title: Spatial_Aged_3dpi_rep2

city: Miami

first: Jae

last: Lee

state: FL

address: 1095 NW 14th Terrace #48

institute: University of Miami

description: Library name: D-19421

data_processing:
Spatial - Sequences were aligned and filtered with the mm10-2020-A genome using Space Ranger V2.0.0. SP and S1 runs for each sample were combined. Passing reads recorded as over tissue were then loaded into R and processed as a Seurat object.  Single cell -  The resulting sequences were then aligned and filtered using the CellRanger 6.0.2 pipeline. Briefly, reads from FASTQ files were were aligned to the mm10-3.0.0 reference genome. Using the STAR splice-aware aligner, the reads were aligned and excluded if they mapped to <50% of an exonic sequence or contained single base substitution errors, then UMIs were removed. The final count matrix was generated containing all passing UMIs in each droplet.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values in a matrix file of genes by cells
Library strategy: Spatial Transcriptomics

source_name: 10uM sagittal section from the midline of 8mm of spinal cord, centered on t19

extract_protocol:
Spatial - On the day of tissue collection, animals were deeply anesthetized with avertin (250 mg/kg, i.p) and then transcardially perfused with ice-cold PBS. A 4mm section of the spinal cord centered at the injury site was dissected, blotted dry with kimwipe, and embedded in OCT for parasagittal cryosectioning. Tissue blocks were stored at -80 ˚C until sectioning.   Tissue permeabilization time was determined in accordance with the Visium Tissue Optimization (TO) user guide (10x Genomics CG000238 Rev E). Briefly, 10 µm thick tissue sections were placed on the TO slide. One capture area was left empty as a negative control and 2 ug bulk-extracted spinal cord RNA (Qiagen RNeasy plus kit) was added to another empty well as a positive control. Following cDNA synthesis and tissue removal, fluorescent cDNA footprints were visualized using Nikon Eclipse microscope and 12 minutes was identified as the optimal permeabilization time. Prior to sectioning, the tissue blocks and Visium Spatial Gene Expression slide were equilibrated to the cryostat chamber for 30 minutes. To correctly identify the injury epicenter, we sampled the tissue after every eighth 10 µm section on a separate slide. Myelin was stained for 5 minutes with 1% Sudan Black in propylene glycol pre-warmed to 56˚C in a water bath and washed with running tap water until the water ran clear.  A 10 µm tissue section containing toward the midline of the tissue and containing a large injury site was captured on the Spatial Gene Expression slide. These steps were repeated for a total of four biological replicates (one per capture area) on a single slide.  The full slide was transported on dry ice to a thermocycler fitted with the Visium thermocycler adapter (3000380, 10x Genomics) pre-warmed to 37˚C. After thawing on the thermocycler adapter for 1 minute, the slide was fixed in ice-cold methanol at -20˚C for 30 minutes. Myelin was again stained with 1% Sudan Black in propylene glycol for 5 minutes at room temperature. The excess staining solution was discarded, and the slide was carefully immersed 3 times in a 50 mL conical tube of ultrapure water, then 15 times each in two additional beakers with 800 mL ultrapure water. The slide was cover slipped with 85% glycerol mounting media according to the manufacturer’s instruction and imaged using Nikon Eclipse inverted microscope using brightfield microscopy.  Single Cell - Each mouse was anesthetized with Avertin (250 mg/kg i.p.) prior to transcardial perfusion with a pre-oxygenated artificial cerebrospinal fluid (aCSF) solution. From each, an 8-mm section of the spinal cord centered at the injury site was then dissected and placed in ice-cold cutting solution upon extraction until the final dissection.  For every 8 mm spinal cord (approximately 400 mg ), 50μL of Enzyme P dissolved in 1.9 mL of buffer X was prepared. The solution was then pre-warmed for at least 10min in 37°C water bath. After peeling away the meninges, the parenchymal tissue was finely chopped 10-15x in horizontal and vertical directions with a razor blade, washed with 5 ml of cutting solution, and centrifuged at 300 g for 2 minutes at RT. The resulting cell pellet was processed using the Miltenyi Neural Tissue Dissociation Kit-P (cat #130–092–628) following the manufacturer's protocol to obtain a single-cell suspension. The cell suspensions were manually triturated (slowly, 10 times) using a large-opening (1,000 um diameter) fire-polished pipette. After a 10-minute incubation at 37°C, the suspensions were further triturated with medium- and then small-opening (750 um and 500 um diameter, respectively) fire-polished pipettes to create a single-cell suspension. The suspensions were then filtered through a 70 μm cell strainer into a 50 mL conical, washed with 10 ml of HBSS with Ca2+/Mg2+, and centrifuged at 4°C and 300 g for 5 minutes. The supernatant was aspirated, and the cell pellets were resuspended in 1mL ACK Lysis Buffer for 1 minute at RT, immediately followed by the addition of 5 mL HBSS with Ca2+/Mg2+, and then centrifuged at 300 g for 5 minutes at 4°C, and the supernatant was discarded. Samples were then processed using Miltenyi Myelin Removal Beads according to manufacturer guidelines. The injury site from a separate mouse was processed as above followed by Miltenyi anti-ACSA-2 magnetic beads to enrich for astrocytes (keeping the cells retained in the column and discarding the flowthrough). The resulting cell suspension was then centrifuged at 300 g for 5 minutes at 4°C, and the supernatant was discarded. One non-enriched and one astrocyte-enriched samples were pooled to generate one biological replicate.
Spatial - After imaging, the spatial gene expression slide was immersed in 3X SSC at a 45˚angle to allow the coverslip to gently separate from the slide. The tissue was enzymatically permeabilized for 12 minutes as determined by the above tissue optimization experiment and cDNA synthesis and library preparation was performed following the manufacturer’s guidelines (Visium Spatial Gene Expression Reagents Kits User Guide CG000160, Rev F). cDNA amplification cycle number was determined by the Cq (defined by 25% peak RFU) value obtained by qPCR.  Each spatial sequencing sample consisted of a single animal per-10X Visium V1 sequencing area. The cDNA library generated was sequenced on an Illumina NovaSeq with a SP-200 and S1 flow cell for paired-end sequencing targeting 50 million reads per sample.   Single Cell - Each single cell sequencing sample consisted of two pooled animals with one sample enriched for astrocytes. The eight biological replicates consisted of one young uninjured, one young 3 days post-injury (dpi), three middle-aged uninjured, and three middle-aged 3dpi samples. Prior to sequencing, cell suspensions were assessed for purity, concentration, and viability with AOPI Stain imaged on a Nexcelom K2 Cellometer. After confirming viability was above 80%, cells were diluted when necessary to achieve approximately 10,000 cells per-capture. ~7,000 cells were sequenced per-sample with a mean of ~95k reads per-cell and a mean of ~11k UMIs per-cell. Sample libraries were prepared with the 10X Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) and multiplexed on the sequencer with Dual Index Kit TT (Set A) according to manufacturer’s protocols. These libraries were then sequenced using paired-end sequencing on eight channels of an Illumina Novaseq X 10-billion-read flow cell with a 300-cycle kit.

treatment_protocol: Female C57BL/6J (Jackson Labs, stock 000664) mice aged 2-3 months (young) or 10-12 months (middle-aged) were anesthetized with a combination of ketamine (100 mg/kg) and xylazine (15 mg/kg) administered intraperitoneally. Following anesthesia, T8 laminectomy was performed to expose the mid-thoracic spinal cord, and the spinal column stabilized with spinal clamps on the adjacent T7 and T9 vertebrae. A contusion injury was then inflicted induced using an Infinite Horizon Impactor device (Precision Systems and Instrumentation, LLC), delivering a force of between 65 and 70 kilodynes. Post-operative care included the subcutaneous administration of slow-release buprenorphine (3.25 mg/kg) for analgesia injected immediately after surgery. Lactated Ringer’s solution (1 ml) and gentamicin (5 mg/kg) were injected subcutaneously once immediately after surgery and once daily for three days following surgery to prevent dehydration and infection. Bladders were manually expressed twice daily until the conclusion of the experiment. All procedures adhered to the guidelines of the University of Miami Institutional Animal Care and Use Committee and the National Institutes of Health.

value: Unenriched whole-tissue

tag: injury

value: Aged

tag: tagnumber


title: PIM010

status: Public on Jul 23 2025

type: SRA

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

country: USA

institute: University of Texas

description: Library name: PIM010

library_source: transcriptomic

data_processing:
The gene expression data was sequenced in six separate batches and preprocessed using the same pipeline.
We processed the data using the BETSY system, which aligned the reads to the hg19 genome with STAR estimated the transcript abundance as transcripts per million (TPM) with RSEM.
We applied ComBat to log_2 TPM values for batch effect normalization.
Assembly: hg19
Supplementary files format and content: expression.counts.txt.  Read counts for each gene and sample.  Tab-delimited text file.
Supplementary files format and content: expression.tpm.txt.  Transcripts per million for each gene and sample.  Tab-delimited text file.
Supplementary files format and content: expression.combat.txt.  ComBat normalized transcripts per million.  Includes only genes with positive variance in all batches before correction.  Tab-delimited text file.

molecule: polyA RNA

organism: Homo sapiens

source_name: patient-derived xenograft (PDX) model of TNBC from tumor

growth_protocol: The fourth mammary fat pads of 4-to-8-week-old female NOD/SCID mice were implanted with 500,000 PDX tumor cells suspended in 30 µL of a 50:50 mixture of DMEM/F12 media and Matrigel. Cells in Matrigel were maintained on ice until engraftment.

extract_protocol:
The RNA was extracted using PicoPure RNA isolation kit and RNA concentration was quantified by Nanodrop.
Whole transcriptome RNA-seq libraries were prepared using RNA HyperPrep kit with RiboErase following the manufacturer's instructions. Paired-end sequencing was performed on Illumina instruments, which varied across batches.

treatment_protocol: Patients were treated with neoadjuvant chemotherapy.  Tumors were extracted and engrafted into xenograft mouse models before (pre), during (mid), and after (post) treatment.

tag: tissue

value: tumor

tag: treatment

tag: time point

value: pre

tag: batch


title: dog3_punctured_pbs_right

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

description: Library name: 5R

data_processing:
Raw fastq was aligned to canine reference genome with hisat2 v2.1.0; gene counts were quantified by using featureCounts software.
Assembly: CanFam3.1
Supplementary files format and content: gene expression matrix

molecule: total RNA

organism: Canis lupus familiaris

source_name: Dorsal Root Ganglion

growth_protocol: All animal experiments were approved by The Ohio State University Institutional Animal Care and Use Committee (IACUC). Female beagles (3-4 y.o. N=6) were obtained from Marshall BioResources and group housed according to federal regulations and institutional policies.

extract_protocol:
DRGs from L4/5 (internal control) and T12/L1 (puncture) were dissected and RNA isolated using the TRIzol Plus RNA Purification Kit (Cat#12183555). RNA-seq was performed at The Ohio State University Genomics Core with library generation using a NEBNext rRNA Depletion and Prep Kit.
cDNA libraries were sequenced on Novaseq SP system (Illumina, USA).

