title: BMSC-derived exosomes, OVX 3

value: Sprague-Dawley

tag: cell type

value: Bone marrow mesenchymal stem cells (BMSCs)

tag: treatment

tag: sample type


title: Targeted RNA of patient number 56

status: Public on Jul 07 2022

type: SRA

city: Lyon

first: PIERRE

last: SAINTIGNY

address: 28 Rue Laennec

country: France

institute: Centre Léon Bérard

library_source: transcriptomic

data_processing:
Illumina bcl2fastq is used for generation of FASTQ files
HTG EdgeSeq Parser software (version 5.1) is used for alignment to a priori defined target sequences.  Requirements include %Q30 >= 85%, %PF >= 75%, and 180 < CD < 290
Post-sequencing quality control using three quality control metrics: 1) Percent of reads allocated to the Positive control probe must not exceed 15%, 2) Total aligned reads must exceed 1,500,000, and 3) Relative Standard Deviaion (CV) of counts within a sample must exceed 0.1 (CV is calculated after removal of counts from ANT and POS control probes and log2 transformation after addition of 2 to avoid taking the log of 0). A log2 CPM normalization is then processed.

molecule: total RNA

organism: Homo sapiens

source_name: Oropharynx

extract_protocol:
10mm2 of 5 micrometer FFPE tumour macrodissection tissue were lysed using HTG Lysis Buffer, followed by proteinase K digestion, and then transferred to an HTG EdgeSeq platform according to manufacturer protocols (HTG Molecular Diagnostics, Inc., Tucson, AZ).
The Oncology Biomarker Panel was used to  capture RNA expression levels of gene targets  on the HTG EdgeSeq platform according to manufacturer protocols (HTG Molecular Diagnostics, Inc., Tucson, AZ). The resulting DNA probes were quantitatively amplified with polymerase chain reaction adding extended primers ,including sequencing primer and sample barcode sequences.
Library samples were cleaned up to remove excess primers, quantitated, pooled and sequenced using Illumina NextSeq500 sequencer using 50-cycles single end ((Illumina, Inc.).

tag: site

value: Oropharynx

tag: age

tag: Sex

value: M

tag: tobacco status

tag: alcohol status

tag: hpv status (0 or 1 or 2 if unknown)

tag: immunotherapy line

tag: best response on immunotherapy (recist)

value: SD

tag: os (month)

tag: os (event)

tag: pfs (month)

tag: pfs (event)

tag: hot phenotype

tag: hot score

value: HOT


title: Targeted RNA of patient number 47

source_name: Oral cavity

value: Oral cavity

value: PD

value: COLD


title: Targeted RNA of patient number 59

source_name: Hypopharynx

value: Hypopharynx


title: Targeted RNA of patient number 48


title: C_103_H2

type: genomic

city: Granada

first: AUGUSTO

middle: MIGUEL

last: ANGUITA-RUIZ

state: Granada

address: Cruz, 6.

country: Spain

institute: ISGLOBAL

description: genomic DNA from whole blood

hyb_protocol: The EZ-96 DNA Methylation Kit (Zymo Research Corporation, Irvine, CA) was used to treat DNA samples (≥ 500 ng) of high quality with bisulfite

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software (lastest version)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from whole-blood samples using Blood Mini Kit (QIAgen Systems, Inc., Valencia, CA, USA). The DNA Clean and Concentrator kit from Zymo Research (Zymo Research, Irvine, CA, USA) were used to purify the samples.

tag: gender

value: Female

value: whole blood

tag: time point


title: btAANAT-1 [ribosome profiling]

city: La Jolla

first: Wun Kiat Justin

last: Tan

state: California

address: 9500 Gilman Drive #0412, PFBH 414

country: USA

institute: UCSD

data_processing:
library strategy: Ribosome profiling
Base calls were made on Illumina's BaseSpace
Adapters were trimmed with CutAdapt v1.8
Adapter trimmed reads were aligned to tRNA and rRNA sequences from E. coli MG1655 and aligned reads were discarded. Unaligned reads were kept for the next step
RNA-unaligned reads were aligned to E. coli MG1655 (NC_000913.3) genome using Bowtie ver. 1.0.0 into BAM files
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Comma-delimited raw read counts for all samples

organism: Escherichia coli

source_name: btAANAT

growth_protocol: Gly2 cells transformed with heterologous gene expressing plasmid were grown in M9 with 0.2% w/v glycerol as carbon source

extract_protocol:
Protocol was modified from Latif et al.2015. Cultures were centrifuged and cell pellets were bathed in liquid nitrogen to flash freeze. Cell pellets were then lysedby grinding in a liquid nitrogen cooled mortar and pestle with frozen lysis buffer.
Ribosomal RNA was depleted using Illumina's Ribo-Zero rRNA removal kit and libraries were constructed using NEBNext Small RNA kit

treatment_protocol: At A600 OD = 0.3 rhamnose was added to a final concentration of 1mM for induction of heterologous gene expression. Cells were harvested 2hrs after induction for total RNA extraction.

tag: strain

tag: gene expressed

value: btAANAT

tag: induction concentration

value: 1mM Rhamnose

tag: induction od

tag: induction time


title: Targeted RNA of patient number 46

tag: site

tag: age

tag: Sex

value: F

tag: tobacco status

tag: alcohol status


title: BRCA_v2-2 [ribosome profiling]


title: CC1-1 [ribosome profiling]


title: btASMT-1 [ribosome profiling]

source_name: btASMT

value: btASMT


title: Targeted RNA of patient number 45

source_name: COLUMELLE

value: COLUMELLE

tag: hpv status (0 or 1 or 2 if unknown)

tag: immunotherapy line

tag: best response on immunotherapy (recist)

tag: os (month)

tag: os (event)


title: Targeted RNA of patient number 44

tag: pfs (month)

tag: pfs (event)

tag: hot phenotype

tag: hot score


title: E_106_H1

description: genomic DNA from whole blood

tag: gender

tag: sample type

tag: time point

value: Baseline


title: BRCA_v2-1 [ribosome profiling]

tag: strain

tag: gene expressed

tag: induction concentration

tag: induction od

tag: induction time


title: E_92_H1

description: genomic DNA from whole blood


title: BRCA_v1-2 [ribosome profiling]


title: Targeted RNA of patient number 40

tag: site

tag: age

tag: Sex

tag: tobacco status

tag: alcohol status

tag: hpv status (0 or 1 or 2 if unknown)


title: Targeted RNA of patient number 39

source_name: Larynx

value: Larynx

tag: immunotherapy line

tag: best response on immunotherapy (recist)

tag: os (month)

tag: os (event)

tag: pfs (month)

tag: pfs (event)


title: C_96_H1

description: genomic DNA from whole blood

tag: gender

value: Male

tag: sample type

tag: time point


title: E_73_H1

description: genomic DNA from whole blood


title: E_84_H1

description: genomic DNA from whole blood


title: Targeted RNA of patient number 37

tag: hot phenotype

tag: hot score


title: Targeted RNA of patient number 41

tag: site

value: M


title: BRCA_v1-1 [ribosome profiling]

tag: strain

tag: gene expressed

tag: induction concentration

tag: induction od

tag: induction time


title: Targeted RNA of patient number 38

tag: age

tag: Sex

tag: tobacco status

tag: alcohol status

tag: hpv status (0 or 1 or 2 if unknown)

tag: immunotherapy line

value: SD


title: E_68_H2

description: genomic DNA from whole blood

tag: gender


title: BRCA-1 [ribosome profiling]

source_name: BRCA

value: BRCA


title: E_80_H2

description: genomic DNA from whole blood

tag: sample type


title: Targeted RNA of patient number 36

tag: best response on immunotherapy (recist)

tag: os (month)

tag: os (event)

tag: pfs (month)

tag: pfs (event)

value: HOT


title: bpTDC-2 [ribosome profiling]

source_name: bpTDC

tag: strain

tag: gene expressed

value: bpTDC


title: Targeted RNA of patient number 34

tag: site

value: Oral cavity

value: PD

tag: hot phenotype

tag: hot score

value: COLD


title: Targeted RNA of patient number 35

tag: age

tag: Sex


title: Targeted RNA of patient number 33

source_name: Sinus maxillaire

value: Sinus maxillaire

tag: tobacco status

tag: alcohol status


title: bpTDC-1 [ribosome profiling]

tag: induction concentration

tag: induction od

tag: induction time


title: Targeted RNA of patient number 32

value: Oropharynx

tag: hpv status (0 or 1 or 2 if unknown)

tag: immunotherapy line

tag: best response on immunotherapy (recist)


title: Targeted RNA of patient number 42

tag: os (month)

tag: os (event)

tag: pfs (month)


title: E_84_H2

description: genomic DNA from whole blood

tag: gender

tag: sample type

value: whole blood

tag: time point


title: E_93_H1

description: genomic DNA from whole blood


title: BRCA-2 [ribosome profiling]

tag: strain

tag: gene expressed

value: 1mM Rhamnose


title: Targeted RNA of patient number 43

tag: site

tag: age

tag: Sex

tag: pfs (event)

tag: hot phenotype

tag: hot score


title: Targeted RNA of patient number 30

value: F

tag: tobacco status

tag: alcohol status

tag: hpv status (0 or 1 or 2 if unknown)


title: Targeted RNA of patient number 31

tag: immunotherapy line

tag: best response on immunotherapy (recist)

tag: os (month)


title: atASMT-325G-2 [ribosome profiling]

tag: induction concentration

tag: induction od

tag: induction time


title: Targeted RNA of patient number 28

tag: os (event)

tag: pfs (month)


title: E_87_H2

description: genomic DNA from whole blood

tag: gender

value: Female

tag: sample type

tag: time point


title: Targeted RNA of patient number 29

tag: site

tag: age

tag: Sex

tag: pfs (event)


title: atASMT-325G-1 [ribosome profiling]

tag: strain

tag: gene expressed


title: E_69_H2

description: genomic DNA from whole blood


title: E_100_H1

description: genomic DNA from whole blood

value: Baseline


title: TCKO 5hmC-Seal rep1

city: Hangzhou

first: Dengfeng

last: Ruan

state: China

address: 88 Jie Fang Road

department: Department of Orthopedic Surgery

country: China

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

library_source: genomic

data_processing:
Library strategy: 5hmC-Seal
Illumina Casava software used for basecalling.
5hmC-Seal data were aligned to the reference GRCm38.99 Mus musculus genome using STAR(v2.7.0e) by using EndToEnd alignEndsType and allowing only uniquely mapping reads with fewer than three mismatches and only 1 for maximum intron length.
Genome_build: GRCm38.99

organism: Mus musculus

source_name: Primary osteoblasts

extract_protocol:
Primary osteoblasts were isolated from 3-day-old WT and TCKO mice.
The 5hmC-Seal library constructions and sequencing were utilized 2 repeats per group in WT and TCKO osteoblasts according to the previous protocol (Song et al.,Nat Biotechnol.,2011).

treatment_protocol: Tet1fl/fl Tet2fl/fl Tet3fl/fl mice were crossed with the Prx1-Cre strain to generate Prx1-Cre, Tet1fl/fl Tet2fl/fl Tet3fl/fl mice.

