk, baseline, E9, RNA

description: Library name: bulk_E9A_RNA

value: baseline

tag: cell type


title: 01R_Ctl

description: Library name: 01R


title: Ref-1_S21_L003

description:
In vivo screen Sample Ref-1-lane3
220106_WP_PM1608.count.txt

value: Murine ovarian cancer cell line

tag: treatment

value: In vivo screen


title: Ref-2_S22_L004

description:
In vivo screen Sample Ref-2-lane4
220106_WP_PM1608.count.txt


title: 79_TNY9V21

description: Library name: lib32935


title: bulk, stimulated, E3, RNA

description: Library name: bulk_E3B_RNA

value: M

value: general anesthesia


title: Ref-1_S21_L002

description:
In vivo screen Sample Ref-1-lane2
220106_WP_PM1608.count.txt


title: 78_TNY8U69

description: Library name: lib32934

value: whole blood

value: ATG


title: 80_TNY9N8C

description: Library name: lib32936

value: female

value: ATG-GCSF


title: bulk, baseline, E3, RNA

description: Library name: bulk_E3A_RNA

value: anterior temporal lobe

value: left


title: 77_TNY8HXY

description: Library name: lib32933


city: Baltimore

first: Hangnoh

middle: Joseph

last: Lee

state: MD

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

description:
Library name: W6_WT_Sham_Sp_5
Mouse Spleen, wild-type, Sham, 6 weeks after SCI, Replicate 5

data_processing:
Base calling was performed using CASAVA version 1.8.2 (Illumina, San Diego, CA).
The GENCODE mouse gene annotation (version M33) was used for alignment and quantification.
Gene-level quantification was performed using RSEM version 1.3.3 (PMID: 21816040).
Assembly: Mouse reference genome GRCm39
Supplementary files format and content: Tab-delimited text files containing Ensembl gene identifiers and gene/isoform expression values in TPM (transcripts per million).

molecule: polyA RNA

source_name: Spleen

extract_protocol:
Following euthanasia 7 days and 6 weeks after SCI, mice were perfused with 50 mL of ice-cold normal saline. Total RNA was extracted from the spinal cord, lung, and spleen tissue with the miRNeasy Mini Kit (Qiagen, Cat# 74104).  In brief, approximately 600ul of QIAzol were added to each sample and disrupted in a Precellys 24 Touch homogenizer. The aqueous phase containing RNA was collected, mixed with ethanol, and applied to a silica membrane spin column. After a series of washes to remove contaminants, RNA was eluted in RNase-free water. A minimum of 100ng was sent to Novogene Bioinformatics Technology Co., Ltd. (Sacramento, CA) for downstream sequencing assays.
Library preparations were carried out by Novogene (Sacramento, CA) for sequencing on the Illumina platform (paired-end, 150 bp reads). mRNA was enriched through poly-A pulldown.

value: Spleen

tag: strain

value: male

value: 19 to 22 months old

tag: genotype

value: wild-type

value: Sham

tag: collection time

value: 6 weeks after SCI

tag: replicate


title: R1_CpG-A

description:
Library name: r1_sam2
MobiNova-100

value: PBMC

value: CpG-A

tag: batch


title: PD1-9_S8_L004

description:
In vivo screen Sample PD1-9-lane4
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

source_name: Tissue sample from Xenograft tumor

tag: tissue

value: Tissue sample from Xenograft tumor

tag: cell line

value: Murine ovarian cancer cell line

value: In vivo screen


title: bulk, stimulated, E2, RNA

description: Library name: bulk_E2B_RNA

value: stimulated

value: neurons/glia

value: M

tag: age

value: epilepsy

value: awake


title: Ref-1_S21_L001

description:
In vivo screen Sample Ref-1-lane1
220106_WP_PM1608.count.txt

value: Cell line


title: 83_TNYALXK

description: Library name: lib32939

value: whole blood

tag: donor id

tag: gender

tag: visit

tag: group

value: ATG


title: 01N_Ctl

description: Library name: 01N

value: Liver


description:
Library name: W6_WT_Sham_Sp_3
Mouse Spleen, wild-type, Sham, 6 weeks after SCI, Replicate 3

value: Spleen

tag: Sex

value: male

value: 19 to 22 months old

value: wild-type


title: 76_TNY9R4U

description: Library name: lib32932

value: ATG-GCSF


title: PD1-9_S8_L003

description:
In vivo screen Sample PD1-9-lane3
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor


title: 75_TNY95WP

description: Library name: lib32931

value: Placebo


description:
Library name: W6_WT_Sham_Sp_2
Mouse Spleen, wild-type, Sham, 6 weeks after SCI, Replicate 2

value: Sham

value: 6 weeks after SCI


title: bulk, stimulated, E1, RNA

description: Library name: bulk_E1B_RNA

value: anterior temporal lobe

tag: hemisphere

value: left

tag: condition

value: stimulated

value: neurons/glia

value: F

tag: diagnosis

tag: anesthesia

tag: paradigm


title: PD1-9_S8_L002

description:
In vivo screen Sample PD1-9-lane2
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

tag: cell type

value: Murine ovarian cancer cell line

tag: treatment

tag: screen

value: In vivo screen


title: 74_TNY5XX8

description: Library name: lib32930

value: whole blood


description:
Library name: W6_WT_Sham_Sp_1
Mouse Spleen, wild-type, Sham, 6 weeks after SCI, Replicate 1

value: Spleen

tag: strain

tag: genotype

tag: collection time

tag: replicate


title: PD1-9_S8_L001

description:
In vivo screen Sample PD1-9-lane1
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

tag: tissue

tag: cell line


description:
Library name: W6_WT_Sham_SC_5
Mouse Spinal Cord, wild-type, Sham, 6 weeks after SCI, Replicate 5

source_name: Spinal Cord

value: Spinal Cord

value: male

tag: age


title: bulk, unstimulated, E8, RNA

description: Library name: bulk_E8B_RNA

value: unstimulated

value: epilepsy

value: general anesthesia


title: 73_TNY89PG

description: Library name: lib32929

tag: donor id

tag: gender

tag: visit

tag: group

value: Placebo


title: bulk, baseline, E1, RNA

description: Library name: bulk_E1A_RNA

tag: hemisphere

tag: condition

value: baseline

tag: Sex

tag: diagnosis

value: awake


title: PD1-8_S7_L004

description:
In vivo screen Sample PD1-8-lane4
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor

tag: cell type

tag: treatment


title: PD1-8_S7_L003

description:
In vivo screen Sample PD1-8-lane3
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

tag: screen


title: bulk, baseline, E8, RNA

description: Library name: bulk_E8A_RNA

value: anterior temporal lobe

value: left

tag: anesthesia

tag: paradigm


description:
Library name: W6_WT_Sham_Sp_4
Mouse Spleen, wild-type, Sham, 6 weeks after SCI, Replicate 4

tag: strain

value: 19 to 22 months old

tag: genotype

value: wild-type

value: Sham

tag: collection time

value: 6 weeks after SCI

tag: replicate


title: 72_TNYPR9

description: Library name: lib32928

tag: tissue

value: whole blood

tag: donor id

tag: age

value: female

value: ATG-GCSF


title: PD1-8_S7_L002

description:
In vivo screen Sample PD1-8-lane2
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

tag: cell line

value: Murine ovarian cancer cell line

value: In vivo screen


description:
Library name: W6_WT_Sham_SC_3
Mouse Spinal Cord, wild-type, Sham, 6 weeks after SCI, Replicate 3

value: Spinal Cord

value: male


title: bulk, baseline, E7, RNA

description: Library name: bulk_E7A_RNA

tag: hemisphere

value: neurons/glia

value: F

value: epilepsy

value: unstimulated


title: 70_TNY7TXH

description: Library name: lib32926

tag: gender

tag: visit

tag: group

value: ATG


title: PD1-8_S7_L001

description:
In vivo screen Sample PD1-8-lane1
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor

tag: cell type


description:
Library name: W6_WT_Sham_SC_2
Mouse Spinal Cord, wild-type, Sham, 6 weeks after SCI, Replicate 2

tag: Sex

value: 19 to 22 months old

tag: treatment


title: bulk, baseline, E2, RNA

description: Library name: bulk_E2A_RNA

value: anterior temporal lobe

value: left

tag: condition

value: baseline

value: M

tag: diagnosis

tag: anesthesia

value: awake

value: stimulated


title: 69_TNY8K90

description: Library name: lib32925

value: whole blood

value: female

value: ATG-GCSF


description:
Library name: W6_WT_Sham_SC_1
Mouse Spinal Cord, wild-type, Sham, 6 weeks after SCI, Replicate 1

value: Spinal Cord

tag: strain

value: male

tag: genotype

value: wild-type

value: Sham

value: 6 weeks after SCI


title: bulk, unstimulated, E6, RNA

description: Library name: bulk_E6B_RNA

value: unstimulated

value: neurons/glia

value: F

value: epilepsy

value: general anesthesia

tag: paradigm


title: 68_TNY7WLY

description: Library name: lib32924

tag: tissue

value: Placebo


description:
Library name: W6_WT_Sham_Lg_5
Mouse Lung, wild-type, Sham, 6 weeks after SCI, Replicate 5

source_name: Lung

value: Lung

value: 19 to 22 months old

tag: collection time

tag: replicate


title: PD1-7_S6_L004

description:
In vivo screen Sample PD1-7-lane4
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor

tag: cell line

value: Murine ovarian cancer cell line

tag: screen

value: In vivo screen


title: PD1-7_S6_L003

description:
In vivo screen Sample PD1-7-lane3
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt


title: bulk, baseline, E6, RNA

description: Library name: bulk_E6A_RNA

value: anterior temporal lobe

tag: hemisphere

value: left

value: baseline

tag: age


title: 67_TNY0KC7

description: Library name: lib32923

value: whole blood

tag: donor id

tag: gender

value: female

tag: visit

tag: group

value: ATG-GCSF


description:
Library name: W6_WT_Sham_SC_4
Mouse Spinal Cord, wild-type, Sham, 6 weeks after SCI, Replicate 4

value: Spinal Cord

tag: Sex

value: male

value: wild-type

tag: treatment

value: Sham

value: 6 weeks after SCI


title: bulk, unstimulated, E5, RNA

description: Library name: bulk_E5B_RNA

value: right

tag: condition

value: unstimulated

tag: cell type

value: neurons/glia

value: F

tag: diagnosis

value: epilepsy

tag: anesthesia

value: general anesthesia


description:
Library name: W6_WT_Sham_Lg_3
Mouse Lung, wild-type, Sham, 6 weeks after SCI, Replicate 3

tag: tissue

value: Lung

tag: strain

value: 19 to 22 months old

tag: genotype


title: 71_TNY8A63

description: Library name: lib32927

value: ATG


title: PD1-7_S6_L001

description:
In vivo screen Sample PD1-7-lane1
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor

tag: cell line

value: Murine ovarian cancer cell line

value: In vivo screen


description:
Library name: W6_WT_Sham_Lg_2
Mouse Lung, wild-type, Sham, 6 weeks after SCI, Replicate 2

tag: collection time

tag: replicate


title: PD1-7_S6_L002

description:
In vivo screen Sample PD1-7-lane2
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

tag: screen


title: bulk, unstimulated, E7, RNA

description: Library name: bulk_E7B_RNA

value: anterior temporal lobe

tag: hemisphere

value: left

tag: age

value: awake

tag: paradigm


title: bulk, baseline, E5, RNA

description: Library name: bulk_E5A_RNA

value: baseline


title: 66_TNY7WT1

description: Library name: lib32922

value: whole blood

tag: donor id

tag: gender

value: female

tag: visit

tag: group

value: ATG-GCSF


title: 65_TNXUV9

description: Library name: lib32921


title: PD1-6_S5_L004

description:
In vivo screen Sample PD1-6-lane4
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

tag: cell type

tag: treatment


title: 64_TNY8J91

description: Library name: lib32920

value: male


description:
Library name: W6_WT_Sham_Lg_1
Mouse Lung, wild-type, Sham, 6 weeks after SCI, Replicate 1

tag: Sex

value: wild-type

value: Sham

value: 6 weeks after SCI


title: multiomics, stimulated, G2, GEX

description: Library name: multiomics_G2B_RNA

molecule: nuclear RNA

source_name: frontal lobe

tag: tissue

value: frontal lobe

tag: condition

value: stimulated

value: neurons/glia

value: F

tag: diagnosis

value: glioblastoma

tag: anesthesia


title: multiomics, stimulated, G2, ATAC

description: Library name: multiomics_G2B_ATAC

library_source: genomic single cell


title: 63_TNY878T

description: Library name: lib32919


title: multiomics, baseline, G2, GEX

description: Library name: multiomics_G2A_RNA


description:
Library name: W6_WT_SCI_Sp_5
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 5

value: Spleen

tag: strain

value: 19 to 22 months old

tag: genotype

value: Spinal Cord Injury (SCI)

tag: collection time


description:
Library name: W6_WT_SCI_Sp_4
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 4

tag: replicate


title: PD1-6_S5_L003

description:
In vivo screen Sample PD1-6-lane3
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor

tag: cell line

value: Murine ovarian cancer cell line

tag: screen

value: In vivo screen


title: 62_TNY6V8A

description: Library name: lib32918

value: whole blood

tag: donor id

tag: age

value: female

value: ATG


title: PD1-6_S5_L001

description:
In vivo screen Sample PD1-6-lane1
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt


description:
Library name: W6_WT_Sham_Lg_4
Mouse Lung, wild-type, Sham, 6 weeks after SCI, Replicate 4

value: Lung

value: male

value: wild-type


title: multiomics, baseline, G2, ATAC

description: Library name: multiomics_G2A_ATAC

value: frontal lobe

tag: hemisphere

value: left

value: baseline

value: awake

tag: paradigm


description:
Library name: W6_WT_SCI_Sp_3
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 3

value: 6 weeks after SCI


title: 60_TNY506M

description: Library name: lib32916

tag: gender

tag: visit

tag: group

value: Placebo


description:
Library name: W6_WT_SCI_Sp_2
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 2

tag: tissue

value: Spleen

tag: Sex

value: 19 to 22 months old

tag: treatment


title: PD1-5_S4_L003

description:
In vivo screen Sample PD1-5-lane3
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor

tag: cell type


title: 59_TNY5MJA

description: Library name: lib32915

value: ATG-GCSF


title: multiomics, stimulated, G1, ATAC

description: Library name: multiomics_G1B_ATAC

source_name: temporal lobe

value: temporal lobe

tag: condition

value: stimulated

value: neurons/glia

value: M

tag: diagnosis

value: glioblastoma

tag: anesthesia


description:
Library name: W6_WT_SCI_Sp_1
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 1

tag: strain

value: male

tag: genotype

value: Spinal Cord Injury (SCI)

tag: collection time

tag: replicate


title: multiomics, baseline, G1, GEX

description: Library name: multiomics_G1A_RNA

tag: age


title: PD1-5_S4_L002

description:
In vivo screen Sample PD1-5-lane2
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

tag: cell line

value: Murine ovarian cancer cell line

tag: screen

value: In vivo screen


title: multiomics, baseline, G1, ATAC

description: Library name: multiomics_G1A_ATAC

tag: hemisphere

value: left

value: baseline

tag: paradigm


description:
Library name: W6_WT_SCI_SC_5
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 5

value: Spinal Cord

value: wild-type

value: 6 weeks after SCI


title: 58_TNY56JY

description: Library name: lib32914

value: whole blood

tag: donor id

tag: gender

value: female

tag: visit

tag: group

value: Placebo


title: 57_TNY6V9J

description: Library name: lib32913

tag: tissue

value: ATG


title: PD1-5_S4_L001

description:
In vivo screen Sample PD1-5-lane1
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor

tag: cell type

tag: treatment


title: 56_TNY6V9L

description: Library name: lib32912


title: PD1-4_S3_L004

description:
In vivo screen Sample PD1-4-lane4
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt


title: multiomics, stimulated, E4, GEX

description: Library name: multiomics_E4B_RNA

source_name: middle temporal gyrus

value: middle temporal gyrus

tag: condition

value: stimulated

value: neurons/glia

tag: Sex

value: F

tag: diagnosis

value: epilepsy

tag: anesthesia

value: general anesthesia


title: PD1-4_S3_L003

description:
In vivo screen Sample PD1-4-lane3
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: Murine ovarian cancer cell line

value: In vivo screen


title: PD1-6_S5_L002

description:
In vivo screen Sample PD1-6-lane2
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt


description:
Library name: W6_WT_SCI_SC_4
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 4

tag: strain

value: male

value: 19 to 22 months old

tag: genotype

value: Spinal Cord Injury (SCI)

tag: collection time

tag: replicate


description:
Library name: W6_WT_SCI_SC_3
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 3

value: Spinal Cord

tag: age

value: wild-type

value: 6 weeks after SCI


description:
Library name: W6_WT_SCI_SC_2
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 2


title: multiomics, stimulated, E4, ATAC

description: Library name: multiomics_E4B_ATAC

tag: hemisphere

value: left

tag: paradigm


description:
Library name: W6_WT_SCI_SC_1
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 1


title: multiomics, stimulated, G1, GEX

description: Library name: multiomics_G1B_RNA

value: temporal lobe

value: M

value: glioblastoma

value: awake


title: 55_TNY56J6

description: Library name: lib32911

value: whole blood

tag: donor id

tag: gender

value: female

value: ATG


title: 61_TNY78N6

description: Library name: lib32917

tag: visit

tag: group

value: Placebo


title: multiomics, baseline, E4, GEX

description: Library name: multiomics_E4A_RNA

tag: tissue

value: middle temporal gyrus

value: baseline

tag: cell type

value: neurons/glia

value: F

value: epilepsy

value: general anesthesia

value: stimulated


title: PD1-4_S3_L002

description:
In vivo screen Sample PD1-4-lane2
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor

tag: cell line

value: Murine ovarian cancer cell line

tag: treatment

tag: screen

value: In vivo screen


title: PD1-5_S4_L004

description:
In vivo screen Sample PD1-5-lane4
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt


description:
Library name: W6_WT_SCI_Lg_5
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 5

value: Lung

tag: Sex

value: male

value: 19 to 22 months old

value: wild-type

value: Spinal Cord Injury (SCI)

value: 6 weeks after SCI


title: 54_TNY667R

description: Library name: lib32910

value: whole blood

value: female

value: Placebo


title: multiomics, stimulated, E3, GEX

description: Library name: multiomics_E3B_RNA

value: anterior temporal lobe

value: left

tag: condition

value: neurons/glia

value: M

tag: diagnosis

tag: anesthesia


title: 53_TNY6669

description: Library name: lib32909


title: PD1-4_S3_L001

description:
In vivo screen Sample PD1-4-lane1
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt


title: multiomics, baseline, E4, ATAC

description: Library name: multiomics_E4A_ATAC

value: middle temporal gyrus

value: baseline

value: F

value: epilepsy

value: general anesthesia

value: stimulated


title: PD1-3_S2_L004

description:
In vivo screen Sample PD1-3-lane4
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor

value: Murine ovarian cancer cell line

value: In vivo screen


title: multiomics, stimulated, E3, ATAC

description: Library name: multiomics_E3B_ATAC


title: 52_TNY44NU

description: Library name: lib32908

value: male

value: ATG-GCSF


title: PD1-3_S2_L003

description:
In vivo screen Sample PD1-3-lane3
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt


title: multiomics, baseline, E3, GEX

description: Library name: multiomics_E3A_RNA


description:
Library name: W6_WT_SCI_Lg_4
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 4

value: Lung

tag: strain

value: 19 to 22 months old

tag: genotype

value: wild-type

value: Spinal Cord Injury (SCI)

tag: collection time

value: 6 weeks after SCI

tag: replicate


title: 51_TNY679P

description: Library name: lib32907

value: whole blood

tag: donor id

tag: age


description:
Library name: W6_WT_SCI_Lg_2
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 2


title: 50_TNY6635

description: Library name: lib32906

tag: gender

value: female

tag: visit

value: Placebo


title: PD1-3_S2_L001

description:
In vivo screen Sample PD1-3-lane1
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

tag: tissue


title: PD1-3_S2_L002

description:
In vivo screen Sample PD1-3-lane2
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

tag: cell type


title: multiomics, stimulated, E2, GEX

description: Library name: multiomics_E2B_RNA

value: anterior temporal lobe

tag: hemisphere

value: left

value: neurons/glia

value: M

value: awake

tag: paradigm


title: multiomics, baseline, E3, ATAC

description: Library name: multiomics_E3A_ATAC

value: baseline

value: epilepsy

value: general anesthesia

value: stimulated


title: 49_TNY6LX5

description: Library name: lib32905

value: male

tag: group

value: ATG-GCSF


title: PD1-2_S1_L004

description:
In vivo screen Sample PD1-2-lane4
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor

tag: cell line

value: Murine ovarian cancer cell line

tag: treatment

tag: screen

value: In vivo screen


description:
Library name: W6_WT_SCI_Lg_1
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 1

value: Lung

tag: Sex

value: 19 to 22 months old

value: wild-type

value: Spinal Cord Injury (SCI)

value: 6 weeks after SCI


title: 48_TNY7UNY

description: Library name: lib32904

value: whole blood


description:
Library name: W6_Hv1KO_Sham_Sp_5
Mouse Spleen, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 5

value: Spleen

tag: strain

value: Hv1 knockout

value: Sham


title: PD1-2_S1_L003

description:
In vivo screen Sample PD1-2-lane3
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt


title: 47_TNYJPCL

description: Library name: lib32903

value: ATG


title: PD1-2_S1_L002

description:
In vivo screen Sample PD1-2-lane2
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt


title: multiomics, baseline, E2, GEX

description: Library name: multiomics_E2A_RNA

value: anterior temporal lobe

value: left

tag: condition

value: baseline

value: neurons/glia

value: M

tag: diagnosis

value: epilepsy

tag: anesthesia

value: awake


description:
Library name: W6_Hv1KO_Sham_Sp_4
Mouse Spleen, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 4

value: male

tag: genotype

tag: collection time

tag: replicate


title: multiomics, baseline, E2, ATAC

description: Library name: multiomics_E2A_ATAC

tag: age

value: stimulated


description:
Library name: W6_Hv1KO_Sham_Sp_3
Mouse Spleen, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 3

tag: tissue

value: 19 to 22 months old


title: PD1-2_S1_L001

description:
In vivo screen Sample PD1-2-lane1
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor

tag: cell type

value: Murine ovarian cancer cell line

value: In vivo screen


title: 46_TNYJX8P

description: Library name: lib32902

value: whole blood

tag: donor id

tag: gender

tag: visit

value: Placebo


description:
Library name: W6_Hv1KO_Sham_Sp_2
Mouse Spleen, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 2

value: Spleen

value: Hv1 knockout

value: Sham

value: 6 weeks after SCI


description:
Library name: W6_WT_SCI_Lg_3
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 3

value: Lung

value: wild-type

value: Spinal Cord Injury (SCI)


title: 45_TNYH7K0

description: Library name: lib32901

value: female

tag: group

value: ATG


title: multiomics, stimulated, E1, GEX

description: Library name: multiomics_E1B_RNA

value: anterior temporal lobe

tag: hemisphere

value: left

value: neurons/glia

value: F

value: epilepsy

value: awake

tag: paradigm


title: PD1-1_S10_L004

description:
In vivo screen Sample PD1-1-lane4
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor

tag: cell line

value: Murine ovarian cancer cell line

tag: treatment

tag: screen

value: In vivo screen


title: multiomics, stimulated, E1, ATAC

description: Library name: multiomics_E1B_ATAC

tag: condition

value: stimulated

tag: Sex

tag: diagnosis


title: PD1-1_S10_L003

description:
In vivo screen Sample PD1-1-lane3
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt


title: 44_TNYHN31

description: Library name: lib32900

value: whole blood

value: male


description:
Library name: W6_Hv1KO_Sham_Sp_1
Mouse Spleen, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 1

value: Spleen

tag: strain

value: 19 to 22 months old

tag: genotype

value: Hv1 knockout

value: Sham

tag: collection time

value: 6 weeks after SCI


title: multiomics, stimulated, E2, ATAC

description: Library name: multiomics_E2B_ATAC

tag: tissue

value: anterior temporal lobe

value: M

tag: age

tag: anesthesia


title: 43_TNYG9WP

description: Library name: lib32899

tag: donor id

tag: gender

value: female

value: ATG-GCSF


title: multiomics, baseline, E1, GEX

description: Library name: multiomics_E1A_RNA

value: left

value: baseline

tag: cell type

value: neurons/glia

value: F

value: epilepsy


title: PD1-1_S10_L002

description:
In vivo screen Sample PD1-1-lane2
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor

value: Murine ovarian cancer cell line

value: In vivo screen


title: 42_TNYGW81

description: Library name: lib32898

value: whole blood

tag: visit

tag: group

value: Placebo


description:
Library name: W6_Hv1KO_Sham_SC_3
Mouse Spinal Cord, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 3

value: Spinal Cord

value: male

value: 19 to 22 months old

value: Hv1 knockout

tag: replicate


title: multiomics, baseline, E1, ATAC

description: Library name: multiomics_E1A_ATAC

value: anterior temporal lobe

tag: hemisphere

value: awake

tag: paradigm

value: stimulated


description:
Library name: W6_Hv1KO_Sham_SC_5
Mouse Spinal Cord, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 5

tag: treatment

value: Sham

value: 6 weeks after SCI


title: 41_TNYCXRL

description: Library name: lib32897

value: ATG-GCSF


description:
Library name: W6_Hv1KO_Sham_SC_2
Mouse Spinal Cord, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 2

tag: Sex


title: Donor_9_10_11,PBMC,CD4,PMAiIL2,rep1,ADT

city: Chapel Hill

first: Edward

middle: Patrick

last: Browne

state: NC

address: 120 Mason Farm Road

institute: UNC-Chapel Hill

description:
Library name: Donor9_10_11_CD4_PMAiIL2_sample1_ADT
ADT matrix includes antibody surface staining and hash tagging oligos. Cells from three donors pooled after cell-hashing. Donor 9:HTO_2 , Donor 10:HTO_1, and Donor 11:HTO_3

library_source: other

data_processing:
Alignment and cell-calling was performed on the UNC high performance computing cluster with cellranger v7.1.0 (10x Genomics) against a custom human-HIV reference genome. Alignment was performed for all files using cellranger count function with default parameters but --jobmode=slurm to run on the UNC high-performance computing cluster.
CITE-seq analysis was performed with cellranger v7.1.0 (10x Genomics) using the human-HIV reference genome and a feature reference .csv. The feature reference file: "TotalSeq_B_Human_Universal_Cocktail_V1_399904_Antibody_reference_UMI_counting_CellRanger_addHTO.csv"  was derived from the manufacturer supplied document with 6 TotalSeq B anti-human hashtag antibodies (TotalSeq B0251-B0256) added as the final 6 entries in the feature reference file. Gene expression (GEX) and CITE-seq surface (ADT) data were split in Seurat from the contents of the cellranger output directories "filtered_feature_barcode_matrix", renamed, and uploaded as separate files for each GEX and ADT library.
The custom human-HIV reference genome was generated from concatenating GRCh38 fasta and .gtf files to an additional contig containing consensus clade B HIV sequence fasta and .gtf files and compiling with the cellranger mkref function.
Assembly: human genome (GRCh38), version 32 (Ensembl 98)
Supplementary files format and content: hdf5 files containing machine readable scRNA seq cell-by-feature matrices
Supplementary files format and content: separate matrix.mtx, barcodes.tsv, and features.tsv files split for GEX and ADT data
Library strategy: CITE-seq

molecule: protein

growth_protocol: After isolation (colon-derived) or thawing (blood-derived), cells were rested overnight at >1M/mL in complete RPMI-1640 (Gibco) containing 10U/mL of IL-2, 10µM ZVAD-FMK caspase inhibitors (Selleck Chem,), and 500nM Raltegravir (Selleck Chem).