treatment_protocol: Following a dorsolateral approach to the thoracolumbar vertebral column, the thoracolumbar fascia was incised and epaxial muscles reflected laterally on one side to reveal the dorsolateral aspect of the intervertebral disc spaces from T11 to L1. The T11/T12, T12/T13, and T13/LI IVDs were identified and punctured with a 26G needle containing either 10 µL of 1x phosphate buffered saline (PBS) (injury control; N=3) or 100 µM PAR2A and 25 µM CS (treatment; N=3).

value: Dorsal Root Ganglion

tag: Sex

value: Female


title: Spatial_Aged_3dpi_rep1

description: Library name: C-19417

organism: Mus musculus

source_name: 10uM sagittal section from the midline of 8mm of spinal cord, centered on t18

tag: cell type

tag: genotype

tag: age


title: dog2_control_right

description: Library name: 4R


title: VC_snRNAseq-12_Animal5_Accessory_Basal__AP2_AP3_

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

library_source: transcriptomic single cell

data_processing:
FASTQ files were pre-processed with the 10x CellRanger pipeline
Human reads were aligned to reference genome GRCh38, rhesus macaque reads were aligned to reference genome Mmul_10, and Olive Baboon reads with aligned to refernce genome Panubis1.0.
Assembly: GRCh38, Mmul_10, and Panubis1.0
Supplementary files format and content: Raw FASTQ files and data processed with the 10x CellRanger pipeline with barcode, feature, and matrix files for each sample.

organism: Macaca mulatta

source_name: brain (amygdala)

extract_protocol:
For human samples, the amygdala was dissected from fresh frozen postmortem human tissue and 100 micron coronal sections of amygdala from fresh frozen postmortem human tissue were obtained by cryosectioning. For nonhuman primates, coronal brain blocks were flash-frozen immediately prior to tissue punches localized to specific amygdala subregions. All nuclei were isolated and barcoded with 10x Genomics Chromium.
Libraries were prepared using 10x Chromium Next GEM Single Cell 3’ v3.1 (dual-index) kit according to manufacturer's instructions.
single-nucleus RNA-sequencing

value: brain (amygdala)


title: VC_snRNAseq-12_Animal3_Central_Nucleus


title: P3 3hr

city: Rochester

first: Renzo

middle: Emanuel

last: Vera

state: Minnesota

address: 305 4th Ave SW

institute: Mayo Clinic

description: Library name: P3_2

data_processing:
RNA-seq FASTq files were processed and trimmed with Trim Galore 0.6.4 and cutadapt 2.10 with Python 3.6.5.
Read quality was evaluated with FastQC and aligned with MAPRseq v.2.0 and HG19 genome as reference.
Reads were assigned by FeatureCounts (Galaxy Version 1.6.4).
Assembly: HG19
Supplementary files format and content: normalized counts for all samples

source_name: pancreatic cancer cell line

growth_protocol: PANC-1 cells were cultured in DMEM + 10% FBS (10-040-CV). Cells were maintained at 37°C and 5% CO2.

extract_protocol:
RNA was extracted with TRIzol reagent and then isolated using Qiagen RNeasy kit per manufacturer instructions.
cDNA libraries were prepared using 200 ng of total RNA according to the manufacturer’s instructions for the Illumina TruSeq Stranded mRNA Sample Prep Kit.

treatment_protocol: For RNA-seq studies, PANC-1 cells were starved overnight with DMEM 1% FBS. Next, the cells were treated for 0, 3, and 24 h in DMEM media supplemented with 10% FBS and 10 µg/mL of collagen I.

value: pancreatic cancer cell line

tag: cell line

value: primary pancreatic ductal adenocarcinoma

value: WT

value: Collagen I treatment

tag: time


title: Spatial_Young_3dpi_rep2

description: Library name: B-19422

source_name: 10uM sagittal section from the midline of 8mm of spinal cord, centered on t17

value: Young


title: dog3_punctured_pbs_left

description: Library name: 5L


title: Spatial_Young_3dpi_rep1

description: Library name: A-19425

source_name: 10uM sagittal section from the midline of 8mm of spinal cord, centered on t16


title: dog2_control_left

description: Library name: 4L


title: VC_snRNAseq-9_Animal4_LV2


title: dog2_punctured_par2acs_right

description: Library name: 3R


title: P3 0hr

description: Library name: P3_1


title: Young_Uninj_rep2

description: Library name: 11A0516

data_processing:
Spatial - Sequences were aligned and filtered with the mm10-2020-A genome using Space Ranger V2.0.0. SP and S1 runs for each sample were combined. Passing reads recorded as over tissue were then loaded into R and processed as a Seurat object.  Single cell -  The resulting sequences were then aligned and filtered using the CellRanger 6.0.2 pipeline. Briefly, reads from FASTQ files were were aligned to the mm10-3.0.0 reference genome. Using the STAR splice-aware aligner, the reads were aligned and excluded if they mapped to <50% of an exonic sequence or contained single base substitution errors, then UMIs were removed. The final count matrix was generated containing all passing UMIs in each droplet.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values in a matrix file of genes by cells

molecule: cytoplasmic RNA

source_name: 8mm of spinal cord, centered on t15

value: 8mm of spinal cord, centered on t15

value: one unenriched whole-tissue sample combined with one astrocyte-enriched sample

value: Uninjured


title: P2 24hr

description: Library name: P2_4


title: PIM014

description: Library name: PIM014


title: Aged_Uninj_rep4

description: Library name: 9A0516

source_name: 8mm of spinal cord, centered on t14

value: 8mm of spinal cord, centered on t14


title: VC_snRNAseq-9_Animal4_LV1


title: VC_snRNAseq-9_Animal4_LD


title: dog2_punctured_par2acs_left

description: Library name: 3L


title: Aged_Uninj_rep2

description: Library name: 7A0513

source_name: 8mm of spinal cord, centered on t13

value: 8mm of spinal cord, centered on t13


title: P3 24hr

description: Library name: P3_4


title: dog1_control_right

description: Library name: 2R


title: P2 3hr

description: Library name: P2_2


title: VC_snRNAseq-9_Animal4_L-Comb


title: Aged_Uninj_rep1

description: Library name: 6A0513

source_name: 8mm of spinal cord, centered on t12

value: 8mm of spinal cord, centered on t12


title: VC_snRNAseq-9_Animal4_BV


title: VC_snRNAseq-12_Animal2_Central_Nucleus


title: P1 24hr

description: Library name: P1_4


title: P2 0hr

description: Library name: P2_1


title: VC_snRNAseq-9_Animal4_BD


title: dog1_control_left

description: Library name: 2L


title: P1 3hr

description: Library name: P1_2


title: Aged_3dpi_rep2

description: Library name: 4A0513

source_name: 8mm of spinal cord, centered on t10

value: 8mm of spinal cord, centered on t10

value: Aged


title: dog1_punctured_par2acs_right

description: Library name: 1R


title: dog1_punctured_par2acs_left

description: Library name: 1L


title: VC_snRNAseq-9_Animal4_B-Comb


title: P1 0hr

description: Library name: P1_1


title: VC_snRNAseq-9_Animal4_AB


title: primary tumor, validation cohort, YCC-105, 3' scRNA-seq

city: Seoul

first: IlSeok

last: Choi

address: 50, Yonsei-ro, Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

description: 10x Genomics 3'

data_processing:
Sequencing reads were aligned to the human reference genome (GRCh38) using Cell Ranger software (v6.0.0).
Assembly: GRCh38
Supplementary files format and content: CellRanger output .h5 file containing filtered gene by cell count data

source_name: colorectal adenocarcinoma

extract_protocol:
Single-cell isolation was performed using a Human Tumor Dissociation Kit (Miltenyi Biotec, USA) following the manufacturer’s instructions. Fresh surgical tissues were cut into small pieces (<1 mm3) and placed into a gentleMACS C Tube (Miltenyi Biotec, USA) containing a mixture of Enzyme H, Enzyme R, and Enzyme A in RPMI 1640 medium. The tube was then processed on a gentleMACS Dissociator (Miltenyi Biotec, USA) using the GentleMACS programs h_tumor_01 and h_tumor_02, each followed by a 30-minute incubation at 37°C with rotation. The dissociated tissues were filtered through a 70 μm MACS SmartStrainer (Miltenyi Biotec, USA) to achieve a single-cell suspension. The filtrate was centrifuged at 300 × g for 10 minutes at 4°C. The resultant cell pellet was resuspended in 4 mL of RPMI 1640 medium (Thermo Fisher Scientific, USA), and dead cells were removed using Ficoll-Paque PLUS (GE Healthcare, USA). The cells were subsequently washed and resuspended in PBS supplemented with 0.1% bovine serum albumin (BSA, Invitrogen, USA). Cell viability was assessed using the LIVE/DEAD™ Viability/Cytotoxicity Kit (Invitrogen, USA), and the single-cell suspension was further enriched for viability with a Dead Cell Removal Kit (Miltenyi Biotec, USA).
Single-cell suspensions were processed on a Chromium system (10x Genomics, USA). For the discovery cohort consisting of 24 samples, we prepared 5’ scRNA-seq libraries using the Chromium Next GEM Single Cell 5′ Library and Gel Bead Kit v1.1 (PN-1000165). For the validation cohort of 18 samples, 3’ scRNA-seq libraries were generated using the Chromium Next GEM Single Cell 3ʹ v3.1 Library and Gel Bead Kit v3.1 (PN-1000121). The libraries were sequenced on an Illumina NovaSeq 6000 for the 5’ scRNA-seq and an Illumina HiSeq 2000 for the 3’ scRNA-seq.

value: colorectal adenocarcinoma

tag: primary tumor_location

value: sigmoid

tag: msi

value: MSS

tag: kras

value: wild

tag: fusobacterium positivity

value: POS


title: Aged_3dpi_rep1

description: Library name: 1A0512

source_name: 8mm of spinal cord, centered on t8

value: 8mm of spinal cord, centered on t8

value: Female


title: DH12075-Leaf-rep3

city: Saskatoon

first: Isobel

last: Parkin

address: 107 Science Pl

country: Canada

institute: Agriculture and Agri-Food Canada

data_processing:
Raw RNA-seq data were filtered using Trimmomatic (version 0.32) with the following settings (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10; SLIDINGWINDOW:4:15; LEADING:15; TRAILING:15; MINLEN:55) to remove adapter and low-quality sequences. For expression profiling, clean reads were aligned to reference transcriptome using salmon (v1.10.0) and gene expression levels were summarized by tximport (version 1.30.0).
Assembly: Camelina sative (GCF_000633955.1); Brassica napus (DH12075 v3.1); Thlaspi arvense (GCA_911865555)
Supplementary files format and content: TPM_N99.csv, TPM_DH12075.csv, TPM_DH55.csv, and TPM_pennycress.csv, all files contain the TPM values summarized by tximport

organism: Brassica napus

source_name: Leaves

extract_protocol:
We collected the fully expanded cotyledons and true leaves from the young seedlings to extract their total RNA using the RNeasy plant mini kit (Qiagen) according to the manufacturer’s protocol.
The concentration and integrity of total RNA were examined by BioAnalyzer with RNA 6000 Nano Kit (Agilent). cDNA sequencing libraries were constructed according to the standard TruSeq RNA library preparation guide

value: Leaves

value: plant cell


title: HiC 72hr siATAT1 MOI5 Rep3

city: Chicago

first: Derek

last: Walsh

state: Illinois

address: 303 East Chicago Avenue, Ward 6165

department: Microbiology Immunology

institute: Northwestern University

description: Library name: HiC21

library_source: genomic

data_processing:
Samples were processed using nfcore/hic (v2.1.0) HiCPro pipeline with a concatinated hg38 (GCA_000001405.15_GRCh38) and TB40E (MW439039) genome.
hicpro2juicer was used to generate .hic files
Assembly: hg38+TB40E
Supplementary files format and content: .hic files for loading into Juicebox

molecule: genomic DNA

source_name: NHDF

growth_protocol: Cells used in this study were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM; Fisher Scientific) supplemented 2 mM L-glutamine, penicillin/streptomycin and 5% Fetal Bovine Serum (FBS) and incubated at 37°C and 5% CO2. Single donor primary normal human dermal fibroblasts (NHDFs) were isolated from human male neonatal foreskin (Lonza: CC-2509).

