title: Human_PFV, scRNA-seq

city: Guangzhou

first: Cheng

last: Wu

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen University

description: BD Rhapsody system

data_processing:
We applied fastp with default parameter filtering the adaptor sequence and removed the low quality reads to achieve the clean data. UMI-tools was applied for Single Cell Transcriptome Analysis to identify the cell barcode whitelist. The UMI-based clean data was mapped to human genome (Ensemble version 100) utilizing STAR mapping with customized parameter from UMI-tools standard pipeline to obtain the UMIs counts of each sample. Cells contained over 200 expressed genes and mitochondria UMI rate below 40% passed the cell quality filtering and mitochondria genes were removed in the expression table.
Assembly: CRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Eye

extract_protocol:
Persistent fetal vasculature (PFV) tissue samples from patient were collected in ice-cold PBS and then centrifuged at 200×g for 2min. The supernatant was removed and 500µl 0.25% trypsin were added . The PFV tissue was then incubated at 37°C for a total 15-20 min, pipet every 5 min to digest into single cells. Finally, DMEM medium with 10% fetal bovine serum was added to stop digestion and centrifuged at 200×g for 2min. The supernatant was removed and cells were suspended in ice-cold PBS to subjected to single-cell RNA sequencing.
BD Rhapsody system was used to capture the transcriptomic information of the single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). Sequencing was performed by illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.

value: Goblet cells

value: Eye


title: JB_14 [WGS]

status: Public on May 31 2023

type: SRA

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

country: Germany

institute: Martin Luther University Halle-Wittenberg

description:
shallow whole genome sequencing (sWGS)
CN_NB_tumor_NT_pool.csv

library_source: genomic

data_processing:
Library strategy: WGS
Sequenced strand specific paired-end reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20 –trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters -q --no-spliced-alignment --rna-strandness RF --dta -k
Secondary alignments were filtered out using samtools (v 1.10).
Copy number variations were analysed using R/cn.MOPS (v 1.36.0) using chromosome normalization (poisson) excluding sex chromosomes.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: CN_NB_tumor_NT_pool.csv: Comma-separated text file including genomic regions, log ratios of read counts and copy number values for each sample.

molecule: genomic DNA

organism: Homo sapiens

source_name: primary neuroblastoma tumor

extract_protocol:
Genomic DNA was extracted using the AllPrep Kit (Qiagen). 10mg of snap-frozen tissue was homogenized in RLT Plus buffer with a Precellys 24 tissue homogenizer (Bertin Instruments) and processed, according to the manufacturer's instructions. Integrity of genomic DNA was tested on an agarose gel.
A total amount of 1.0μg DNA per sample was used as input material for the DNA sample preparations. Sequencing libraries were generated using NEBNext DNA Library Prep Kit following manufacturer's recommendations and indices were added to each sample. The genomic DNA is randomly fragmented to a size of 350bp by shearing, then DNA fragments were end polished, A-tailed, and ligated with the NEBNext adapter for Illumina sequencing, and further PCR enriched by P5 and indexed P7 oligos. The PCR products were purified (AMPure XP system) and resulted libraries were analyzed for size distribution by Agilent 2100 Bioanalyzer and quantified using real-time PCR.

tag: tissue

value: primary neuroblastoma tumor

tag: tumor stage

tag: mycn status

value: not amplified


title: JB_16 [WGS]

value: amplified


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 43

city: Chicago

first: Yogesh

last: Goyal

state: IL

address: 303 E Superior St

country: USA

institute: Northwestern University

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample43

library_source: transcriptomic

data_processing:
We aligned RNA-seq reads to the human genome (hg19) with STAR v2.5.2a and counted uniquely mapping reads with HTSeq v0.6.1 and outputs count matrix.
The counts matrix was used to obtain tpm and other normalized values for each gene.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts, TPM, RPKM, RPM values for each sample

molecule: total RNA

growth_protocol: WM989 A6-G3 melanoma cell line, first described in Shaffer et al, 2017, and kindly provided by the lab of Dr. Meenhard Herlyn, were derived by twice single-cell bottlenecking the WM989 melanoma cell line. The identities of WM989 A6-G3 was verified by DNA STR microsatellite fingerprinting at the Wistar Institute. Cells were cultured in Tu2% media (80% MCDB 153, 10% Leibovitz’s L-15, 2% FBS, 2.4mM CaCl2, 50 U/mL penicillin, and 50 μg/mL streptomycin) in a 10cm dish.

extract_protocol:
We conducted standard bulk paired-end (37:8:8:38) RNA sequencing using RNeasy Micro (Qiagen 74004) for RNA extraction, NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L), NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB E7770L), NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) oligos (NEB E7600S), and an Illumina NextSeq 550 75 cycle high-output kit (Illumina 20024906).
Prior to extraction and library preparation, the samples were randomized to avoid any experimental and human biases.

treatment_protocol:
We prepared stock solutions in DMSO of 4 mM vemurafenib (PLX4032, Selleck Chemicals, S1267) and 100 μM trametinib (Selleck Chemicals, S2673). We prepared small aliquots (10-15ul) for each drug and stored them at −20 °C to minimize freeze–thaw cycles. For drug treatment experiments, we diluted the stock solutions in culture medium to a final concentration of 1 µM and 100nM for vemurafenib and 5 nM for trametinib.
The dose of vemurafenib (1µM) was chosen as per Shaffer et al. (Nature 2017), which was optimized for growth arrest without overt cytotoxicity. The doses of trametinib used were 5 nM for WM989 A6-G3, 10 nM for WM3623 P4E7, and 25nM for WM3451 P2G7. These doses were also chosen based on a dose curve to obtain virtually complete growth arrest. WM989 A6-G3 cells were treated with either vemurafenib or 5 nM trametinib for 3-4 weeks, and the media was replaced every 3-4d. Resistant colonies were isolated and cultured in either 1µM vemurafenib or 5 nM trametinib in Tu2% (Goyal et al. 2021) for several weeks to months.

tag: cell line

tag: cell type

value: Human melanoma cells

tag: genotype

value: BRAF - V600E

tag: treatment

value: Treatment with therapy drugs

tag: time

value: Experiment set 2, Expanded over months


title: LuCaP35_ORY_3X_rep3

city: Boston

first: Changmeng

last: Cai

state: MA

address: 100 William T Morrissey Blvd

institute: University of Massachusetts Boston

description: Xenograft_LuCaP35CR_ORY_samples_count_table.txt.gz

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were aligned to the human reference genome (hg19) using STAR (version 2.7.2) followed by counting with featureCounts (version 1.6.4) from GRCh37 Ensembl reference.
Assembly: hg19
Supplementary files format and content: txt file for raw counts of sequence reads

source_name: CRPC PDX

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol.
RNA-seq libraries  were performed by using TruSeq® Strnd Total RNA LT (Illumina).

value: CRPC PDX

value: 0.06mg/kg ORY-1001 (3 times/week)


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 44

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample44


title: LuCaP35_ORY_3X_rep2


title: JB_12 [WGS]


title: JB_13 [WGS]


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 42

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample42


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 48

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample48


title: LuCaP35_ORY_3X_rep1


title: JB_11 [WGS]


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 41

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample41


title: LuCaP35_VEH_3X_rep3

value: DMSO(3 times/week)


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 40

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample40


title: JB_10 [WGS]


title: LuCaP35_VEH_3X_rep2


title: PN00159_D5-5

city: Belfast

first: David

middle: Arthur

last: Simpson

state: N. Ireland

address: The Wellcome – Wolfson Institute for Experimental Medicine, 97 Lisburn Road

department: Wellcome-Wolfson Institite for Experimental Medicine

country: United Kingdom

institute: Queen's University Belfast

description:
Merged_raw_counts.txt
PN0159_0055_S55

data_processing:
Raw sequence reads were inspected for quality using FastQC
Sequence reads were mapped to the Mus musculus reference genome (GRCm38.p5) and annotated using Gencode (M15) with the STAR aligner program (v2.7.4a)
HTSeq-count (v0.11.1) was used to generate the raw counts for each sample, and the resultant read count matrix was normalized together using DESeq2 (v1.26.0)
Assembly: GRCm38.p5
Supplementary files format and content: tab-delimited text files include counts for each sample

organism: Mus musculus

source_name: retina

growth_protocol: Mice were bred at Indiana University according to approved IACUC. Male Ins2Akita heterozygous mice were bred with female C57Bl6 mice, and heterozygous male Ins2Akita exhibited consistent hyperglycemia (>250mg/dL), while littermate males without phenotype considered controls. Mice were kept at constant temperature and humidity under a 12h:12h Light/Dark (12L/12D) schedule from birth, with ad libitum access to food and water, and when they reached four months of age were euthanized for sample collection.

extract_protocol:
Rotal RNA isolation was performed using the Qiagen RNeasy Mini Kit.
Complementary DNA (cDNA) libraries were constructed using the KAPA RNA HyperPrep Kit with RiboErase (HMR) amplification

treatment_protocol: Terminal perfusion was conducted using cold phosphate-buffered saline (PBS) solution (without Ca2+ and Mg2+), eyes enucleated, and retinas were dissected under a microscope. For the night points (ZT12-ZT24), all processes were performed under dim red light. Following isolation, retinas were immediately frozen in liquid nitrogen and stored at -80°C.

value: retina


title: PN00159_C13-5

description:
Merged_raw_counts.txt
PN0159_0054_S54


title: PN00159_D1-5

description:
Merged_raw_counts.txt
PN0159_0058_S58


title: PN00159_C1-6

description:
Merged_raw_counts.txt
PN0159_0057_S57


title: PN00159_C5-5

description:
Merged_raw_counts.txt
PN0159_0056_S56


title: JB_9 [WGS]


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 39

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample39


title: JB_8 [WGS]


title: PN00159_D17-5

description:
Merged_raw_counts.txt
PN0159_0052_S52


title: LuCaP35_GSK_rep3

description: Xenograft_LuCaP35CR_GSK_samples_count_table.txt.gz

value: 33mg/kg GSK2879552 (6 times/week)


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 38

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample38


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 37

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample37


title: JB_7 [WGS]


title: JB_6 [WGS]


title: LuCaP35_GSK_rep2


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 36

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample36


title: PN00159_D13-5

description:
Merged_raw_counts.txt
PN0159_0050_S50


title: LuCaP35_GSK_rep1


title: JB_5 [WGS]


title: PN00159_D9-5

description:
Merged_raw_counts.txt
PN0159_0049_S49


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 35

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample35


title: LuCaP35_VEH_6X_rep3

value: DMSO(6 times/week)


title: JB_4 [WGS]


title: PN00159_C9-5

description:
Merged_raw_counts.txt
PN0159_0048_S48


title: LuCaP35_VEH_6X_rep2


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 34

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample34


title: JB_3 [WGS]


title: PN00159_D21-5

description:
Merged_raw_counts.txt
PN0159_0053_S53


title: LuCaP35_VEH_3X_rep1


title: LuCaP35_VEH_6X_rep1


title: PN00159_C5-6

description:
Merged_raw_counts.txt
PN0159_0047_S47


title: JB_2 [WGS]