extract_protocol:
PBMCs were isolated by Ficoll gradient centrifugation with ammonium-chloride-potassium buffer-based red-blood cell lysis and viably frozen in liquid nitrogen. Intra-epithelial lymphocytes (IEL) and Lamina propria-resident immune cells (LP cells) were isolated in the method of Trapecar et al. DOI:10.1089/aid.2017.0208 and pooled after isolation. Epithelial stripping was performed in an EDTA+DTT buffer with mechanical disruption on a gentleMACS dissociator, with IEL cells liberated to the supernatant. The remaining lamina propria fraction was digested in CLSPA+DNAse buffer and subjected to additional gentleMACS dissociation and mechanical disruption by syringe. LP cells were isolated by filtration of the supernatant through a 70 micron filter. LP and IEL cells were treated with DNAse, filtered through a 40 micron filter, and rinsed in complete RPMI culture media. Cells were then subjected to a dead cell removal protocol (Biolegend) to remove epithelial debris.
scRNAseq libraries were prepared according to manufacturer instructions (10x Genomics scRNAseq v3.1 3’ sequencing, catalog 1000269, protocol ). Gel-bead and cell emulsions (GEMs) were generated using the Chromium controller, subjected to reverse transcription, and first-strand cDNA was extracted from GEMs. Purified cDNA was PCR pre-amplified (12-cycles, 1-minute extension) with primers binding the P7 region and the Template Switching Oligo, cleaned up by solid-phase reversible immobilization (SPRI) beads, analyzed by HS DNA 5000 capillary electrophoresis (Agilent), and concentration calculated by Qubit (ThermoFisher).  From this material, 25% was used for Illumina NGS library construction involving fragmentation, end-repair/A-tailing, adapter TA ligation, and SPRI double-sided size selection to remove adapters and unfragmented products.  Libraries were amplified with Illumina indexing/sequencing i5 and i7 primers (13 cycles), then cleaned with SPRI beads before being quantified by Qubit and the fragment size determined using a Tapestation (Agilent).  Libraries were then pooled at an equimolar concentration and sequencing was performed using NovaSeq or NovaseqX sequencing (Illumina). CITE seq was performed as above, but with the following additional steps. The TotalSeq-B Universal Human antibody panel (Biolegend, catalog 399904) of lyophilized DNA-tagged antibodies was resuspended and spun down according to manufacturer’s instructions.  Meanwhile, cells were treated with Human TruStain FcX (Biolegend, catalog 422301) to prevent antibody binding by human Fc receptors.  Next, cells from each donor were stained with Totalseq-B hash-tag oligonucleotide antibodies (Biolegend, catalog 155831, 155833, and 155835) then added to three pools comprising untreated PBMCs, untreated CD4 cells, and PMA/ionomycin stimulated CD4 T cells. Pooled samples were stained in parallel with the TotalSeq-B Universal Human antibody panel, washed, and prepared for scRNA seq library construction as above but with additional PCR amplification of cell surface feature libraries following manufacturer instructions (10x Genomics protocol #CG000206).

treatment_protocol: Following overnight rest, cultures were split and treatment cultures were stimulated with PMA/ionomycin (16nM/1μM) and IL-2 (100U/mL) for 6 hours

value: PBMC

value: isolated CD4

tag: hto

value: ADT_BC1/HashBC1:Donor 10. ADT_BC2/HashBC2:Donor 9. ADT_BC3/HashBC3:Donor 11


title: PD1-10_S9_L003

description:
In vivo screen Sample PD1-10-lane3
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor

tag: cell line

value: Murine ovarian cancer cell line

tag: screen


title: PD1-1_S10_L001

description:
In vivo screen Sample PD1-1-lane1
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt

value: In vivo screen


description:
Library name: W6_Hv1KO_Sham_SC_1
Mouse Spinal Cord, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 1

tag: strain

tag: genotype

tag: collection time


title: 40_TNY9T29

description: Library name: lib32896

tag: tissue

value: whole blood

tag: age

value: Placebo


title: 39_TNYAV7V

description: Library name: lib32895

tag: donor id

tag: gender

value: male

value: ATG


title: Donor_9_10_11,PBMC,CD4,PMAiIL2,rep2,ADT

description:
Library name: Donor9_10_11_CD4_PMAiIL2_sample2_ADT
ADT matrix includes antibody surface staining and hash tagging oligos. Cells from three donors pooled after cell-hashing. Donor 9:HTO_2 , Donor 10:HTO_1, and Donor 11:HTO_3

tag: cell type


title: PD1-10_S9_L004

description:
In vivo screen Sample PD1-10-lane4
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt


title: PD1-10_S9_L002

description:
In vivo screen Sample PD1-10-lane2
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt


description:
Library name: W6_Hv1KO_Sham_Lg_5
Mouse Lung, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 5

value: Lung

value: 19 to 22 months old

value: Hv1 knockout


title: Donor_9_10_11,PBMC,CD4,Untreated,rep2,ADT

description:
Library name: Donor9_10_11_CD4_sample2_ADT
ADT matrix includes antibody surface staining and hash tagging oligos. Cells from three donors pooled after cell-hashing. Donor 9:HTO_2 , Donor 10:HTO_1, and Donor 11:HTO_3

value: Untreated


title: 38_TNYCWGL

description: Library name: lib32894

tag: visit

tag: group


title: PD1-10_S9_L001

description:
In vivo screen Sample PD1-10-lane1
220106_WP_PM1608.count.txt
220106_WP_PM1608_PD1_Ctrl.sgrna_summary.txt
220106_WP_PM1608_PD1_Ctrl.gene_summary.txt


title: 37_TNY77X1

description: Library name: lib32893


description:
Library name: W6_Hv1KO_Sham_SC_4
Mouse Spinal Cord, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 4

value: Spinal Cord

value: Sham

tag: replicate


title: Donor_9_10_11,PBMC,total,Untreated,rep2,ADT

description:
Library name: Donor9_10_11_totalPBMC_sample2_ADT
ADT matrix includes antibody surface staining and hash tagging oligos. Cells from three donors pooled after cell-hashing. Donor 9:HTO_2 , Donor 10:HTO_1, and Donor 11:HTO_3

value: total immune cells


title: NSG-5_S20_L004

description:
In vivo screen Sample NSG-5-lane4
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt


description:
Library name: W6_Hv1KO_Sham_Lg_3
Mouse Lung, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 3

value: 6 weeks after SCI


description:
Library name: W6_Hv1KO_Sham_Lg_4
Mouse Lung, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 4


title: Donor_9_10_11,PBMC,total,Untreated,rep1,ADT

description:
Library name: Donor9_10_11_totalPBMC_sample1_ADT
ADT matrix includes antibody surface staining and hash tagging oligos. Cells from three donors pooled after cell-hashing. Donor 9:HTO_2 , Donor 10:HTO_1, and Donor 11:HTO_3

value: PBMC


title: 36_TNYAKN6

description: Library name: lib32892


description:
Library name: W6_Hv1KO_Sham_Lg_2
Mouse Lung, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 2


title: 35_TNYAU00

description: Library name: lib32891

value: female


title: NSG-5_S20_L003

description:
In vivo screen Sample NSG-5-lane3
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor


title: Donor_9_10_11,PBMC,CD4,PMAiIL2,rep2,GEX

description:
Library name: Donor9_10_11_CD4_PMAiIL2_sample2_cDNA
Cells from three donors pooled after cell-hashing. Donor 9:HTO_2 , Donor 10:HTO_1, and Donor 11:HTO_3

value: isolated CD4


title: 34_TNYCA4R

description: Library name: lib32890


title: NSG-5_S20_L002

description:
In vivo screen Sample NSG-5-lane2
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt

value: Murine ovarian cancer cell line

value: In vivo screen


title: Donor_9_10_11,PBMC,CD4,PMAiIL2,rep1,GEX

description:
Library name: Donor9_10_11_CD4_PMAiIL2_sample1_cDNA
Cells from three donors pooled after cell-hashing. Donor 9:HTO_2 , Donor 10:HTO_1, and Donor 11:HTO_3


title: NSG-5_S20_L001

description:
In vivo screen Sample NSG-5-lane1
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt


description:
Library name: W6_Hv1KO_SCI_Sp_4
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 4

value: Spleen

value: Spinal Cord Injury (SCI)


title: 33_TNYA3K3

description: Library name: lib32889

value: whole blood

value: male

value: Placebo


description:
Library name: W6_Hv1KO_SCI_Sp_5
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 5

value: 19 to 22 months old

value: Hv1 knockout


title: Donor_9_10_11,PBMC,CD4,Untreated,rep1,ADT

description:
Library name: Donor9_10_11_CD4_sample1_ADT
ADT matrix includes antibody surface staining and hash tagging oligos. Cells from three donors pooled after cell-hashing. Donor 9:HTO_2 , Donor 10:HTO_1, and Donor 11:HTO_3

value: Untreated

value: ADT_BC1/HashBC1:Donor 10. ADT_BC2/HashBC2:Donor 9. ADT_BC3/HashBC3:Donor 11


title: Donor_9_10_11,PBMC,CD4,Untreated,rep1,GEX

description:
Library name: Donor9_10_11_CD4_sample1_cDNA
Cells from three donors pooled after cell-hashing. Donor 9:HTO_2 , Donor 10:HTO_1, and Donor 11:HTO_3


title: NSG-4_S19_L003

description:
In vivo screen Sample NSG-4-lane3
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt


title: NSG-4_S19_L004

description:
In vivo screen Sample NSG-4-lane4
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt


title: 31_TNY24CA

description: Library name: lib32887

value: ATG


description:
Library name: W6_Hv1KO_SCI_Sp_3
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 3

value: 6 weeks after SCI


title: Donor_9_10_11,PBMC,total,Untreated,rep2,GEX

description:
Library name: Donor9_10_11_totalPBMC_sample2_cDNA
Cells from three donors pooled after cell-hashing. Donor 9:HTO_2 , Donor 10:HTO_1, and Donor 11:HTO_3

value: PBMC

value: total immune cells


title: NSG-4_S19_L002

description:
In vivo screen Sample NSG-4-lane2
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor


description:
Library name: W6_Hv1KO_SCI_Sp_2
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 2