extract_protocol:
Cells were trypsinized, washed in PBS, and collected for Hi-C crosslinking and library prep. Approximately 1 million cells per Hi-C experiment were used.
The Arima Hi-C kit (#A410231) was used to generate Hi-C libraries. Breifly, in-situ HiC was performed by fixing cells with PFA. Samples were sheared to 400pb using Covaris and made into sequencing libraries using the NEB Ultra II DNA Library Prep Kit (#E7645S). Libraries were sequenced 2x150bp.

treatment_protocol: Cells were either mock infected or infected at an MOI of 5 with TB40E-UL99-mCherry for designated timepoints. For siRNA experiments, cells were infected 12hrs before siRNA treatment.

value: NHDF

value: Normal human fibroblasts

value: WT

value: siATAT1-B, MOI5


title: primary tumor, validation cohort, YCC-104, 3' scRNA-seq

description: 10x Genomics 3'

value: ascending

value: NEG


title: HiC 72hr siControl MOI5 Rep3

description: Library name: HiC19

value: siControl-A, MOI5


title: DH12075-Leaf-rep2


title: VC_snRNAseq-8_Animal3_LV

value: brain (amygdala)


title: primary tumor, validation cohort, YCC-103, 3' scRNA-seq

description: 10x Genomics 3'

value: colorectal adenocarcinoma

value: cecum


title: Aged_3dpi_rep3

description: Library name: 5A0513

source_name: 8mm of spinal cord, centered on t11

value: 8mm of spinal cord, centered on t11

value: one unenriched whole-tissue sample combined with one astrocyte-enriched sample

value: Aged


title: VC_snRNAseq-8_Animal3_LD


title: DH12075-COT-rep3

source_name: Cotyledons

value: Cotyledons


title: HiC 72hr siSUN1 MOI5 Rep3

description: Library name: HiC20

value: siSUN1-B, MOI5


title: primary tumor, validation cohort, YCC-102, 3' scRNA-seq

description: 10x Genomics 3'

value: Male

value: sigmoid

value: MSS

value: wild


title: VC_snRNAseq-8_Animal3_BV2


title: VC_snRNAseq-8_Animal3_LV3


title: Young_3dpi_rep1

description: Library name: 2A0512

source_name: 8mm of spinal cord, centered on t9

value: 8mm of spinal cord, centered on t9

value: Female

value: Young


title: primary tumor, validation cohort, YCC-097, 3' scRNA-seq

description: 10x Genomics 3'

value: NEG


title: DH12075-Leaf-rep1

value: Leaves

value: plant cell


title: DH12075-COT-rep2


title: primary tumor, validation cohort, YCC-087, 3' scRNA-seq

description: 10x Genomics 3'

value: colorectal adenocarcinoma

value: ascending

value: POS


title: VC_snRNAseq-8_Animal3_BV1

value: brain (amygdala)


title: VC_snRNAseq-8_Animal3_Bd_Bv


title: DH12075-COT-rep1


title: HiC 96hr MOI5 Rep2

description: Library name: HiC16

value: NHDF

value: Normal human fibroblasts

value: WT


title: HiC 72hr siATAT1 MOI5 Rep2

description: Library name: HiC18

value: siATAT1-B, MOI5


title: HiC 96hr MOI5 Rep1

description: Library name: HiC15


title: VC_snRNAseq-8_Animal3_BD


title: N99-Leaf-rep3


title: primary tumor, validation cohort, YCC-081, 3' scRNA-seq

description: 10x Genomics 3'


title: primary tumor, validation cohort, YCC-080, 3' scRNA-seq

description: 10x Genomics 3'

value: MSI-H


title: VC_snRNAseq-8_Animal3_AB__


title: N99-Leaf-rep2


title: HiC 72hr siATAT1 MOI5 Rep1

description: Library name: HiC11


title: HiC 72hr siSUN1 MOI5 Rep2

description: Library name: HiC17

value: siSUN1-B, MOI5


title: HiC 72hr siSUN1 MOI5 Rep1

description: Library name: HiC10


title: primary tumor, validation cohort, YCC-065, 3' scRNA-seq

description: 10x Genomics 3'

value: Male

value: sigmoid

value: MSS


title: N99-Leaf-rep1


title: HiC 72hr siControl MOI5 Rep1

description: Library name: HiC09

value: siControl-A, MOI5


title: N99-COT-rep3

value: Cotyledons


title: VC_snRNAseq-7_LateralVentralAP1_-1


title: primary tumor, validation cohort, YCC-074, 3' scRNA-seq

description: 10x Genomics 3'

value: Female

value: wild

value: NEG


title: N99-COT-rep2

value: plant cell


title: VC_snRNAseq-7_LateralDorsalAP1AP2_-8


title: primary tumor, validation cohort, YCC-064, 3' scRNA-seq

description: 10x Genomics 3'

value: colorectal adenocarcinoma

value: ascending


title: VC_snRNAseq-7_BasalVentralAP2_-5

value: brain (amygdala)


title: HiC 120hr MOI5 Rep2

description: Library name: HiC08

value: NHDF

value: Normal human fibroblasts


title: HiC 120hr Mock Rep2

description: Library name: HiC07

value: WT

value: Mock


title: VC_snRNAseq-7_BasalVentralAP1_-4


title: primary tumor, validation cohort, YCC-061, 3' scRNA-seq

description: 10x Genomics 3'

value: cecum

value: POS


title: HiC 72hr MOI5 Rep2

description: Library name: HiC06


title: VC_snRNAseq-7_LateralVentralAP2_-2


title: Leaf, NaCl stress, 14d, rep3

city: Kunming

first: mengjie

last: Zhang

address: Qingyun Street Panlong District

country: China

institute: southwest forestry university

data_processing:
Sequencing data were removed using Fastp to remove sequences with junctions at the 3' end and to remove Reads with average quality scores lower than Q20; the filtered Reads were compared to the reference genome using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml). Data quality was checked using FastaQC to ensure that all transcriptome data had a Q value greater than 30, resulting in high-quality Clean Data.Read Count values were statistically compared to each gene using HTSeq and normalised using FPKM values.
Assembly: Using the Citrus sinensis genome as a reference genome

organism: Citrus sinensis

source_name: leaf

growth_protocol: Citrus sinensis seedling

extract_protocol:
0.5g of each sample from the treatment and control were sent to Suzhou Panomic Biomedical Technology Co. for transcriptome sequencing.
Filtered Reads were compared to the reference genome using the upgraded HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml ) software for TopHat2.
HISAT2 uses an improved BWT algorithm for library construction. Default parameters are used for non-strand-specific libraries, while strand-specific libraries require the library type to be specified (i.e., use --rna-strandness RF for first, --rna-strandness FR for second).

treatment_protocol: Sweet orange histocultured seedlings treated at 0.01 mg/L boron for 25 days

value: leaf

value: Add 2% NaCl


title: VC_snRNAseq-7_BasalDorsalAP1_-3B

source_name: brain (amygdala)


title: primary tumor, validation cohort, YCC-050, 3' scRNA-seq

description: 10x Genomics 3'

value: Male

value: rectum

value: MSS


title: primary tumor, validation cohort, YCC-040, 3' scRNA-seq

description: 10x Genomics 3'

value: Female


title: HiC 72hr Mock Rep2

description: Library name: HiC05


title: Leaf, NaCl stress, 14d, rep2


title: VC_snRNAseq-7_BasalDorsalAP1_-3A


title: Leaf, NaCl stress, 14d, rep1


title: N99-COT-rep1

value: Cotyledons


title: HiC 120hr MOI5 Rep1

description: Library name: HiC04


title: primary tumor, validation cohort, YCC-038, 3' scRNA-seq

description: 10x Genomics 3'

value: sigmoid

value: NEG


title: primary tumor, validation cohort, YCC-036, 3' scRNA-seq

description: 10x Genomics 3'

value: colorectal adenocarcinoma

value: ascending


title: HiC 72hr MOI5 Rep1

description: Library name: HiC02

value: NHDF


title: HiC 120hr Mock Rep1

description: Library name: HiC03

value: Normal human fibroblasts


title: VC_snRNAseq-7_AccBasalAP1AP2_-7

value: brain (amygdala)


title: Leaf blades, sterile water, 14d,  rep2

value: No NaCl was added


title: LIB210527RC_AB_1B


title: primary tumor, validation cohort, YCC-020, 3' scRNA-seq

description: 10x Genomics 3'

value: rectosigmoid junction

value: wild


title: LIB210527RC_AB_1A


title: TOV-112D cells, CPT, 24 hours, biological replicate 3

status: Public on Jul 22 2025

city: Tsuruoka-shi

first: Yuki

last: Iimori

address: 246-2 Kakuganji Aza, Mizukami

country: Japan

institute: Keio University

description: Library name: CPT_24h_biol rep 3

data_processing:
The reference used in proteomic analysis (uniprot human reference) was first mapped from UniProt IDs to RefSeq IDs using an ID mapping tool. Subsequently, the Entrez Programming Utilities (https://www.ncbi.nlm.nih.gov/books/NBK25497/) were employed to construct a reference for RNA-seq quantification. Samples collected at 10 hours and 24 hours after treatment were analyzed separately. Transcript abundance was quantified using Kallisto (v0.51.1). Differential expression analysis for RNA-seq datasets was performed using the R package edgeR (v4.4.1).
Assembly: Custom transcriptome reference built by mapping UniProt human reference (downloaded in April 2023) to RefSeq transcript IDs using UniProt ID mapping tools and NCBI Entrez Programming Utilities.
Supplementary files format and content: Tab-delimited text files containing gene-level raw counts and TPM values per sample (genes in rows)
Supplementary files format and content: Tab-delimited text files containing differential expression results from edgeR (log2FC, P-value, FDR) with genes in rows.