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 33

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample33


title: LNCaP_BRD4-rep2

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were mapped to the hg19 human genome using bwa (version 0.7.9a) with aln and samse sub-commands.
Samtools (version 1.2) was used to convert sam files to bam format.
MACS2 (version 2.1.0) was used to call peak on the bam files.
bedGraph files generated from MACS2 were converted into bigwig files with UCSC tools (version 369).
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

source_name: LNCaP Cell

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed using the SMARTer ThruPLEX DNA-Seq Prep Kit (Takara Bio USA).

value: LNCaP Cell

value: prostate cancer cell line

tag: chip antibody

value: anti-BRD4 (Bethyl Laboratories)


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 32

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample32

source_name: WM989 A6-G3, clone 99

value: WM989 A6-G3, clone 99


title: JB_1 [WGS]

description:
shallow whole genome sequencing (sWGS)
CN_NB_tumor_NT_pool.csv

value: primary neuroblastoma tumor


title: PN00159_C17-5

description:
Merged_raw_counts.txt
PN0159_0051_S51


title: LNCaP_BRD4-rep1


title: PN00159_D21-4

description:
Merged_raw_counts.txt
PN0159_0046_S46


title: PN00159_C21-4

description:
Merged_raw_counts.txt
PN0159_0045_S45


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 30

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample30

source_name: WM989 A6-G3, clone 97

value: WM989 A6-G3, clone 97


title: PN00159_D17-4

description:
Merged_raw_counts.txt
PN0159_0044_S44


title: Platelet Sample from Subject 182493, 28 Days Post Vaccination

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

data_processing:
Raw data was demultiplexed and converted to FASTQ format using bcl2fastq.
FASTQ files were quality trimmed using Trimmomatic.
FASTQ files were quality assessed with FASTQC.
Quality-trimmed FASTQ files were aligned against human reference with STAR aligner.
Read counts for each gene were genereated with htseq-count.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Each processed file contains the read counts for each gene for one sample. The format is plain text, gzip compressed.

source_name: platelet

extract_protocol:
Whole blood was collected in a yellow-cap tube and stored at room temperature. The tube was centrifuged and the platelet-rich plasma (PRP) was collected. The PRP was aliquoted and further centrifuged to isolate the platelet pellet. The platelet pellet was dissolved in 700 microliter Qiasol/TRISol. RNA was extracted using the Qiagen miRNA Easy Kit (Cat. # 217004) following the manufacturer’s instructions using a QIACUBE.
RNA-seq libraries were prepared using the Takara Bio SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian per the manufacturer’s instructions.

tag: subject id

tag: gender

value: Male

value: Young

tag: time point relative to flu vaccination

value: 28 Days Post-Vaccination


title: PN00159_C17-4

description:
Merged_raw_counts.txt
PN0159_0043_S43


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 29

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample29

source_name: WM989 A6-G3, clone 96

value: WM989 A6-G3, clone 96

value: Human melanoma cells

value: BRAF - V600E

value: Treatment with therapy drugs


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 31

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample31

source_name: WM989 A6-G3, clone 98

value: WM989 A6-G3, clone 98

value: Experiment set 2, Expanded over months


title: NFIX, sh2, Day7, Rep2, ATACseq

city: Cambridge

first: Mudit

last: Chaand

address: 35 Cambridgepark Drive

institute: Syros Pharmaceuticals

description: bm_nfix_shrna_kd_atacseq_reads_in_peaks.txt

data_processing:
Raw fastq files were processed using the ENCODE ATAC-seq pipeline: https://github.com/ENCODE-DCC/atac-seq-pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: Text files containing read count matrices for union ATAC-seq peak sets.

source_name: Blood

growth_protocol:
BM-derived erythroid progenitor NFIX knockdown cells were differentiated using the three phase EDM.  The differentiation state of the cells was determined by staining the cells with fluorescently conjugated antibodies specific to erythroid surface markers: CD36-FITC (Becton, Dickinson, and Company, 20 µL/test), CD71-APC (Becton, Dickinson, and Company, 20 µL/test) and CD235a-BV421 (Becton, Dickinson, and Company, 5 µL/test).
See sample-specific growth protocols.

extract_protocol:
50,000 cells were treated with 2.5 ul transposase for 30 minutes, then amplified for an initial 5 cycles using custom Illumina adapters.
ATAC libraries were prepared used the Nextera DNA Library Prep Kit. 50,000 cells were treated with 2.5 ul transposase for 30 minutes, then amplified for an initial 5 cycles using custom Illumina adapters. The library was quantified using SYBR Gold in a qPCR assay and amplified for a calculated number of additional cycles.

value: Blood

value: bone marrow derived erythroblasts

tag: shRNA target

value: NFIX

tag: markers

value: differentiation day 7


title: NFIX, sh2, Day7, Rep1, ATACseq


title: NFIX, sh2, Day4, Rep2, ATACseq

value: differentiation day 4


title: PN00159_D13-4

description:
Merged_raw_counts.txt
PN0159_0042_S42

value: retina


title: Platelet Sample from Subject 182493, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 27

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample27

source_name: WM989 A6-G3, clone 94

value: WM989 A6-G3, clone 94


title: Platelet Sample from Subject 182492, 28 Days Post Vaccination

value: Female


title: NFIX, sh2, Day4, Rep1, ATACseq


title: PN00159_D9-4

description:
Merged_raw_counts.txt
PN0159_0040_S40


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 26

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample26

source_name: WM989 A6-G3, clone 93

value: WM989 A6-G3, clone 93


title: NFIX, sh1, Day7, Rep2, ATACseq


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 25

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample25

source_name: WM989 A6-G3, clone 92

value: WM989 A6-G3, clone 92


title: Platelet Sample from Subject 182492, 2 Days Post Vaccination

value: Young


title: PN00159_D5-4

description:
Merged_raw_counts.txt
PN0159_0038_S38


title: Platelet Sample from Subject 182493, 7 Days Post Vaccination

value: Male

value: 7 Days Post-Vaccination


title: NFIX, sh1, Day7, Rep1, ATACseq


title: NFIX, sh1, Day4, Rep2, ATACseq


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 23

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample23

source_name: WM989 A6-G3, clone 90

value: WM989 A6-G3, clone 90

value: Human melanoma cells

value: BRAF - V600E

value: Treatment with therapy drugs


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 24

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample24

source_name: WM989 A6-G3, clone 91

value: WM989 A6-G3, clone 91

value: Experiment set 2, Expanded over months


title: PN00159_C9-4

description:
Merged_raw_counts.txt
PN0159_0039_S39


title: Control, Day7, Rep2, ATACseq

growth_protocol:
Control BM-derived erythroid progenitor were differentiated using the three phase EDM.  The differentiation state of the cells was determined by staining the cells with fluorescently conjugated antibodies specific to erythroid surface markers: CD36-FITC (Becton, Dickinson, and Company, 20 µL/test), CD71-APC (Becton, Dickinson, and Company, 20 µL/test) and CD235a-BV421 (Becton, Dickinson, and Company, 5 µL/test).
See sample-specific growth protocols.

value: Blood

value: bone marrow derived erythroblasts

value: Control

value: differentiation day 7


title: Platelet Sample from Subject 182491, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: Platelet Sample from Subject 182491, 7 Days Post Vaccination

value: Female


title: Control, Day7, Rep1, ATACseq


title: Platelet Sample from Subject 182490, 28 Days Post Vaccination

value: 28 Days Post-Vaccination


title: PN00159_C5-4

description:
Merged_raw_counts.txt
PN0159_0037_S37

value: retina


title: Platelet Sample from Subject 182491, 28 Days Post Vaccination

value: Young


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 22

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample22

source_name: WM989 A6-G3, clone 89

value: WM989 A6-G3, clone 89


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 28

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample28

source_name: WM989 A6-G3, clone 95

value: WM989 A6-G3, clone 95


title: PN00159_C13-4

description:
Merged_raw_counts.txt
PN0159_0041_S41


title: Control, Day5, Rep1, ATACseq

value: differentiation day 5


title: PN00159_C1-4

description:
Merged_raw_counts.txt
PN0159_0035_S35


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 20

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample20

source_name: WM989 A6-G3, clone 87

value: WM989 A6-G3, clone 87

value: Human melanoma cells


title: Platelet Sample from Subject 182490, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: Platelet Sample from Subject 182490, 2 Days Post Vaccination


title: CB, Population7, Donor1, ATACseq

growth_protocol:
BM- and CB-derived erythroid progenitor cells were differentiated using the three phase EDM.  The differentiation state of the cells was determined by staining the cells with fluorescently conjugated antibodies specific to erythroid surface markers: CD36-FITC (Becton, Dickinson, and Company, 20 µL/test), CD71-APC (Becton, Dickinson, and Company, 20 µL/test) and CD235a-BV421 (Becton, Dickinson, and Company, 5 µL/test). The antibody co-stained cells were subjected to FACS (Sony SH800, Sony Biotechnology) and were gated based on differential expression of CD36, CD71 and CD235a on different days of erythroid differentiation.
See sample-specific growth protocols.