title: NSG-4_S19_L001

description:
In vivo screen Sample NSG-4-lane1
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt


title: Donor_9_10_11,PBMC,total,Untreated,rep1,GEX

description:
Library name: Donor9_10_11_totalPBMC_sample1_cDNA
Cells from three donors pooled after cell-hashing. Donor 9:HTO_2 , Donor 10:HTO_1, and Donor 11:HTO_3


title: 30_TNYA4RV

description: Library name: lib32886

value: ATG-GCSF


title: 29_TNYAC1H

description: Library name: lib32885


description:
Library name: W6_Hv1KO_Sham_Lg_1
Mouse Lung, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 1

value: Lung

value: Sham


title: 28_TNY9VXL

description: Library name: lib32884


title: Donor_11,Colon,total,PMAiIL2,rep1

description: Library name: Donor11_sample1

data_processing:
Alignment and cell-calling was performed on the UNC high performance computing cluster with cellranger v7.1.0 (10x Genomics) against a custom human-HIV reference genome. Alignment was performed for all files using cellranger count function with default parameters but --jobmode=slurm to run on the UNC high-performance computing cluster.
CITE-seq analysis was performed with cellranger v7.1.0 (10x Genomics) using the human-HIV reference genome and a feature reference .csv. The feature reference file: "TotalSeq_B_Human_Universal_Cocktail_V1_399904_Antibody_reference_UMI_counting_CellRanger_addHTO.csv"  was derived from the manufacturer supplied document with 6 TotalSeq B anti-human hashtag antibodies (TotalSeq B0251-B0256) added as the final 6 entries in the feature reference file. Gene expression (GEX) and CITE-seq surface (ADT) data were split in Seurat from the contents of the cellranger output directories "filtered_feature_barcode_matrix", renamed, and uploaded as separate files for each GEX and ADT library.
The custom human-HIV reference genome was generated from concatenating GRCh38 fasta and .gtf files to an additional contig containing consensus clade B HIV sequence fasta and .gtf files and compiling with the cellranger mkref function.
Assembly: human genome (GRCh38), version 32 (Ensembl 98)
Supplementary files format and content: hdf5 files containing machine readable scRNA seq cell-by-feature matrices
Supplementary files format and content: separate matrix.mtx, barcodes.tsv, and features.tsv files split for GEX and ADT data

source_name: Sigmoid Colon

value: Sigmoid Colon


title: NSG-3_S18_L003

description:
In vivo screen Sample NSG-3-lane3
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt

value: Murine ovarian cancer cell line

value: In vivo screen


title: Donor_10,Colon,total,PMAiIL2,rep4

description: Library name: Donor10_sample5


description:
Library name: W6_Hv1KO_SCI_SC_5
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 5

value: Spinal Cord

value: male

value: Spinal Cord Injury (SCI)


title: NSG-3_S18_L004

description:
In vivo screen Sample NSG-3-lane4
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt


title: 27_TNYA03T

description: Library name: lib32883

value: whole blood

value: female


description:
Library name: W6_Hv1KO_SCI_SC_4
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 4

value: 19 to 22 months old

value: Hv1 knockout


title: 32_TNYAKHU

description: Library name: lib32888

value: Placebo


title: Donor_9_10_11,PBMC,CD4,Untreated,rep2,GEX

description:
Library name: Donor9_10_11_CD4_sample2_cDNA
Cells from three donors pooled after cell-hashing. Donor 9:HTO_2 , Donor 10:HTO_1, and Donor 11:HTO_3

value: PBMC

value: isolated CD4

value: Untreated


description:
Library name: W6_Hv1KO_SCI_SC_3
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 3

value: 6 weeks after SCI


title: NSG-3_S18_L001

description:
In vivo screen Sample NSG-3-lane1
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor


description:
Library name: W6_Hv1KO_SCI_SC_2
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 2


title: NSG-3_S18_L002

description:
In vivo screen Sample NSG-3-lane2
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt


title: 25_TNY9T49

description: Library name: lib32881


title: Donor_10,Colon,total,PMAiIL2,rep1

description: Library name: Donor10_sample2

value: total immune cells


title: NSG-2_S17_L004

description:
In vivo screen Sample NSG-2-lane4
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt


title: Donor_10,Colon,total,PMAiIL2,rep3

description: Library name: Donor10_sample4

value: Sigmoid Colon


title: 26_TNY9V6V

description: Library name: lib32882

value: ATG


description:
Library name: W6_Hv1KO_SCI_Sp_1
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 1

value: Spleen


title: NSG-2_S17_L003

description:
In vivo screen Sample NSG-2-lane3
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt

value: Murine ovarian cancer cell line

value: In vivo screen


description:
Library name: W6_Hv1KO_SCI_Lg_5
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 5

value: Lung

value: male

value: Spinal Cord Injury (SCI)


title: Donor_9,Colon,total,PMAiIL2,rep2

description: Library name: Donor9_sample2

source_name: Colon

value: Colon


title: 23_TNY40YU

description: Library name: lib32879

value: whole blood

value: ATG-GCSF


title: NSG-2_S17_L002

description:
In vivo screen Sample NSG-2-lane2
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt


description:
Library name: W6_Hv1KO_SCI_Lg_4
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 4

value: 19 to 22 months old

value: Hv1 knockout


title: 24_TNY743K

description: Library name: lib32880


title: 22_TNY40YR

description: Library name: lib32878


title: Donor_9,Colon,total,PMAiIL2,rep1

description: Library name: Donor9_sample1


description:
Library name: W6_Hv1KO_SCI_Lg_3
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 3


title: NSG-2_S17_L001

description:
In vivo screen Sample NSG-2-lane1
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt


title: Donor_3,PBMC,total,PMAiIL2,rep1

description: Library name: Donor3_sample6

value: PBMC


title: 20_TNY5CGY

description: Library name: lib32876

value: female


description:
Library name: W6_Hv1KO_SCI_Lg_2
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 2

value: 6 weeks after SCI


title: Donor_10,Colon,total,PMAiIL2,rep2

description: Library name: Donor10_sample3

value: total immune cells


title: Donor_3,PBMC,total,Untreated,rep1

description: Library name: Donor3_sample5

value: Untreated


title: 21_TNY953G

description: Library name: lib32877

value: Placebo


description:
Library name: W6_Hv1KO_SCI_SC_1
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 1

value: Spinal Cord


description:
Library name: W6_Hv1KO_SCI_Lg_1
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 1


title: NSG-1_S16_L003

description:
In vivo screen Sample NSG-1-lane3
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt

value: Tissue sample from Xenograft tumor

value: Murine ovarian cancer cell line


title: NSG-1_S16_L002

description:
In vivo screen Sample NSG-1-lane2
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt

value: In vivo screen


title: Donor_3,Colon,total,PMAiIL2,rep1

description: Library name: Donor3_sample3

value: Sigmoid Colon


title: Donor_3,Colon,total,PMAiIL2,rep2

description: Library name: Donor3_sample4


title: Donor_10,Colon,total,Untreated,rep1

description: Library name: Donor10_sample1


title: NSG-1_S16_L001

description:
In vivo screen Sample NSG-1-lane1
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt


description:
Library name: D7_WT_Sham_Sp_4
Mouse Spleen, wild-type, Sham, 7 days after SCI, Replicate 4

value: Spleen

value: male

value: wild-type

value: Sham

value: 7 days after SCI


title: 18_TNY24JU

description: Library name: lib32874

value: whole blood

value: ATG


title: 19_TNY1L1H

description: Library name: lib32875

value: female


title: 17_TNY960L

description: Library name: lib32873


description:
Library name: D7_WT_Sham_Sp_3
Mouse Spleen, wild-type, Sham, 7 days after SCI, Replicate 3

value: 19 to 22 months old


title: Mock-5_S15_L004

description:
In vivo screen Sample Mock-5-lane4
220106_WP_PM1608.count.txt

value: PBS


title: 16_TNY95V0

description: Library name: lib32872


description:
Library name: D7_WT_Sham_Sp_2
Mouse Spleen, wild-type, Sham, 7 days after SCI, Replicate 2


title: Mock-5_S15_L003

description:
In vivo screen Sample Mock-5-lane3
220106_WP_PM1608.count.txt


title: Donor_3,Colon,total,Untreated,rep1

description: Library name: Donor3_sample1

value: total immune cells

value: Untreated


description:
Library name: D7_WT_Sham_Sp_1
Mouse Spleen, wild-type, Sham, 7 days after SCI, Replicate 1


title: NSG-1_S16_L004

description:
In vivo screen Sample NSG-1-lane4
220106_WP_PM1608.count.txt
220106_WP_PM1608_NSG_Ctrl.sgrna_summary.txt
220106_WP_PM1608_NSG_Ctrl.gene_summary.txt


title: 15_TNY8HYG

description: Library name: lib32871

value: Placebo


title: Mock-5_S15_L002

description:
In vivo screen Sample Mock-5-lane2
220106_WP_PM1608.count.txt

value: Tissue sample from Xenograft tumor


title: Donor_2,PBMC,total,PMAiIL2,rep1

description: Library name: Donor2_sample10

value: PBMC


description:
Library name: D7_WT_Sham_SC_4
Mouse Spinal Cord, wild-type, Sham, 7 days after SCI, Replicate 4

value: Spinal Cord


title: Donor_2,PBMC,total,Untreated,rep1

description: Library name: Donor2_sample9


title: 14_TNY82WG

description: Library name: lib32870


title: Mock-5_S15_L001

description:
In vivo screen Sample Mock-5-lane1
220106_WP_PM1608.count.txt

value: Murine ovarian cancer cell line

value: In vivo screen


title: 13_TNY9009

description: Library name: lib32869

value: ATG-GCSF


description:
Library name: D7_WT_Sham_SC_3
Mouse Spinal Cord, wild-type, Sham, 7 days after SCI, Replicate 3