tag: cell type

value: Primary osteoblasts

tag: genotype

value: TET1/2/3 Triple knockout


title: Targeted RNA of patient number 25

value: M

tag: tobacco status

tag: alcohol status

tag: hpv status (0 or 1 or 2 if unknown)

tag: immunotherapy line

tag: best response on immunotherapy (recist)

tag: os (month)

tag: hot phenotype

tag: hot score


title: Targeted RNA of patient number 26

tag: os (event)

tag: pfs (month)


title: Targeted RNA of patient number 24

tag: site

tag: age


title: Targeted RNA of patient number 23

tag: Sex

tag: pfs (event)


title: Targeted RNA of patient number 27


title: E_93_H2

description: genomic DNA from whole blood

tag: gender

value: Male

tag: sample type

tag: time point


title: E_100_H2

description: genomic DNA from whole blood


title: WT 5hmC-Seal rep2

tag: cell type

tag: strain

tag: genotype

value: wild type


title: Targeted RNA of patient number 22

tag: tobacco status

tag: alcohol status

tag: hpv status (0 or 1 or 2 if unknown)

tag: immunotherapy line

value: PR


title: TCKO 5hmC-Seal rep2


title: Targeted RNA of patient number 21

tag: best response on immunotherapy (recist)

tag: os (month)

tag: hot phenotype

tag: hot score

value: HOT


title: Targeted RNA of patient number 19

tag: site

value: Larynx

tag: age

value: SD

tag: os (event)

tag: pfs (month)


title: Targeted RNA of patient number 20

value: Hypopharynx

tag: Sex

value: PD

tag: pfs (event)

value: COLD


title: WT 5hmC-Seal rep1

tag: cell type


title: E_92_H2

description: genomic DNA from whole blood

tag: gender

tag: sample type

value: whole blood

tag: time point


title: Targeted RNA of patient number 18

value: Oral cavity

tag: tobacco status

tag: alcohol status


title: Targeted RNA of patient number 17

value: Oropharynx

tag: hpv status (0 or 1 or 2 if unknown)

tag: immunotherapy line


title: Targeted RNA of patient number 16

tag: best response on immunotherapy (recist)

tag: os (month)


title: TCKO RNA-seq rep2

data_processing:
Illumina Casava software used for basecalling.
The RNA sequencing reads were aligned to GRCm38.99 Mus musculus reference genome with STAR(v2.7.0e) using a supplied set of known transcripts in GTF format (RefSeq GRCm38.99; Mus musculus, Ensembl).
Count of each gene was calculate by using featureCounts (v2.0.0).
Differentially expressed genes were calculated using DESeq2 with cutoff (Fold change greater than 2, FDR less than 0.05, and RPKM greater than 0.24 - the lower quartile), and RPKM values were calculated with a custom R script.
Genome_build: GRCm38.99
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample，

molecule: polyA RNA

extract_protocol:
Primary osteoblasts were isolated from 3-day-old WT and TCKO mice. RNA was extracted by TRIzol (Sigma, T9424).
The RNA-seq library constructions and sequencing were utilized 3 repeats per group in WT and TCKO osteoblasts by using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®(E7760L).

tag: strain

tag: genotype

value: TET1/2/3 Triple knockout


title: E_69_H1

description: genomic DNA from whole blood

value: Baseline


title: E_73_H2

description: genomic DNA from whole blood

value: Female


title: Targeted RNA of patient number 15

tag: site

tag: age

tag: hot phenotype

tag: hot score


title: Targeted RNA of patient number 14

tag: Sex

value: F

tag: os (event)

tag: pfs (month)

tag: pfs (event)


title: TCKO RNA-seq rep1


title: Targeted RNA of patient number 13

value: M


title: Targeted RNA of patient number 12


title: Targeted RNA of patient number 11


title: E_80_H1

description: genomic DNA from whole blood

tag: gender

value: Male

tag: sample type

tag: time point


title: Targeted RNA of patient number 10

tag: tobacco status

tag: alcohol status

tag: hpv status (0 or 1 or 2 if unknown)


title: WT RNA-seq rep2

value: wild type


title: E_87_H1

description: genomic DNA from whole blood


title: E_68_H1

description: genomic DNA from whole blood


title: Targeted RNA of patient number 9

tag: immunotherapy line

tag: best response on immunotherapy (recist)

tag: os (month)


title: TCKO RNA-seq rep3

tag: strain

tag: genotype


title: Targeted RNA of patient number 8

tag: site

tag: age

value: PR

tag: hot phenotype


title: Targeted RNA of patient number 7

tag: Sex

tag: os (event)

tag: hot score


title: Targeted RNA of patient number 5

tag: pfs (month)

tag: pfs (event)

value: HOT


title: Targeted RNA of patient number 6

value: Larynx


title: TCKO ATAC-seq rep2

data_processing:
Illumina Casava software used for basecalling.
ATAC-seq data were aligned to the reference GRCm38.99 Mus musculus genome using STAR(v2.7.0e) by using EndToEnd alignEndsType and allowing only uniquely mapping reads with fewer than three mismatches and only 1 for maximum intron length.
After merging replicates, peaks were called using MACS2 with call-summits method and other default parameters (v 2.1.6).To find peaks specific to one condition (e.g. TCKO), specific peaks to each state were defined with a two-fold relative enrichment cutoff after merging the replicates.
Genome_build: GRCm38.99
Supplementary_files_format_and_content: peak text files

extract_protocol:
Primary osteoblasts were isolated from 3-day-old WT and TCKO mice.
The ATAC-seq library constructions and sequencing were utilized 3 repeats per group in WT and TCKO osteoblasts by using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®(E7760L).


title: Targeted RNA of patient number 4


title: C_103_H1

description: genomic DNA from whole blood

tag: gender

tag: sample type

tag: time point


title: C_90_H1

description: genomic DNA from whole blood


title: WT RNA-seq rep1


title: TCKO ATAC-seq rep1


title: Targeted RNA of patient number 2

tag: tobacco status

tag: alcohol status

tag: hpv status (0 or 1 or 2 if unknown)


title: C_99_H1

description: genomic DNA from whole blood


title: WT ATAC-seq rep2


title: Targeted RNA of patient number 3

tag: immunotherapy line

tag: best response on immunotherapy (recist)

tag: os (month)


title: C_70_H2

description: genomic DNA from whole blood


title: WT ATAC-se rep1

tag: strain

tag: genotype


title: E_106_H2

description: genomic DNA from whole blood


title: P4D8_day13_Rep2

city: Los Angeles

first: Min

last: Yu

state: CA

address: 1450 Biggy Street, NRT 3507

department: USC Norris Comprehensive Cancer Center, Keck School of Medicine

institute: University of Southern California

description:
compound description:
LY 231617

data_processing:
RNA-sequencing reads were trimmed for Nextera and Illumina adapter sequences using Trim Galore under default parameters. Trimmed reads were then mapped to the human genome build GRCh37 from Ensembl (ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna_sm.primary_assembly.fa.gz) using STAR under optimized parameters for single-end sequenced data.
Aligned reads were then counted via featureCounts (47) and piped into DESeq2 (48) for normalization to sequencing depth and downstream analysis. For purposes of producing the PCA plot, count data was transformed via the vst function to eliminate the experiment-wide trend of variance over mean and the plot was produced using ggplot2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw counts

source_name: The breast cancer CTC line BRx68

growth_protocol: Single cells were cultured in the presence of EGF, bFGF containing RPMI media for either 6 days or 13 days at 37°C, 5% CO2 and 4% O2, and media was changed every 3 days.

extract_protocol:
At day 6 or day 13 cells were harvested and flash frozen in liquid nitrogen and stored at -80c. On the day of RNA extraction, samples were retrived from -80 c and processed using SMARTer chemistry (SMART Seq® v4 Ultra® Low Input RNA Kit for Sequencing, Takara Clontech).
cDNA libraries were prepared using the Nextera XT DNA Library Prep Kit (Illumina) with Nextera index kit index 1 (i7) and index 2 (i5) adapters.

treatment_protocol: Single cells were treated with either 1μM of P1C2, P4D8, or P1G7, or 0.3mM of NAC or a combination of 1μM of P1C2 and 0.3 mM of NAC. Cells cultured in media containing DMSO served as a control. Cells were cultured under treatment for either 6 days or 13 days.

tag: cell line

tag: treatment

tag: batch

value: B


title: WT RNA-seq rep3

tag: age


title: P4D8_day6_Rep2

description:
compound description:
LY 231617


title: C_71_H2

description: genomic DNA from whole blood


title: P1G7_day6_Rep2

description:
compound description:
Sodium Salicylate (P1G7)


title: P1G7_day13_Rep2


title: P1C2_day13_Rep2

description:
compound description:
Diclofenac Sodium  (P1C2)


title: C_74.2_H2

description: genomic DNA from whole blood


title: P1C2_day6_Rep2


title: NAC-0.3mM_day13_Rep3

description:
compound description:
N-Acetyl-L-cysteine (NAC) 0.3mM


title: NAC-0.3mM_day6_Rep2


title: NAC-0.3mM_day6_Rep3


title: C_90_H2

description: genomic DNA from whole blood


title: Targeted RNA of patient number 1

tag: site

tag: Sex

tag: os (event)

tag: pfs (month)

tag: hot phenotype

tag: hot score


title: C_67_H1

description: genomic DNA from whole blood

tag: gender

tag: sample type

tag: time point


title: Sham_4

city: Bethesda

first: Joshua

last: Stone

state: Maryland

address: 37 Convent Drive Room 3050

institute: NIH

library_source: transcriptomic single cell

data_processing:
Data processing was performed using Seurat v4.1.0.
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Lung adenocarcinoma

extract_protocol:
Lung tissues were perfused then collected and dissected and then digested using the Mouse Tumor Dissociation Kit (Miltenyi Biotec) according to the manufacturer's instructions. Tissue digests were filtered through a 40 µm strainer and RBCs were lysed prior to staining with PE-conjugated anti-CD45 antibody (BD, clone 104) and sorting on a BD FACSAria.
Single cells were droplet captured according to the manufacturer's protocol (10X Genomics Chromium 3' Dual Index v3.2).
Sequencing was performed on Illumina NovaSeq S2 with 10 bp indices i5 and i7, 28 bp R1, and 90 bp R2 length reads with a target depth of 50,000 reads per cell.

treatment_protocol: Mice aged 5-9 w.o. were instilled with Adcre to activate the mutant Kras/p53 alleles. PBS (sham) or A. temperans were first instilled two weeks later and bacterial doses were repeated biweekly an additional five times, with mice sacrificed for tissue collection 14 weeks post-Adcre.

tag: tissue

value: Lung adenocarcinoma

value: KrasLSL-G12D/+; Trp53LSL-R172H/+

value: Sham


title: Sham_1


title: Sham_2


title: At_4

value: Acidovorax temperans


title: CTGeneral_day6_Rep2

description:
compound description:
1ul/ml DMSO

value: Control_(1ul/ml DMSO)


title: NAC-0.3mM_day13_Rep2


title: CTGeneral_day6_Rep3

description:
compound description:
1ul/ml DMSO


title: CTGeneral_day13_Rep3

description:
compound description:
1ul/ml DMSO


title: At_3


title: C_104_H2

description: genomic DNA from whole blood

value: whole blood


title: CTGeneral_day13_Rep2

description:
compound description:
1ul/ml DMSO


title: Sham_3


title: At_2


title: C_28_H1

description: genomic DNA from whole blood


title: C_28_H2

description: genomic DNA from whole blood


title: At_1


title: Combined_day6_Rep2

description:
compound description:
N-Acetyl-L-cysteine (NAC) + Diclofenac Sodium  (P1C2)


title: Combined_day6_Rep1


title: C_96_H2

description: genomic DNA from whole blood


title: 4NQO-KO-1

city: Beijing

first: Xukun

last: Li

address: No.17 Panjiayuan Nanli, Chaoyang District

department: Department of Radiation Oncology

institute: NCC

data_processing:
Clean reads were obtained after the removal of reads containing adapter and ploy-N and having low quality.
Differential expression was assessed using DESeq by using read counts as input.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: esophagus

extract_protocol:
Esophageal tumors were removed,  liquid nitrogen storage, and RNA was harvested using Trizol reagent.
RNA libraries were constructed using an Illumina TruSeq RNA Sample Preparation kit.

tag: mice

value: esophageal tumor

value: 4NQO induced-tumor

value: S100A14 CKO


title: 4NQO-KO-8


title: C_74.2_H1

description: genomic DNA from whole blood

value: Baseline


title: P4D8_day6_Rep1

description:
compound description:
LY 231617

value: A


title: C_78_H2

description: genomic DNA from whole blood

value: Female


title: 4NQO-WT-3

value: wild type


title: 4NQO-WT-6


title: C_99_H2

description: genomic DNA from whole blood


title: C_74.1_H2

description: genomic DNA from whole blood


title: P4D8_day13_Rep1

description:
compound description:
LY 231617


title: HT29_TM_Buf

type: RNA

city: Koto-ku

first: Hitomi

last: Shirahama

state: Tokyo

address: Ariake 3-8-31

country: Japan

institute: Japanese Foundation for Cancer Research

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hours at 45℃ on GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix, CA, USA). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Thermo Fisher Scientific, MA, USA).

data_processing: Normalization of microarray data was carried out by the MAS5.0 method.

label: biotin

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 µg total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were cultured in RPMI1640 supplemented with 10% fetal bovine serum and 100 µg/ml kanamycin.