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin-amphotericin B at 37 °C in 5% CO2.

extract_protocol:
Total RNAs were isolated using the Monarch Total RNA Miniprep Kit (New England Biolabs).
Poly(A)+ RNA was purified using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) according to the manufacturer’s instructions. RNA-seq libraries were prepared using a NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs).

value: ovarian endometrioid adenocarcinoma

value: Transfection reagent treatment, followed by 100 nM Camptothecin for 24 hours


title: TOV-112D cells, CPT+tRNALeu(TAA), 24 hours, biological replicate 3

description: Library name: CPT_TAA_24h_biol rep 3

value: Transfection reagent and 10 nM tRNALeu(TAA), followed by 100 nM Camptothecin for 24 hours


title: Leaf blades, sterile water, 14d,  rep1

value: leaf


title: TOV-112D cells, CPT+tRNALeu(TAA), 24 hours, biological replicate 2

description: Library name: CPT_TAA_24h_biol rep 2


title: TOV-112D cells, CPT, 24 hours, biological replicate 2

description: Library name: CPT_24h_biol rep 2


title: TOV-112D cells, CPT, 24 hours, biological replicate 1

description: Library name: CPT_24h_biol rep 1


title: TOV-112D cells, CPT+tRNALeu(TAA), 24 hours, biological replicate 1

description: Library name: CPT_TAA_24h_biol rep 1


title: primary tumor, validation cohort, YCC-078, 3' scRNA-seq

description: 10x Genomics 3'

value: MSS


title: HiC 72hr siControl MOI5 Rep2

description: Library name: HiC12

value: WT

value: siControl-A, MOI5


title: TOV-112D cells, DMSO, 24 hours, biological replicate 3

description: Library name: DMSO_24h_biol rep 3

value: Transfection reagent treatment, followed by DMSO for 24 hours


title: TOV-112D cells, CPT+tRNALeu(TAA), 10 hours, biological replicate 3

description: Library name: CPT_TAA_10h_biol rep 3

value: Transfection reagent and 10 nM tRNALeu(TAA), followed by 100 nM Camptothecin for 10 hours


title: TOV-112D cells, CPT+tRNALeu(TAA), 10 hours, biological replicate 1

description: Library name: CPT_TAA_10h_biol rep 1


title: TOV-112D cells, CPT+tRNALeu(TAA), 10 hours, biological replicate 2

description: Library name: CPT_TAA_10h_biol rep 2


title: TOV-112D cells, DMSO, 24 hours, biological replicate 2

description: Library name: DMSO_24h_biol rep 2


title: TOV-112D cells, DMSO, 24 hours, biological replicate 1

description: Library name: DMSO_24h_biol rep 1


title: Leaf blades, sterile water, 14d,  rep3


title: TOV-112D cells, CPT, 10 hours, biological replicate 1

description: Library name: CPT_10h_biol rep 1

value: Transfection reagent treatment, followed by 100 nM Camptothecin for 10 hours


title: TOV-112D cells, CPT, 10 hours, biological replicate 2

description: Library name: CPT_10h_biol rep 2


title: TOV-112D cells, DMSO, 10 hours, biological replicate 3

description: Library name: DMSO_10h_biol rep 3

value: Transfection reagent treatment, followed by DMSO for 10 hours


title: HiC 72hr Mock Rep1

description: Library name: HiC01

value: NHDF

value: Mock


title: TOV-112D cells, DMSO, 10 hours, biological replicate 1

description: Library name: DMSO_10h_biol rep 1


title: TOV-112D cells, DMSO, 10 hours, biological replicate 2

description: Library name: DMSO_10h_biol rep 2


title: PBMC6 activated, TCR

city: Bethesda

first: Farid

last: Rashidi Mehrabadi

address: Building 37, Room 3044A

institute: NCI

description: Library name: SCAF4131t_PBMC6_post

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v8.0.1 (https://support. 10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Downstream analysis, including preprocessing, clustering, annotation, and visualization were done with Scanpy (v1.10.1) following best-practice guidelines. For quality control, we used stringent criteria in which cells with over 15% mitochondrial, over 2% hemoglobin, or under 5% ribosomal gene counts were excluded. Ambient mRNA contamination was removed using SoupX (v1.6.0). Doublets were excluded with scDblFinder (v1.8.0), ultimately removing 8,811 cells and retaining 25,149 cells for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
The sample concentration and viability were assessed using the LunaFX7 fluorescence cell counter and diluted as necessary with PBS + 0.04% BSA. The cellular samples were loaded in the lanes according to the 10X Genomics Chromium Next GEM Single Cell 5’v3 (Dual Index) User Guide with a single capture lane per sample targeting a recovery of 12,000 cells per lane. Cell partitioning completed successfully with uniform emulsion consistency and the reverse transcription PCR was run overnight. All subsequent steps of library preparation, TCR enrichment, and quality control were performed as described in 10X Genomics 5’ v3 Single Cell User Guide. Libraries were prepared using the 10X validated automation platform, Chromium Connect.
PBMCs from PBMC6 and PBMC12 were included in the single-cell studies. For peptide-naïve PBMCs, PBMC6 and PBMC12 were thawed from frozen and incubated at a high density (1x10^7 /mL) one day before single-cell capture. For peptide-activated PBMCs, 5x10^6 PBMCs underwent weekly peptide stimulation as described earlier, with a slight difference in the duration of stimulation (6 weeks for PBMC12 and 5 weeks for PBMC6). Three days after the final peptide stimulation, the PBMCs were thoroughly mixed, and a portion of the cells was harvested for single-cell studies. The scRNA and scTCRseq libraries were sequenced two runs on a NovaSeq X-plus system, using read lengths of 28 bp for read 1, 10 bp for index 1, 10 bp for index 2, and 90 bp for read 2.

value: Blood

value: PBMC

value: Immune cells


title: PBMC12 naïve, TCR

description: Library name: SCAF4132t_PBMC12_pre


title: PBMC12 activated, TCR

description: Library name: SCAF4133t_PBMC12_post


title: PBMC6 naïve, TCR

description: Library name: SCAF4130t_PBMC6_pre


title: PBMC12 activated, GEX

description: Library name: SCAF4133_PBMC12_post


title: PBMC6 activated, GEX

description: Library name: SCAF4131_PBMC6_post


title: A549 Cas9 Cell RNASeq

city: New Haven

first: Yubao

last: Cheng

state: Connecticut

address: 333 Cedar Street, 387A: Nathan Smith Bldg

institute: Yale University

description: Library name: A549 Cas9 Cell RNASeq

data_processing:
Quality control and adapter trimming were performed using Fastp109 (v0.24.0). Cleaned reads were aligned to the human reference genome GRCh38 using HISAT2110 (v2.2.1). The resulting alignments were sorted and indexed with SAMtools111 (v1.19) to generate BAM files for expression quantification. FPKM values were calculated using Cufflinks112 (v2.2.1), with gene annotations provided by the GENCODE Release 46 (GRCh38.p14) GTF file.
Assembly: GENCODE Release 46
Supplementary files format and content: Text file with gene FPKM

source_name: NSCKC Adenocarcinoma

growth_protocol: A549-Cas9 cells were cultured in F-12K media (Corning, 10-025-CV) supplemented with 15% FBS (VWR, 97068-091) and 1% Pen-Strep (Thermo Fisher Scientific, 15140122) at 37°C in 5% CO2.

extract_protocol:
A549-Cas9 cells were harvested for total RNA extraction. RNA was extracted using the RNeasy Mini Kit (QIAGEN, Cat. 74104). Total RNA quality is determined by nanodrop, based on A260/A280 and A260/A230 ratios.
RNA-Seq library was then prepared using the KAPA RNA HyperPrep Kit with RiboErase (Roche, Cat. KR1351), which includes ribosomal RNA depletion.

value: NSCKC Adenocarcinoma

value: Cancer cell

value: Cas9 protein expressing

value: No


title: PBMC12 naïve, GEX

description: Library name: SCAF4132_PBMC12_pre


title: Control Mesenchymal stem cell-derived extracellular vesicles

city: 달성군

first: Jun-Kook

last: Park

state: 대구광역시

address: 대구광역시 테크노북로

institute: DGIST

description: Library name: C-MEV

data_processing:
The data were analyzed using the Bowtie2 software tool to generate a bam file (alignment file). Mapping was based on the mature miRNA sequence. Read counts mapped to the mature miRNA sequences were extracted from the alignment file using the bed tool (version 2.25.0) and Bioconductor, which uses the R (version 3.2.2) statistical programming language (R Development Core Team, 2011). These read counts were used to assess the miRNA expression levels, with comparisons between samples performed using the quantile normalization method. miRWalk 2.0 was used for miRNA target exploration. Data mining and visualization were performed using ExDEGA (Ebiogen Inc., Republic of Korea). GO (Gene Ontology) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed for target genes using the online computational resource DIANA-miRPath v4.0 with target selection from TargetScan v.8.0 (26).
Assembly: mirBase
Supplementary files format and content: A XLSX with fold change, normalized data, raw data, etc

source_name: Mesenchymal stem cell

extract_protocol:
RNA was isolated from EVs using TRIzol LS reagent (10296028; Invitrogen; Thermo Fisher Scientific) according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 bioanalyzer equipped with an RNA 6000 Nano Chip (Agilent Technologies, Santa Clara, CA, USA). RNA quantification was performed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific).
A small RNA library was prepared using the NEBNext Multiplex Small RNA Library Prep kit (New England Biolabs, Ipswich, MA, USA) according to the manufacturer's protocol. To construct the library, cDNA synthesis was initiated by adaptor ligation using 1 μg of total RNA from each sample, followed by reverse transcription using adaptor-specific primers. The library was amplified by PCR and purified using the QIAquick PCR Purification kit (Qiagen, Hilden, Germany) and AMPure XP beads (Beckman Coulter). Then, the yield and size distribution of the small RNA libraries were analyzed using an Agilent 2100 Bioanalyzer alongside a high-sensitivity DNA assay (Agilent Technologies, USA). High-throughput sequencing was performed by single-ended 75 sequencing using the NextSeq550 system (Illumina, San Diego, CA, USA).

value: Mesenchymal stem cell


title: TOV-112D cells, CPT, 10 hours, biological replicate 3

description: Library name: CPT_10h_biol rep 3

value: ovarian endometrioid adenocarcinoma


title: Primed Mesenchymal stem cell-derived extracellular vesicles

description: Library name: P-MEV

value: stimulated them with IFN-γ and TNF-α


title: HUT2365, wheat bran/soy bean, day3, replicate B

city: Khlong Luang

first: Wuttichai

last: Mhuantong

state: Pathum Thani

address: National Center for Genetic Engineering and Biotechnology (BIOTEC)

country: Thailand

institute: BIOTEC

data_processing:
The raw reads were processed using FASTP software. Clean reads were obtained from removing low quality reads from raw data using default parameters (the quality score cutoff of 20).
The reads after quality control were then mapped to respective genomes of the three A. aculeatus constructed in our earlier study (Mhuangthong et al. 2021; https://doi.org/10.3389/fbioe.2020.607176), using HISAT2 version 2.1.0. The Picard Tool (https://broadinstitute.github.io/picard/) was used to mark and remove duplicates (https://broadinstitute.github.io/picard/). The alignedment reads were then assembled and quantified for the relative transcript estimation using StringTie software (Pertea et al. 2015).
Assembly: The genomes of three A. aculeatus strains were completely sequenced using the PacBio RS II platform (Pacific Biosciences, USA), giving the total circular consensus sequencing of 345.3 – 463.3 Mb. The final genome sizes after assembly were between 36.0-37.7 Mb, similar to the size (36.01 Mb) of the most closely-related publicly available genome A. aculeatus ATCC16872 (Mhuangthong et al. 2021; https://doi.org/10.3389/fbioe.2020.607176)
Supplementary files format and content: normalizedReadCount.csv

organism: Aspergillus aculeatus

growth_protocol: Fungal mycelium cultured for 72 and 144 hrs in an aerobic cultivation condition at 30°C.