value: male

value: wild-type


title: Donor_2,Colon,total,PMAiIL2,rep4

description: Library name: Donor2_sample7

value: Sigmoid Colon


title: Donor_2,Colon,total,PMAiIL2,rep5

description: Library name: Donor2_sample8


description:
Library name: D7_WT_Sham_SC_2
Mouse Spinal Cord, wild-type, Sham, 7 days after SCI, Replicate 2

value: Sham

value: 7 days after SCI


title: 12_TNY98W3

description: Library name: lib32868

value: whole blood

value: ATG


title: Mock-4_S14_L004

description:
In vivo screen Sample Mock-4-lane4
220106_WP_PM1608.count.txt

value: PBS


title: Donor_2,Colon,total,PMAiIL2,rep3

description: Library name: Donor2_sample6

value: total immune cells


title: Mock-4_S14_L003

description:
In vivo screen Sample Mock-4-lane3
220106_WP_PM1608.count.txt


description:
Library name: D7_WT_Sham_SC_1
Mouse Spinal Cord, wild-type, Sham, 7 days after SCI, Replicate 1

value: 19 to 22 months old


title: Donor_2,Colon,total,PMAiIL2,rep2

description: Library name: Donor2_sample5


title: 11_TNY771T

description: Library name: lib32867


title: Mock-4_S14_L002

description:
In vivo screen Sample Mock-4-lane2
220106_WP_PM1608.count.txt


description:
Library name: D7_WT_Sham_Lg_4
Mouse Lung, wild-type, Sham, 7 days after SCI, Replicate 4

value: Lung


title: Donor_3,Colon,total,Untreated,rep2

description: Library name: Donor3_sample2

value: Untreated


title: Mock-4_S14_L001

description:
In vivo screen Sample Mock-4-lane1
220106_WP_PM1608.count.txt

value: Tissue sample from Xenograft tumor


title: 9_TNY7WMC

description: Library name: lib32865

value: female

value: Placebo


title: Mock-3_S13_L004

description:
In vivo screen Sample Mock-3-lane4
220106_WP_PM1608.count.txt

value: Murine ovarian cancer cell line

value: In vivo screen


title: Donor_2,Colon,total,PMAiIL2,rep1

description: Library name: Donor2_sample4


description:
Library name: D7_WT_Sham_Lg_3
Mouse Lung, wild-type, Sham, 7 days after SCI, Replicate 3

value: male


description:
Library name: D7_WT_Sham_Lg_2
Mouse Lung, wild-type, Sham, 7 days after SCI, Replicate 2

value: wild-type


title: Donor_2,Colon,total,Untreated,rep3

description: Library name: Donor2_sample3

value: Sigmoid Colon


title: 8_TNY87WU

description: Library name: lib32864

value: ATG-GCSF


title: 7_TNY87VP

description: Library name: lib32863


description:
Library name: D7_WT_Sham_Lg_1
Mouse Lung, wild-type, Sham, 7 days after SCI, Replicate 1

value: Sham

value: 7 days after SCI


title: Donor_2,Colon,total,Untreated,rep2

description: Library name: Donor2_sample2


title: 6_TNXV6W

description: Library name: lib32862

value: whole blood


title: 10_TNY8NXM

description: Library name: lib32866


description:
Library name: D7_WT_SCI_Sp_5
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 5

value: Spleen

value: Spinal Cord Injury (SCI)


title: Donor_2,Colon,total,Untreated,rep1

description: Library name: Donor2_sample1

value: total immune cells


title: Mock-3_S13_L001

description:
In vivo screen Sample Mock-3-lane1
220106_WP_PM1608.count.txt

value: PBS


description:
Library name: D7_WT_SCI_Sp_4
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 4

value: 19 to 22 months old


title: 4_TNY6V8J

description: Library name: lib32860


title: Mock-3_S13_L002

description:
In vivo screen Sample Mock-3-lane2
220106_WP_PM1608.count.txt

value: Tissue sample from Xenograft tumor


description:
Library name: D7_WT_SCI_Sp_3
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 3


title: Mock-2_S12_L003

description:
In vivo screen Sample Mock-2-lane3
220106_WP_PM1608.count.txt


description:
Library name: D7_WT_SCI_Sp_2
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 2


title: 3_TNY56H0

description: Library name: lib32859


title: Donor_1,Colon,total,PMAiIL2,rep1

description: Library name: Donor1_sample2


title: Mock-2_S12_L004

description:
In vivo screen Sample Mock-2-lane4
220106_WP_PM1608.count.txt


title: Mock-2_S12_L002

description:
In vivo screen Sample Mock-2-lane2
220106_WP_PM1608.count.txt


title: Donor_1,PBMC,total,Untreated,rep1

description: Library name: Donor1_sample3

value: PBMC

value: Untreated


title: Mock-3_S13_L003

description:
In vivo screen Sample Mock-3-lane3
220106_WP_PM1608.count.txt

value: Murine ovarian cancer cell line


title: Mock-2_S12_L001

description:
In vivo screen Sample Mock-2-lane1
220106_WP_PM1608.count.txt

value: In vivo screen


description:
Library name: D7_WT_SCI_SC_5
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 5

value: Spinal Cord

value: male


description:
Library name: D7_WT_SCI_Sp_1
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 1

value: wild-type


title: Donor_1,Colon,total,Untreated,rep1

description: Library name: Donor1_sample1

value: Sigmoid Colon


title: Mock-1_S11_L004

description:
In vivo screen Sample Mock-1-lane4
220106_WP_PM1608.count.txt


description:
Library name: D7_WT_SCI_SC_4
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 4


title: Donor_1,PBMC,total,PMAiIL2,rep1

description: Library name: Donor1_sample4


title: Carotid, Asymptomatic, Subject 6

city: New Orleans

first: Thomas

middle: Cooper

last: Woods

state: LA

address: 1430 Tulane Avenue

department: Physiology

institute: Tulan

description:
Library name: Asymp6
Bulk RNA-seq of human carotid plaque tissue collected from a diabetic patient; single-end rRNA-depleted library.

data_processing:
Illumina instrument software was used for basecalling. Sequencing reads were trimmed for adapter sequences and low-quality bases using standard Illumina trimming tools. Transcript-level abundances were quantified using RSEM (v1.3.0) with default parameters, aligning single-end reads to the Homo sapiens GRCh38 transcriptome. Gene-level expected counts, TPM, and FPKM values were generated by RSEM. Gene-level expected counts were imported into DESeq2 via tximport for normalization and downstream analysis.
Assembly: Homo_sapiens.GRCh38.76
Supplementary files format and content: Processed data file contains a gene-by-sample matrix of raw integer counts generated from RSEM gene-level expected counts imported via tximport. Rows represent Ensembl gene identifiers; columns represent samples. Values reflect estimated gene-level counts prior to normalization.

source_name: carotid plaque

growth_protocol: not applicable; samples were obtained directly from human carotid atherosclerotic plaques collected during carotid endarterectomy.

extract_protocol:
Carotids obtained from patients undergoing carotid endarterectomy and flash frozen in liquid nitrogen. RNA was harvested using the Qiagen miReasy Mini Kit (Cat#217004). rRNA was removed using Ribo-Zero rRNA removal mix.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no experimental treatment was applied; samples represent symptomatic or asymptomatic carotid plaques collected from diabetic patients.

value: carotid plaque

value: mixed vascular cells

tag: batch


title: 5_TNY3JMH

description: Library name: lib32861

value: whole blood

value: female

value: Placebo


title: Mock-1_S11_L003

description:
In vivo screen Sample Mock-1-lane3
220106_WP_PM1608.count.txt

tag: treatment


title: MM134+vehicle; DNA repair

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

description:
Library name: JH210_control_haircut
Single cell DNA repair activity library from the 10X genomics 3´ end kit (v2 chemistry).

data_processing:
Data analysis pipeline and custom scripts are provided in a github repository (https://github.com/rnabioco/rhumba/tree/master/haircut).
Single cell RNA-Seq libraries were preprocessed using the 10x genomics software cellranger (3.0.2).
The single cell DNA repair libraries were preprocessed to append the read 1 sequence to the paired read 2 read id using umi_tools extract(v 1.0.0 --bc-pattern CCCCCCCCCCCCCCCCNNNNNNNNNN)(Smith et al. 2017) followed by poly(A) tail and template switching oligo removal from read 2 using cutadapt (v. 1.8.3 -a AAAAAAAAAAA -g AAGCAGTGGTATCAACGCAGAGTACATGGG --minimum-length=2) (Martin 2011).
Reads were next aligned with bowtie2 (v 2.3.2 Langmead B, Salzberg S. 2012) to a repair substrate reference.
Following alignment, BAM files were processed to extract the alignment hairpin and position into a tag (XT) within the BAM file (tag_bam).
UMI groups were identified and added as a tag (CB) using umi_tools group (--read-length = True --per-cell --output-bam = True --output-unmapped = True).
BAM files were then sorted by cell barcode tag using samtools sort (v 1.5-4 -t CB -@ 23) (Li 2009).
BAM files were then sorted by cell barcode tag using samtools sort (v 1.5-4 -t CB -@ 23) (Li 2009). UMIs per hairpin_position were enumerated per cell using umi-tools count (v 0.5.3) (Smith et al. 2017) using the directional method to disambiguate similar UMI sequences.
Count tables produced by umi_tools are then converted into sparseMatrix format using the scrunchy R package (https://github.com/hesselberthlab/scrunchy, umitools_to_mtx).
Matrices are the filtered to include only the cell-associated barcodes using the scrunchy R package (filter_matrix). Cell-associated barcodes are identified from the mRNA data using cellranger (v 3.0.2) from the filtered barcodes.tsv output.
Assembly: hg38, custom repair substrate reference
Supplementary files format and content: metadata and expression matrix, tsv files

molecule: other

source_name: MDA MB 134VI

growth_protocol: MDA MB 134VI (MM134; ATCC HTB-23; RRID:CVCL_0617) were routinely maintained in a 1:1 mix of DMEM (Gibco 11965) and L-15 (Gibco 11415), supplemented with 10% fetal bovine serum (Gibco A5670).