value: cord blood derived erythroblasts

value: differentiation day 11


title: PN00159_D1-4

description:
Merged_raw_counts.txt
PN0159_0036_S36


title: Platelet Sample from Subject 182489, 2 Days Post Vaccination

value: Male


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 18

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample18

source_name: WM989 A6-G3, clone 85

value: WM989 A6-G3, clone 85

value: BRAF - V600E

value: Treatment with therapy drugs

value: Experiment set 2, Expanded over months


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 16

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample16

source_name: WM989 A6-G3, clone 83

value: WM989 A6-G3, clone 83


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 19

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample19

source_name: WM989 A6-G3, clone 86

value: WM989 A6-G3, clone 86


title: Platelet Sample from Subject 182488, 28 Days Post Vaccination

value: Female

value: 28 Days Post-Vaccination


title: Platelet Sample from Subject 182489, 7 Days Post Vaccination

value: Young


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 17

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample17

source_name: WM989 A6-G3, clone 84

value: WM989 A6-G3, clone 84


title: Platelet Sample from Subject 182489, 28 Days Post Vaccination


title: Platelet Sample from Subject 182492, 7 Days Post Vaccination


title: PN00159_C13-3

description:
Merged_raw_counts.txt
PN0159_0029_S29

source_name: retina

value: retina


title: PN00159_D17-3

description:
Merged_raw_counts.txt
PN0159_0032_S32


title: PN00159_C21-3

description:
Merged_raw_counts.txt
PN0159_0033_S33


title: CB, Population3, Donor1, ATACseq

value: Blood

value: differentiation day 4


title: PN00159_D9-3

description:
Merged_raw_counts.txt
PN0159_0028_S28


title: CB, Population6, Donor1, ATACseq


title: PN00159_D13-3

description:
Merged_raw_counts.txt
PN0159_0030_S30


title: CB, Population4, Donor1, ATACseq


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 21

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample21

source_name: WM989 A6-G3, clone 88

value: WM989 A6-G3, clone 88

value: Human melanoma cells


title: CB, Population2, Donor1, ATACseq

value: cord blood derived erythroblasts

value: differentiation day 0


title: Platelet Sample from Subject 182488, 2 Days Post Vaccination

source_name: platelet

value: 2 Days Post-Vaccination


title: PN00159_D21-3

description:
Merged_raw_counts.txt
PN0159_0034_S34


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 13

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample13

source_name: WM989 A6-G3, clone 80

value: WM989 A6-G3, clone 80

value: BRAF - V600E


title: Control, Day4, Rep2, ATACseq

source_name: Blood

value: bone marrow derived erythroblasts

value: Control


title: CB, Population5, Donor1, ATACseq

value: differentiation day 11


title: PN00159_C17-3

description:
Merged_raw_counts.txt
PN0159_0031_S31


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 15

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample15

source_name: WM989 A6-G3, clone 82

value: WM989 A6-G3, clone 82

value: Treatment with therapy drugs

value: Experiment set 2, Expanded over months


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 14

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample14

source_name: WM989 A6-G3, clone 81

value: WM989 A6-G3, clone 81


title: CB, Population1, Donor1, ATACseq


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 11

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample11

source_name: WM989 A6-G3, clone 78

value: WM989 A6-G3, clone 78


title: Platelet Sample from Subject 182488 Pre-vaccination

value: Female

value: Young

value: Pre-vaccination


title: Platelet Sample from Subject 182487, 28 Days Post Vaccination

value: Male

value: 28 Days Post-Vaccination


title: Platelet Sample from Subject 182487, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: PN00159_D5-3

description:
Merged_raw_counts.txt
PN0159_0026_S26

value: retina


title: PN00159_C9-3

description:
Merged_raw_counts.txt
PN0159_0027_S27


title: BM, Population5, Donor1, ATACseq

value: Blood

value: differentiation day 10


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 10

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample10

source_name: WM989 A6-G3, clone 77

value: WM989 A6-G3, clone 77

value: Human melanoma cells

value: BRAF - V600E


title: BM, Population6, Donor1, ATACseq

value: bone marrow derived erythroblasts


title: PN00159_C5-3

description:
Merged_raw_counts.txt
PN0159_0025_S25


title: BM, Population4, Donor1, ATACseq

value: differentiation day 4


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 08

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample8

source_name: WM989 A6-G3, clone 75

value: WM989 A6-G3, clone 75

value: Treatment with therapy drugs

value: Experiment set 2, Expanded over months


title: Platelet Sample from Subject 182487, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: Platelet Sample from Subject 182487 Pre-vaccination

value: Young


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 12

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample12

source_name: WM989 A6-G3, clone 79

value: WM989 A6-G3, clone 79


title: PN00159_C1-3

description:
Merged_raw_counts.txt
PN0159_0023_S23


title: Platelet Sample from Subject 182486, 28 Days Post Vaccination

value: Female


title: BM, Population3, Donor1, ATACseq


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 07

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample7

source_name: WM989 A6-G3, clone 74

value: WM989 A6-G3, clone 74


title: PN00159_D21-2

description:
Merged_raw_counts.txt
PN0159_0021_S21


title: PN00159_C21-2

description:
Merged_raw_counts.txt
PN0159_0022_S22


title: BM, Population7, Donor1, ATACseq


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 06

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample6

source_name: WM989 A6-G3, clone 73

value: WM989 A6-G3, clone 73


title: BM, Population1, Donor1, ATACseq

value: differentiation day 0


title: Platelet Sample from Subject 182486, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: PN00159_D1-3

description:
Merged_raw_counts.txt
PN0159_0024_S24

value: retina


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 09

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample9

source_name: WM989 A6-G3, clone 76

value: WM989 A6-G3, clone 76


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 05

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample5

source_name: WM989 A6-G3, clone 72

value: WM989 A6-G3, clone 72

value: Human melanoma cells


title: Platelet Sample from Subject 182486, 2 Days Post Vaccination


title: PN00159_C17-2

description:
Merged_raw_counts.txt
PN0159_0020_S20


title: PN00159_C13-2

description:
Merged_raw_counts.txt
PN0159_0019_S19


title: HUDEP2, ATACseq

description: hudep1_hudep2_atacseq_reads_in_peaks.txt

source_name: Umbilical cord blood

growth_protocol:
Cells were maintained in StemSpan™ SFEM (Stemcell Technologies) supplemented with dexamethasone (Sigma), doxycycline (Sigma), SCF (R&D Systems), and erythropoietin (R&D Systems).
See sample-specific growth protocols.

value: Umbilical cord blood


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 04

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample4

source_name: WM989 A6-G3, clone 71

value: WM989 A6-G3, clone 71

value: BRAF - V600E


title: BM, Population2, Donor1, ATACseq

value: Blood

value: bone marrow derived erythroblasts


title: PN00159_D9-2

description:
Merged_raw_counts.txt
PN0159_0018_S18

source_name: retina


title: PN00159_C9-2

description:
Merged_raw_counts.txt
PN0159_0017_S17


title: HUDEP1, ATACseq


title: PN00159_D5-2

description:
Merged_raw_counts.txt
PN0159_0016_S16


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 03

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample3

source_name: WM989 A6-G3, clone 70

value: WM989 A6-G3, clone 70

value: Treatment with therapy drugs

value: Experiment set 2, Expanded over months


title: PN00159_C5-2

description:
Merged_raw_counts.txt
PN0159_0015_S15


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 02

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample2

source_name: WM989 A6-G3, clone 69

value: WM989 A6-G3, clone 69


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 01

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample1

source_name: WM989 A6-G3, clone 68

value: WM989 A6-G3, clone 68


title: Platelet Sample from Subject 182419, 2 Days Post Vaccination

source_name: platelet

value: Female

value: Older

value: 2 Days Post-Vaccination


title: Platelet Sample from Subject 182420, 2 Days Post Vaccination

value: Male


title: Platelet Sample from Subject 182419, 28 Days Post Vaccination

value: 28 Days Post-Vaccination


title: PN00159_D1-2

description:
Merged_raw_counts.txt
PN0159_0014_S14

value: retina


title: Isolated and expanded melanoma WM989 resistant clone 67

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC67

source_name: WM989 A6-G3, clone 67

value: WM989 A6-G3, clone 67

value: Human melanoma cells

value: Experiment set 1, Expanded over months


title: Isolated and expanded melanoma WM989 resistant clone 66

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC66

source_name: WM989 A6-G3, clone 66

value: WM989 A6-G3, clone 66

value: BRAF - V600E


title: Platelet Sample from Subject 182418, 28 Days Post Vaccination


title: PN00159_C1-2

description:
Merged_raw_counts.txt
PN0159_0013_S13


title: Isolated and expanded melanoma WM989 resistant clone 65

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC65

source_name: WM989 A6-G3, clone 65

value: WM989 A6-G3, clone 65


title: Platelet Sample from Subject 182420, 28 Days Post Vaccination


title: Platelet Sample from Subject 182488, 7 Days Post Vaccination

value: Young

value: 7 Days Post-Vaccination


title: PN00159_D21-1

description:
Merged_raw_counts.txt
PN0159_0012_S12


title: wild type R4

city: Cassina Rizzardi

first: Veronica

middle: Maria

last: Beretta

state: Co

address: Via A. Vivaldi 36

country: Italy

institute: Università degli Studi di Milano

data_processing:
The raw RNA-seq files were processed using the TuxNet interface (Spurney et al., 2019).
Reads were cleaned, mapped on the O. sativa reference genome (IRGSP-1.0), normalised, and FPKMs (Fragment per kilobase of transcript per million mapped reads) were calculated
performing a pairwise differential expression analysis between the wild type and mutant, the TuxNet interface generated Differentially Expressed Gene (DEG) datasets
Assembly: reference genome IRGSP-1.0
Supplementary files format and content: FPKM_Replicates.xlsx excel file that contains the FPKM values of each of the replicates
Supplementary files format and content: complete_table.xlsx excel file that contains the expression values, log2 fold changes, and q-values

organism: Oryza sativa Japonica Group

source_name: meristems at early developmental stages enriched in PBMs and ePBM/Ams

growth_protocol: pants sown in growth chamber under LD condition (70% humidity, 16h light at 28°C/8h dark at 26°C) sampled after 12 day of induction in SD conditions (70% humidity, 12h light at 28°C/12h dark at 26°C)

extract_protocol:
RNA was extracted from the samples using RNeasy Plant Mini Kit from Qiagene.
cDNA libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (E7370) according to the manufacturer’s instructions.

tag: cultivar

value: Nipponbare

value: meristematic cells

value: wild type control

value: pants sown in growth chamber under LD conditions, sampled after 12 days in SD conditions


title: Platelet Sample from Subject 182418, 7 Days Post Vaccination

value: Female

value: Older


title: wild type R2

treatment_protocol: 12 day of induction in SD conditions (70% humidity, 12h light at 28°C/12h dark at 26°C)

value: meristems at early developmental stages enriched in PBMs and ePBM/Ams


title: Platelet Sample from Subject 182419, 7 Days Post Vaccination


title: Platelet Sample from Subject 182418, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: PN00159_C17-1

description:
Merged_raw_counts.txt
PN0159_0009_S9

value: retina


title: Isolated and expanded melanoma WM989 resistant clone 61

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC61

source_name: WM989 A6-G3, clone 61

value: WM989 A6-G3, clone 61

value: Treatment with therapy drugs


title: PN00159_D13-1

description:
Merged_raw_counts.txt
PN0159_0008_S8


title: Isolated and expanded melanoma WM989 resistant clone 64

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC64

source_name: WM989 A6-G3, clone 64

value: WM989 A6-G3, clone 64

value: Human melanoma cells

value: Experiment set 1, Expanded over months


title: Platelet Sample from Subject 182417, 28 Days Post Vaccination

value: Male

value: 28 Days Post-Vaccination


title: Platelet Sample from Subject 182417, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: osg1l2 R4

value: Nipponbare

value: osg1l2 single mutant


title: osg1l2 R3

value: meristematic cells


title: Isolated and expanded melanoma WM989 resistant clone 60

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC60

source_name: WM989 A6-G3, clone 60

value: WM989 A6-G3, clone 60

value: BRAF - V600E


title: PN00159_C13-1

description:
Merged_raw_counts.txt
PN0159_0007_S7


title: osg1l2 R2

value: pants sown in growth chamber under LD conditions, sampled after 12 days in SD conditions


title: Platelet Sample from Subject 182417, 2 Days Post Vaccination

value: Older


title: Isolated and expanded melanoma WM989 resistant clone 59

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC59

source_name: WM989 A6-G3, clone 59

value: WM989 A6-G3, clone 59


title: wild type R3

value: meristems at early developmental stages enriched in PBMs and ePBM/Ams

value: wild type control


title: PN00159_C21-1

description:
Merged_raw_counts.txt
PN0159_0011_S11

value: retina


title: osg1l2 R1


title: Isolated and expanded melanoma WM989 resistant clone 58

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC58

source_name: WM989 A6-G3, clone 58

value: WM989 A6-G3, clone 58

value: Treatment with therapy drugs


title: PN00159_D17-1

description:
Merged_raw_counts.txt
PN0159_0010_S10


title: Platelet Sample from Subject 182417 Pre-vaccination

value: Pre-vaccination


title: Isolated and expanded melanoma WM989 resistant clone 62

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC62

source_name: WM989 A6-G3, clone 62

value: WM989 A6-G3, clone 62

value: Human melanoma cells

value: Experiment set 1, Expanded over months


title: PN00159_C9-1

description:
Merged_raw_counts.txt
PN0159_0005_S5


title: Platelet Sample from Subject 182418 Pre-vaccination

value: Female


title: Platelet Sample from Subject 182416, 28 Days Post Vaccination

value: Male

value: 28 Days Post-Vaccination


title: Isolated and expanded melanoma WM989 resistant clone 57

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC57

source_name: WM989 A6-G3, clone 57

value: WM989 A6-G3, clone 57


title: PN00159_D9-1

description:
Merged_raw_counts.txt
PN0159_0006_S6


title: Platelet Sample from Subject 182416, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: PN00159_C5-1

description:
Merged_raw_counts.txt
PN0159_0003_S3


title: Platelet Sample from Subject 182416, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: Isolated and expanded melanoma WM989 resistant clone 55

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC55

source_name: WM989 A6-G3, clone 55

value: WM989 A6-G3, clone 55

value: BRAF - V600E


title: Treg_FE_Rep1

city: Luxembourg

first: Etienne

last: Moussay

address: 6 rue Nicolas-Ernest Barblé

department: Cancer Research

country: Luxembourg

institute: Luxembourg Institute of Health

description: healthy

data_processing:
After initial QCs using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/), fastq files were processed using a local Snakemake workflow including the following main steps.
First, raw reads were trimmed from their UMI index, poly A and adapter sequences using a combination of dedicated scripts and cutadapt (v2.10).
Next, filtered reads were submitted for mapping (STAR v2.5.3a) on the Mouse Reference genome (GRCm38).
Collapsing of reads originating from the same fragment was achieved with umi_tools (v 1.0.0) and counting was perfomed with featureCounts (subread v2.0.0).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Table with raw gene counts for every gene and every sample

source_name: Spleen

extract_protocol:
Spleens were removed, gently dissociated on ice, and cells were antibody-stained and sorted by FACS (Aria III). Cells were activated in vitro with plate-bound anti-CD3 (2μg/ml), anti-CD28 (2μg/ml) and IL-2 (10 ng/mL) for 72h. RNA was harvested and isolated using NucleoZOL reagent and columns. QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina was used with 500 ng of total RNA for the construction of sequencing libraries. UMI were added to the protocol.
Libraries were prepared for sequencing using standard protocols
3'-RNA-Seq

tag: strain

value: Foxp3 YFP/cre Ebi3 -/-

value: T cells

tag: phenotype

value: Treg


title: Treg_FE_Rep2

description: healthy


title: Treg_F_Rep3

description: healthy

value: Foxp3 YFP/cre


title: Isolated and expanded melanoma WM989 resistant clone 54

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC54

source_name: WM989 A6-G3, clone 54

value: WM989 A6-G3, clone 54

value: Treatment with therapy drugs


title: Platelet Sample from Subject 182416 Pre-vaccination

value: Older

value: Pre-vaccination


title: Treg_F_Rep2

description: healthy


title: PN00159_C1-1

description:
Merged_raw_counts.txt
PN0159_0001_S1

source_name: retina

tag: tissue

value: retina


title: Platelet Sample from Subject 182420, 7 Days Post Vaccination


title: wild type R1

value: Nipponbare

value: meristems at early developmental stages enriched in PBMs and ePBM/Ams

value: meristematic cells

value: wild type control

value: pants sown in growth chamber under LD conditions, sampled after 12 days in SD conditions


title: Platelet Sample from Subject 182415, 28 Days Post Vaccination

value: Female

value: 28 Days Post-Vaccination


title: Treg_FE_Rep3

description: healthy


title: Treg_F_Rep1

description: healthy


title: Isolated and expanded melanoma WM989 resistant clone 53

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC53

source_name: WM989 A6-G3, clone 53

value: WM989 A6-G3, clone 53

value: Human melanoma cells

value: BRAF - V600E

value: Experiment set 1, Expanded over months


title: Isolated and expanded melanoma WM989 resistant clone 52

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC52

source_name: WM989 A6-G3, clone 52

value: WM989 A6-G3, clone 52


title: Platelet Sample from Subject 182415, 7 Days Post Vaccination

source_name: platelet

value: 7 Days Post-Vaccination


title: PN00159_D5-1

description:
Merged_raw_counts.txt
PN0159_0004_S4


title: Platelet Sample from Subject 182415, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: Isolated and expanded melanoma WM989 resistant clone 51

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC51

source_name: WM989 A6-G3, clone 51

value: WM989 A6-G3, clone 51

value: Treatment with therapy drugs


title: CD4_FE_Rep3

description: healthy

value: Foxp3 YFP/cre Ebi3 -/-

value: T cells


title: PN00159_D1-1

description:
Merged_raw_counts.txt
PN0159_0002_S2

value: retina


title: Isolated and expanded melanoma WM989 resistant clone 56

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC56

source_name: WM989 A6-G3, clone 56

value: WM989 A6-G3, clone 56


title: Platelet Sample from Subject 182414, 28 Days Post Vaccination

value: Older


title: Isolated and expanded melanoma WM989 resistant clone 49

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC49

source_name: WM989 A6-G3, clone 49

value: WM989 A6-G3, clone 49


title: Isolated and expanded melanoma WM989 resistant clone 50

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC50

source_name: WM989 A6-G3, clone 50

value: WM989 A6-G3, clone 50


title: CD4_FE_Rep2

description: healthy


title: CD4_FE_Rep1

description: healthy


title: CD4_F_Rep3

description: healthy

value: Foxp3 YFP/cre


title: CD4_F_Rep2

description: healthy


title: Platelet Sample from Subject 182414, 2 Days Post Vaccination

value: Female


title: Isolated and expanded melanoma WM989 resistant clone 48

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC48

source_name: WM989 A6-G3, clone 48

value: WM989 A6-G3, clone 48

value: Human melanoma cells


title: Platelet Sample from Subject 182414, 7 Days Post Vaccination


title: Isolated and expanded melanoma WM989 resistant clone 47

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC47

source_name: WM989 A6-G3, clone 47

value: WM989 A6-G3, clone 47

value: BRAF - V600E

value: Experiment set 1, Expanded over months


title: Platelet Sample from Subject 182414 Pre-vaccination

value: Pre-vaccination


title: Platelet Sample from Subject 182413, 28 Days Post Vaccination

value: Male

value: 28 Days Post-Vaccination


title: Isolated and expanded melanoma WM989 resistant clone 45

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC45

source_name: WM989 A6-G3, clone 45

value: WM989 A6-G3, clone 45

value: Treatment with therapy drugs


title: CD8_FE_Rep3

description: healthy

value: Foxp3 YFP/cre Ebi3 -/-

value: T cells


title: Isolated and expanded melanoma WM989 resistant clone 46

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC46

source_name: WM989 A6-G3, clone 46

value: WM989 A6-G3, clone 46


title: CD8_FE_Rep2

description: healthy


title: Isolated and expanded melanoma WM989 resistant clone 44

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC44

source_name: WM989 A6-G3, clone 44

value: WM989 A6-G3, clone 44


title: frotal cortex, CSS_control, rep7 [MC_C2A4]

city: Gold Coast

first: Kevin

middle: John

last: Ashton

state: QLD

address: University Drive

department: Health Sciences & Medicine

country: Australia

institute: Bond University

data_processing:
Length normalization, transcript quantification and quasi-mapping against the mouse reference genome (Ensembl release 99) was performed using Salmon v1.1.0
Transcript reads were imported into R/Bioconductor and summarised at the gene level using the tximport package
Assembly: mm10
Supplementary files format and content: Count data summarized at gene level, saved as CSV

source_name: frontal cortex

extract_protocol:
At the end of experimental periods, mice were anaesthetised and brains rapidly removed into ice-cold PBS. One hemisphere was stored in RNAlater and then dissected to obtain FC. Frontal cortex tissue was analysed for 6 T2D and 6 age-matched control mice, and 8 CSS and 8 age-matched control mice. Total RNA extraction  was performed using the Maxwell RSC simplyRNA Tissue Kit (Promega Corporation) on the Maxwell® RSC instrument per manufacturer’s instructions. RNA was eluted into nuclease‑free water, quantitated and RNA integrity (via RIN) assessed.
Library preparation (1.5ug total RNA) was undertaken for whole transcriptome sequencing using the TruSeq® Stranded Total RNA Library Prep kit, with the Ribo Zero Gold rRNA depletion kit, both of which are available from llumina.

treatment_protocol: Mice subjected to either chronic social stress (CSS) - social isolation for 7 wks + twice daily social confrontation in final 20 days; type 2 diabetes (T2D) - 75 mg.kg-1 streptozotocin/21 wk high-fat diet (43.2% kcal as fat); or control conditions.