extract_protocol:
RNA was extracted following the Tri Reagent® protocol (MRC, USA). On-column DNase digestion kit (Qiagen, Germany) was used to further remove DNA traces.
RNA-seq library preparation and sequencing were performed through service by Macrogen (Korea). Ribosomal RNA was removed from 10 μg of total RNA using the Ribominus™ Eukaryotic kit (Life Technologies, USA). The RNA was enriched using the Absolutely mRNA Purification kit (Agilent Technologies, USA), and further quantified by BioAnalyzer 2100 (Agilent Technologies, USA), before cDNA library construction. The cDNA libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA). Illumina paired-end adapters and barcode sequences were ligated onto the cDNA fragments. The quality and quantity of the libraries were then assessed, before being sequenced using the Illumina HiSeq2000 platform (Illumina, USA).

treatment_protocol: The three A. aculeatus strains were investigated for their relative transcription levels under different growth media across two key time points (Day-3 and Day-6), and related to their phenotyppes in terms of cellulolytic enzyme activities

tag: strain

tag: medium

value: wheat bran/soy bean (WS)

value: Day 3

tag: biological replicate

value: B


title: HUT2365, glucose, day6, replicate A

value: glucose (G)

value: Day 6

value: A


title: HUT2365, wheat bran/soy bean, day6, replicate A


title: HUT2365, wheat bran/soy bean, day3, replicate A


title: HUT2365, glucose, day3, replicate A


title: HUT2365, glucose, day6, replicate B


title: HUT2365, glucose, day3, replicate B


title: BCC199, wheat bran/soy bean, day3, replicate B


title: BCC199, glucose, day6, replicate B


title: BCC199, glucose, day3, replicate B


title: BCC199, wheat bran/soy bean, day3, replicate A


title: BCC199, wheat bran/soy bean, day6, replicate A


title: BCC199, glucose, day3, replicate A


title: BCC199, glucose, day6, replicate A


title: BCC56535, wheat bran/soy bean, day6, replicate B


title: BCC56535, glucose, day6, replicate B


title: BCC56535, wheat bran/soy bean, day3, replicate B


title: PBMC6 naïve, GEX

description: Library name: SCAF4130_PBMC6_pre

tag: tissue


title: BCC56535, wheat bran/soy bean, day3, replicate A


title: HUT2365, wheat bran/soy bean, day6, replicate B


title: BCC56535, glucose, day6, replicate A


title: BCC56535, wheat bran/soy bean, day6, replicate A


title: BCC56535, glucose, day3, replicate B


title: EX-1-385_Pre_Anesthesia

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description: Library name: lib91781

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.  The FASTQs were aligned to the GRCh38 human reference genome, using STAR v.2.4.2a and gene counts were generated using htseq-count.  QC and metrics analysis was performed using the Picard family of tools (v1.134).
Assembly: GRCh38.91
Supplementary files format and content: csv file voom normalized counts

source_name: Whole Blood

extract_protocol:
Whole blood was collected in Tempus Blood RNA Tubes (ThermoFisher), and RNA was extracted using MagMax for Stabilized Blood Tubes RNA Isolation Kit, followed by globin reduction using GlobinClear Human (ThermoFisher ).  To generate sequencing libraries, total RNA 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).  Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer (Illumina) with paired-end 59-base reads, with a target depth of 5 million reads per sample.

value: Whole Blood

tag: tube

value: Pre-Sevo 9ml Tempus for RNA Box

tag: anesthesia status

value: F

tag: median cv_coverage

tag: mapped reads


title: EX-1-383_Post_Anesthesia

description: Library name: lib91779

value: 9ml Tempus for RNA Box

tag: Sex


title: EX-1-386_Post_Anesthesia

description: Library name: lib91784


title: BCC199, wheat bran/soy bean, day6, replicate B


title: EX-1-386_Pre_Anesthesia

description: Library name: lib91783


title: EX-1-383_Pre_Anesthesia

description: Library name: lib91778


title: EX-1-382_Post_Anesthesia

description: Library name: lib91777


title: EX-1-381_Pre_Anesthesia

description: Library name: lib91774


title: EX-1-381_Post_Anesthesia

description: Library name: lib91775


title: EX-1-380_Post_Anesthesia

description: Library name: lib91773

value: M


title: EX-1-379_Pre_Anesthesia

description: Library name: lib91770


title: EX-1-379_Post_Anesthesia

description: Library name: lib91771


title: EX-1-378_Pre_Anesthesia

description: Library name: lib91768


title: EX-1-378_Post_Anesthesia

description: Library name: lib91769


title: EX-1-376_Post_Anesthesia

description: Library name: lib91767


title: EX-1-376_Pre_Anesthesia

description: Library name: lib91766


title: hNECs, delta_bteA::bteA_infected, 24h, rep2

city: Prague

first: Martin

last: Zmuda

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Microbiology of the Czech Academy of Sciences

description: Library name: comp.BteA3

data_processing:
Sequencing was performed on the NextSeq 2000 Illumina platform with 122 bp single-end reads.  Raw sequencing reads were processed with the nf-core/RNAseq pipeline (version 3.10.1) using the default settings for STAR + Salmon (https://nf-co.re/rnaseq/3.18.0). Reads were mapped to the ENSEMBL reference genome and transcriptome (Homo_sapiens GRCh38.dna_sm.primary assembly genome and GRCh38.110 transcriptome.
Assembly: GRCh38
Supplementary files format and content: tab-delimited salmon.merged.gene_tpm.tsv file contains tpm for each sample
Supplementary files format and content: tab-delimited salmon.merged.gene_counts.tsv contains raw gene counts for each sample

source_name: primary nasal epithelial cells, air-liquid interface culture, day 30

growth_protocol: Air-liquid interface cultures of primary human nasal epithelial cells (hNECs) were prepared as previously described in Malcova I, Kamanova J. 2024. Bsp22 protein polymerization drives dynamic adaptation of the Bordetella type III secretion system injectisome. bioRxiv doi:10.1101/2024.03.04.583273:2024.03.04.583273

extract_protocol:
hNECs on the Transwell membranes were lysed in situ using 0.3 mL of RLT lysis solution from the Qiagen RNeasy plus micro kit (Cat# 74134) per membrane. Homogenization was carried out by repeated pipetting. Total RNA was then isolated according to the instructions of the RNeasy plus micro kit (Qiagen, Cat# 74134) using single Transwell membrane per sample. During the RW1 wash step, 80 µl of the RDD buffer containing 10 µl of DNase I solution was pipetted directly onto the spin column, and incubated 15 minutes at room temperature. RNA concentration and quality were assessed using the DS-11 spectrophotometer (DeNovix), and RNA integrity was analyzed using an Agilent Bioanalyzer 2100 (Agilent Technologies).
The libraries were prepared using the KAPA mRNA HyperPrep Kit with polyA selection (Roche, Cat#08098123702), with 300 ng of RNA as input per sample. Only samples with a minimum RNA integrity number (RIN) of 6 were used in library preparation.

treatment_protocol: Differentiated air-liquid interface cultures of hNECs were infected apically with 3×10^6 CFU of B. pertussis B1917 wild-type, a BteA deletion mutant, or a BteA-complemented strain, using 200 μL of ALI medium. Control uninfected cells were treated with ALI medium only. After 6 hours, the medium was carefully removed without washing. The cultures were then further incubated and processed for RNA extraction 24 hours post-infection.

tag: cell type

value: primary cells

tag: treatment

value: infected with BteA complemented delta-bteA::bteA strain of B.pertussis B1917, MOI 10:1, 24 h


title: hNECs, delta_bteA_infected, 24h, rep1

description: Library name: dBteA1

value: primary nasal epithelial cells, air-liquid interface culture, day 30

value: infected with delta-bteA mutant of B. pertussis B1917, MOI 10:1, 24 h


title: hNECs, delta_bteA::bteA_infected, 24h, rep3

description: Library name: comp.BteA4


title: hNECs, delta_bteA_infected, 24h, rep3

description: Library name: dBteA3


title: hNECs, delta_bteA::bteA_infected, 24h, rep1

description: Library name: comp.BteA2


title: hNECs, WT-infected, 24h, rep2

description: Library name: WT3

value: infected with wild type B.pertussis B1917, MOI 10:1, 24 h


title: BCC56535, glucose, day3, replicate A


title: hNECs, delta_bteA_infected, 24h, rep2

description: Library name: dBteA2


title: hNECs, WT-infected, 24h, rep1

description: Library name: WT2


title: EX-1-382_Pre_Anesthesia

description: Library name: lib91776

tag: age


title: EX-1-380_Pre_Anesthesia

description: Library name: lib91772


title: hNECs, uninfected, 24h, rep1

description: Library name: Non.infected_1

value: uninfected


title: hNECs, uninfected, 24h, rep2

description: Library name: Non.infected_3


title: EX-1-384_Post_Anesthesia

description: Library name: lib91780


title: Small intestinal dendritic cells from WT mice

city: Aachen

first: Hieu

middle: Trong

last: Nguyen

address: Pauwelstrasse 30

country: Germany

institute: RWTH Aachen University Hospital

description: Library name: SI LP DCs WT

data_processing:
FASTQ files were aligned and processed with CellRanger pipeline, default parameters.
Assembly: mmu10
Supplementary files format and content: h5

source_name: small intestine

extract_protocol:
SI LP cells were isolated from 5 female C57BL/6 (WT) mice mice and dendritic cells (DCs) were identified as live, single cells,  MHCII+ ,CD11c+, CD64-, B220-, CD19-, Nk1.1- and sorted using a FACSAria Ilu (BD).
Chromium Next GEM Chip K and the Next GEM Single Cell 5’ Kit v2, 16rxns PN-1000263 were used for GEM generation and library was prepared using the Library Construction Kit according  to the Chromium Next GEM Single Cell 5-v2 User guide (10x Genomics). Sequencing was performed on a NextSeq 2000 sequencing system (Illumina).

value: small intestine

value: dendritic cells

tag: genotype

value: WT


title: Mouse BMDCs treated with 5A-MPLA #2 for 24 h

city: Boston

first: Hyoung-Soo

last: Cho

state: Massachusetts

address: 77 Avenue Louis Pasteur, NRB 1058

department: Immunology

institute: Harvard Medical School

description: Library name: Sample 8 (S8)

data_processing:
To perform the RNA Sequencing analysis reads (FASTQ format) were first inspected for quality using FastQC and Qualimap.
Second reads were then mapped to the mouse genome (mm10 assembly) using the STAR Aligner.
Third the aligned reads had their lanes combined, and sorted using SamTools.
Forth the sorted read files were counted using HTSEQ Count using the name and union flags.
Finally, the gene expression count files were processed using DESeq2 in order to determine which genes were differentially expressed.
Assembly: mm10
Supplementary files format and content: Excel (.xlsx) files include RPKM values for each sample

source_name: Bone marrow

growth_protocol: BM precursors were isolated from the tibia and femur of WT B6 mice by flushing the cavity of marrow with serum-free RPMI 1640 medium (Gibco). Red blood cells (RBCs) from the harvested BM cells were lysed with ACK Lysing Buffer (Invitrogen), washed with complete medium, and then stained with 0.4% Trypan Blue (Invitrogen) for cell counting. 2.0 x 106 cells of BM cells were plated in 10 cm tissue culture plate and cultured for 9 days in the presence of 20 ng/mL murine GM-CSF (PeproTech) while the medium was changed in every 3 days. Loosely attached or semi-suspended cells in the plate were collected and counted.