extract_protocol:
Single cell suspensions were prepared according to 10X Genomics recommendations. Briefly, cells were quickly washed with 0.25% trypsin (ThermoFisher) and then incubated in 0.25% trypsin for 5 min at 37°C. Trypsin digestion was quenched by the addition of cell culture medium. Cells were isolated by centrifugation at 150 × g for 3 min (these same conditions were used for all cell washes). Cells were washed twice with cold PBS containing 0.04% BSA. Cells were resuspended in 500 μl PBS with 0.04% BSA and filtered through a Flowmi™ Tip Strainer.
RNA-Seq

treatment_protocol: MM134 cells were hormone-deprived in phenol red-free IMEM (Gibco 10488) supplemented with 10% charcoal-stripped FBS, prepared as previously described (PMID: 27459541). After hormone deprivation, cells were treated with vehicle (0.01% EtOH) or estradiol (E2, 100nM) for 24 hours.

value: MDA MB 134VI

value: lobular carcinoma of the breast

value: WT

value: 0.01% Ethanol, 24hrs


title: MM134+E2; DNA repair

description:
Library name: JH210_E2_haircut
Single cell DNA repair activity library from the 10X genomics 3´ end kit (v2 chemistry).

value: 100nM Estradiol, 24hrs


description:
Library name: D7_WT_SCI_SC_3
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 3

tag: Sex

value: 19 to 22 months old

value: Spinal Cord Injury (SCI)

value: 7 days after SCI


title: MM134+E2; mRNA

description:
Library name: JH212_E2_targetedmrna
Targeted gene expression panel; 10X genomics Pan-Cancer panel; https://www.10xgenomics.com/support/universal-five-prime-gene-expression/documentation/steps/targeted-gene-expression/human-pan-cancer-panel


title: Mock-1_S11_L002

description:
In vivo screen Sample Mock-1-lane2
220106_WP_PM1608.count.txt

value: Tissue sample from Xenograft tumor

value: Murine ovarian cancer cell line

value: PBS

value: In vivo screen


title: Carotid, Asymptomatic, Subject 4

description:
Library name: Asymp4
Bulk RNA-seq of human carotid plaque tissue collected from a diabetic patient; single-end rRNA-depleted library.

value: carotid plaque


title: MM134+vehicle; mRNA

description:
Library name: JH212_control_targetedmrna
Targeted gene expression panel; 10X genomics Pan-Cancer panel; https://www.10xgenomics.com/support/universal-five-prime-gene-expression/documentation/steps/targeted-gene-expression/human-pan-cancer-panel


title: Carotid, Asymptomatic, Subject 5

description:
Library name: Asymp5
Bulk RNA-seq of human carotid plaque tissue collected from a diabetic patient; single-end rRNA-depleted library.

value: mixed vascular cells


title: Mock-1_S11_L001

description:
In vivo screen Sample Mock-1-lane1
220106_WP_PM1608.count.txt


description:
Library name: D7_WT_SCI_SC_2
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 2

value: Spinal Cord

value: male

value: wild-type


description:
Library name: D7_WT_SCI_SC_1
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 1


title: 2_TNY6622

description: Library name: lib32858

value: whole blood

value: Placebo


title: ET1-4_S11_L004

description:
In vitro screen Sample ET1-4-lane4
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.gene_summary.txt

value: Cell line

value: Pmel T cell treated

value: In vitro screen


description:
Library name: D7_WT_SCI_Lg_5
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 5

value: Lung

value: 19 to 22 months old


title: Carotid, Symptomatic, Subject 5

description:
Library name: Symp5
Bulk RNA-seq of human carotid plaque tissue collected from a diabetic patient; single-end rRNA-depleted library.


title: EPCAM- in d109 cochlear organoids with T4

city: Indianapolis

first: Tsubasa

last: Saeki

state: IN

address: 980 W Walnut St

department: Otolaryngology-Head and Neck Surgery

institute: Indiana University School of Medicine

description: Library name: T4_d140_EPCAM-

data_processing:
Illumina’s CellRanger v4.0.0 program generated BCL files, which were demultiplexed and converted to FASTQ files via bcl2fastq Conversion Software. The FASTQ files were then aligned to the GRCh38-3.0.0 human reference genome using the STAR (Spliced Transcripts Alignment to a Reference) aligner. Mapped reads were grouped by cell barcode, and single-cell gene expression was quantified using unique molecular identifiers (UMIs). The resulting filtered gene-barcode (count) matrices were used as input for downstream analysis.
Assembly: GRCh38/hg38
Supplementary files format and content: Gene expression matrix

source_name: cochlear organoids

growth_protocol: PAX2-2A-nGFP/POU4F3-2A-ntdTomato hESCs were dissociated with Accutase and distributed at 2500-3500 cells per well onto low-adhesion 96-well U-bottom plates in E8fn containing Y-27632. 100μL of E8fn was added to each well after >4 h of incubation. After 48 h of incubation (day 0; d0), aggregates were washed in Essential 6 medium and transferred to new 96-well U-bottom plates with 100 μL of E6 medium with Normocin (E6n) containing FGF-2, SB-431542, and 2% Martigel. On d3, FGF-2 and LDN-193189 were added. Culture media was changed on d7 and d8 with E6n containing CHIR99021, LDN, and FGF-2. On d11, aggregates were washed and transferred to 6-well culture dishes in Organoid Maturation Medium (OMM) containing 1% Matrigel and CHIR99021. OMM consists of a 50:50 mixture of advanced DMEM:F12 and Neurobasal Medium with N2 Supplement, B27 minus Vitamin A, GlutaMAX, β-Mercaptoethanol, and Normocin. Cultures were maintained in OMM containing CHIR99021 and Purmorphamine from d13-18, and maintained in OMM containing Purmorphamine and IWP2 from d18-22, with media changes on d15, 18, and 20, then maintained in OMM for the remainder of the culture.

extract_protocol:
Aggregates were dissected to enrich the otic epithelial cell types 2-3 days prior to single-cell dissociation. On the day of cell sorting, aggregates were incubated with Accumax at 37°C for 120 min. During incubation, the samples were mechanically dissociated by gentle pipetting with wide-orifice P1000 tips. After confirming that most cells, especially those with reporter expression, were completely dissociated, they were filtered through a 40-μm cell strainer and then transferred into 2-ml tubes. After spinning down at 200 ×g for 5 min, dissociated cells were resuspended in FACS buffer consisting of 2% fetal bovine serum in 1× DPBS. Then, cells were stained with 1:100 PE conjugated EPCAM antibody at 4℃ for 30 min in dark. After antibody staining, cells were washed and resuspended in FACS buffer. Cells were stored on ice in the dark prior to sorting. Both PE-EPCAM+ and PE-EPCAM- populations were collected in separate tubes for separate downstream scRNA-seq reactions.
scRNA-seq for all samples was performed using the 10x Genomics Chromium 3’ v3 platform for cDNA library construction and the NovaSeq 6000 system for sequencing.

value: cochlear organoids


title: 1_TNY662L

description: Library name: lib32857


title: anti-HER2/neu and non-transduced T-cells (n=4 pool each)

city: Novosibirsk

first: Saleh

last: Alrhmoun

address: Yadrintscvskaya street 14

country: Russia

institute: Federal State Budgetary Scientific Institution Research Institute of Fundamental and Clinical Immunology

description:
Sex: male (n =4), female (n=4)
Library name: Her2_Non-TD

data_processing:
The SampleTag sample demultiplexing, barcode processing, gene UMI counting and aggregation were made using the BD Rhapsody pipeline v1.9 (https://bd-rhapsody-bioinfo-docs.genomics.bd.com/release_notes.html).
Assembly: BD Rhapsody™ Onco-BC Panel Hs (https://scomix.bd.com/hc/en-us/article_attachments/360059289812).
Supplementary files format and content: Comma-separated gene expressiom matrices demultiplexed via SampleTag HTO's.

source_name: Blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from peripheral blood by centrifugation using Ficoll. T cells were isolated from PBMCs using CD3 antibodies. T cells were transduced using a lentiviral-based anti-HER2/enu construct.

extract_protocol:
Cells were harvested following tumor co-culture, washed in PBS, stained with BD SampleTag antibodies, and counted. Single-cell suspensions were loaded onto the BD Rhapsody platform according to the manufacturer’s instructions.
Library was performed according to the manufacter’s instructions (BD Rhapsody™ System Targeted mRNA and Sample Tag Library Preparation Protocol).

treatment_protocol: TCR-T and non-transduced T cells were co-cultured with HER2/neu-expressing tumor cell lines (e.g., SK-Mel-37, SK-Mel-5, HCT-116) for 16–18 hours prior to single-cell analysis.

value: T-cells

value: Blood

value: 24-48 years

tag: instrument

value: BD Rhapsody


title: ET1-4_S11_L003

description:
In vitro screen Sample ET1-4-lane3
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.gene_summary.txt

source_name: Cell line

tag: cell line

value: Murine ovarian cancer cell line


title: Carotid, Asymptomatic, Subject 3

description:
Library name: Asymp3
Bulk RNA-seq of human carotid plaque tissue collected from a diabetic patient; single-end rRNA-depleted library.