extract_protocol: Total RNA was extracted from cultured cells using QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).

treatment_protocol: HT-29 cells were treated with vehicle (DMSO), spautin-1 (10 µM), or buformin (300 mM) under 2DG (10 mM)- or tunicamycin (1 mg/mL)-stressed conditions for 18 hours.

value: 1 mg/mL tunicamycin+ 300 mM buformin, 18 h


title: C_67_H2

description: genomic DNA from whole blood

value: Male


title: HT29_TM_Spa

value: 1 mg/mL tunicamycin+ 10 mM spautin-1, 18 h


title: HT29_Buf

value: 300 microM buformin, 18 h


title: P1G7_day13_Rep1


title: P23 single cell TCR of post-Tx HNSCC tumor

city: Boston

first: Shengbao

last: Suo

state: MA

address: 360 Longwood Ave

institute: Dana-Farber Cancer Institute

data_processing:
Raw PBMC scRNA-sequencing reads were demultiplexed and aligned to the human reference genome (GRCh38-2020-A from 10x Genomics) for each pooled library using Cell Ranger (v4.0.0). Each pooled library contained multiple patient samples and timepoints; cells from each sample were labelled with distinct Hashtag oligonucleotides (HTO, Cell Hashing). Sequencing files for Gene Expression (measure mRNA level of cells) and Antibody Capture (measure HTO levels of cells) were fed to the “cellranger count” function with the –libraries flag, and the sequences of all HTO used in the library were fed to this function with –feature-ref flag. This generated a digital gene expression matrix, which measured the number of unique molecular identifier (UMI) for each gene and each cell barcode.
The raw gene-by-barcode count matrix was then processed to filter potential empty drops using emptyDrops function from DropletUtils (v1.8.0, R package) (Lun et al., 2019) with the parameters of “lower = 500, ignore = 5”. We initially selected droplets as containing a cell if total UMI counts of this droplet exceed the 99th percentile of the top 10,000 barcodes divided by 10. Finally, only cells with FDR<=0.01 were retained as real cells for the following analysis. The raw HTO-by-barcode matrix was subsequently filtered based on identified real cells.
The filtered HTO-by-barcode matrix for each pooled library was processed using GMM-demux to distinguish singlets from doublets or multiplets based on detection of HTOs with default parameters (Xin et al., 2020). Predicted singlets with a confidence score>=0.8 were defined as true singlet cells. Cell barcodes were then classified and allocated to respective patient samples based on hashtag identities. After processing, the gene-by-barcode count matrix was refined based on these identified singlets and used for the following analyses.
Raw tumor scRNA-sequencing reads were demultiplexed to FASTQ files using Cell Ranger mkfastq (v3.0.0, 10x Genomics), and the Cumulus cellranger-workflow implementation of Cell Ranger count (v4.0.0) on Terra (https://terra.bio/) was used to align reads to the human reference genome (GRCh38-2020-A) and generate a raw counts matrix (Li et al., 2020). Cumulus was used to filter cells from the Cell Ranger raw counts matrix with fewer than 400 UMIs, 200 genes, or greater than 20% of UMIs mapped to mitochondrial genes.
To generate the single-cell V(D)J sequences and annotate each library, we aligned TCR FASTQ reads to human GRCh38 V(D)J reference (v4.0.0 from 10X Genomics, modified to remove TRDD segments) using “cellranger vdj” function from Cell Ranger (v4.0.0). The filtered contig annotations, which contained high-level annotations of each high-confident cellular contig, were further filtered by removing records with ‘raw_consensus_id’ as ‘none’. For blood single-cell V(D)J analysis, the identities of different patient samples in each pooled library were labelled based on demultiplexing of the gene expression matrix.
Assembly: GRCh38
Supplementary files format and content: Each scRNA sequenting sample contains a .h5 file including Gene Expression (tumor and PBMC) and Antibody Capture (PBMC) information. Single cell TCR sequencing data for each sample were saved in a csv file, which is generated by 'cellranger vdj' function and shows the detailed clonotype information. Bulk TCR sequencing data for each sample were provided by Adaptive Biotech and were saved in a tsv file. Hashtag files contain the sequence of each hashtag and the corresponding patient sample information.

source_name: HNSCC tumor

extract_protocol:
Fresh tumor tissue was transferred to a 6 cm tissue culture dish in a small volume of DMEM media and cut into <2 mm pieces with a razor blade. Tissue pieces were centrifuged (400 g for 5 minutes at 4°C for all centrifuge steps) and resuspended in 2-5 mL of a collagenase-containing enzymatic digestion solution (Miltenyi Human Tumor Dissociation Kit #30-095-929), based on the weight of collected tissue, according to manufacturer’s instructions. Biopsies were incubated at 37°C for 20-30 minutes with mixing using a 5-10 mL serological pipet and intermittent gentle vortexing at 2-5-minute intervals. The extent of tumor tissue dissociation was variable and likely dependent on extracellular matrix abundance. The resulting cell suspension was passed through a 70 um nylon mesh filter and washed with an additional 5-10 mL of RPMI media. Filtered tumor cell suspensions were centrifuged and resuspended in 3 mL ACK red blood cell lysis buffer (Gibco #A1049201) for 1 minute at RT, then immediately diluted with 10 mL of PBS (Life Technologies #10437028). Cells were pelleted and resuspended in Zombie NIR (Biolegend) viability dye solution (1:500 in PBS), followed by a 15 minute incubation at RT in the dark. Cells were counted with a hemocytometer, yielding on average 1.3x104 live cells/mg of tumor tissue. Up to 500,000 live cells were then resuspended in 100 uL of FACS wash buffer (FWB; PBS, 2% FBS, 1 mM EDTA) with the addition of the following antibodies: TruStain FcX (Biolegend 422302), CD3-PE/Dazzle (Biolegend 300450), CD45-Pacific Blue (Biolegend 304022), CD66b-PE/Cy7 (Biolegend 305116) and CD15-APC (Biolegend 301908). Cells were incubated on ice for 20 minutes, washed with 1 mL FWB, filtered through 40 um flow-cap strainers, and then resuspended in 500 uL FWB. Cells were sorted using a FACS Aria II or III instrument (BD Biosciences). For most samples, 12-15 x 103 live CD45+CD66b- mononuclear cells (MNC) cells were sorted into T cell media (RPMI + 10% FBS) and immediately transferred to ice. All scRNA-seq was performed using the 10x Genomics 5’ V1 assay and protocols (10x Genomics). CD45+ cells isolated as above were centrifuged and washed with PBS containing 0.05% RNase-free BSA (ThermoFisher Scientific #AM2616), leaving a volume of <32 uL after the final wash. Up to 15,000 cells based on cell sorter count were loaded into a Single Cell Chip A channel, along with reverse transcriptase reagent mixture and 5’ gel beads according to the manufacturer’s protocol.
Libraries were prepared accordingn to 10X Genomics protocols for 5' barcoded GEX and V(D)J TCR (Version 1)

tag: cell marker

value: TCR:ab chains

tag: single cell or bulk

value: Single cell

tag: state

value: Post-Tx

tag: patient diagnosis

value: Head and neck squamous cell Carcinoma (HNSCC)

tag: molecule

value: T cell receptor


title: P24 single cell TCR of post-Tx HNSCC tumor


title: P1C2_day6_Rep1

tag: cell line

tag: treatment

tag: batch


title: C_74.1_H1

description: genomic DNA from whole blood

value: whole blood


title: Combined_day13_Rep2

value: B


title: C_71_H1

description: genomic DNA from whole blood


title: C_70_H1

description: genomic DNA from whole blood


title: P22 single cell TCR of post-Tx HNSCC tumor


title: HT29_2DG_Buf

value: 10 mM 2DG + 300 mM buformin, 18 h


title: HT29_TM

value: 1 mg/mL tunicamycin, 18 h


title: HT29_Cont

value: Vehicle (DMSO), 18 h


title: HT29_2DG_Spa

value: 10 mM 2DG + 10 mM spautin-1, 18 h


title: NAC-0.3mM_day6_Rep1

value: A


title: C_85_H2

description: genomic DNA from whole blood

value: Female


title: P21 single cell TCR of post-Tx HNSCC tumor


title: P1C2_day13_Rep1


title: HT29_Spa

value: 10 microM spautin-1, 18 h


title: C_85_H1

description: genomic DNA from whole blood

value: Baseline


title: CTGeneral_day6_Rep1

description:
compound description:
1ul/ml DMSO

value: Control_(1ul/ml DMSO)


title: C_78_H1

description: genomic DNA from whole blood


title: ChIP-seq in Beko cells, Normoxia_RBPJ_2

city: Philadelphia

first: Tobias

last: Friedrich

state: Pennsylvania

address: 421 Curie Boulevard

institute: University of Pennsylvania

data_processing:
Quality control of FASTQ files was done using the seeFastq command within systemPipeR.
The fastq files were aligned using TopHat v.2.1.1. or Hisat2  v.2.2.1
Count tables were generated from BAM files using the summarizeOverlaps function.
ChIP-seq aligment was performed using Bowite 2 v.2.3.5.1.
Duplicated reads were removed using Picard tools.
bigWig files were generated using bamCoverage.
Peak calling was done using Peakranger v.1.18 and followed by MSPC to combine peak sets.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Count tables of raw read counts per gene in csv format.
Supplementary_files_format_and_content: ChIP-seq: bigWig files.

source_name: Beko pre-T cell line

growth_protocol: Mouse pre-T (Beko) cells were grown at 37°C with 5% CO2 in IMDM medium (Gibco 21980-065) supplemented with 2% FCS, peptone, insulin, nonessential aminoacids and penicillin/streptomycin.

extract_protocol:
ChIP was done essentially as previously described (Giaimo et al. Jove 2017, doi:  10.3791/55907)
Library-prep kit: Diagenode MicropPlex Library Preparation kit v2 (C05010012).

treatment_protocol: Mouse pre-T (Beko) cells were treated with DMSO for 24 hours.

value: Beko

tag: cell type

value: pre-T cells

value: kept for 12 hours at 5% oxygen

tag: chip antibody

value: RBPJ; Cell Signaling #5313


title: NAC-0.3mM_day13_Rep1


title: P19 single cell TCR of post-Tx HNSCC tumor

value: TCR:ab chains

value: Single cell

value: Post-Tx

value: Head and neck squamous cell Carcinoma (HNSCC)


title: P1G7_day6_Rep1


title: C_104_H1

description: genomic DNA from whole blood

value: Male

value: whole blood


title: P20 single cell TCR of post-Tx HNSCC tumor

value: T cell receptor


title: Input_ChIP-seq in Beko cells, Normoxia_Input_2


title: Combined_day13_Rep1


title: P13 single cell TCR of post-Tx HNSCC tumor

extract_protocol:
Fresh tumor tissue was transferred to a 6 cm tissue culture dish in a small volume of DMEM media and cut into <2 mm pieces with a razor blade. Tissue pieces were centrifuged (400 g for 5 minutes at 4°C for all centrifuge steps) and resuspended in 2-5 mL of a collagenase-containing enzymatic digestion solution (Miltenyi Human Tumor Dissociation Kit #30-095-929), based on the weight of collected tissue, according to manufacturer’s instructions. Biopsies were incubated at 37°C for 20-30 minutes with mixing using a 5-10 mL serological pipet and intermittent gentle vortexing at 2-5-minute intervals. The resulting cell suspension was passed through a 70 m nylon mesh filter and washed with an additional 5-10 mL of RPMI media.Tumor-infiltrating immune cells were isolated with anti-CD45 magnetic beads. Following filtering of dissociated tumor suspension, cells were centrifuged and then resuspended in 80 mL of MACS buffer (0.5% FBS, 2 mM EDTA in PBS). Human CD45 MicroBeads (20 mL, Miltenyi) were mixed with cells, and then incubated at 4°C for 15 minutes per manufacturer’s protocol. After washing with MACS buffer, beads were applied to a MS magnetic column (Miltenyi) placed in a magnetic MACS separator and washed with 3x500 mL of MACS buffer. To elute cells, the column was removed from the magnet and flushed with 1 mL of MACS buffer. CD45+ cells isolated as above were centrifuged and washed with PBS containing 0.05% RNase-free BSA (ThermoFisher Scientific #AM2616). Up to 15,000 cells based on cell sorter count were loaded into a Single Cell Chip A channel, along with reverse transcriptase reagent mixture and 5’ gel beads according to the manufacturer’s protocol.
Libraries were prepared accordingn to 10X Genomics protocols for 5' barcoded GEX and V(D)J TCR (Version 1)


title: HT29_2DG


title: P16 single cell TCR of post-Tx HNSCC tumor


title: Input_ChIP-seq in Beko cells, Normoxia_Input_1


title: 3' PBMC Illumina

city: Cambridge

last: Levin

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description: 3' PBMC data, sequenced with Illumina

data_processing:
cellranger mkfastq v5.0 was used to generate fastq files for Illumina data
For Ultima and Single End Illumina data, Cutadapt v2.10 was used to remove adapters and qualitfy filter. For 3' data reads without 8 T's from the poly(T) region were discarded. Cutadapt and SeqKit v0.15.0 were used to split these read into 2 pieces for later processing. We removed reads whose cDNA sequence was < 50bp.
seqtk v1.0 was used to downsample the Ultima data to the appropriate level
CellRanger count v5.0 was used to quanifty the number of UMIs per cell in each sample, with CellRanger vdj being used for TCR and BCR data.
CellSNP-lite v1.2.0  and Vireo v0.5.5 were used to identify genotype clusters in the 5' mixture data
Demux-EM v0.1.7  was used to assign cells to hash tag IDs in the Perturb-seq data
Seurat v4.0.0 was used for clustering and downstream analysis
Assembly: hg38
Supplementary files format and content: Most processed data are in MM format, with 3 files per sample: the cell names file, the gene names file, and the MM file with gene by cell UMI count matrix. In addition have h5 files from CellRanger for the Perturb-seq results, including UMI counts from the HTO, ADT, and Guide data. The csv files are for TCR and BCR data produeced by CellRanger vdj.