extract_protocol:
DCs treated with lipid A analogs were harvested and centrifuged for 1 min at 18,000 rpm at 4°C. After discarding supernatant, cell pellets were treated with 500 μL of TRIzol (Invitrogen) and incubated for 5 min at RT, then for 1 h or overnight at -80°C. Thawed samples were treated with 100 μL of chloroform and then vigorously vortexed for 15 sec. After incubation at RT for 5 min, the samples were centrifuged 15 min at 18,000 rpm at 4°C, and the aqueous fractions were collected into new tubes in ice. 1.0 μL of Glycoblue Coprecipitant (Invitrogen) was treated to each tube, and 250 μL of isopropanol was treated to each sample. After incubation for 1 h at -80°C, the samples were centrifuged for 20 min at 18,000 rpm at 4°C. Supernatants were discarded, and the pellets were washed with 500 μL of 75% ice-cold ethanol. After centrifugation, the pellets were air-dried for 1 h and resuspended with nuclease-free water (Invitrogen).
RNA library was prepared using NEBNext Ultra II Directional RNA Libaray Prep Kit for Illumina by following the manufacturer's protocol.

treatment_protocol: Synthetic lipid A analogs (1.0 μg/mL) were treated to the BDMC culture for 24 h.

value: Bone marrow

tag: cell line

value: Primary cells

value: Mouse BMDCs


title: Mouse BMDCs treated with 6A-DPLA #1 for 24 h

description: Library name: Sample 11 (S11)


title: EX-1-385_Post_Anesthesia

description: Library name: lib91782

value: Whole Blood


title: Mouse BMDCs treated with 4A-MPLA #2 for 24 h

description: Library name: Sample 6 (S6)


title: hNECs, uninfected, 24h, rep3

description: Library name: Non.infected_4


title: Mouse BMDCs treated with 3A-MPLA #2 for 24 h

description: Library name: Sample 4 (S4)


title: Mouse BMDCs treated with 4A-MPLA #1 for 24 h

description: Library name: Sample 5 (S5)


title: Mouse BMDCs treated with 3A-MPLA #1 for 24 h

description: Library name: Sample 3 (S3)


title: Mouse BMDCs treated with Control #1 (PBS) for 24 h

description: Library name: Sample 1 (S1)

value: PBS (Control)


title: Mouse BMDCs treated with Control #2 (PBS) for 24 h

description: Library name: Sample 2 (S2)


title: hNECs, WT-infected, 24h, rep3

description: Library name: WT4


title: muscle, PH238, week 16, rest

city: Dayton

first: Madhavi

last: Kadakia

address: 3640 Colonel Glenn Hwy

department: Biochemistry and Molecular Biology

institute: Wright State University

description:
PH238w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

library_source: other

data_processing:
Data processing performed in Partek Flow v10.0.21.0706
Reads were trimmed to a fixed length based on an average PHRED quality score greater than 20.
Trimmed reads were alighed to miRbase v21/hg38 using Bowtie aligner (seed mismatch =1, seed length = 10) and quantitated using miRBase v21.
Reads were normalized using the Trimmed Mean of M values (TMM) normalization method with an offset of 1.0.
Assembly: miRBase v21 of the hg38 (GRCh38) assembly.
Supplementary files format and content: tab-delimited text files listing raw read counts for each sample
Supplementary files format and content: tab-delimited text files listing TMM-normalized read counts for each sample

molecule: other

source_name: vastus lateralis muscle

extract_protocol:
Muscle: Total RNA isolated using mirVana Paris Kit (Fisher); Serum exosomes: Exosomes isolated using Total Exosome Isolation from Serum Kit (Life Tech) and exosomal RNA purified using the Total Exosome RNA and Protein Isolation Kit (Life Tech).  XX RNA was used for construction of sequencing libraries.
cDNA was barcoded with IonExpress RNA-Seq Barcode 1-16 kit (Life Tech). 7.5picomoles each of 8-10 barcoded libraries were pooled and clonally amplified onto IonSphere Particles and enriched using the OneTouch2 (Life Tech).

treatment_protocol: All participants completed 12 weeks of either TRAD or HITT exercise followed by a 4 week detraining period.

value: vastus lateralis muscle

tag: participant id

value: TRAD

tag: week

value: week 16

tag: time

value: rest

value: Female


title: SUM149 treated with gapmer 4,,replicate 3

type: RNA

city: Halifax

first: Paola

last: Marcato

address: 5850 College street

department: Pathology

institute: Dalhousie university

hyb_protocol: Hybridized to Affymetrix Human Gene 2.0 ST, 16 hr at 45°C

scan_protocol: Affymetrix GeneChip Scanner 3000(Scanner#4)

data_processing: Expresion Console

label: biotin

source_name: Wildtype

label_protocol: Sample preparaton with Affymetrix WT PLUS Kit

growth_protocol: SUM149 cells were cultured in Ham’s F-12 Nutrient Mix (F-12; Life Technologies, Life Technologies, ThermoFisher Scientific) supplemented with 5% FBS, AA, HEPES buffer, 1ug/mL hydrocortisone (Millipore Sigma, Mississauga, Canada), and 5ug/mL human insulin (Millipore Sigma) at 37oC, with 5% CO2

extract_protocol: Cells were collected in TRIzol and RNA purified using a PureLink RNA kit (Invitrogen Thermo Fisher Scientific) following the manufacturer’s instructions.

treatment_protocol: SUM149 cells were treated for 48 hours with 15nM screening-grade modified antisense oligonucleotices GapmeRs, (Qiagen) admixed with TransIT-BrCa (MS Biolnyx) as per the manufacturer’s instructions.

tag: tumor type

value: TNBC


title: muscle, PH238, week 12, pre

description:
PH238w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 12

value: pre


title: muscle, PH238, week 0, 24hr

description:
PH238w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 0


title: Mouse BMDCs treated with 6A-DPLA #2 for 24 h

description: Library name: Sample 12 (S12)


title: muscle, PH238, week 12, 24hr

description:
PH238w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH238, week 0, pre

description:
PH238w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH237, week 16, rest

description:
PH237w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: HITT

value: Male


title: muscle, PH237, week 12, pre

description:
PH237w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH238, week 12, 3hr

description:
PH238w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH238, week 0, 3hr

description:
PH238w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH237, week 0, pre

description:
PH237w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH237, week 12, 24hr

description:
PH237w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH237, week 0, 24hr

description:
PH237w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: SUM149 treated with negative  control gapmer ,replicate 3

description: SUM149 treated with control gapmer ,replicate 3


title: muscle, PH229, week 16, rest

description:
PH229w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH237, week 0, 3hr

description:
PH237w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: SH1

city: Guangzhou

first: Mei

last: Song

address: Zhongshan No.2 Road 1th, Nonglin Street

institute: Sun Yat-sen University

description: Library name: Sample 4

data_processing:
Base-calling was performed with the BGISEQ-500 software.
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were alignment to the reference genome, GRCh38.p13 using HISAT2 (v2.1.0).
Bowtie2 (2.3.4.3) was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: csv file includes FPKM, TPM and read_count values for each sample and each gene

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (#RC112-01, Vazyme), according to manufacturer’s instructions.
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads, then fragmented. Then cDNA were sythesized, added A and adaptor ligation, and put into PCR system. Finally, PCR products were circularized and single-stranded circle DNA molecules were replicated via rolling cycle amplificationa to generate a DNA nanoball (DNB), which were then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: colon cancer cells

value: UBR5 knockdown


title: SUM149 treated with gapmer 3 ,replicate 3


title: SUM149 treated with gapmer 3 ,replicate 1


title: PL3

description: Library name: Sample 3

value: WT


title: SUM149 treated with gapmer 4 ,replicate 2


title: SUM149 treated with gapmer 3 ,replicate 2


title: muscle, PH237, week 12, 3hr

description:
PH237w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: Mouse BMDCs treated with 5A-MPLA #1 for 24 h

description: Library name: Sample 7 (S7)

value: Bone marrow

value: Primary cells

value: Mouse BMDCs


title: SUM149 treated with negative control gapmer ,replicate 1

description: SUM149 treated with control gapmer ,replicate 1


title: SH3

description: Library name: Sample 6


title: SH2

description: Library name: Sample 5


title: muscle, PH229, week 12, pre

description:
PH229w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: vastus lateralis muscle


title: SUM149 treated with gapmer 4,replicate 1


title: PL2

description: Library name: Sample 2


title: PL1

description: Library name: Sample 1


title: muscle, PH229, week 12, 24hr

description:
PH229w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH229, week 12, 3hr

description:
PH229w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH229, week 0, 3hr

description:
PH229w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH229, week 0, pre

description:
PH229w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Tim3_day28_LAG3_25

city: Noda-shi

first: Mikiya

last: Tsunoda

state: Chiba

department: Molecular Preventive Medicine

institute: The University of Tokyo

description: Library name: Sample 164

data_processing:
Adapter trimming and quality filtering of sequencing data were performed by using Cutadapt-3.2 and PRINSEQ-0.20.4. Sequencing data were processed by MiXCR-3.0.5.
In MiXCR, Filtered reads were aligned to reference mouse TCR V/D/J sequences registered in the international ImMunoGeneTics information system: -starting-material=rna, -5-end=no-v-primers-, -3-end=c-primers, -adapters=no-adapters, vParameters.geneFeatureToAlign=VTranscript, -vjAlignmentOrder=JThenV, then identical sequences were assembled and grouped in clones with PCR and sequencing error correlation with the following parameters: -badQualityThreshold=15, –separateByV=true, –separateByJ=true, -only-productive=true, –region-of-interest=CDR3.
The Variable (V) and Joining (J) segment of TCRs were represented in IMGT gene nomenclature. List of final clones were analyzed by VDJtools-1.2.1. Then, the sequencing reads of sample was normalized to the six times of cell count in each sample by “DownSample” command of VDJtools. T-cell clones were determined as TCR reads with the same TCR V segment, J segment and CDR3 nucleotide sequence.
Assembly: IMGT reference sequences of mouse TRB
Supplementary files format and content: text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones

source_name: Tumor

growth_protocol: Lewis lung carcinoma (LLC) cells (5 × 10^5 cells /mouse) were inoculated subcutaneously (s.c.) into the left flank, right flank and the left hip of C57BL/6 mice.