value: carotid plaque

value: mixed vascular cells


title: EPCAM+ in d109 cochlear organoids with T4

description: Library name: T4_d109_EPCAM+


title: ET1-4_S11_L002

description:
In vitro screen Sample ET1-4-lane2
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.gene_summary.txt

tag: screen


description:
Library name: D7_WT_SCI_Lg_4
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 4

tag: strain

value: male

value: Spinal Cord Injury (SCI)

value: 7 days after SCI


title: ET1-4_S11_L001

description:
In vitro screen Sample ET1-4-lane1
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.gene_summary.txt


title: EPCAM- in d109 cochlear organoids without T4

description: Library name: CTR_d109_EPCAM-


description:
Library name: D7_WT_SCI_Lg_3
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 3

tag: genotype

value: wild-type


title: Carotid, Symptomatic, Subject 4

description:
Library name: Symp4
Bulk RNA-seq of human carotid plaque tissue collected from a diabetic patient; single-end rRNA-depleted library.


title: EPCAM+ in d109 cochlear organoids without T4

description: Library name: CTR_d109_EPCAM+


description:
Library name: D7_WT_SCI_Lg_1
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 1

tag: collection time


title: Carotid, Symptomatic, Subject 2

description:
Library name: Symp2
Bulk RNA-seq of human carotid plaque tissue collected from a diabetic patient; single-end rRNA-depleted library.

tag: tissue


description:
Library name: D7_WT_SCI_Lg_2
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 2

tag: age


title: ET1-3_S10_L003

description:
In vitro screen Sample ET1-3-lane3
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.gene_summary.txt

value: Cell line


title: Carotid, Symptomatic, Subject 1

description:
Library name: Symp1
Bulk RNA-seq of human carotid plaque tissue collected from a diabetic patient; single-end rRNA-depleted library.


description:
Library name: D7_Hv1KO_Sham_Sp_5
Mouse Spleen, Hv1 knockout, Sham, 7 days after SCI, Replicate 5

value: Spleen

value: Hv1 knockout

value: Sham


title: ET1-3_S10_L002

description:
In vitro screen Sample ET1-3-lane2
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.gene_summary.txt

value: Pmel T cell treated

value: In vitro screen


title: TGTGCCCA_F8

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

description:
Library name: nk_d958_t6_r3
Donor 958, DPI=6, Biological replicate 3

data_processing:
For data pre-processing, sequenced reads were demultiplexed and trimmed using Cutadapt v3.4 to acquire ORF library barcodes (settings: -e 0.1 -m 4 –-discard-untrimmed -g atatcttgtggaaaggacga...tgcatcgatcgagtcagctagctgat), which were subsequently aligned using Bowtie v1.3.0 (settings: -v 0 -m 1 --chunkmbs 2000 --best) 83. Next, the random nucleotide UMIs were extracted from the demultiplexed fastq files, described above, using Cutadapt to identify and trim flanking sequences (settings: -e 0.1 -m 4 --discard-untrimmed -g gatcgagtcagctagctgat...ttaagtcgacaatcaacctc). The ORF barcode reads were matched to the UMIs using the individual read IDs, and the unique barcode-UMI pairs were quantified. Finally, the mini-screen data were analyzed using SAMBA, similar to the CRISPRa screen, but UMIs were used instead of sgRNAs for distinct constructs targeting the same gene.
Assembly: GRCh38.p14
Supplementary files format and content: The processed data file has a tab-delimited format, with the first column as the UMI ID, the second column as the ORF ID, and the following columns with UMI counts for all samples.
Library strategy: CRISPR Screen

source_name: Tumor-infiltrating CAR-PBNK

extract_protocol:
Primary human peripheral blood NK cells from two healthy donors were first transduced with HER2-CAR lentivirus and then with the ORF library lentivirus at an MOI of ~0.2. A total of 20 million library-transduced CAR-NK cells were injected into each HT29 tumor-bearing mouse (n = 5 mice for Donor 0957 and n = 3 for Donor 0958 for each time point). Genomic DNA was extracted from tumors at day 3 and 6 post-treatment, as well as from pre-injection cells, and subjected to NGS to quantify ORF and UMI barcode representations.
To generate the ORF library, the top 35 gene targets (cDNA length ≤ 1 kb) were chosen from the CRISPRa screen, along with five fluorescent reporter genes as null controls. The ORF library was synthesized as individual eBlocks (IDT), pooled at equimolar ratios, and amplified with primers containing four-nucleotide random barcodes (UMIs; NNNN) to introduce molecular redundancy targeting the same gene. The ORF expression vector plasmid was bought from Addgene (#145026). The barcoded ORF library was pool-cloned into the expression vector using Gibson assembly.

value: Tumor-infiltrating CAR-PBNK

value: Primary peripheral blood NK cell

value: Natural Killer cell

value: Donor 958


title: Carotid, Symptomatic, Subject 6

description:
Library name: Symp6
Bulk RNA-seq of human carotid plaque tissue collected from a diabetic patient; single-end rRNA-depleted library.


description:
Library name: D7_Hv1KO_Sham_Sp_4
Mouse Spleen, Hv1 knockout, Sham, 7 days after SCI, Replicate 4

value: 19 to 22 months old


title: Carotid, Asymptomatic, Subject 2

description:
Library name: Asymp2
Bulk RNA-seq of human carotid plaque tissue collected from a diabetic patient; single-end rRNA-depleted library.

value: carotid plaque


title: TGTGCCCA_F6

description:
Library name: nk_d958_t6_r1
Donor 958, DPI=6, Biological replicate 1


description:
Library name: D7_Hv1KO_Sham_Sp_3
Mouse Spleen, Hv1 knockout, Sham, 7 days after SCI, Replicate 3


title: Carotid, Asymptomatic, Subject 1

description:
Library name: Asymp1
Bulk RNA-seq of human carotid plaque tissue collected from a diabetic patient; single-end rRNA-depleted library.

value: mixed vascular cells


title: TGTGCCCA_F5

description:
Library name: nk_d957_t6_r5
Donor 957, DPI=6, Biological replicate 5

value: Donor 957


title: ET1-3_S10_L001

description:
In vitro screen Sample ET1-3-lane1
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.gene_summary.txt

value: Murine ovarian cancer cell line


description:
Library name: D7_Hv1KO_Sham_Sp_2
Mouse Spleen, Hv1 knockout, Sham, 7 days after SCI, Replicate 2

value: male

value: 7 days after SCI


title: TGTGCCCA_F4

description:
Library name: nk_d957_t6_r4
Donor 957, DPI=6, Biological replicate 4


title: ET1-2_S9_L003

description:
In vitro screen Sample ET1-2-lane3
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.gene_summary.txt

value: Cell line


title: ET1-3_S10_L004

description:
In vitro screen Sample ET1-3-lane4
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.gene_summary.txt


description:
Library name: D7_Hv1KO_Sham_Sp_1
Mouse Spleen, Hv1 knockout, Sham, 7 days after SCI, Replicate 1

value: Spleen


title: Carotid, Symptomatic, Subject 3

description:
Library name: Symp3
Bulk RNA-seq of human carotid plaque tissue collected from a diabetic patient; single-end rRNA-depleted library.


title: TGTGCCCA_F3

description:
Library name: nk_d957_t6_r3
Donor 957, DPI=6, Biological replicate 3


title: SFI_Pt21

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

department: Pathology

country: South Korea

institute: Asan Medical Center

description:
Library name: Pt21
Pt21

data_processing:
Sequenced reads mapped to the GRCh38 reference genome using HISAT2 program
assembly and quantification using the StringTie program
Assembly: GRCh38
Supplementary files format and content: raw read count txt file

source_name: kidney

extract_protocol:
FFPE tissues were used.
SureSelectXT RNA Direct Library Preparation Kit

value: kidney

value: Renal cell carcinoma

value: SFI


description:
Library name: D7_Hv1KO_Sham_SC_5
Mouse Spinal Cord, Hv1 knockout, Sham, 7 days after SCI, Replicate 5

value: Spinal Cord

value: Hv1 knockout

value: Sham


title: ET1-2_S9_L002

description:
In vitro screen Sample ET1-2-lane2
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.gene_summary.txt

value: Pmel T cell treated

value: In vitro screen


title: SFI_Pt22

description:
Library name: Pt22
Pt22


title: ET1-2_S9_L001

description:
In vitro screen Sample ET1-2-lane1
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.gene_summary.txt


title: TGTGCCCA_F2

description:
Library name: nk_d957_t6_r2
Donor 957, DPI=6, Biological replicate 2

value: Tumor-infiltrating CAR-PBNK

value: Primary peripheral blood NK cell

value: Natural Killer cell


title: SFI_Pt20

description:
Library name: Pt20
Pt20


title: TGTGCCCA_F7

description:
Library name: nk_d958_t6_r2
Donor 958, DPI=6, Biological replicate 2

value: Donor 958


title: ET02-4_S8_L004

description:
In vitro screen Sample ET02-4-lane4
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.gene_summary.txt

value: Murine ovarian cancer cell line


title: TGTGCCCA_F1

description:
Library name: nk_d957_t6_r1
Donor 957, DPI=6, Biological replicate 1

value: Donor 957


description:
Library name: D7_Hv1KO_Sham_SC_3
Mouse Spinal Cord, Hv1 knockout, Sham, 7 days after SCI, Replicate 3

value: male

value: 19 to 22 months old

value: 7 days after SCI


title: GTGTAAAC_F8

description:
Library name: nk_d958_t3_r3
Donor 958, DPI=3, Biological replicate 3