source_name: peripheral blood mononuclear cells (PBMCs)

growth_protocol: Perturb-seq only: Perturbed cells selection with puromycin, details see manuscript

extract_protocol: 10x Chromium Next GEM single cell 3' (v3.1) and 5' (v2) gene expression assays

treatment_protocol: Perturb-seq only: Selected perturb-seq cells treated with recombinant IFNγ, details see manuscript

tag: 10x technology

value: PBMC


title: ChIP-seq in Beko cells, Normoxia_HIF1alpha_Diagenode

value: Diagenode C15410234


title: P24 single cell TCR of pre-Tx HNSCC tumor

value: Pre-Tx


title: WT_B_0PQ_ribo

data_processing:
Base calls were made using Illumina's bcl2fastq
For RNAseq samples, Sequenced reads were aligned to E. coli MG1655 (NC_000913.3) genome and plasmid sequences using Bowtie 2 ver. 2.1.0 into BAM files
For RNAseq samples, BAM files were processed using HTSeq to generate raw read count files, and these were normalized to get TPM
For Riboseq samples, adapters were removed from raw reads using cutadapt ver 1.8, trimmed reads were then aligned to E. coli MG1655 (NC_000913.3) genome. Aligned reads longer than 25bp were assigned to the position at their 3' end. This was written to a file containing the total number of reads with 3' ends at each position in the genome.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Comma-delimited raw read counts for all samples

source_name: GLU4_without paraquat

growth_protocol: Cells were grown in M9 minimal media with 0.4% glucose w/v as a carbon source

extract_protocol:
Ribosome profiling libraries were generated using the protocol from Latif et. al. 2015. Briefly, cultures were harvested by centrifuging, and flash frozen in liquid nitrogen. Cell pellets were ground in liquid nitrogen with the addition of lysis buffer and total RNA was isolated. MNase was used to shear RNA leaving behind ribosome protected regions. RiboZero rRNA removal kit was used to deplete ribosomal RNA, and libraries were constructed using the NEBNext Small RNA kit.
Total RNA was isolated using Qiagens RNAProtect Bacteria Reagent kit
Ribosomal RNA was depleted using Illumina's Ribo-Zero rRNA removal kit and libraries were constructed using KAPA RNA-Seq Library Preparation kit

treatment_protocol: At A600 OD = 0.3 paraquat was added to a final concentration of 250uM for paraquat stressed samples. Cells were harvested 20mins after addition of paraquat for total RNA extraction.

tag: strain


title: WT_B_PQ_ribo

source_name: GLU4_250uM Paraquat

tag: stressor

value: 250uM Paraquat

tag: stress time


title: CTGeneral_day13_Rep1

description:
compound description:
1ul/ml DMSO

value: A


title: ChIP-seq in Beko cells, Normoxia_HIF1alpha_abcam

value: abcam ab228649


title: patient 21 post-treatment

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

state: OH

address: 400 W 12th Ave

department: Comprehensive Cancer Center

institute: Ohio State University

data_processing:
FASTQs, BAM files and cell barcode-gene matrices were generated using Cellranger v3.1.0 using the 10X-supplied GRCh38 reference (version 2020-A).
QC functions from scater were used to remove cells with a proportion of counts mapped to mitochondrial genes that was more than 2 median absolute deviations (MADs) above the median, a feature count that was more than 2 MADs below the median or cells with more than 1% of counts mapped to a globin gene.
High likelihood doublets were predicted using Doubletfinder and removed.
Patient to patient variation was reduced by aligning according to mutual nearest neighbors with Batchelor.  Following alignment according to patient ID, a second round of alignment by sample tissue type (blood or bone marrow) was performed.
Dimension reduction, clustering, top marker identification, gene module analysis and quantification of gene expression was performed using functions from Monocle3.
Cell clustering was performed using the partitioning method.
Descriptive labels were attached to cell partitions by inspection of top specific markers, aggregated gene module expression, and by label transfer from reference PBMC and bone marrow data sets using Seurat.
Pseudobulk differential gene expression was performed by generating aggregate gene expression profiles for indicated strata of cells using Monocle3 functions and then comparing across conditions using DESeq2.  Each patient served as an independent biological replicate in this analysis.
Assembly: GRCh38 (10X Genomics prebuilt reference, version 2020-A)
Supplementary files format and content: *.barcodes.tsv.gz:  tab separated values file containing filtered cell barcode ids
Supplementary files format and content: *.features.tsv.gz:  tab separated values file containing feature (gene) ids
Supplementary files format and content: *.matrix.mtx.gz:  Matrix Market format sparse matrix containing cell barcode/feature counts

source_name: bone marrow

extract_protocol:
scRNASeq was carried out on viable frozen ficoll enriched myeloblast samples from matched patient samples before and during gilteritinib treatment.   Cells were thawed, washed with PBS and dead cells were removed using Dead Cell Removal Kit (Miletnyi).  Cells were then washed twice using scRNASeq Buffer (PBS + 0.04% BSA) to remove any Ca2+ and resuspended at a concentration of 1x106/mL.  Approximately 6000 cells per lane were loaded and processed for cDNA according to the 10X Genomics Chromium Single Cell 3’ Reagent Kit v.3.1 in the OSUCCC Genomics Shared Resource.  Samples with less than 10% myeloblasts, estimated by diagnostic pathology report, were run in duplicate or triplicate.
Libraries were constructed using the 10X Genomics Chromium Single Cell 3’ Reagent Kit v.3.1 and according to the manufacturer's instructions. Libraries were sequenced on an Illumina NovaSeq 6000 using 300 cycles with paired 150bp reads.  A minimum of 20,000 read pairs per cell were obtained.

tag: categorical timepoint

value: post-treatment

tag: day of treatment

tag: gilteritinib response

value: unresponsive


title: patient 21 pre-treatment

value: pre-treatment


title: WT_A_PQ_ribo


title: patient 20 post-treatment

value: sensitive


title: ChIP-seq in Beko cells, Normoxia_RBPJ_1

value: Beko

value: pre-T cells

value: kept for 12 hours at 5% oxygen

value: RBPJ; Cell Signaling #5313


title: WT_A_0PQ_ribo


title: ChIP-seq in Beko cells, Hypoxia_RBPJ_2

value: kept for 12 hours at 1% oxygen


title: patient 20 pre-treament


title: PQ2B_PQ_ribo

source_name: PQ2_250uM Paraquat


title: Ctrl-2_spinal

city: Suita

first: Masayuki

last: Nakamori

state: Osaka

address: 2-2, D-4, Yamadaoka

department: Neurology

institute: Osaka University Graduate School of Medicine

data_processing:
The libraries were sequenced on an Illumina HiSeq 2500(Illumina).
For gene expression analysis, the quality of sequence read data was verified using FastQC version 0.11.8.
Adapter and quality trimming of sequence reads was performed using Trimmomatic version 0.36 30, followed by alignment with human reference genome (GRCh37) sequence using STAR version 2.5.2b software.
FPKM (fragments per kilobase of exon per million mapped fragments) values were calculated using Genedata Profiler Genome version 10.1.15a.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: spinal neurons

extract_protocol:
Total RNA was extracted from human brain tissues and spinal cords using an ALL Prep DNA/RNA Micro Kit (Qiagen).
Nextera XT DNA Library Preparation (Illumina) kits were used to prepare RNA-seq libraries.

value: spinal motor neurons

tag: disease

value: Control


title: ChIP-seq in Beko cells, Hypoxia_RBPJ_1


title: PQ2B_0PQ_ribo

source_name: PQ2_without paraquat


title: Ctrl-1_spinal


title: Input_ChIP-seq in Beko cells, Hypoxia_Input_2


title: DM1-Pt5_spinal


title: DM1-Pt4_spinal


title: PQ2A_PQ_ribo


title: patient 2 post-treatment 3

source_name: peripheral blood


title: patient 2 post-treatment 2


title: PQ2A_0PQ_ribo


title: Input_ChIP-seq in Beko cells, Hypoxia_Input_1


title: DM1-Pt1_spinal


title: ChIP-seq in Beko cells, Hypoxia_HIF1alpha_Diagenode


title: Ctrl-3_white_matter

source_name: brain

value: white matter glial cells


title: MP_A_ribo

source_name: MP_250uM Paraquat

value: MP


title: RNA-seq in Beko cells, USP10_KD_3

extract_protocol:
RNA-Seq samples were prepared essentially as as previously described (Giaimo et al. NAR 2018, doi:  10.1093/nar/gky551)
Illumina TruSeq Stranded Total RNA Sample Preparation kit.

treatment_protocol: Mouse pre-T (Beko) cells were treated for 24 hours with 0.5 mM DMOG or DMSO as a control. Alternatively, Beko cells were kept for 12 hours at 1% oxygen to induce hypoxia or at 5% oxygen as a control.