extract_protocol:
Tumors were cut into small fragments and digested for 45 minutes at 37°C with 0.2% collagenase (FUJIFILM Wako) and DNase I (Sigma-Aldrich), except for experiments for single-cell analysis, in which tumors were digested with 0.2% collagenase NB8 (Nordmark Pharma GmbH). The cells were then subjected to two-phase density separation with upper 35% Percoll PLUS (GE Healthcare) (1000g, 10 minutes at room temperature). Leukocytes were recovered, washed and resuspended in preparation medium (PM) [5%FBS, 10mM HEPES (Nacalai), Penicillin-Streptomycin (Nacalai) in RPMI-1640 (Nacalai)]. After RBC lysis with ACK buffer [155mM of NH4Cl (Nacalai), 10mM of KHCO3 (Nacalai), and 0.5mM EDTA pH8.0 (NIPPON GENE)] for 1 minute at room temperature, cells were washed and resuspended in PM, and the cell concentrations were measured using Flow-Count fluorospheres (Beckman Coulter) and a CytoFLEX S flow cytometer (Beckman Coulter).Cells were stained with a mix of Fc Block (anti-mouse CD16/CD32 mAb; clone 2.4G2, BioLegend) and fluorophore-conjugated anti-mouse monoclonal antibodies (Supplementary Table 5). Antibody mixtures were prepared using BD Horizon Brilliant Stain Buffer Plus (BD) diluted 5x with FACS buffer (D-PBS(-) supplemented with 2% FBS, and 0.05% Sodium Azide). Staining was performed for 20 minutes at 4°C. Before sorting, T cells were enriched from tumor suspensions by further staining with BD IMag APC Magnetic Particles-DM (BD Biosciences), then placed on magnetic plate. After washing by MACS buffer (D-PBS(-) supplemented with 10% BSA, and 2 mM EDTA pH8.0), APC and APC-Cy7(CD8, mouse TCRb)-positive cells were collected as positive fraction. Cell sorting was performed using a FACS Aria II or Aria III (BD Biosciences). Cells were stained with 5µg/mL of propidium iodide (PI, Sigma-Aldrich) immediately before sorting. Nonviable cells were excluded from the analysis based on forward and side scatter profiles and PI staining. For bulk TCR repertoire analysis and bulk RNA-seq analysis, cells were sorted into Lysis buffer [1% w/v LiDS, 100 mM Tris-HCl pH7.5, 500 mM LiCl, 5 mM dithiothreitol, and 10 mM EDTA pH8.0] and stored at −80°C. Cells were sorted from the CD8+, CD8+PD-1+Ly108+TIM-3-, CD8+PD-1+Ly108+TIM-3+, CD8+PD-1+Ly108-TIM-3+ and CD8+PD-1- fractions to produce five datasets per mouse.
TCR libraries were prepared on purified T cells lysed in lysis buffer [1% LiDS, 100 mM Tris-HCl (pH 7.5), 500 mM LiCl, and 10 mM EDTA]. PolyA RNAs were isolated according to a previous report with some modifications (GSE110711).To perform reverse transcription and template-swiching, beads were then suspended in 10 µL of RT mix [1× First Strand buffer (Thermo Fisher Scientific), 1 mM dNTP, 2.5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma-Aldrich), 9 mM MgCl2, 1 U/µL RNaseIn Plus Rnase Inhibitor (Promega), 10 U/µL Superscript II (Thermo Fisher Scientific), and 1µM of i5-TSO], and incubated for 60 min at 42ºC and immediately cooled on ice. Beads were washed once with with B&W-T buffer [5 mM Tris-HCl (pH 7.5), 1 M NaCl, 0.5 mM EDTA, and 0.1% Tween-20], and once with Tris-HCl (pH 8.0). To amplify the TCR cDNA containing complementarity determining region 3 (CDR3), nested PCR of the TCR locus was performed as follows. Beads with containing cDNA was resuspended with the 25 µL of first PCR mixture [0.4 µM of primers (i5, Trac_ex, and Trbc_ex), and 1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems, Wilmington, MA, #KK2602)], and the thermal cycling was performed as following condition: denaturation at 95°C for 3 min, 10 cycles of denaturation for 20 sec at 98°C, annealing for 15 sec at 65°C and extension for 30 sec at 72°C, followed by a final extension at 72°C for 2 min. Then, 2.5 µL of first PCR product was mixed with the 22.5 µl of second PCR mixture [0.35 µM of primers (i5_2nd, i7-BC_mTrac, and i7-BC_mTrbc), and 1x KAPA Hifi Hotstart ReadyMix], , and the thermal cycling was performed as following condition: denaturation at 95°C for 3 min, 18 cycles of denaturation for 20 sec at 98°C, annealing for 15 sec at 65°C and extension for 30 sec at 72°C, followed by a final extension at 72°C for 2 min.. The second-PCR products were purified by an Agencort AM Pure XP kit (Bexkman-Coulter, CA, #A63881) at a 0.7:1 ratio of beads to sample, and eluted with 20 µL of Tris-HCl (pH 8.0).To amplify TCR library and add adaptor sequence for next generation sequencer, the third PCR was performed as follows. 5µL of purified second PCR product was mixed with the 20 µl of third PCR mixture [0.4 µM of primers (i5-BC and i7-BC), and 1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems, Wilmington, MA, USA, #KK2602)], and the thermal cycling was performed under the same condition as first PCR, excepted for the number of cycles (23 cycles). The third-PCR products were purified as second PCR. The products were pooled and then purified and subjected to dual size selection using ProNex size-selective purification system (Promega) and eluted with 25 μL of Tris-HCl (pH 8.5). Final TCR libraries, whose lengths were about 600 base pairs were sequenced using an Illumina Novaseq 6000 S4 flowcell (67 bp read 1 and 140 bp read 2) (Illumina, USA). Only read2 contained the sequence regarding the definition of T cell clones.

value: Tumor

value: Lewis lung carcinoma

value: lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRb+,  CD4-, CD8+, PD-1+, Ly108- and Tim3+ T cells


title: ExT13_Tumor_Tim3_day28_LAG3_29

description: Library name: Sample 165


title: muscle, PH227, week 16, rest

description:
PH227w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: TRAD

value: week 16

value: rest

value: Female


title: ExT13_Tumor_Tim3_day28_LAG3_2

description: Library name: Sample 160


title: muscle, PH229, week 0, 24hr

description:
PH229w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 0


title: ExT13_Tumor_Tim3_day28_LAG3_4

description: Library name: Sample 161


title: muscle, PH227, week 12, pre

description:
PH227w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 12

value: pre


title: muscle, PH227, week 12, 24hr

description:
PH227w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Tim3_day28_cont_28

description: Library name: Sample 158


title: muscle, PH227, week 0, pre

description:
PH227w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH227, week 12, 3hr

description:
PH227w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Tim3_day28_cont_30

description: Library name: Sample 159


title: muscle, PH227, week 0, 3hr

description:
PH227w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH227, week 0, 24hr

description:
PH227w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Tim3_day28_cont_21

description: Library name: Sample 157


title: ExT13_Tumor_Tim3_day21_LAG3_29

description: Library name: Sample 154


title: ExT13_Tumor_Tim3_day28_cont_19

description: Library name: Sample 156


title: ExT13_Tumor_Tim3_day28_cont_3

description: Library name: Sample 155


title: muscle, PH225, week 16, rest

description:
PH225w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: HITT


title: ExT13_Tumor_Tim3_day21_LAG3_25

description: Library name: Sample 153


title: muscle, PH225, week 12, pre

description:
PH225w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Tim3_day21_LAG3_16

description: Library name: Sample 152


title: ExT13_Tumor_Tim3_day28_LAG3_16

description: Library name: Sample 163


title: muscle, PH225, week 12, 24hr

description:
PH225w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Tim3_day28_LAG3_14

description: Library name: Sample 162


title: muscle, PH225, week 12, 3hr

description:
PH225w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Tim3_day21_LAG3_14

description: Library name: Sample 151


title: muscle, PH225, week 0, pre

description:
PH225w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Tim3_day21_LAG3_4

description: Library name: Sample 150


title: muscle, PH225, week 0, 24hr

description:
PH225w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Tim3_day21_cont_30

description: Library name: Sample 148


title: ExT13_Tumor_Tim3_day21_cont_28

description: Library name: Sample 147


title: muscle, PH224, week 16, rest

description:
PH224w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: Male


title: ExT13_Tumor_Tim3_day21_cont_21

description: Library name: Sample 146

value: WT


title: ExT13_Tumor_Tim3_day21_cont_19

description: Library name: Sample 145


title: ExT13_Tumor_Tim3_day14_LAG3_29

description: Library name: Sample 143


title: muscle, PH224, week 0, 3hr

description:
PH224w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH224, week 0, pre

description:
PH224w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH224, week 12, pre

description:
PH224w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Tim3_day14_LAG3_16

description: Library name: Sample 141


title: ExT13_Tumor_Tim3_day21_cont_3

description: Library name: Sample 144


title: muscle, PH224, week 0, 24hr

description:
PH224w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH216, week 16, rest

description:
PH216w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Tim3_day14_LAG3_14

description: Library name: Sample 140


title: ExT13_Tumor_Tim3_day21_LAG3_2

description: Library name: Sample 149


title: ExT13_Tumor_Tim3_day14_LAG3_2

description: Library name: Sample 138


title: muscle, PH216, week 12, pre

description:
PH216w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Tim3_day14_cont_30

description: Library name: Sample 137


title: ExT13_Tumor_Tim3_day14_LAG3_4

description: Library name: Sample 139


title: muscle, PH216, week 12, 24hr

description:
PH216w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH216, week 12, 3hr

description:
PH216w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH225, week 0, 3hr

description:
PH225w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Tim3_day14_cont_28

description: Library name: Sample 136


title: muscle, PH224, week 12, 3hr

description:
PH224w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Tim3_day14_cont_21

description: Library name: Sample 135


title: muscle, PH216, week 0, pre

description:
PH216w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH224, week 12, 24hr

description:
PH224w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Tim3_day14_LAG3_25

description: Library name: Sample 142


title: ExT13_Tumor_Tim3_day14_cont_19

description: Library name: Sample 134


title: muscle, PH207, week 16, rest

description:
PH207w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH216, week 0, 3hr

description:
PH216w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Tim3_day14_cont_3

description: Library name: Sample 133


title: muscle, PH207, week 12, pre

description:
PH207w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_PD1nega_day28_LAG3_29

description: Library name: Sample 132

value: lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRb+,  CD4-, CD8+ and PD-1- T cells


title: muscle, PH207, week 12, 3hr

description:
PH207w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_PD1nega_day28_LAG3_25

description: Library name: Sample 131


title: muscle, PH207, week 12, 24hr

description:
PH207w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_PD1nega_day28_LAG3_14

description: Library name: Sample 129


title: ExT13_Tumor_PD1nega_day28_LAG3_16

description: Library name: Sample 130


title: ExT13_Tumor_PD1nega_day28_LAG3_2

description: Library name: Sample 127


title: muscle, PH205, week 16, rest

description:
PH205w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH207, week 0, 3hr

description:
PH207w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH205, week 12, 3hr

description:
PH205w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_PD1nega_day28_LAG3_4

description: Library name: Sample 128


title: muscle, PH207, week 0, 24hr

description:
PH207w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH205, week 12, pre

description:
PH205w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH207, week 0, pre

description:
PH207w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_PD1nega_day21_cont_19

description: Library name: Sample 112


title: ExT13_Tumor_PD1nega_day21_cont_28

description: Library name: Sample 114


title: ExT13_Tumor_PD1nega_day21_LAG3_14

description: Library name: Sample 118


title: ExT13_Tumor_PD1nega_day21_LAG3_25

description: Library name: Sample 120


title: ExT13_Tumor_PD1nega_day21_LAG3_4

description: Library name: Sample 117


title: ExT13_Tumor_PD1nega_day21_cont_30

description: Library name: Sample 115


title: ExT13_Tumor_PD1nega_day28_cont_21

description: Library name: Sample 124


title: ExT13_Tumor_PD1nega_day21_LAG3_29

description: Library name: Sample 121


title: ExT13_Tumor_PD1nega_day21_LAG3_2

description: Library name: Sample 116


title: ExT13_Tumor_PD1nega_day28_cont_3

description: Library name: Sample 122


title: ExT13_Tumor_PD1nega_day21_LAG3_16

description: Library name: Sample 119


title: ExT13_Tumor_PD1nega_day28_cont_28

description: Library name: Sample 125


title: ExT13_Tumor_PD1nega_day28_cont_19

description: Library name: Sample 123


title: ExT13_Tumor_PD1nega_day28_cont_30

description: Library name: Sample 126


title: muscle, PH205, week 12, 24hr

description:
PH205w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH204, week 0, pre