value: frontal cortex

tag: Sex

value: male

tag: age weeks

tag: rin


title: frotal cortex, CSS_control, rep8 [MC_C3A4]


title: Isolated and expanded melanoma WM989 resistant clone 43

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC43

source_name: WM989 A6-G3, clone 43

tag: cell line

value: WM989 A6-G3, clone 43

tag: cell type


title: frotal cortex, CSS_control, rep6 [MC_C2A3]

tag: treatment


title: CD8_FE_Rep1

description: healthy

source_name: Spleen


title: CD4_F_Rep1

description: healthy

value: Foxp3 YFP/cre


title: Platelet Sample from Subject 182413, 7 Days Post Vaccination

value: Older

value: 7 Days Post-Vaccination


title: Isolated and expanded melanoma WM989 resistant clone 42

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC42

source_name: WM989 A6-G3, clone 42

value: WM989 A6-G3, clone 42

value: Human melanoma cells

tag: genotype

value: BRAF - V600E

tag: time


title: Platelet Sample from Subject 182412, 28 Days Post Vaccination

tag: subject id

value: Male


title: Platelet Sample from Subject 182413, 2 Days Post Vaccination

tag: gender

value: 2 Days Post-Vaccination


title: Isolated and expanded melanoma WM989 resistant clone 41

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC41

source_name: WM989 A6-G3, clone 41

value: WM989 A6-G3, clone 41

value: Experiment set 1, Expanded over months


title: CD8_F_Rep2

description: healthy


title: Platelet Sample from Subject 182412, 2 Days Post Vaccination

tag: time point relative to flu vaccination


title: frotal cortex, CSS_control, rep4 [MC_C1A4]


title: frotal cortex, CSS_control, rep5 [MC_C2A2]


title: Platelet Sample from Subject 182412, 7 Days Post Vaccination


title: Isolated and expanded melanoma WM989 resistant clone 40

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC40

source_name: WM989 A6-G3, clone 40

value: WM989 A6-G3, clone 40

value: Treatment with therapy drugs


title: Isolated and expanded melanoma WM989 resistant clone 63

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC63

source_name: WM989 A6-G3, clone 63

value: WM989 A6-G3, clone 63


title: CD8_F_Rep1

description: healthy

value: T cells


title: frotal cortex, CSS_control, rep3 [MC_C1A3]

value: frontal cortex


title: Platelet Sample from Subject 182411, 7 Days Post Vaccination

source_name: platelet


title: ko, ADT

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

description:
P14 RosaYFP+/- Stat5a/bfl/fl  treated with tat-cre in vitro, transferred into LCMV Cl13 mice and isolated  at D27p.i.,ADT-derived cDNA
wt cell surface protein library
Antibody-derived oligonucleotide (ADT)

library_source: other

data_processing:
A UMI count matrix was created for P14 WT and P14 Stat5iKO cells using CellRanger 4.0.0. and the two matrixes were used to create Seurat objects. For each sample, an antibody (“adt”) assay was created and added to its cognate Seurat object (WT or Stat5iKO) that were subsequently merged into one object containing rna and adt counts for each sample
Cells with fewer than 200 or greater than 2500 detected genes were excluded from downstream analysis as of cells with >12% of mitochondrial gene counts. Genes which expression was detected in 3 cells or less were excluded
A total of 4377 P14 WT and 4906 P14 Stat5iKO cells passed filters with an average sequencing depth of 1210 genes per cell and were considered for downstream analysis. Counts (rna assay) were then normalized, and the top 2000 variable features were scaled before running linear dimensional reduction (PCA). The 30 most significant PCs were used as input for unsupervised clustering using the “FindNeighbors” and “FindClusters” functions of Seurat with a resolution of 0.1
DEGs were identified by the Seurat function “FindAllMarkers” with min.pct=0.25 and logfc.threshold=0.25
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: P14 Cells

extract_protocol:
CITEseq samples from duplicate experiments were prepared as described above (scRNAseq section) and processed according to the CITE-seq protocol from the New York Center Technology Innovation Lab (https://cite-seq.com/protocols/). Briefly, enriched CD8 T cells were incubated for 10’ at 4oC in Staining buffer (2%BSA/0.01% Tween in PBS) containing FcBlock (1/10 dilution ;TruStainTM FcX, Biolegend) followed by a 30’ incubation in Staining Buffer containing TotalSeqB antibodies against Ly108, CD69, Tim-3, PD-1, CD127, CD122, Lag-3, CD38 and KLRG1 (BioLegend) previously titrated according to manufacturer’s protocol using PE-conjugated version of each antibodies
Samples were then washed, sorted as described above, down-sampled and equivalent number of cells (104) between samples were loaded onto the Chip (Chromium Next GEM Chip G) of a Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Dual Index, 10x Genomics) and run onto a Chromium Controller. Samples were then processed according to manufacturer’s protocol.
Gene expression and Cell surface Protein libraries were constructed using Dual Index TT Set A and Dual Index NT Set A (10x Genomics) respectively. Libraries were quantified by qPCR using a KAPA Library Quant Kit (KAPA Biosystems). Normalized libraries were pooled (0.23nM), diluted to 1.8pg/ml and loaded onto a NextSeq 500/550 High Output Kit v2.5 (150 cycles, Illumina) and paired-end sequencing was performed on a NextSeq 550 (Illumina).

value: ko

value: P14 Cells

tag: library type

value: ADT


title: Platelet Sample from Subject 182411, 28 Days Post Vaccination

value: Older

value: 28 Days Post-Vaccination


title: Isolated and expanded melanoma WM989 resistant clone 39

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC39

source_name: WM989 A6-G3, clone 39

value: WM989 A6-G3, clone 39


title: frotal cortex, CSS_control, rep2 [MC_C1A2]

value: male


title: wt, ADT

description:
P14 RosaYFP+/- Stat5a/b+/+  treated with tat-cre in vitro, transferred into LCMV Cl13 mice and isolated  at D27p.i.,ADT-derived cDNA
wt cell surface protein library
Antibody-derived oligonucleotide (ADT)

value: wt


title: CD8_F_Rep3

description: healthy

value: Foxp3 YFP/cre


title: Isolated and expanded melanoma WM989 resistant clone 38

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC38

source_name: WM989 A6-G3, clone 38

value: WM989 A6-G3, clone 38

value: Human melanoma cells

value: BRAF - V600E


title: Platelet Sample from Subject 182411, 2 Days Post Vaccination

value: Male

value: 2 Days Post-Vaccination


title: frotal cortex, CSS_control, rep1 [MC_C1A1]


title: frotal cortex, CSS, rep8 [MSS_C4A3]

value: CSS


title: Isolated and expanded melanoma WM989 resistant clone 37

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC37

source_name: WM989 A6-G3, clone 37

value: WM989 A6-G3, clone 37

value: Treatment with therapy drugs

value: Experiment set 1, Expanded over months


title: ko, GEX

description:
P14 RosaYFP+/- Stat5a/bfl/fl  treated with tat-cre in vitro, transferred into LCMV Cl13 mice and isolated  at D27p.i.,mRNA-derived cDNA
ko gene expression library
poly A RNA

molecule: polyA RNA

value: ko

value: P14 Cells

value: mRNA


title: Platelet Sample from Subject 182410, 28 Days Post Vaccination

value: Female

value: Older

value: 28 Days Post-Vaccination


title: wt, GEX

description:
P14 RosaYFP+/- Stat5a/b+/+  treated with tat-cre in vitro, transferred into LCMV Cl13 mice and isolated  at D27p.i., mRNA-derived cDNA
wt gene expression library
poly A RNA

value: wt


title: Isolated and expanded melanoma WM989 resistant clone 36

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC36

source_name: WM989 A6-G3, clone 36

value: WM989 A6-G3, clone 36


title: Isolated and expanded melanoma WM989 resistant clone 35

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC35

source_name: WM989 A6-G3, clone 35

value: WM989 A6-G3, clone 35


title: frotal cortex, CSS, rep7 [MSS_C4A2]

value: frontal cortex

value: male


title: Platelet Sample from Subject 182409, 28 Days Post Vaccination


title: Platelet Sample from Subject 182410, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: Platelet Sample from Subject 182410, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: frotal cortex, CSS, rep5 [MSS_C3A4]

value: CSS


title: postChallenge, T3

description: P14 CD8 T cells transduced with a retrovirus encoding an orthogonal IL2Rb, isolated at d26p.i. from LCMV Cl13 infected mice, sorted based on Ly108+RV(YFP)+ transferred into naive secondary recipient, re-challenged with LCMV Arm and isolated at D8 post challenge from mice treated with ortho-IL2 during challenge (D3-7).

data_processing:
The fastqs were aligned to mm10 using bowtie2.
Unmapped, unpaired, and mitochondrial reads were removed using samtools.
ENCODE Blacklist regions were removed.
PCR duplicates were removed using Picard.
Peak calling was performed with MACS2 with a FDR q-value < 0.001
Normalization and differential accessibility analysis was done with DESeq2.
Assembly: mm10
Supplementary files format and content: bw, bed

source_name: P14 CD8 T cell

extract_protocol:
Transposed DNA fragments were purified using a Qiagen Reaction MiniElute Kit, barcoded with NEXTERA dual indexes (Illumina) and amplified by PCR for 11 cycles using NEBNext High Fidelity 2x PCR Master Mix (New England Biolabs)
PCR products were purified using a PCR Purification Kit (Qiagen) and amplified fragments size was verified on a 2200 TapeStation (Agilent Technologies) using High Sensitivity D1000 ScreenTapes (Agilent Technologies). Libraries were quantified by qPCR using a KAPA Library Quant Kit (KAPA Biosystems). Normalized libraries were pooled, diluted to 1.8pM, loaded onto a NextSeq 500/550 High Output Kit v2.5 (150 cycles, Illumina) and paired-end sequencing was performed on a NextSeq 550 (Illumina)

treatment_protocol: Sorted cells (2-to-5x10^4) were washed twice in cold PBS and resuspended in 50ml of cold lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2 and  0.1% IGEPAL CA-630),Lysates were centrifuge (750xg, 10min, 4oC) and nuclei were resuspended in 50ul of transposition reaction mix (TD buffer [25ul], Tn5 Transposase [2.5ul], nuclease-free water [22.5ul]; (Illumina)) and incubated for 30min at 37oC

value: P14 CD8 T cell


title: frotal cortex, CSS, rep6 [MSS_C4A1]


title: Platelet Sample from Subject 182409, 7 Days Post Vaccination


title: Isolated and expanded melanoma WM989 resistant clone 34

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC34

source_name: WM989 A6-G3, clone 34

value: WM989 A6-G3, clone 34

value: Human melanoma cells

value: BRAF - V600E

value: Treatment with therapy drugs


title: Isolated and expanded melanoma WM989 resistant clone 32

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC32

source_name: WM989 A6-G3, clone 32

value: WM989 A6-G3, clone 32

value: Experiment set 1, Expanded over months


title: Isolated and expanded melanoma WM989 resistant clone 33

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC33

source_name: WM989 A6-G3, clone 33

value: WM989 A6-G3, clone 33


title: postChallenge, T2


title: postChallenge, T1


title: postChallenge, NT3

description: P14 CD8 T cells transduced with a retrovirus encoding an orthogonal IL2Rb, isolated at d26p.i. from LCMV Cl13 infected mice, sorted based on Ly108+RV(YFP)+ transferred into naive secondary recipient, re-challenged with LCMV Arm and isolated at D8 post challenge from mice treated with PBS during challenge (D3-7).

value: PBS


title: Isolated and expanded melanoma WM989 resistant clone 31

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC31

source_name: WM989 A6-G3, clone 31

value: WM989 A6-G3, clone 31


title: frotal cortex, CSS, rep2 [MSS_C2A3]

source_name: frontal cortex


title: frotal cortex, CSS, rep3 [MSS_C3A2]


title: postChallenge, NT2


title: Platelet Sample from Subject 182409, 2 Days Post Vaccination

value: Female

value: Older


title: Isolated and expanded melanoma WM989 resistant clone 30

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC30

source_name: WM989 A6-G3, clone 30

value: WM989 A6-G3, clone 30


title: Platelet Sample from Subject 182408, 7 Days Post Vaccination


title: Platelet Sample from Subject 182408, 28 Days Post Vaccination

value: 28 Days Post-Vaccination


title: Platelet Sample from Subject 182408, 2 Days Post Vaccination


title: postChallenge, NT1


title: postChallenge, Memory3

description: P14 CD8 T cells isolated at d≥30p.i. from LCMV Armstrong infected mice, transferred into naive secondary recipient, re-challenged with LCMV Arm and isolated at D8 post challenge

value: Memory


title: frotal cortex, CSS, rep4 [MSS_C3A3]

value: frontal cortex

value: male


title: Isolated and expanded melanoma WM989 resistant clone 29

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC29

source_name: WM989 A6-G3, clone 29

value: WM989 A6-G3, clone 29


title: Platelet Sample from Subject 182407, 28 Days Post Vaccination

value: Male


title: Isolated and expanded melanoma WM989 resistant clone 28

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC28

source_name: WM989 A6-G3, clone 28

value: WM989 A6-G3, clone 28

value: Human melanoma cells


title: frotal cortex, T2D_control, rep5 [C92]


title: frotal cortex, T2D_control, rep6 [C93]


title: frotal cortex, CSS, rep1 [MSS_C1A1]

value: CSS


title: Isolated and expanded melanoma WM989 resistant clone 27

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC27

source_name: WM989 A6-G3, clone 27

value: WM989 A6-G3, clone 27

value: BRAF - V600E

value: Treatment with therapy drugs


title: frotal cortex, T2D_control, rep4 [C184]


title: postChallenge, Memory1

value: P14 CD8 T cell


title: Platelet Sample from Subject 182407, 7 Days Post Vaccination

source_name: platelet

value: 7 Days Post-Vaccination


title: frotal cortex, T2D_control, rep3 [C182]


title: Platelet Sample from Subject 182407, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: postChallenge, Naive3

description: CD8 T cells isolated from naïve C57B/6 female mice

source_name: CD8 T cell

value: CD8 T cell

value: Naive


title: postChallenge, Memory2


title: Isolated and expanded melanoma WM989 resistant clone 26

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC26

source_name: WM989 A6-G3, clone 26

value: WM989 A6-G3, clone 26

value: Experiment set 1, Expanded over months


title: postChallenge, Naive2


title: Isolated and expanded melanoma WM989 resistant clone 25

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC25

source_name: WM989 A6-G3, clone 25

value: WM989 A6-G3, clone 25


title: frotal cortex, T2D_control, rep2 [C102]

value: frontal cortex

value: male


title: postChallenge, Naive1


title: Isolated and expanded melanoma WM989 resistant clone 24

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC24

source_name: WM989 A6-G3, clone 24

value: WM989 A6-G3, clone 24


title: Platelet Sample from Subject 182406, 7 Days Post Vaccination

value: Female

value: Older


title: Platelet Sample from Subject 182406, 28 Days Post Vaccination

value: 28 Days Post-Vaccination


title: postInfection, Stat5CA4

description: P14 CD8 T cells transduced with a retrovirus encoding STAT5CA and isolated from LCMV Cl13 infected mice at D8p.i.

source_name: cell type: P14 CD8 T cell


title: Platelet Sample from Subject 182406, 2 Days Post Vaccination


title: Isolated and expanded melanoma WM989 resistant clone 23

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC23

source_name: WM989 A6-G3, clone 23

value: WM989 A6-G3, clone 23

value: Human melanoma cells


title: frotal cortex, T2D, rep6 [T224]


title: Isolated and expanded melanoma WM989 resistant clone 22

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC22

source_name: WM989 A6-G3, clone 22

value: WM989 A6-G3, clone 22

value: BRAF - V600E

value: Treatment with therapy drugs


title: frotal cortex, T2D_control, rep1 [C101]


title: postInfection, Stat5CA3

value: P14 CD8 T cell


title: frotal cortex, T2D, rep5 [T214]


title: postInfection, Stat5CA2


title: Platelet Sample from Subject 182405, 28 Days Post Vaccination


title: frotal cortex, T2D, rep4 [T134]


title: Isolated and expanded melanoma WM989 resistant clone 20

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC20

source_name: WM989 A6-G3, clone 20

value: WM989 A6-G3, clone 20


title: postInfection, Stat5CA1


title: Platelet Sample from Subject 182405, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: Isolated and expanded melanoma WM989 resistant clone 19

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC19

source_name: WM989 A6-G3, clone 19

value: WM989 A6-G3, clone 19


title: postInfection, Empty3

description: P14 CD8 T cells transduced with an Empty (control) retrovirius and isolated from LCMV Cl13 infected mice at D8p.i.

value: Empty


title: frotal cortex, T2D, rep2 [T132]


title: frotal cortex, T2D, rep3 [T133]


title: Isolated and expanded melanoma WM989 resistant clone 18

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC18

source_name: WM989 A6-G3, clone 18

value: WM989 A6-G3, clone 18

value: Experiment set 1, Expanded over months


title: Platelet Sample from Subject 182404, 28 Days Post Vaccination

value: Male


title: postInfection, Empty4


title: Platelet Sample from Subject 182407 Pre-vaccination

value: Pre-vaccination


title: postInfection, Empty2


title: Platelet Sample from Subject 182404, 7 Days Post Vaccination


title: Isolated and expanded melanoma WM989 resistant clone 17

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC17

source_name: WM989 A6-G3, clone 17

value: WM989 A6-G3, clone 17


title: Platelet Sample from Subject 182404, 2 Days Post Vaccination

value: Older

value: 2 Days Post-Vaccination


title: Isolated and expanded melanoma WM989 resistant clone 16

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC16

source_name: WM989 A6-G3, clone 16

value: WM989 A6-G3, clone 16


title: frotal cortex, T2D, rep1 [T131]

source_name: frontal cortex

value: frontal cortex

value: male


title: postInfection, Empty1


title: postInfection, Teff4

description: P14 CD8 T cells isolated from LCMV Armstrong infected mice at D8p.i.

value: Teff


title: Isolated and expanded melanoma WM989 resistant clone 21

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC21

source_name: WM989 A6-G3, clone 21

value: WM989 A6-G3, clone 21

value: Human melanoma cells

value: BRAF - V600E

value: Treatment with therapy drugs


title: Isolated and expanded melanoma WM989 resistant clone 15

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC15

source_name: WM989 A6-G3, clone 15

value: WM989 A6-G3, clone 15


title: Platelet Sample from Subject 182405, 2 Days Post Vaccination

value: Female


title: postInfection, Teff3

value: P14 CD8 T cell


title: postInfection, Teff2


title: Platelet Sample from Subject 182343, 28 Days Post Vaccination

value: Young

value: 28 Days Post-Vaccination


title: postInfection, Teff1


title: Isolated and expanded melanoma WM989 resistant clone 12

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC12

source_name: WM989 A6-G3, clone 12

value: WM989 A6-G3, clone 12

value: Experiment set 1, Expanded over months


title: Isolated and expanded melanoma WM989 resistant clone 13

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC13

source_name: WM989 A6-G3, clone 13

value: WM989 A6-G3, clone 13


title: W_108_3_C

city: tampa

first: Kristen

last: Dominguez

state: FL

address: 9440 leatherwood ave

department: Molecular Medicine

institute: University of South Florida

data_processing:
Read count extraction and normalization were performed using DESeq2
Supplementary files format and content: tab-delimited text files include normalized counts

source_name: colon

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
mRNA library preparation (poly A enrichment)

value: colon

value: epithelial cells

value: Streptococcus agalactiae

value: COH1 (WT)


title: W_113_3_SI

source_name: small intestine

value: small intestine


title: W_108_2_C


title: W_107_1_SI


title: W_107_2_SI


title: W_108_2_SI


title: Platelet Sample from Subject 182343 Pre-vaccination

source_name: platelet

value: Male

value: Pre-vaccination


title: postInfection, Naive3

description: CD8 T cells isolated from naïve C57B/6 female mice

source_name: cell type: CD8 T cell

value: CD8 T cell

value: Naive


title: W_107_3_C


title: postInfection, Naive2


title: Platelet Sample from Subject 182342, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: Platelet Sample from Subject 182341, 2 Days Post Vaccination


title: Platelet Sample from Subject 182342 Pre-vaccination


title: Isolated and expanded melanoma WM989 resistant clone 11

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC11

source_name: WM989 A6-G3, clone 11

value: WM989 A6-G3, clone 11

value: Human melanoma cells

value: BRAF - V600E

value: Treatment with therapy drugs


title: Platelet Sample from Subject 182341, 7 Days Post Vaccination

value: Young

value: 7 Days Post-Vaccination


title: Isolated and expanded melanoma WM989 resistant clone 10

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC10

source_name: WM989 A6-G3, clone 10

value: WM989 A6-G3, clone 10

value: Experiment set 1, Expanded over months


title: W_107_2_C

value: colon

value: epithelial cells


title: postInfection, Naive1


title: Isolated and expanded melanoma WM989 resistant clone 09

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC09

source_name: WM989 A6-G3, clone 9

value: WM989 A6-G3, clone 9


title: sgPbrm1_e7.1+ Cas9+ P14, Replicate B [RNA_sgPbrm1_e7.1_B]

data_processing:
Basecalls was performed using bcltofastq to get raw FASTQ files.
FASTQ files were aligned using STAR 2.7.1a using mm10 Gencode reference genome
Read counts of genes were quantified by STAR using --quantMode GeneCounts parameter.
Normalized and rlog transformed read counts were generated using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read count and normalized read count by DESeq2 values for each Sample

source_name: Splenocytes

growth_protocol: At day 15 post infection with LCMV clone 13, sgRNA+ Cas9+ P14 CD8 T cells were isolated from the spleens of infected recipients.

extract_protocol:
mRNA was isolated using the RNeasy micro kit (QIAGEN), per manufacturers instructions.
cDNA libraries were generated using the SMARTSeq V4 Ultra Low kit (Takara Bio), per manufacturers insturctions. Libraries were quantified by qPCR (KAPA Library Quant Kit, KAPA Biosystems).

treatment_protocol: Isolated P14 CD8 T cells were collected into DNA loBind tubes (Eppendorf) and centrifuged. Pellets were resuspeneded in 350ul of RLT buffer (Rneasy Plus Micro kit, Qiagen), snap frozen on dry ice and stored at -80oC.

value: Splenocytes

value: P14 CD8 T cells

tag: background strain

value: Cas9+ CD4Cre C57BL/6

value: LCMV clone 13 infection

value: Day 15 post-infection


title: W_107_1_C

value: Streptococcus agalactiae

value: COH1 (WT)


title: Platelet Sample from Subject 182343, 7 Days Post Vaccination

value: Male


title: Isolated and expanded melanoma WM989 resistant clone 14

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC14

source_name: WM989 A6-G3, clone 14

value: WM989 A6-G3, clone 14

value: Human melanoma cells

value: BRAF - V600E


title: Platelet Sample from Subject 182341 Pre-vaccination

value: Young

value: Pre-vaccination


title: sgPbrm1_e7.1+ Cas9+ P14, Replicate A [RNA_sgPbrm1_e7.1_A]


title: Isolated and expanded melanoma WM989 resistant clone 08

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC08

source_name: WM989 A6-G3, clone 8

value: WM989 A6-G3, clone 8

value: Treatment with therapy drugs

value: Experiment set 1, Expanded over months


title: Platelet Sample from Subject 182340, 28 Days Post Vaccination

value: Female

value: 28 Days Post-Vaccination


title: sgPbrm1_e4.1+ Cas9+ P14, Replicate B [RNA_sgPbrm1_e4.1_B]

value: Splenocytes

value: P14 CD8 T cells


title: Isolated and expanded melanoma WM989 resistant clone 07

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC07

source_name: WM989 A6-G3, clone 7

value: WM989 A6-G3, clone 7


title: Platelet Sample from Subject 182340, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: P_94_5_SI

value: small intestine

value: epithelial cells

value: Vehicle control (phosphate buffered saline)


title: P_84_6_SI


title: Platelet Sample from Subject 182340, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: Isolated and expanded melanoma WM989 resistant clone 03

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC03

source_name: WM989 A6-G3, clone 3

value: WM989 A6-G3, clone 3

value: Human melanoma cells


title: P_94_1_C

value: colon


title: Isolated and expanded melanoma WM989 resistant clone 06

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC06

source_name: WM989 A6-G3, clone 6

value: WM989 A6-G3, clone 6

value: BRAF - V600E


title: Isolated and expanded melanoma WM989 resistant clone 02

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC02

source_name: WM989 A6-G3, clone 2

value: WM989 A6-G3, clone 2

value: Treatment with therapy drugs


title: sgArid2_e13.1+ Cas9+ P14, Replicate A [RNA_sgArid2_13e1_A]

value: Cas9+ CD4Cre C57BL/6

value: LCMV clone 13 infection

value: Day 15 post-infection


title: P_84_4_SI


title: sgPbrm1_e4.1+ Cas9+ P14, Replicate A [RNA_sgPbrm1_e4.1_A]

value: Splenocytes

value: P14 CD8 T cells


title: Isolated and expanded melanoma WM989 resistant clone 01

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC01

source_name: WM989 A6-G3, clone 1

value: WM989 A6-G3, clone 1

value: Experiment set 1, Expanded over months


title: Platelet Sample from Subject 182338, 2 Days Post Vaccination

value: Female

value: Young


title: sgArid2_e3.1+ Cas9+ P14, Replicate B [RNA_sgArid2_3e1_B]


title: Isolated and expanded melanoma WM989 resistant clone 05

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC05

source_name: WM989 A6-G3, clone 5

value: WM989 A6-G3, clone 5


title: Platelet Sample from Subject 182338 Pre-vaccination

value: Pre-vaccination


title: Platelet Sample from Subject 182340 Pre-vaccination


title: Isolated and expanded melanoma WM989 resistant clone 04

description:
deRandomized_BulkColonySeq_20200220_meltedData_hg19_normalizedRevised.tsv
WM989_RC04

source_name: WM989 A6-G3, clone 4

value: WM989 A6-G3, clone 4

value: Human melanoma cells


title: P_94_5_C

source_name: colon

value: colon

value: epithelial cells

value: Vehicle control (phosphate buffered saline)


title: D_115_3_SI

source_name: small intestine

value: small intestine

value: Streptococcus agalactiae

value: COH1delcylE (KO)


title: sgArid2_e3.1+ Cas9+ P14, Replicate A [RNA_sgArid2_3e1_A]

value: Cas9+ CD4Cre C57BL/6

value: LCMV clone 13 infection

value: Day 15 post-infection


title: 11_PRERT

city: Daegu

first: Incheol

last: Seo

address: 680 gukchaebosang-ro, Jung-gu

country: South Korea

institute: KYUNGPOOK NATIONAL UNIVERSITY INDUSTRY-ACADEMIC COOPERATION FOUNDATION

data_processing:
For quality control, low-quality bases and adapter sequences were trimmed from the raw sequencing reads using Trimmomatic software with default parameters, except that the minimum length of reads to be dropped was 38 bp.
Trimmed sequencing reads were mapped to the hg38 human reference genome using STAR aligner with default parameters.
Reads per gene was counted simultaneously by STAR using the ‘--quantMode GeneCounts’ parameter.
Count normalization were performed DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: primary tumor

extract_protocol:
Total RNA was extracted using TRIzol RNA Isolation Reagent (Life Technologies) from the samples. The quantity and quality of the total RNA were evaluated using an Agilent 2100 bioanalyzer RNA kit.
The isolated total RNA was processed for preparation of an RNA-seq library using an Illumina TruSeq Stranded mRNA Sample Preparation kit according to the manufacturer’s protocol.

value: primary tumor

value: Male

tag: age

value: conventional long-course neoadjuvant CRT (five cycles of 5-fluorouracil (5-FU)-based chemotherapy and 50.4 Gy radiation)

value: before CRT


title: Platelet Sample from Subject 182339, 28 Days Post Vaccination

source_name: platelet

value: Female

value: Young

value: 28 Days Post-Vaccination


title: Platelet Sample from Subject 182337, 28 Days Post Vaccination


title: sgArid2_e13.1+ Cas9+ P14, Replicate B [RNA_sgArid2_13e1_B]

value: Splenocytes

value: P14 CD8 T cells


title: D_112_2_SI

value: epithelial cells


title: Platelet Sample from Subject 182337, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: 10_PRERT


title: P_84_4_C

value: colon

value: Vehicle control (phosphate buffered saline)


title: Platelet Sample from Subject 182338, 28 Days Post Vaccination


title: P_114_4_C


title: sgAno9+ Cas9+ P14, Replicate C [RNA_sgAno9_C]

value: Wild type


title: sgPbrm1_e7.1+ Cas9+ P14, Replicate A [ATAC_sgPbrm1-e71-A_S5]

data_processing:
Paired-end reads were aligned to mm10 reference genome using Bowtie2 v2.3.5.
Picard tools v1.96 was used to remove presumed PCR duplicates using the MarkDuplicates command.
Bam files containing uniquely mapped reads were created using Samtools v1.1
Blacklist regions defined by ENCODE, random chromosomes and mitochondria were removed, and filtered bam files were used for downstream analysis.
Read per million (RPM/CPM) normalized bigwig files were created using deepTools bamCoverage. Replicates were pooled together using wiggleTools and UCSC toolkit bedGraphToBigWig.
Enrichment signals of each sample were called using MACS v2. (adjusted p-value cutoff of 0.01). Consensus peaks shown in at least two replicates per condition were identified using findOverlapsOfPeaks function of R package ChIPpeakAnno. All peaks from each condition were merged using BEDTools to create the final used union peak list for downstream analysis.
Genes proximal to peaks were annotated against the mm10 genome using rGREAT and Homer.
The number of reads under union peak list were determined using BEDTools coverage.
Assembly: mm10
Supplementary files format and content: bigWig, peak with annotation, tab-delimited raw and normalized read count data

extract_protocol:
Transposed DNA fragments were purified using a Qiagen Reaction MiniElute Kit, per manufacturers instrcutions.
DNA fragments were barcoded with NEXTERA dual indexes (Illumina) and amplified by PCR using NEBNext High Fidelity 2x PCR Master Mix (New England Biolabs).

treatment_protocol: Isolated P14 CD8 T cells were collected into DNA loBind tubes (Eppendorf) and centrifuged. Pellets were washed twice in PBS and lysed in lysis buffer (10nM Tris-HCl, pH 7.4, 10mM NaCl, 3mM  MgCl2, 0.1% IGEPAL). Nuclei were centrifuged and resuspended in transposition reaction mix (25ul TD buffer, 2.5ul Tn5 Transposase, 22.5 nuclease-free water per sample; (Illumina)) and incubated for 30min at 37oC.

value: Cas9+ CD4Cre C57BL/6


title: P_114_4_SI

value: small intestine


title: 11_POSTRT

value: after CRT


title: D_115_3_C

value: Streptococcus agalactiae

value: COH1delcylE (KO)


title: sgAno9+ Cas9+ P14, Replicate B [RNA_sgAno9_B]

value: LCMV clone 13 infection

value: Day 15 post-infection


title: Platelet Sample from Subject 182339, 7 Days Post Vaccination

value: Female


title: 9_PRERT

value: primary tumor

value: Male

value: conventional long-course neoadjuvant CRT (five cycles of 5-fluorouracil (5-FU)-based chemotherapy and 50.4 Gy radiation)

value: before CRT


title: sgAno9+ Cas9+ P14, Replicate A [RNA_sgAno9_A]

value: Splenocytes

value: P14 CD8 T cells


title: Platelet Sample from Subject 182336, 28 Days Post Vaccination

value: Young

value: 28 Days Post-Vaccination


title: sgPbrm1_e4.1+ Cas9+ P14, Replicate A [ATAC_sgPbrm1-e41-A_S3]


title: D_112_4_C

value: colon

value: epithelial cells


title: sgPbrm1_e7.1+ Cas9+ P14, Replicate B [ATAC_sgPbrm1-e71-B_S4]

value: Cas9+ CD4Cre C57BL/6


title: D_111_6_C


title: Platelet Sample from Subject 182337, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: D_115_8_SI

value: small intestine

value: Streptococcus agalactiae


title: sgArid2_e3.1+ Cas9+ P14, Replicate B [ATAC_sgArid2-e131-B_S9]

value: LCMV clone 13 infection


title: sgPbrm1_e4.1+ Cas9+ P14, Replicate B [ATAC_sgPbrm1-e41-B_S6]

value: Day 15 post-infection


title: D_111_4_C

value: COH1delcylE (KO)


title: 10_POSTRT

value: primary tumor

value: after CRT


title: 8_PRERT

value: Male

value: conventional long-course neoadjuvant CRT (five cycles of 5-fluorouracil (5-FU)-based chemotherapy and 50.4 Gy radiation)


title: 8_POSTRT


title: sgArid2_e3.1+ Cas9+ P14, Replicate A [ATAC_sgArid2-e131-A_S8]

value: Splenocytes


title: 7_POSTRT


title: D_115_8_C


title: 9_POSTRT


title: Platelet Sample from Subject 182336, 7 Days Post Vaccination

value: Female

value: 7 Days Post-Vaccination


title: 6_POSTRT


title: sgArid2_e13.1+ Cas9+ P14, Replicate B [ATAC_sgArid2-e31-B_S1]

value: P14 CD8 T cells


title: 7_PRERT

value: before CRT


title: Platelet Sample from Subject 182335, 2 Days Post Vaccination

value: Young


title: Platelet Sample from Subject 182335, 7 Days Post Vaccination


title: sgArid2_e13.1+ Cas9+ P14, Replicate A [ATAC_sgArid2-e31-A_S7]

value: Cas9+ CD4Cre C57BL/6


title: LCMV7: Cl13D30, scATAC

description: P14 CD8 T cells from LCMV Clone13 infection 30 days post infection

data_processing:
scRNA-seq and scATAC-seq sample demultiplexing, barcode processing, alignment, filtering, unique molecular identifier (UMI) counting and aggregating sequencing runs were performed using 10x Cell Ranger pipeline (6.0.0) and mm10 genome.
Downstream scRNA-seq amd scATAC-seq analysis was performed in R (version 4.0.2) using Signac and Archr packages
Union peak list was generated using peaks called in ArchR and using macs2 with sample bam files.
Assembly: GRCm38/mm10
Supplementary files format and content: Filtered feature-barcode matrices containing only cellular barcodes corresponding to gene expression and chromatin accessibility

source_name: P14 CD8 T cells

extract_protocol:
Cells were loaded onto the Chromium Controller (10x Genomics) for a target recovery of 10,000 single cells.
The scRNAseq and scATACseq libraries were generated using 10x Genomics multiome coAssay according to the manufacturer’s protocol.

treatment_protocol: PD1 blockade was performed with 5 treatments of 200ug aPD-L1 antibody (10F.9G2, BioXCell) i.p. every 3 days starting 16 days after infection with LCMV Cl13. Analysis was performed one day after final treatment. For control treatments, phosphate-buffered saline (PBS) was administered i.p.

value: CD8 T cells


title: LCMV8: Cl13D30+aPDL1, scATAC

description: P14 CD8 T cells from LCMV Clone13 infection+anti PDL1 treatment


title: sgAno9+ Cas9+ P14, Replicate C [ATAC_sgAno9-C_S2]

value: Wild type


title: 6_PRERT


title: Platelet Sample from Subject 182336, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: sgAno9+ Cas9+ P14, Replicate B [ATAC_sgAno9-B_S10]

value: LCMV clone 13 infection


title: Platelet Sample from Subject 182334, 28 Days Post Vaccination

value: 28 Days Post-Vaccination


title: Platelet Sample from Subject 182334, 7 Days Post Vaccination


title: 5_PRERT


title: LCMV7: Cl13D30, scRNA

library_source: transcriptomic single cell

value: LCMV Clone13 infection 30 days post infection


title: 5_POSTRT

value: primary tumor


title: LCMV6: Cl13D15, scATAC

description: P14 CD8 T cells from LCMV Clone13 infection 15 days post infection


title: Platelet Sample from Subject 182335, 28 Days Post Vaccination


title: LCMV8: Cl13D30+aPDL1, scRNA

value: LCMV Clone13 infection+anti PDL1 treatment


title: CD45_cells

first: Bryan

middle: B

last: Bryson

address: 77 Massachusetts Avenue

department: Department of Biological Engineering

institute: Massachusetts Institute of Technology

description: Pooled treatment groups from sorted CD45+ cells 5 days post-infection

data_processing:
Data were processed using Cell Ranger Count v6.0.1 aligned to mm10 reference.
LMO and GEX count matrices were analyzed using Seurat. Samples were demuxed using HTODemux.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix with raw counts
Supplementary_files_format_and_content: Gene list corresponding to matrix rownames
Supplementary_files_format_and_content: Barcode list corresponding to matrix column names
Supplementary_files_format_and_content: Seurat object containing count matrices, metadata, and MULTI-seq LMO barcode counts.
Supplementary_files_format_and_content: Cell-level metadata, "cell_barcode" column corresponds to matrix column names

source_name: CD45+ cells from the lung

extract_protocol:
6-week-old female C57Bl/6 mice were purchased from Jackson Laboratories and injected with PBS or 100ug of aLAM-mIgG2a or -mIgG2a N297A (5mg/kg) i.p. (3 mice/group) one day prior to aerosol infection (Biaera AeroMP-Hope aerosolization unit) with YFP-expressing H37Rv. On day 5 post infection, mice were sacrificed, and a single cell suspension of lungs cells was generated for flow sorting. Prior to sorting for CD45+ cells, samples were then quenched with FACS buffer (PBS with 2% FBS and 2 mM EDTA), washed once, and counted before proceeding with MULTI-seq barcoding. Samples were multiplexed as previously described. In brief, samples were barcoded with 2.5uM of the LMO anchor and barcode for 5 minutes on ice in PBS before adding 2.5 uM of the LMO co-anchor and incubating for an additional 5 minutes. Samples were quenched with 1% BSA in PBS and washed once before staining with the antibodies of the above flow staining method. CD45+ cells were sorted on a BD FACS AriaFusion. Sorted cells were processed using the 10X Genomics NextGEM Single Cell 3’ kit v3.1 per the manufacturer’s protocol in 2 microfluidic lanes. Again, 0.5 U/uL RNase inhibitor (Roche) was added to the single-cell suspension and cDNA was heat-inactivated at 95C for 15 minutes prior to BSL3 removal.
Chromium Single Cell 3' Gene Expression Kit (10X Genomics, v3.1)

tag: strain

value: Multiple

tag: replicate


title: LCMV6: Cl13D15, scRNA

value: LCMV Clone13 infection 15 days post infection


title: SB/AKT/NRas + TAA 5

city: Sydney

first: Vincent

middle: Lok Hang

last: Chiu

state: NSW

address: 1 Campbell St Liverpool

institute: Ingham Institute for Applied Medical Research

data_processing:
Raw fastq files have been analysed with RNAsik pipeline (Tsyganov et al. 2018) to produce raw genes count matrix and various quality control metrics.
For this analysis RNAsik pipeline (Tsyganov et al. 2018) ran with STAR aligner option (Dobin et al. 2013 ) and reads were quantified with featureCounts (Liao, Smyth, and Shi 2014).
The reference GRCm38 was used with transgenes appended into the reference
Raw counts were then analysed with Degust (Powell 2015) web tool to do differential expression analysis to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots
In this analysis limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell 2015) largely follows limma voom workflow with typical counts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation (Robinson and Oshlack 2010) for RNA composition normalisation.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw gene counts, text file, tab separated

source_name: Mouse liver

extract_protocol:
Liver tissue was snap-frozen in liquid nitrogen; RNA extracted using RNAzol reagent.
Library was prepared as described in Grubman et al. (2021). Briefly, index was added during initial pA priming and pooled samples amplified using template switching oligo. P5 is added by PCR and P7 by Nextera transposase. Sequencing was performed according to Illumina protocols using NextSeq 550 v2.5 kit.

treatment_protocol: 14-15 wk old male C57BL/6JAusb mice received HTVI of 0.8 µg SB plasmid, alone or with AKT (10 µg) and c-Met (10 µg) plasmids (SB/AKT/c-Met), or AKT (10 µg) and NRas (10 µg) plasmids (SB/AKT/NRas). 8-10 days post-HTVI, mice received 10-11 i.p. injections of TAA dissolved in saline, or equal volume of saline. The first i.p. injection was 100 mg/kg TAA body weight dissolved in 0.5% body weight saline, with subsequent injections 200 mg/kg TAA body weight dissolved in 1% body weight saline. i.p. injections were given twice per week for 5-6 weeks.

tag: tissue

value: Liver

value: male

tag: plasmid-htvi treatment

value: Sleeping Beauty (SB) + myr-AKT + NRasV12

tag: injury treatment

value: thioacetamide

tag: mouse id


title: Platelet Sample from Subject 182333, 28 Days Post Vaccination

value: Female


title: LCMV5: Cl13D8, scATAC

description: P14 CD8 T cells from LCMV Clone13 infection 8 days post infection


title: 4_PRERT

tag: Sex

value: Male

value: conventional long-course neoadjuvant CRT (five cycles of 5-fluorouracil (5-FU)-based chemotherapy and 50.4 Gy radiation)

value: before CRT


title: 4_POSTRT

value: after CRT


title: Platelet Sample from Subject 182335 Pre-vaccination

value: Young

value: Pre-vaccination


title: LCMV5: Cl13D8, scRNA

tag: cell type

value: CD8 T cells

value: LCMV Clone13 infection 8 days post infection


title: Platelet Sample from Subject 182333, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: 3_POSTRT

value: primary tumor

tag: treatment


title: SB/AKT/NRas + TAA 4


title: LCMV4: ArmD30, scATAC

description: P14 CD8 T cells from LCMV Armstrong infection 30 days post infection


title: 3_PRERT


title: SB/AKT/NRas + TAA 3


title: Platelet Sample from Subject 182333, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: LCMV4: ArmD30, scRNA

value: LCMV Armstrong infection 30 days post infection


title: Platelet Sample from Subject 182332, 28 Days Post Vaccination

value: 28 Days Post-Vaccination


title: 2_POSTRT


title: YFPMtb_cells

description: Pooled treatment groups from sorted YFP Mtb+ cells 5 days post-infection

value: Multiple


title: 2_PRERT


title: Platelet Sample from Subject 182334, 2 Days Post Vaccination


title: LCMV3: ArmD15, scRNA

description: P14 CD8 T cells from LCMV Armstrong infection 15 days post infection


title: LCMV3: ArmD15, scATAC

value: LCMV Armstrong infection 15 days post infection


title: 1_POSTRT


title: 1_PRERT


title: LCMV2: ArmD8, scRNA

description: P14 CD8 T cells from LCMV Armstrong infection 8 days post infection


title: Platelet Sample from Subject 182332, 2 Days Post Vaccination


title: Platelet Sample from Subject 182332 Pre-vaccination


title: Platelet Sample from Subject 182332, 7 Days Post Vaccination


title: SB/AKT/NRas + saline 4

value: Liver

value: male

value: Sleeping Beauty (SB) + myr-AKT + NRasV12

value: saline


title: SB/AKT/NRas + saline 2


title: Platelet Sample from Subject 182331, 28 Days Post Vaccination

value: Female


title: SB/AKT/NRas + TAA 2

value: thioacetamide


title: SB/AKT/NRas + saline 3


title: LCMV1: Naive, scATAC

description: P14 naïve CD8 T cells

value: naïve


title: SB/AKT/NRas + saline 1


title: LCMV1: Naive, scRNA

description: P14 naïve CD8 T cells