value: infected with plasmids driving the expression of shRNAs against Usp10


title: Ctrl-3_spinal


title: patient 22 post-treatment 2


title: MP_B_ribo

value: 250uM Paraquat


title: ChIP-seq in Beko cells, Hypoxia_HIF1alpha_abcam


title: RNA-seq in Beko cells, Scrambled_3

value: infected with plasmids driving the expression of scrambled shRNAs as control


title: DM1-Pt3_white_matter


title: WT_B_PQ

description:
processed data file: 20190623_rnaseq_tpm.csv
ERS_HRS_ALE4B_PQ_RNA_S26_L007

extract_protocol:
Total RNA was isolated using Qiagens RNAProtect Bacteria Reagent kit
Ribosomal RNA was depleted using Illumina's Ribo-Zero rRNA removal kit and libraries were constructed using KAPA RNA-Seq Library Preparation kit


title: patient 22 post-treatment 1


title: RNA-seq in Beko cells, USP10_KD_2


title: patient 22 post-treatment 3


title: DM1-Pt1_white_matter


title: WT_A_PQ

description:
processed data file: 20190623_rnaseq_tpm.csv
ERS_HRS_ALE4A_PQ_RNA_S27_L007


title: patient 2 post-treatment 1


title: WT_B_0PQ

description:
processed data file: 20190623_rnaseq_tpm.csv
ERS_HRS_ALE4B_0PQ_RNA_S23_L007


title: patient 22 pre-treatment


title: DM1-Pt2_white_matter


title: patient 2 pre-treatment


title: patient 17 pre-treatment


title: RNA-seq in Beko cells, USP10_KD_1


title: patient 17 post-treatment


title: RNA-seq in Beko cells, Normoxia_2


title: Ctrl-1_white_matter


title: PQ2B_0PQ

description:
processed data file: 20190623_rnaseq_tpm.csv
ERS_HRS_18_36B_0PQ_S46_L004


title: Ctrl-2_white_matter


title: Ctrl-3_cortical

value: cortical neurons


title: PQ2B_PQ

description:
processed data file: 20190623_rnaseq_tpm.csv
ERS_HRS_18_36B_PQ_S46_L004


title: RNA-seq in Beko cells, Normoxia_1


title: RNA-seq in Beko cells, Scrambled_1


title: patient 5 post-treatment 2

value: post-treatment


title: Ctrl-2_cortical


title: WT_A_0PQ

description:
processed data file: 20190623_rnaseq_tpm.csv
ERS_HRS_ALE4A_0PQ_RNA_S24_L007


title: patient 5 post-treatment 1

value: unresponsive


title: patient 5 pre-treatment

value: pre-treatment


title: RNA-seq in Beko cells, Scrambled_2


title: PQ2A_PQ

description:
processed data file: 20190623_rnaseq_tpm.csv
ERS_HRS_18_36A_PQ_S46_L004


title: Ctrl-1_cortical


title: PQ2A_0PQ

description:
processed data file: 20190623_rnaseq_tpm.csv
ERS_HRS_18_36A_0PQ_S0_L000


title: RNA-seq in Beko cells, Hypoxia_2


title: DM1-Pt3_cortical


title: DM1-Pt2_cortical


title: ChIP-seq in Beko cells, DMSO_RBPJ_5

value: treated for 24 hours with DMSO


title: PQ1B_0PQ

description:
processed data file: 20190623_rnaseq_tpm.csv
ERS_HRS_16_32B_0PQ_S0_L000

source_name: PQ1_without paraquat


title: patient 4 post-treatment 2

value: sensitive


title: PQ1B_PQ

description:
processed data file: 20190623_rnaseq_tpm.csv
ERS_HRS_16_32B_PQ_S0_L000

source_name: PQ1_250uM Paraquat


title: ChIP-seq in Beko cells, DMSO_RBPJ_4

value: Beko

value: pre-T cells


title: patient 4 post-treatment 1


title: DM1-Pt1_cortical


title: iPSCs dopa, MPP+, 100uM, t24, 9C

city: Maastricht

first: Julian

last: Krauskopf

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

data_processing:
STAR alignemnt
RSEM
Genome_build: Human Build 38.99
Supplementary_files_format_and_content: RSEM files (expected_count, TPM, FPKM)

source_name: endothelial cells

extract_protocol:
Qiagen miRNeasy Mini Kit
Perkin Elmer Rapid Directional RNA-Seq kit 2.0 with NextFlex RNA-Seq Unique dual index barcodes

value: MPP+

tag: dose

tag: time

value: iPSC-derived dopaminergic neurons


title: i14G1-12_Ti-seq_1

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

description: Ribosome protected RNA

data_processing:
Library strategy: Ti-seq
Removing first base and adapter and keeping only sequences of length 20 to 50 (initial length 61) that had adapter, no trimming by quality.   cutadapt -a CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --discard-untrimmed --times 1 -u 1 -m 20 -M 50
rRNA removal was done by bowtie to make fastq file with non-RNA sequences (bowtie run with parameter norc)
Filtering for  reads of length 28-33  using cutadapt (-m 28 -M 33)
Mapping the reads to hg38 human using TopHat2  with parameters : --no-novel-juncs --library-type fr-firststrand
UTR and CDS gtf files were created from refseq gtf file, avoiding regions found in both files. HTSeq was used for the quantification (parameters -s yes -t exon -m intersection-nonempty). The option intersection-nonempty allows to assign junction reads to either the CDS or UTR, depending where most of read is placed.
Counts presented were normalized with DESeq2 (normalization was computed for the sum 5' UTR and CDS)
Genome_build: hg38
Supplementary_files_format_and_content: "Ribo-seq norm counts" sheet contains normalized DESeq2 counts for 5' UTR and CDS

source_name: HEK293T cells

growth_protocol: HEK293T cells were grown in standard growth condition in 10 cm plates

extract_protocol:
cell lysate was treated with Rnase I followed by ultracentrifugation according to Ingolia et al. 2012
purified RNA was processed to make ribosome profiling and translation initiation sequencing liberaries (Ingolia et al. 2012). Both libraries were sequenced on HiSeq2500 High-Output instrument (Illumina) to yield 60 bp single-end reads
Ribosome Profiling Ribo-seq and Translation Initiation (TI)-Seq

treatment_protocol: HEK293T cells were treated with DMSO (vehicle Control) or i14G1-10 (20uM) or i14G1-12 (10 uM) for 3h. Followed by treatment with Cycloheximide only for Ribo-seq, and Harringtonin and Cycloheximide for TI-seq.

value: Human embryonic kidney cells

tag: passage

value: passages 5-8


title: RNA-seq in Beko cells, Hypoxia_1

value: kept for 12 hours at 1% oxygen


title: patient 4 pre-treatment


title: PQ1A_0PQ

description:
processed data file: 20190623_rnaseq_tpm.csv
ERS_HRS_16_32A_0PQ_S0_L000


title: i14G1-12_Ti-seq_2

description: Ribosome protected RNA


title: PQ1A_PQ

description:
processed data file: 20190623_rnaseq_tpm.csv
ERS_HRS_16_32A_PQ_S0_L000


title: Input_ChIP-seq in Beko cells, DMSO_Input_2


title: ChIP-seq in Beko cells, DMSO_RBPJ_3

value: RBPJ; Cell Signaling #5313


title: i14G1-10_Ti-seq_2

description: Ribosome protected RNA


title: MLN-DSS 4

city: Kumamoto

first: Hitoshi

last: Takizawa

address: 2-2-1 Honjo, Chu-ku

institute: Kumamoto University

data_processing:
mRNA profile generated by deep-sequencing using Illumina NextSeq 500
Quality check and trimming of single-end sequences were completed with the trim_galore (version 0.4.3) package. Quality and length parameters were --quality 30 and --length 30.
Filtered sequences were processed to remove mitochondrial mRNA with the SortMeRNA and were aligned to mouse reference sequences (GRCm38, M17 version) from (http://www.genecodesgenes.org/mouse/release.html) with ultrafast RNA-seq aligner STAR (version 2.5.3a).
All aligned bam files were used with mouse GFF annotation files (GRCm38, M17 version) as input into the featureCounts program from the Subreads program (version 1.6.1) to count the raw reads for each gene and sample, and to create a gene count matrix for MLN and BM samples.
Assembly: GRCm38
Supplementary files format and content: Excel files include normalized counts for each sample.

source_name: mesenteric lymph node

extract_protocol:
Cells were lysed with cell lysis buffer (Roche). The first strand of cDNA was synthesized with the PrimeScript RT reagent kit (TAKARA Bio Inc.) and NSR (not-so random) primers. The second strand was synthesized with Klenow Fragments (3′-5′exo-; New England Biolabs Inc.) and complement chains of NSR primers. The double-stranded cDNA was purified with AMPure XP beads (Beckman Coulter, Inc. CA).
The library was preparation with the Nextera XT DNA sample Prep kit. The quantity and quality of the isolated cDNA library was determined with Multina (Shimadzu Corporation, Japan) and Bioanalyzer 2100 (Agilent, Waldbronn, Germany).

tag: tissue

value: mesenteric lymph node

value: Multipotent progenitor 2 (MPP2)

tag: age

value: 8-10 weeks


title: RNA-seq in Beko cells, DMSO_2

tag: cell line

tag: treatment


title: MLN-DSS 3

tag: cell type


title: iPSCs dopa, MPP+, 100uM, t24, 7C


title: i14G1-10_Ti-seq_1

description: Ribosome protected RNA


title: Control_Ti-seq_2

description: Ribosome protected RNA

value: DMSO


title: RNA-seq in Beko cells, DMSO_1


title: iPSCs dopa, control, 0, t24, 6C

value: control


title: MLN-DSS 1


title: RNA-seq in Beko cells, DMOG_2

value: treated for 24 hours with 0.5 mM DMOG


title: iPSCs dopa, control, 0, t24, 4C


title: Control_Ti-seq_1

description: Ribosome protected RNA


title: iPSCs dopa, MPP+, 100uM, t24, 8C


title: MLN-ddW 6

value: ddW


title: iPSCs dopa, MPP+, 400uM, t74, 27C


title: i14G1-12_Ribo-seq_2

description: Ribosome protected RNA

data_processing:
Library strategy: Ribo-seq
Removing first base and adapter and keeping only sequences of length 20 to 50 (initial length 61) that had adapter, no trimming by quality.   cutadapt -a CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --discard-untrimmed --times 1 -u 1 -m 20 -M 50
rRNA removal was done by bowtie to make fastq file with non-RNA sequences (bowtie run with parameter norc)
Filtering for  reads of length 28-33  using cutadapt (-m 28 -M 33)
Mapping the reads to hg38 human using TopHat2  with parameters : --no-novel-juncs --library-type fr-firststrand
UTR and CDS gtf files were created from refseq gtf file, avoiding regions found in both files. HTSeq was used for the quantification (parameters -s yes -t exon -m intersection-nonempty). The option intersection-nonempty allows to assign junction reads to either the CDS or UTR, depending where most of read is placed.
Counts presented were normalized with DESeq2 (normalization was computed for the sum 5' UTR and CDS)
Genome_build: hg38
Supplementary_files_format_and_content: "Ribo-seq norm counts" sheet contains normalized DESeq2 counts for 5' UTR and CDS


title: MLN-ddW 5


title: MLN-ddW 4


title: i14G1-12_Ribo-seq_1

description: Ribosome protected RNA


title: iPSCs dopa, MPP+, 400uM, t74, 26C


title: shMettl3_dox_RNA-seq_Replicate 3

city: Stanford

first: Nitin

last: Raj

address: 269 Campus Drive, CCSR-South, Rm 1240, MC5152

department: Radiation Oncology

institute: Stanford University

data_processing:
fastp was used to obtain clean data (clean reads) by removing reads containing adapter and poly-N sequences and reads with low quality from raw data
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software
Featurecounts 1.5.3 was used to count the read numbers mapped of each gene
RPKM (Reads Per Kilobase of exon model per Million mapped reads) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package
Genome_build: mm10

source_name: E1A;HRasV12 expressing mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts were maintained in Dulbecco’s Modified Eagle Medium (Gibco) supplemented with 10% Fetal Calf Serum (FCS), 1% penicillin/streptomycin, 50 μg/mL gentamicin and incubated at 37°C in a carbon dioxide incubator.

extract_protocol:
Total RNA extracted TRIzol method were used for RNA-seq
Novogene generated and sequenced RNA-seq libraries using the NEBNext UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Cells were treated with 0,2 ug/ml of Doxorubicin for 6 hours

tag: genotype

value: Doxorubicin


title: shMettl3_dox_RNA-seq_Replicate 2

value: E1A;HRasV12 expressing mouse embryonic fibroblasts


title: MLN-DSS 2


title: iPSCs dopa, MPP+, 200uM, t74, 24C


title: i14G1-10_Ribo-seq_2

description: Ribosome protected RNA


title: iPSCs dopa, MPP+, 400uM, t74, 25C


title: shLuc_dox_RNA-seq_Replicate 3


title: Control_Ribo-seq_2

description: Ribosome protected RNA


title: shMettl3_dox_RNA-seq_Replicate 1


title: RNA-seq in Beko cells, DMOG_1

source_name: Beko pre-T cell line

value: Beko


title: MLN-ddW 1


title: i14G1-10_Ribo-seq_1

description: Ribosome protected RNA


title: iPSCs dopa, MPP+, 100uM, t74, 21C


title: iPSCs dopa, control, 0, t24, 5C


title: MLN-ddW 2


title: shLuc_dox_RNA-seq_Replicate 2


title: iPSCs dopa, MPP+, 200uM, t74, 23C


title: Control_Ribo-seq_1

description: Ribosome protected RNA


title: iPSCs dopa, MPP+, 200uM, t74, 22C


title: MLN-ddW 3


title: Y1 Dexamethasone 24H rep2

city: Auburn

first: Sophia

last: Zheng

state: AL

address: 1130 Wire Road

department: Anatomy, Physiology 7 Pharmacology

institute: Auburn University

data_processing:
Raw data was transformed by Casava version1.8 base calling
Reads were removed with adaptor contamination. The trimmed reads were then aligned to the mouse genome (mm10, GRCm38.95) using STAR (v. 2.5). Reads were mapped to each gene and counted using HTSeq (v.0.6.1).
Fragments Per Kilobase of transcript sequence per Millions (FPKM) were calculated using sequencing depth and gene length on counting of fragments (Mortazavi et al. 2008).
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft excel open XML spreadsheet include read counts

source_name: Y1 Dexamethasone 24H rep2

growth_protocol: Y-1 cells were cultured in DMEM/F12 media supplemented with 10% fetal bovine serum and 1% streptomycin/penicillin.

extract_protocol:
Total RNA from cell cultures was extracted using TRIzol.
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Pre Kit for Illumina.

treatment_protocol: Cells were subcultured separately onto three groups. Cells were subcultured separately onto three groups. The control group treated with vehicle. One group treated with 100nM dexamethasone with 1h. One group treated with 100nM dexamethasone with 24h.

value: Y-1 adrenocortical cells

tag: agent

value: dexamethasone


title: BM-DSS 3

value: bone marrow

tag: strain


title: shLuc_dox_RNA-seq_Replicate 1


title: Y1 Dexamethasone 24H rep3

source_name: Y1 Dexamethasone 24H rep3


title: Y1 Dexamethasone 24H rep1

source_name: Y1 Dexamethasone 24H rep1


title: BM-DSS 2

source_name: bone marrow


title: iPSCs dopa, MPP+, 100uM, t74, 20C

value: MPP+

value: iPSC-derived dopaminergic neurons


title: iPSCs dopa, control, 0, t74, 18C


title: BM-DSS 1


title: iPSCs dopa, control, 0, t74, 17C


title: iPSCs dopa, MPP+, 100uM, t74, 19C


title: Cell_HN30_CR_rep1

city: Shanghai

first: tong

last: tong

address: 639 Zhizaoju Road

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Cell,HN30,cisplatin resistance replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human HNSCC cell lines HN4 and HN30 were maintained in DMEM with 10% FBS and cultured at  37°C  with 5% CO2. Cisplatin-resistant cells (HN4_CR and HN30_CR) were maintained in the culture medium containing 20 μM cisplatin for 48 hours.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

value: head and neck squamous cell carcinoma (HNSCC)


title: BM-ddW 4


title: Y1 Dexamethasone 1H rep3

source_name: Y1 Dexamethasone 1H rep3


title: BM-ddW 2


title: Y1 Dexamethasone 1H rep2

source_name: Y1 Dexamethasone 1H rep2


title: Y1 Dexamethasone 1H rep1

source_name: Y1 Dexamethasone 1H rep1


title: iPSCs dopa, control, 0, t74, 16C


title: BM-ddW 1


title: Y1 Control rep3

source_name: Y1 Control rep3

value: 0.05percent ethanol


title: Cell_HN30_rep1


title: Plasma MVs - Control rep4

city: Torino

first: Giovanni

last: Birolo

state: TO

address: Via Santena 19

department: Medical Sciences

country: Italy

institute: University of Turin

data_processing:
basecalling with bcl2fastq
adapter removal with cutadapt 1.10
alignment to miRbase with SHRiMP 2.2.3
Genome_build: murine mature miRNAs from mirBase 21
Supplementary_files_format_and_content: tab separated tables of raw counts

source_name: Plasma MVs - Control

growth_protocol: C26 cells were were cultured for 48 hours in serum-free media containing DMEM, 100 U/mL penicillin, 100 μg/mL streptomycin, 100 μg/mL sodium pyruvate, 2 mmol/L l-glutamine and maintained at 37°C in a humidified atmosphere of 5% CO2 in air.

extract_protocol:
Serum-free conditioned media or plasma were centrifuged at 300 × g for 10 min to eliminate cell debris. The supernatant was then recovered and successive centrifugations at increasing speed were performed: one at 2,000 × g for 20 min to eliminate dead cells, then one at 10,000 × g for 30 min to remove cell debris, and finally one at 100,000 × g for 70 min to pellet MVs. The resulting pellet was then washed in sterilized PBS and ultracentrifuged again at the same speed. The obtained pellet was finally re-suspended in 1 mL TriPure and total RNA was isolated following the manufacturer’s instructions
NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs Inc., Ipswich, MA, USA);Protocol E7330)
The obtained sequence libraries were subjected to the Illumina sequencing pipeline, passing through clonal cluster generation on a single-read flow cell (Illumina Inc., San Diego, CA, USA) by bridge amplification and were sequenced at ultrahigh throughput on NextSeq500 (Illumina Inc., San Diego, CA, USA). One flowcell in 24-plex could produce about six million single reads per sample, 75 base pairs (bp) long

treatment_protocol: C26-bearing mice were subcutaneously inoculated on the back with 5 × 10^5 C26 carcinoma cells and sacrified 14 days after tumor injection.

value: Balb/C

tag: disease state

value: Healthy

tag: sample type

value: plasma-derived MVs


title: Y1 Control rep2

source_name: Y1 Control rep2


title: BM-ddW 3

value: Multipotent progenitor 2 (MPP2)

value: 8-10 weeks


title: Plasma MVs - Control rep3


title: ESCC4 (KYSE410 cells_defactinib_24 hours)

first: lingyuan

last: zhang

address: 52 Fucheng Road, Haidian District, Beijing, China

institute: BEIJING INSTITUTE FOR CANCER RESEARCH

hyb_protocol: 1.5ug of Cy3-labelled cRNA (specific activity > 10.0 pmol Cy3/ug cRNA) was fragmented at 60 ℃ for 30 minutes in a reaction volume of 250 ml containing 1× Agilent fragmentation buffer and 2× Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2× Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays for 17 hours at 65 ℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 ℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned using Agilent Scanner G2505C.

data_processing: Data was extracted and normalized using Feature Extraction v10.7.1.1 software. Further Data analysis was performed using Agilent GeneSpring v13.1 software.

source_name: KYSE410 24H treatment.txt

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy  column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100U/ml), and streptomycin (100 μg/ml).

extract_protocol: Total RNA was extracted using mirVanaTM RNA Isolation Kit (ABI, AM1561).

treatment_protocol: KYSE410 cells were treated with or without 10 uM defactinib for 4 hours and 24 hours.

value: KYSE410 cells

value: 10 uM FAK inhibitor (defactinib) for 24 hours


title: Plasma MVs - Control rep2


title: Cell_HN4_rep1


title: P13, P19, P26 and P32 single cell TCR of sorted B2 CD4+ HNSCC PBMC (Hashtag) 1

source_name: HNSCC PBMC

extract_protocol:
Frozen PBMC samples were sorted using T cell activation markers identified in scRNA-seq data. Cells were thawed in two groups (B1 or B2), diluted in FWB, and counted with a hemacytometer. Up to 5x106 cells were then centrifuged and resuspended in 1:500 Zombie Aqua (Biolegend) in PBS and incubated at RT for 15 minutes. Cells were resuspended in TruStainFx FcBlock (1:20 dilution) in FWB, incubated at 4°C for 15 minutes. Additional antibodies for sorting/analysis were then added Unique sample-specific hashtag TotalSeqC antibodies (Biolegend, #1-4) were added to each sample (10 uL per sample) for identification of cells from individual specimens. Cells were stained for 20 minutes at 4°C, washed twice with FWB and filtered through a 40 um flow-cap strainer. Using a BD FACS Aria II instrument (BD Biosciences), live CD3+ CD4+ HLA-DR-high cells were sorted into PBS+BSA. Sorted cells were washed with 0.25% BSA and counted if numbers permitted (>30,000 cells). Cells from patient were pooled, using all sorted cells or up to 10,000 cells per patient. Each pool of cells was loaded into single Chip A channel, along with the reverse transcriptase reagent mixture and 5’ gel beads according to the 10x Genomics 5’ V1 assay protocol.
Libraries were prepared accordingn to 10X Genomics protocols for 5' barcoded GEX, feature barcode, and V(D)J TCR (Version 1)

tag: cell marker

value: TCR:ab chains

tag: single cell or bulk

value: Single cell

tag: state

tag: patient diagnosis

value: Head and neck squamous cell Carcinoma (HNSCC)

tag: molecule

value: T cell receptor


title: ESCC3 (KYSE410 cells_24 hours_control)

source_name: KYSE410 24H control.txt

value: control 24 hours


title: Cell_HN4_CR_rep1

source_name: Cell,HN4,cisplatin resistance replicate 1


title: Y1 Control rep1

source_name: Y1 Control rep1

value: Y-1 adrenocortical cells


title: iPSCs dopa, MPP+, 400uM, t24, 14C

source_name: endothelial cells

value: MPP+

tag: dose

tag: time


title: Plasma MVs - Control rep1


title: iPSCs dopa, MPP+, 200uM, t24, 11C

value: iPSC-derived dopaminergic neurons


title: iPSCs dopa, MPP+, 200uM, t24, 12C


title: iPSCs dopa, MPP+, 400uM, t24, 13C


title: Adrenal PBS rep2

data_processing:
Raw data was transformed by Casava version 1.8 base calling
Reads were removed with adaptor contamination. The trimmed reads were then aligned to the mouse genome (mm10, GRCm38.95) using STAR (v. 2.5). Reads were mapped to each gene and counted using HTSeq (v.0.6.1).
Fragments Per Kilobase of transcript sequence per Millions (FPKM) were calculated using sequencing depth and gene length on counting of fragments (Mortazavi et al. 2008).
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft excel open XML spreadsheet include read counts

source_name: Adrenal gland

extract_protocol:
Adrenal glands were removed, and surrounding adipose tissue was trimmed away. The right adrenal gland from each mouse was snap-frozen in liquid nitrogen and stored at -80°C until use. Adrenals from 2-3 animals were pooled as one biological replicate, with two biological replicates per condition (a total of 5 mice were included in each condition). Total RNA was extracted from frozen adrenal glands using Monarch Total RNA Miniprep Kit.
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Pre Kit for Illumina

treatment_protocol: Mice were intraperitoneal  injected with either dexamethasone or vehicle (sterile 1X phosphate-buffered saline). Adrenal gands were collected one hour after injection.

tag: tissue

value: Adrenal gland

value: treated with PBS for 1h

value: adult

tag: Sex

value: male


title: Plasma MVs - C26 rep6

source_name: Plasma MVs - C26

value: Balb/C

value: Cachectic

value: plasma-derived MVs


title: ESCC1 (KYSE410 cells_4 hours_control)

source_name: KYSE410 4H control.txt

tag: cell line

value: KYSE410 cells

value: control 4 hours


title: Adrenal PBS rep1

tag: treatment

tag: age


title: iPSCs dopa, MPP+, 400uM, t24, 15C

tag: cell type


title: P13, P19, P26 and P32 scRNA-seq of sorted B2 CD8+ HNSCC PBMC (Hashtag) 2

extract_protocol:
Frozen PBMC samples were sorted using T cell activation markers identified in scRNA-seq data. Cells were thawed in two groups (B1 or B2), diluted in FWB, and counted with a hemacytometer. Up to 5x106 cells were then centrifuged and resuspended in 1:500 Zombie Aqua (Biolegend) in PBS and incubated at RT for 15 minutes. Cells were resuspended in TruStainFx FcBlock (1:20 dilution) in FWB, incubated at 4°C for 15 minutes. Additional antibodies for sorting/analysis were then added Unique sample-specific hashtag TotalSeqC antibodies (Biolegend, #1-4) were added to each sample (10 uL per sample) for identification of cells from individual specimens. Cells were stained for 20 minutes at 4°C, washed twice with FWB and filtered through a 40 um flow-cap strainer. Using a BD FACS Aria II instrument (BD Biosciences), live CD3+ CD8+ CD38+HLA-DR+ cells were sorted into PBS+BSA. Sorted cells were washed with 0.25% BSA and counted if numbers permitted (>30,000 cells). Cells from patient were pooled, using all sorted cells or up to 10,000 cells per patient. Each pool of cells was loaded into single Chip A channel, along with the reverse transcriptase reagent mixture and 5’ gel beads according to the 10x Genomics 5’ V1 assay protocol.
Libraries were prepared accordingn to 10X Genomics protocols for 5' barcoded GEX, feature barcode, and V(D)J TCR (Version 1)

value: total RNA


title: P13, P19, P26 and P32 single cell TCR of sorted B2 CD8+ HNSCC PBMC (Hashtag) 2

value: TCR:ab chains

value: Single cell


title: Adrenal Dexamethasone rep2

value: treated with dexamethasone for 1h


title: P13, P19, P26 and P32 single cell TCR of sorted B1 CD4+ HNSCC PBMC (Hashtag) 1

value: Head and neck squamous cell Carcinoma (HNSCC)

value: T cell receptor


title: Plasma MVs - C26 rep4


title: iPSCs dopa, MPP+, 200uM, t24, 10C

value: MPP+


title: P13, P19, P26 and P32 scRNA-seq of sorted B2 CD4+ HNSCC PBMC (Hashtag) 1


title: Adrenal Dexamethasone rep1


title: Plasma MVs - C26 rep5


title: P13, P19, P26 and P32 single cell TCR of sorted B1 CD8+ HNSCC PBMC (Hashtag) 2


title: ESCC2 (KYSE410 cells_defactinib_4 hours)

source_name: KYSE410 4H treatment.txt

value: 10 uM FAK inhibitor (defactinib) for 4 hours


title: JHOC5_siXPR1_3

city: Yayoi, Bunkyo-ku

first: Tomoatsu

last: Hayashi

institute: The University of Tokyo

description: JHOC5 cells treated with siXPR1#3 for 48h

data_processing:
BAM-formatted map files were generated using STAR version 2.5.3a with default parameters.
The gene-level expression values (counts and TPM) were estimated by RSEM version 1.3.1 with default paramters.
Differential expression analysis was performed using edgeR-3.32.1 (likehood ratio test) with R version 4.0.1. To filter out the low expression genes, we used 'filterByExpr' command (min.count = 5).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw read counts per gene.
Supplementary_files_format_and_content: tab-delimited text files include transcripts per kilobase million (TPM).

source_name: ovarian cancer cell line

growth_protocol: Human ovarian cancer OVISE and JHOC5 cells were cultured in DMEM and RPMI1640 medium supplemented with 10% fetal bovine serum (FBS), respectively. TOV21G cells were cultured in a 1:1 mixture of MCDB 105 medium and Medium 109 supplemented with 15% FBS. ES2 cells were grown in McCoy 5A supplemented with 10% FBS. All cell lines were cultured at 37°C under a 5% CO2 atmosphere.

extract_protocol:
Cells were collected ad 48h post-transfection and then total RNA was extracted using TRIsure reagent (Bioline)according to the manufacturer’s protocol. RNA concentration and quality were evaluated using a NanoDrop 3000 spectrophotometer (Thermo Fisher Scientific) and a TAPESTATION (Agilent), respectively.
The sequencing library construction (Illumina mRNA-seq) and Illumina sequencing (paired-end 150 bp reads) were performed by AnnoRoad Gene Technology.

treatment_protocol: Silencer select siRNA targeting XPR1 was purchased from Ambion (siXPR1#1; #17614, siXPR1#2; #17615, siXPR1#3; #17616). Cells were transfected with siRNA using Lipofectamine RNAiMax (ThermoFisher) according to the manufacturers instruction. Silencer select siRNA negative controls (ThermoFisher, siNC#1; 4390843, siNC#2; 4390846) were used as a control.

tag: sirna treatment

value: ovarian cancer cell line


title: JHOC5_siXPR1_2

description: JHOC5 cells treated with siXPR1#2 for 48h


title: RNA_2C_K36M_rep8

city: Fukuoka

first: Hiroyuki

last: Sasaki

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Molecular and Structural Biology

institute: Medical Institute of Bioregulation, Kyushu University

data_processing:
For ChIP-seq data, paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with a default setting after removing adaptor sequences and low-quality reads by Trim Galore!. Reads from PCR duplicates were removed by using Samtools ‘markdup’ with an option ‘-r’. To compute normalized enrichment, normalized ChIP read counts were divided by normalized input read counts using deepTools bamCompare with options '--normalizeUsing RPKM'and '--operation ratio'. Spike-in normalization was performed when it is possible.
For CUT&RUN data, paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with a default setting after removing adaptor sequences and low-quality reads by Trim Galore!. Reads from PCR duplicates were removed by using Samtools ‘markdup’ with an option ‘-r’. Normalized read counts were computed using deepTools bamCoverage with options '--normalizeUsing RPKM'.
For WGBS data,Reads were trimmed to remove low quality bases and adaptor sequences using Trim-Galore! and mapped to the mouse genome (mm10) using Bismark v0.14.5. After confirming reproducibility between replicates, the BAM files were merged using Samtools ‘merge’. CG sites covered by four to 100 reads were considered as informative CG sites, and bins containing more than five informative CG sites were used for downstream analyses by custom Perl scripts. To extract bins in which CG methylation levels are unaffected by Dnmt3a KO in oocytes, we used the following criteria: the difference of CG methylation levels between Dnmt3a KO versus control FGOs <10%, and the CG methylation levels in control FGOs >40%.
For RNA-seq data, the first three bases of the Read 2 derived from the SMART-seq Stranded Adaptor were trimmed prior to mapping using Trim Galore!. After the reads were aligned with Hisat2, reads corresponding to ribosomal RNA were removed by using the BEDTools intersectBed function. FeatureCounts was then used to analyze the gene expression level. The resulting read count data were processed by EdgeR to identify differentially expressed transcripts between two groups. A false discovery rate of <0.05 was used to extract differentially expressed transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig and text files

source_name: Embryo

growth_protocol: Fully grown oocytes were collected by punching ovaries of female mice at 3-4 weeks of age. For in vitro fertilization, female mice were super-ovulated by the injection of 0.1 ml of CARD HyperOva followed by hCG injection (5 IU) 46–48 h later. Cumulus-oocyte complexes were collected from the oviducts and fertilized with C57BL/6J or JF1 sperm. Zygotes were cultured in EmbryoMax KSOM medium (Merck Millipore) at 37 ºC and 6% CO2. Late 2-cell embryos were harvested at 31-32 h post-fertilization for RNA-seq.

extract_protocol:
For ChIP-seq, MNase-digested chromatin was used. For CUT&RUN, chromatin digested by protein A/protein G-MNase was used. WGBS libraries were constructed using the post-bisulfite adapter tagging method (Miura et al., 2012). A SMART-Seq stranded kit (TAKARA) was used to prepare RNA-seq libraries.
ULI-NChIP-seq protocol was used to prepare ChIP-seq libraries. CUT&RUN libraries were prepared as described before (Ishiuchi et al., Nat. Struct. Mol. Biol. 2021). The PBAT method was used to prepare WGBS libraries as described before (Au et al., Cell Rep. 2019). A SMART-Seq stranded kit (TAKARA) protocol was used to prepare RNA-seq libraries.
ChIP-seq, CUT&RUN, WGBS, and RNA-seq.

treatment_protocol: For ChIP-seq, CUT&RUN, or WGBS, FGOs were collected from mouse ovaries. Pooled FGOs or single late 2-cell embryos were used for RNA-seq.

tag: strain

value: hybrid C57BL/6 / 129 X JF-1


title: Plasma MVs - C26 rep3

tag: disease state


title: JHOC5_siXPR1_1

description: JHOC5 cells treated with siXPR1#1 for 48h


title: JHOC5_siNC_2

description: JHOC5 cells treated with siNC#2 for 48h


title: RNA_2C_K36M_rep7


title: P13, P19, P26 and P32 scRNA-seq of sorted B1 CD8+ HNSCC PBMC (Hashtag) 2

data_processing:
Raw PBMC scRNA-sequencing reads were demultiplexed and aligned to the human reference genome (GRCh38-2020-A from 10x Genomics) for each pooled library using Cell Ranger (v4.0.0). Each pooled library contained multiple patient samples and timepoints; cells from each sample were labelled with distinct Hashtag oligonucleotides (HTO, Cell Hashing). Sequencing files for Gene Expression (measure mRNA level of cells) and Antibody Capture (measure HTO levels of cells) were fed to the “cellranger count” function with the –libraries flag, and the sequences of all HTO used in the library were fed to this function with –feature-ref flag. This generated a digital gene expression matrix, which measured the number of unique molecular identifier (UMI) for each gene and each cell barcode.
The raw gene-by-barcode count matrix was then processed to filter potential empty drops using emptyDrops function from DropletUtils (v1.8.0, R package) (Lun et al., 2019) with the parameters of “lower = 500, ignore = 5”. We initially selected droplets as containing a cell if total UMI counts of this droplet exceed the 99th percentile of the top 10,000 barcodes divided by 10. Finally, only cells with FDR<=0.01 were retained as real cells for the following analysis. The raw HTO-by-barcode matrix was subsequently filtered based on identified real cells.
The filtered HTO-by-barcode matrix for each pooled library was processed using GMM-demux to distinguish singlets from doublets or multiplets based on detection of HTOs with default parameters (Xin et al., 2020). Predicted singlets with a confidence score>=0.8 were defined as true singlet cells. Cell barcodes were then classified and allocated to respective patient samples based on hashtag identities. After processing, the gene-by-barcode count matrix was refined based on these identified singlets and used for the following analyses.
Raw tumor scRNA-sequencing reads were demultiplexed to FASTQ files using Cell Ranger mkfastq (v3.0.0, 10x Genomics), and the Cumulus cellranger-workflow implementation of Cell Ranger count (v4.0.0) on Terra (https://terra.bio/) was used to align reads to the human reference genome (GRCh38-2020-A) and generate a raw counts matrix (Li et al., 2020). Cumulus was used to filter cells from the Cell Ranger raw counts matrix with fewer than 400 UMIs, 200 genes, or greater than 20% of UMIs mapped to mitochondrial genes.
To generate the single-cell V(D)J sequences and annotate each library, we aligned TCR FASTQ reads to human GRCh38 V(D)J reference (v4.0.0 from 10X Genomics, modified to remove TRDD segments) using “cellranger vdj” function from Cell Ranger (v4.0.0). The filtered contig annotations, which contained high-level annotations of each high-confident cellular contig, were further filtered by removing records with ‘raw_consensus_id’ as ‘none’. For blood single-cell V(D)J analysis, the identities of different patient samples in each pooled library were labelled based on demultiplexing of the gene expression matrix.
Assembly: GRCh38
Supplementary files format and content: Each scRNA sequenting sample contains a .h5 file including Gene Expression (tumor and PBMC) and Antibody Capture (PBMC) information. Single cell TCR sequencing data for each sample were saved in a csv file, which is generated by 'cellranger vdj' function and shows the detailed clonotype information. Bulk TCR sequencing data for each sample were provided by Adaptive Biotech and were saved in a tsv file. Hashtag files contain the sequence of each hashtag and the corresponding patient sample information.


title: P31 and P32 single cell TCR of HNSCC PBMC (Hashtag)

extract_protocol:
PBMCs isolated as described above were thawed in groups in 5-6 vials at a time, with each vial representing an individual blood draw. Thawed PBMCS were immediately diluted into 10 mL PBS, centrifuged (400 g for 5 minutes at 4°C for all centrifugation steps) and resuspended in PBS. Cells were counted with a hemacytometer; viability of thawed cells averaged 55%. Live cells were sorted to ensure the quality of scRNA-seq libraries. Between 0.5-1x10^6 cells were stained with Zombie NIR (Biolegend) diluted 1:500 in PBS for 15 minutes at RT. Cells were centrifuged and then resuspended in 90 uL of FWB, to which the following were added: 5 uL of TruStain Fx FcBlock (Biolegend), 2 uL of aCD45-Pacific Blue (Biolegend), 2 uL of aCD3-PE/Dazzle594 (Biolegend) and 2 uL (1 ug) of a TotalSeqC hashing antibody (Biolegend). For each group of up to six PBMC vials, unique hashtags were used for later identification of cells from individual samples. Cells were incubated for 20 minutes at 4°C, washed twice with 500 uL FWB, and filtered through 40 um flow-cap strainers. Live CD45+ cells (50,000 to 100,000 cells) were then separately sorted using a FACS Aria II instrument for each hashtag-labeled sample. Cells were sorted into 500 uL 0.1% BSA in 1.5 mL DNA LoBind microcentrifuge tubes (Eppendorf). Following sorting, cells were centrifuged, washed with 0.25% BSA, and resuspended in a final volume of 30-50 uL 0.25% BSA. Live cells were counted with a hemacytometer. For generation of single-cell emulsions, 6000 live cells from each sample (up to six samples) were pooled and loaded into a single Chip A channel, along with the reverse transcriptase reagent mixture and 5’ gel beads, according to the 10x Genomics 5’ V1 manufacturer’s protocol.
Libraries were prepared accordingn to 10X Genomics protocols for 5' barcoded GEX, feature barcode, and V(D)J TCR (Version 1)


title: Plasma MVs - C26 rep2

tag: sample type


title: P22 and P23 single cell TCR of HNSCC PBMC (Hashtag)

tag: cell marker


title: P13, P19, P26 and P32 scRNA-seq of sorted B1 CD4+ HNSCC PBMC (Hashtag) 1

tag: single cell or bulk


title: JHOC5_siNC_1

description: JHOC5 cells treated with siNC#1 for 48h


title: C26 cells - TMVs rep3

source_name: C26 cells - TMVs

value: Colon adenocarcinoma 26 (C26) cells

value: Conditioned medium of C26 cells


title: P21, P25 and P28 single cell TCR of HNSCC PBMC (Hashtag)

tag: state


title: RNA_2C_K36M_rep4


title: RNA_2C_K36M_rep5


title: Plasma MVs - C26 rep1

value: Balb/C


title: JHOC5_mock

description: JHOC5 cells treated with transfection reagents for 48h

value: Mock (only transfection reagents)


title: C26 cells - TMVs rep1


title: ES2_siXPR1_3

description: ES2 cells treated with siXPR1#3 for 48h


title: C26 cells - TMVs rep2


title: RNA_2C_K36M_rep6


title: P19 and P20 single cell TCR of HNSCC PBMC (Hashtag)

tag: patient diagnosis


title: p53Notch1__rep6

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: Sample 26

data_processing:
Obtained single-end RNA-seq reads were mapped to the mouse genome assembly, version mm10, with RNA-STAR (Dobin et al., Bioinformatics 2013), with default parameters except for reporting only one hit for multimapping reads ( outFilterMultimapNmax=10, outSAMmultNmax=1) and  filtering reads without evidence in spliced junction table (outFilterType="BySJout").
All subsequent gene expression data analysis was done within the R software (R Foundation for Statistical Computing, Vienna, Austria). Raw reads and mapping quality was assessed by the qQCreport function from the R/Bioconductor software package QuasR (Gaidatzis et al., 2015).
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in December 2015) and the qCount function from QuasR package, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw counts for Entrez Genes , 1.column is EntrezGeneID, 2. column is length of all exons in nt, 3. and remaining columns contain raw counts

source_name: Glioma cells from Notch1 -/- tumor

growth_protocol: Mice were euthanized and their brains were isolated.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sequencing libraries were generated with the TruSeq Stranded RNA LT kit (Illumina). Sequencing was performed on an Illumina NextSeq 500 according to manufacturer specification.

treatment_protocol: Early stage gliomas were identified by the expression of GFP from the Rosa-CAG::GFP Cre-reporter, micro-dissected, and GFP+ tumor cells purified by FACS.

value: ko

value: wt

tag: rbpj

tag: replicate


title: P18, P29 and P30 single cell TCR of HNSCC PBMC (Hashtag)

tag: molecule


title: RNA_2C_K36M_rep3


title: p53__rep6

description: Sample 25

source_name: Glioma cells from control tumor


title: ES2_siXPR1_2

description: ES2 cells treated with siXPR1#2 for 48h


title: ES2_siXPR1_1

description: ES2 cells treated with siXPR1#1 for 48h


title: RNA_2C_K36M_rep2


title: RNA_2C_K36M_rep1


title: ES2_siNC_2

description: ES2 cells treated with siNC#2 for 48h


title: p53N1N2__rep5

description: Sample 24

source_name: Glioma cells from Notch1 -/- Notch2 -/- tumor


title: P15 and P17 single cell TCR of HNSCC PBMC (Hashtag)


title: P13 and P14 single cell TCR of HNSCC PBMC (Hashtag)


title: p53Notch2__rep5

description: Sample 23

source_name: Glioma cells from Notch2 -/- tumor


title: ES2_siNC_1

description: ES2 cells treated with siNC#1 for 48h


title: p53Notch1__rep5

description: Sample 22


title: ES2_mock

description: ES2 cells treated with transfection reagents for 48h


title: RNA_2C_ctrl_rep7


title: RNA_2C_ctrl_rep5


title: RNA_2C_ctrl_rep6


title: P08 and P09 single cell TCR of HNSCC PBMC (Hashtag)


title: p53Rbpj__rep4

description: Sample 21

source_name: Glioma cells from Rbpj -/- tumor


title: TOV21G_siXPR1_2

description: TOV21G cells treated with siXPR1#2 for 48h


title: TOV21G_siXPR1_3

description: TOV21G cells treated with siXPR1#3 for 48h


title: p53__rep5

description: Sample 20


title: RNA_2C_ctrl_rep4


title: p53N1N2__rep4

description: Sample 19


title: P16, P24 and P26 single cell TCR of HNSCC PBMC (Hashtag)

source_name: HNSCC PBMC


title: P01 and P02 single cell TCR of HNSCC PBMC (Hashtag)


title: TOV21G_siXPR1_1

description: TOV21G cells treated with siXPR1#1 for 48h


title: TOV21G_siNC_2

description: TOV21G cells treated with siNC#2 for 48h


title: RNA_2C_ctrl_rep2


title: RNA_2C_ctrl_rep3


title: TOV21G_siNC_1

description: TOV21G cells treated with siNC#1 for 48h


title: p53Notch2__rep4

description: Sample 18


title: P22 and P23 single cell GEX of HNSCC PBMC (Hashtag)


title: p53Notch1__rep4

description: Sample 17


title: P31 and P32 single cell GEX of HNSCC PBMC (Hashtag)


title: TOV21G_mock

description: TOV21G cells treated with transfection reagents for 48h


title: P19 and P20 scRNA-seq of HNSCC PBMC (Hashtag)


title: p53Rbpj__rep3

description: Sample 16


title: p53__rep4

description: Sample 15


title: P18, P29 and P30 scRNA-seq of HNSCC PBMC (Hashtag)


title: P21, P25 and P28 scRNA-seq of HNSCC PBMC (Hashtag)


title: OVISE_siXPR1_3

description: OVISE cells treated with siXPR1#3 for 48h

value: OVISE


title: OVISE_siXPR1_2

description: OVISE cells treated with siXPR1#2 for 48h


title: RNA_FGO_K36M_rep2

source_name: Oocyte

value: hybrid C57BL/6 / 129


title: P04 and P05 single cell TCR of HNSCC PBMC (Hashtag)

value: TCR:ab chains


title: OVISE_siXPR1_1

description: OVISE cells treated with siXPR1#1 for 48h


title: p53N1N2__rep3

description: Sample 14


title: p53Notch2__rep3

description: Sample 13


title: RNA_FGO_K36M_rep1


title: RNA_2C_ctrl_rep8


title: P16, P24 and P26 scRNA-seq of HNSCC PBMC (Hashtag)

value: Single cell

value: total RNA


title: OVISE_siNC_2

description: OVISE cells treated with siNC#2 for 48h


title: RNA_FGO_ctrl_rep3


title: P15 and P17 scRNA-seq of HNSCC PBMC (Hashtag)

value: Head and neck squamous cell Carcinoma (HNSCC)


title: OVISE_siNC_1

description: OVISE cells treated with siNC#1 for 48h


title: RNA_2C_ctrl_rep1


title: RNA_FGO_ctrl_rep2


title: p53Rbpj__rep2

description: Sample 11


title: RNA_FGO_ctrl_rep1


title: RNA_FGO_K36M_rep3


title: P13 and P14 scRNA-seq of HNSCC PBMC (Hashtag)


title: OVISE_mock

description: OVISE cells treated with transfection reagents for 48h


title: WGBS_DM_rep2


title: p53__rep3

description: Sample 10


title: P10 and P12 scRNA-seq of HNSCC PBMC (Hashtag)


title: P10 and P12 single cell TCR of HNSCC PBMC (Hashtag)

value: T cell receptor


title: P08 and P09 scRNA-seq of HNSCC PBMC (Hashtag)


title: p53Notch2__rep2

description: Sample 8


title: p53N1N2__rep2

description: Sample 9


title: CAG-shA5-2

city: Hangzhou

first: Yifan

last: Hou

address: No. 79, Qingchun Rd

institute: Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In  this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: human myeloma cell line

growth_protocol: HMCLs cultured in RPMI-1640 supplemented with 10% FBS

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared using NEB Next® Ultra™ RNA Library Prep Kit

treatment_protocol: Ransduced with indicated lentiviruses

value: CAG


title: P04 and P05 scRNA-seq of HNSCC PBMC (Hashtag)

last: Suo

institute: Dana-Farber Cancer Institute


title: p53Notch1__rep3

description: Sample 12


title: WGBS_setd2_KO


title: WGBS_K36M_rep2


title: CAG-shA5-1


title: p53Notch1__rep2

description: Sample 7


title: p53Rbpj__rep1

description: Sample 6


title: WGBS_K36M_rep1


title: WGBS_ctrl_rep2


title: CAG_shNC_2

value: shNC


title: P31 single cell TCR of post-Tx HNSCC tumor

source_name: HNSCC tumor

extract_protocol:
Fresh tumor tissue was transferred to a 6 cm tissue culture dish in a small volume of DMEM media and cut into <2 mm pieces with a razor blade. Tissue pieces were centrifuged (400 g for 5 minutes at 4°C for all centrifuge steps) and resuspended in 2-5 mL of a collagenase-containing enzymatic digestion solution (Miltenyi Human Tumor Dissociation Kit #30-095-929), based on the weight of collected tissue, according to manufacturer’s instructions. Biopsies were incubated at 37°C for 20-30 minutes with mixing using a 5-10 mL serological pipet and intermittent gentle vortexing at 2-5-minute intervals. The extent of tumor tissue dissociation was variable and likely dependent on extracellular matrix abundance. The resulting cell suspension was passed through a 70 um nylon mesh filter and washed with an additional 5-10 mL of RPMI media. Filtered tumor cell suspensions were centrifuged and resuspended in 3 mL ACK red blood cell lysis buffer (Gibco #A1049201) for 1 minute at RT, then immediately diluted with 10 mL of PBS (Life Technologies #10437028). Cells were pelleted and resuspended in Zombie NIR (Biolegend) viability dye solution (1:500 in PBS), followed by a 15 minute incubation at RT in the dark. Cells were counted with a hemocytometer, yielding on average 1.3x104 live cells/mg of tumor tissue. Up to 500,000 live cells were then resuspended in 100 uL of FACS wash buffer (FWB; PBS, 2% FBS, 1 mM EDTA) with the addition of the following antibodies: TruStain FcX (Biolegend 422302), CD3-PE/Dazzle (Biolegend 300450), CD45-Pacific Blue (Biolegend 304022), CD66b-PE/Cy7 (Biolegend 305116) and CD15-APC (Biolegend 301908). Cells were incubated on ice for 20 minutes, washed with 1 mL FWB, filtered through 40 um flow-cap strainers, and then resuspended in 500 uL FWB. Cells were sorted using a FACS Aria II or III instrument (BD Biosciences). For most samples, 12-15 x 103 live CD45+CD66b- mononuclear cells (MNC) cells were sorted into T cell media (RPMI + 10% FBS) and immediately transferred to ice. All scRNA-seq was performed using the 10x Genomics 5’ V1 assay and protocols (10x Genomics). CD45+ cells isolated as above were centrifuged and washed with PBS containing 0.05% RNase-free BSA (ThermoFisher Scientific #AM2616), leaving a volume of <32 uL after the final wash. Up to 15,000 cells based on cell sorter count were loaded into a Single Cell Chip A channel, along with reverse transcriptase reagent mixture and 5’ gel beads according to the manufacturer’s protocol.
Libraries were prepared accordingn to 10X Genomics protocols for 5' barcoded GEX and V(D)J TCR (Version 1)

value: Post-Tx


title: P01 and P02 scRNA-seq of HNSCC PBMC (Hashtag)


title: p53N1N2__rep1

description: Sample 5


title: CAG_shNC_1


title: p53Notch2__rep1

description: Sample 4


title: P30 single cell TCR of post-Tx HNSCC tumor


title: CAG_shNC_3