description:
PH204w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH204, week 16, rest

description:
PH204w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH204, week 12, 24hr

description:
PH204w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH205, week 0, pre

description:
PH205w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH204, week 12, pre

description:
PH204w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH204, week 0, 3hr

description:
PH204w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH205, week 0, 24hr

description:
PH205w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH204, week 12, 3hr

description:
PH204w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH205, week 0, 3hr

description:
PH205w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH202, week 16, rest

description:
PH202w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH202, week 12, pre

description:
PH202w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_PD1nega_day21_cont_3

description: Library name: Sample 111


title: muscle, PH204, week 0, 24hr

description:
PH204w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_PD1nega_day21_cont_21

description: Library name: Sample 113


title: muscle, PH202, week 12, 3hr

description:
PH202w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_PD1nega_day14_LAG3_16

description: Library name: Sample 108


title: ExT13_Tumor_PD1nega_day14_LAG3_29

description: Library name: Sample 110


title: muscle, PH200, week 16, rest

description:
PH200w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH202, week 0, 24hr

description:
PH202w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH202, week 0, pre

description:
PH202w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_PD1nega_day14_LAG3_4

description: Library name: Sample 106


title: ExT13_Tumor_PD1nega_day14_LAG3_14

description: Library name: Sample 107


title: muscle, PH200, week 12, pre

description:
PH200w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH202, week 12, 24hr

description:
PH202w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_PD1nega_day14_cont_19

description: Library name: Sample 101


title: muscle, PH200, week 12, 24hr

description:
PH200w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_PD1nega_day14_cont_28

description: Library name: Sample 103


title: muscle, PH202, week 0, 3hr

description:
PH202w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day28_LAG3_29

description: Library name: Sample 99

value: lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRb+,  CD4-, CD8+, PD-1+, Ly108+ and Tim3- T cells


title: muscle, PH200, week 0, 24hr

description:
PH200w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_PD1nega_day14_LAG3_25

description: Library name: Sample 109


title: SUM149 treated with negative  control gapmer ,replicate 2

description: SUM149 treated with control gapmer ,replicate 2

value: TNBC


title: muscle, PH199, week 16, rest

description:
PH199w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: vastus lateralis muscle


title: ExT13_Tumor_PD1nega_day14_cont_3

description: Library name: Sample 100

value: Tumor


title: ExT13_Tumor_PD1nega_day14_cont_21

description: Library name: Sample 102

value: Lewis lung carcinoma


title: muscle, PH200, week 0, 3hr

description:
PH200w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH200, week 0, pre

description:
PH200w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH199, week 12, pre

description:
PH199w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH200, week 12, 3hr

description:
PH200w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day28_LAG3_16

description: Library name: Sample 97


title: ExT13_Tumor_Ly108_day28_LAG3_25

description: Library name: Sample 98


title: muscle, PH199, week 12, 3hr

description:
PH199w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_PD1nega_day14_LAG3_2

description: Library name: Sample 105


title: ExT13_Tumor_PD1nega_day14_cont_30

description: Library name: Sample 104


title: ExT13_Tumor_Ly108_day28_LAG3_14

description: Library name: Sample 96


title: muscle, PH199, week 0, pre

description:
PH199w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day28_LAG3_4

description: Library name: Sample 95


title: ExT13_Tumor_Ly108_day28_LAG3_2

description: Library name: Sample 94


title: muscle, PH199, week 0, 3hr

description:
PH199w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day28_cont_30

description: Library name: Sample 93


title: muscle, PH199, week 12, 24hr

description:
PH199w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH199, week 0, 24hr

description:
PH199w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH198, week 16, rest

description:
PH198w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH198, week 12, pre

description:
PH198w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day28_cont_28

description: Library name: Sample 92


title: muscle, PH198, week 12, 3hr

description:
PH198w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH198, week 12, 24hr

description:
PH198w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day28_cont_3

description: Library name: Sample 89


title: ExT13_Tumor_Ly108_day21_LAG3_29

description: Library name: Sample 88


title: muscle, PH198, week 0, pre

description:
PH198w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day28_cont_21

description: Library name: Sample 91


title: muscle, PH198, week 0, 3hr

description:
PH198w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day21_LAG3_16

description: Library name: Sample 86


title: muscle, PH198, week 0, 24hr

description:
PH198w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day21_LAG3_14

description: Library name: Sample 85


title: ExT13_Tumor_Ly108_day21_LAG3_4

description: Library name: Sample 84


title: ExT13_Tumor_Ly108_day21_LAG3_25

description: Library name: Sample 87


title: ExT13_Tumor_Ly108_day21_LAG3_2

description: Library name: Sample 83


title: muscle, PH197, week 16, rest

description:
PH197w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH197, week 12, 3hr

description:
PH197w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH197, week 12, pre

description:
PH197w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH197, week 12, 24hr

description:
PH197w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day21_cont_30

description: Library name: Sample 82


title: ExT13_Tumor_Ly108_day21_cont_28

description: Library name: Sample 81


title: muscle, PH197, week 0, 3hr

description:
PH197w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day21_cont_21

description: Library name: Sample 80


title: muscle, PH196, week 16, rest

description:
PH196w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH197, week 0, 24hr

description:
PH197w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day21_cont_3

description: Library name: Sample 78


title: ExT13_Tumor_Ly108_day14_LAG3_29

description: Library name: Sample 77


title: muscle, PH197, week 0, pre

description:
PH197w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day21_cont_19

description: Library name: Sample 79


title: ExT13_Tumor_Ly108_day28_cont_19

description: Library name: Sample 90


title: muscle, PH196, week 12, 24hr

description:
PH196w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day14_LAG3_16

description: Library name: Sample 75


title: muscle, PH196, week 12, pre

description:
PH196w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day14_LAG3_25

description: Library name: Sample 76


title: muscle, PH196, week 0, pre

description:
PH196w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day14_LAG3_4

description: Library name: Sample 73


title: muscle, PH196, week 0, 3hr

description:
PH196w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH196, week 12, 3hr

description:
PH196w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH196, week 0, 24hr

description:
PH196w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day14_LAG3_2

description: Library name: Sample 72


title: ExT13_Tumor_Ly108_day14_cont_30

description: Library name: Sample 71


title: muscle, PH195, week 16, rest

description:
PH195w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day14_cont_21

description: Library name: Sample 69


title: muscle, PH195, week 12, pre

description:
PH195w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day14_cont_19

description: Library name: Sample 68


title: muscle, PH195, week 12, 24hr

description:
PH195w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH195, week 12, 3hr

description:
PH195w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_DP_day28_LAG3_25

description: Library name: Sample 65

value: lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRb+,  CD4-, CD8+, PD-1+, Ly108+ and Tim3+ T cells


title: muscle, PH195, week 0, pre

description:
PH195w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH195, week 0, 24hr

description:
PH195w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day14_cont_3

description: Library name: Sample 67


title: ExT13_Tumor_DP_day28_LAG3_16

description: Library name: Sample 64


title: ExT13_Tumor_DP_day28_LAG3_29

description: Library name: Sample 66


title: muscle, PH194, week 12, pre

description:
PH194w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: TRAD


title: ExT13_Tumor_DP_day28_LAG3_14

description: Library name: Sample 63


title: muscle, PH194, week 16, rest

description:
PH194w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 16


title: muscle, PH195, week 0, 3hr

description:
PH195w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_DP_day28_LAG3_4

description: Library name: Sample 62


title: muscle, PH194, week 12, 3hr

description:
PH194w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_Ly108_day14_LAG3_14

description: Library name: Sample 74


title: ExT13_Tumor_DP_day28_LAG3_2

description: Library name: Sample 61


title: ExT13_Tumor_DP_day28_cont_30

description: Library name: Sample 60


title: muscle, PH194, week 0, pre

description:
PH194w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_DP_day28_cont_28

description: Library name: Sample 59


title: ExT13_Tumor_Ly108_day14_cont_28

description: Library name: Sample 70


title: ExT13_Tumor_DP_day28_cont_21

description: Library name: Sample 58


title: muscle, PH194, week 0, 3hr

description:
PH194w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH194, week 0, 24hr

description:
PH194w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH193, week 12, pre

description:
PH193w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH193, week 16, rest

description:
PH193w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: rest


title: ExT13_Tumor_DP_day28_cont_3

description: Library name: Sample 56


title: ExT13_Tumor_DP_day28_cont_19

description: Library name: Sample 57


title: ExT13_Tumor_DP_day21_LAG3_29

description: Library name: Sample 55


title: muscle, PH193, week 12, 24hr

description:
PH193w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_DP_day21_LAG3_25

description: Library name: Sample 54


title: muscle, PH193, week 12, 3hr

description:
PH193w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_DP_day21_LAG3_2

description: Library name: Sample 50


title: ExT13_Tumor_DP_day21_LAG3_14

description: Library name: Sample 52


title: muscle, PH191, week 16, rest

description:
PH191w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH193, week 0, 3hr

description:
PH193w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH193, week 0, pre

description:
PH193w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_DP_day21_cont_28

description: Library name: Sample 48


title: ExT13_Tumor_DP_day21_LAG3_16

description: Library name: Sample 53


title: muscle, PH193, week 0, 24hr

description:
PH193w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH194, week 12, 24hr

description:
PH194w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: Female


title: ExT13_Tumor_DP_day21_cont_30

description: Library name: Sample 49


title: muscle, PH191, week 12, pre

description:
PH191w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_DP_day21_cont_21

description: Library name: Sample 47


title: ExT13_Tumor_DP_day21_cont_3

description: Library name: Sample 45


title: ExT13_Tumor_DP_day21_cont_19

description: Library name: Sample 46


title: muscle, PH191, week 0, pre

description:
PH191w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 0


title: ExT13_Tumor_DP_day14_LAG3_29

description: Library name: Sample 44


title: muscle, PH191, week 0, 3hr

description:
PH191w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH191, week 0, 24hr

description:
PH191w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH189, week 16, rest

description:
PH189w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_DP_day14_LAG3_25

description: Library name: Sample 43


title: muscle, PH189, week 12, pre

description:
PH189w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 12


title: muscle, PH189, week 12, 3hr

description:
PH189w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_DP_day14_LAG3_14

description: Library name: Sample 41


title: ExT13_Tumor_DP_day14_LAG3_16

description: Library name: Sample 42


title: ExT13_Tumor_DP_day21_LAG3_4

description: Library name: Sample 51


title: ExT13_Tumor_DP_day14_LAG3_4

description: Library name: Sample 40


title: muscle, PH189, week 12, 24hr

description:
PH189w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH191, week 12, 3hr

description:
PH191w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_DP_day14_LAG3_2

description: Library name: Sample 39


title: muscle, PH189, week 0, 3hr

description:
PH189w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH189, week 0, pre

description:
PH189w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: pre


title: ExT13_Tumor_DP_day14_cont_28

description: Library name: Sample 37


title: muscle, PH191, week 12, 24hr

description:
PH191w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt