title: TCKO WGBS

city: Hangzhou

first: Dengfeng

last: Ruan

state: China

address: 88 Jie Fang Road

department: Department of Orthopedic Surgery

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

data_processing:
Illumina Casava software used for basecalling.
For WGBS data analysis, raw reads were aligned to the reference GRCm38.99 Mus musculus genome using BSMAP (v 2.74) by allowing up to 2 mismatches (-v 2), 1 best hit (-w 1) and aligning to both strands(-n 1).
Methylation levels at each cytosine were then extracted with BSMAP (methratio_32unit_alt.py) scripts by allowing only unique mapped reads (-u).Methylation levels at each cytosine were calculated as #C/(#C+#T).
Genome_build: GRCm38.99
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: Matrix table with base site and CG methylation

source_name: Primary osteoblasts

extract_protocol:
DNA was extracted by DNeasy Blood & Tissue Kit (QIAGEN, 69504).
BS-seq library constructions and sequencing utilized one sample per group.

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.

value: TET1/2/3 Triple knockout

tag: age


title: 3' PBMC Ultima

status: Public on Jul 07 2022

type: SRA

city: Cambridge

first: Joshua

last: Levin

state: MA

address: 75 Ames St

department: Stanley Center

country: USA

institute: Broad Institute

description: 3' PBMC data, sequenced with Ultima

library_source: transcriptomic

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.

molecule: total RNA

organism: Homo sapiens

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

tag: sample type

value: PBMC


title: 5' PBMC Ultima

description: 5' PBMC data, sequenced with Ultima


title: 5' PBMC mixture Ultima

description: 5' PBMC Mixture data, sequenced with Ultima


title: 5' PBMC Single End Illumina

description: 5' PBMC data, sequenced with Illumina as a single ended library


title: Glycine max hypocotyl tissue - null_mock_rep2

city: Corvallis

first: Emily

last: Helliwell

state: OR

address: Oregon State University

institute: Oregon State University

data_processing:
Base-calling was done using RTA (Real-Time Analysis) software, and bcl files were converted to fastq using bcl2fastq
Sequenced reads were trimmed for adaptor sequence using cutadapt2 parameters -b 20 -n 2  and mapped to Glycine max v1.1 using bowtie2 with parameters -c 'tophat --num-threads 8 -P 8 -q
Count tables to quantify the number of reads per gene were generated with the samtools function htseq-count (Li et al., 2009), parameter -f
Normalization of the number of counts was run using EstimateSizeDisperson function with the R package DESeq
Assembly: Wm82.a1.v1.1 (Glyma 1.1), Gmax_189_gene.gff3
Supplementary files format and content: csv file soybean_ncounts include normalized values for each Sample ...
Supplementary files format and content: Matrix table raw_counts with raw gene counts for every gene and every sample

organism: Glycine max

growth_protocol: Six soybean seeds were sown in potting soil in 6-inch pots and maintained in growth chambers at 28˚C light/24˚C dark.

extract_protocol:
Hypocotyl segments, 1 cm long, centered on the inoculated areas were harvested 12 hr later, pooling 18 plants each for mock- and P. sojae-inoculated lines, then snap-frozen in liquid nitrogen and stored in -80˚C.  RNA was extracted using RNeasy (Qiagen) RNA extraction reagent according to the manufacturer’s instructions.
1 µg of total RNA was submitted for sequenceding on an Illumina HiSeq 3000, using a 150 base pair, paired-end module at the Oregon State University Center for Genome Research and Biocomputing

treatment_protocol: Hypocotyls on 10 day-old soybeans were wounded by gently scraping 0.5 cm between the soil line and the cotyledons, and a 2.5 mm2 square of P. sojae mycelia was placed, mycelial side down over the wounded area.  Inoculated plants were maintained in a growth chamber at 28˚C light/24˚C dark for twelve hours

tag: cell type

value: plant cells, hypocotyl tissue

tag: strain

value: null segregant

tag: treatment

value: Inoculated with sterile water


title: 5' PBMC mixture TCR_BCR (BCR)

description: TCR/BCR data for 5' PBMC Mixture data, sequenced with Illumina


title: shLuc_dox_m6A-eCLIP

city: Stanford

first: Nitin

last: Raj

state: CA

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

department: Radiation Oncology

institute: Stanford University

description: m12-m6A-eCLIP_shLuc_dox_S4.adapterTrim.round2

data_processing:
library strategy: m6A-eCLIP-seq
Unique molecular Identifiers (UMIs) were pruned from read sequences using umi_tools (v0.5.1)
3'-adapters were trimmed from reads using cutadapt (v2.7)
Peaks were identified within m6A-eCLIP samples using the peak caller CLIPper (https://github.com/YeoLab/clipper)
Peaks were annotated using transcript information from GENCODE (Release M21)
The RPM value for a particular region was calculated by counting the number of reads in that region and dividing that by the “per million” scaling factor, which is defined as the total number of reads in the sample divided by 1,000,000. The log2 fold changes for a peak are calculated as follows: Log2 (RPM in IP in peak region / RPM in input in peak region). Log2 fold change values (RPM in IP in peak region / RPM in input in peak region) were calculated for individual peaks in each m6A-IP to normalize the IP reads to the total number of reads covering the m6A residue. The differential of Log2 fold change between shLuc and shMettl3 samples treated with dox, was used to identify genes that were most enriched for a specific m6A modification under DNA damage in a Mettl3-dependent manner.
Genome_build: mm10
Supplementary_files_format_and_content: shLuc_dox_m6A-eCLIP vs Input.xlsx: shLuc_dox m6A peaks normalized to Input
Supplementary_files_format_and_content: shMettl3-2_dox_m6A-eCLIP vs Input.xslx: shMettl3-2_dox m6A peaks normalized to Input
Supplementary_files_format_and_content: m12-shLuc_dox_vs_shMettl3_dox_peaks_w_full_read_nums_edited_filter_Column V.xlsx: RNA-seq (Inputs) processed data and calculations to normalize m6A-eCLIP peaks to their respective inputs.

molecule: polyA RNA

organism: Mus musculus

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 were used for RNA-seq and purified mRNAs were used for m6A-eCLIP
Libraries were prepared as described in Van Nostrand et al (Nat Methods. 2016 Jun; 13(6): 508–514.)

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

tag: genotype/variation

value: control shRNAs

value: Doxorubicin


title: WT WGBS

country: China

library_source: genomic

molecule: genomic DNA

tag: genotype

value: wild type


title: shMettl3_dox_m6A-eCLIP

description: m12-m6A_eCLIP_shMettl3-2_dox_S6.adapterTrim.round2

value: E1A;HRasV12 expressing mouse embryonic fibroblasts

value: shRNAs directed against Mettl3


title: shMettl3_dox_input_RNA-seq

description: m12-RNA-seq_shMettl3-2_dox_S16.adapterTrim.round2

data_processing:
Unique molecular Identifiers (UMIs) were pruned from read sequences using umi_tools (v0.5.1)
3'-adapters were trimmed from reads using cutadapt (v2.7)
Peaks were identified within m6A-eCLIP samples using the peak caller CLIPper (https://github.com/YeoLab/clipper)
Peaks were annotated using transcript information from GENCODE (Release M21)
The RPM value for a particular region was calculated by counting the number of reads in that region and dividing that by the “per million” scaling factor, which is defined as the total number of reads in the sample divided by 1,000,000. The log2 fold changes for a peak are calculated as follows: Log2 (RPM in IP in peak region / RPM in input in peak region). Log2 fold change values (RPM in IP in peak region / RPM in input in peak region) were calculated for individual peaks in each m6A-IP to normalize the IP reads to the total number of reads covering the m6A residue. The differential of Log2 fold change between shLuc and shMettl3 samples treated with dox, was used to identify genes that were most enriched for a specific m6A modification under DNA damage in a Mettl3-dependent manner.
Genome_build: mm10
Supplementary_files_format_and_content: shLuc_dox_m6A-eCLIP vs Input.xlsx: shLuc_dox m6A peaks normalized to Input
Supplementary_files_format_and_content: shMettl3-2_dox_m6A-eCLIP vs Input.xslx: shMettl3-2_dox m6A peaks normalized to Input
Supplementary_files_format_and_content: m12-shLuc_dox_vs_shMettl3_dox_peaks_w_full_read_nums_edited_filter_Column V.xlsx: RNA-seq (Inputs) processed data and calculations to normalize m6A-eCLIP peaks to their respective inputs.


title: shLuc_dox_input_RNA-seq

description: m12-RNA-seq_shLuc_dox_S14.adapterTrim.round2


title: 5' PBMC mixture TCR_BCR (TCR)


title: CK_CTRL_1

city: Tokyo

first: Iki

last: Sonn

address: Shinjyuku-ku, Shinanomachi 35

country: Japan

institute: Keio University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg38 genome using HISAT2.
Sequence counts were calculated by Featurecounts.
Genome_build: Hg38
Supplementary_files_format_and_content: Raw counts

growth_protocol: Feeder-free SPI1 plasmid transfected iPSCs were cultured according to protocol published by CiRA. Then cells were transferred into StemPro™-34 SFM  medium and supplied with multiple cytokines according to different stages of differentiation (more details in the text). On Day 16, floating cells were collected and re-plated into PDL-coated plate, cultured in DMEM/F12 medium supplied by IL-34, TGFβ1, MCSF, CD200L and CX3CL1. Half medium change were applied every two days.

extract_protocol:
Cells were collected by RLT buffer and then homogenized by QIAshredder (Qiagen #79656). Total RNAs were isolated by RNeasy Mini Kit (Qiagen #74106) following manufacture’s guideline
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10ng/ml Dox were added into medium from Day 6.

value: iPSCs-derived microglia

tag: iPS strain

value: Cytokine alone


title: 5' PBMC mixture Illumina

description: 5' PBMC Mixture data, sequenced with Illumina


title: 5' PBMC TCR_BCR (TCR)

description: TCR/BCR data for 5' PBMC data, sequenced with Illumina


title: Perturb-seq Barcodes Perturb Guide

description: ADT, HTO, and Guide sequencing data from 3' Perturb-seq data

source_name: A375 cell line

value: Cell Line


title: 5' PBMC Illumina

description: 5' PBMC data, sequenced with Illumina


title: 5' PBMC TCR_BCR (BCR)


title: Resistant- replicate 2

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

description: M229-Res-Replicate 2

data_processing:
The reads were first mapped to the hg38 human genome set using Bowtie2 version 2.1.0 . The mitochondria reads, duplicate reads and non-unique reads were removed bdfore peak calling.MACS2 was used for peak calling using BAMPE mode.
The mitochondria reads, duplicate reads and non-unique reads were removed bdfore peak calling.MACS2 was used for peak calling using BAMPE mode.
Assembly: hg38
Supplementary files format and content: peak txt file

growth_protocol: M229-Par and M229-Res   were grown in DMEM medium with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Cells were trypsinized and purified by centrifugation before being place in nuclei isolation buffer (lysis buffer) containing 0.1% IGEPAL. Nuclei were then counted and 250,000 nuclei were used in ATAC-seq library preparation
Libraries were constructed as described in ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide by Buenrostro et al. 2015 Curr Proc Mol Biol

treatment_protocol: M229 parental and resistant cell lines were used for preparing nuclei to perform ATAC seq

tag: cell line


title: Resistant- replicate 2 [RNA-Seq]

description: M229-Res-Replicate 2

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: M229 parental and resistant cell lines were used for preparing total RNA to perform RNA seq


title: Parental- replicate 1 [RNA-Seq]

description: M229-Par-Replicate 1


title: Resistant- replicate 1 [RNA-Seq]

description: M229-Res-Replicate 1


title: Parental- replicate 3 [RNA-Seq]

description: M229-Par-Replicate 3


title: Parental- replicate 2 [RNA-Seq]

description: M229-Par-Replicate 2


title: Resistant- replicate 3

description: M229-Res-Replicate 3


title: Parental- replicate 3

description: M229-Par-Replicate 3


title: Parental- replicate 2

description: M229-Par-Replicate 2


title: P31 bulk TCR of B3 HNSCC PBMC

city: Boston

first: Shengbao

last: Suo

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 PBMC

extract_protocol:
Between 0.5-2.0 x106 PBMCs were pelleted and snap-frozen on dry-ice. Bulk TCR sequencing was performed from DNA extracted from cell pellets.
Illumina libraries were prepared using the Adaptive Biotechnologies ImmunoSeq deep TCR beta assay.

tag: cell marker

value: TCR:b chains

tag: single cell or bulk

value: Bulk

tag: state

tag: patient diagnosis

value: Head and neck squamous cell Carcinoma (HNSCC)

tag: molecule

value: T cell receptor b chains


title: P32 bulk TCR of B3 HNSCC PBMC


title: P23 bulk TCR of B3 HNSCC PBMC


title: P27 bulk TCR of B3 HNSCC PBMC


title: Parental- replicate 1

description: M229-Par-Replicate 1


title: P21 bulk TCR of B3 HNSCC PBMC


title: P20 bulk TCR of B3 HNSCC PBMC


title: P22 bulk TCR of B3 HNSCC PBMC


title: P19 bulk TCR of B3 HNSCC PBMC


title: P17 bulk TCR of B3 HNSCC PBMC


title: Resistant- replicate 3 [RNA-Seq]

description: M229-Res-Replicate 3


title: P15 bulk TCR of B3 HNSCC PBMC


title: P25 bulk TCR of B3 HNSCC PBMC


title: P13 bulk TCR of B3 HNSCC PBMC


title: P12 bulk TCR of B3 HNSCC PBMC


title: P14 bulk TCR of B3 HNSCC PBMC


title: P10 bulk TCR of B3 HNSCC PBMC


title: P09 bulk TCR of B3 HNSCC PBMC


title: P07 bulk TCR of B3 HNSCC PBMC


title: Resistant- replicate 1

description: M229-Res-Replicate 1


title: P06 bulk TCR of B3 HNSCC PBMC


title: P02 bulk TCR of B3 HNSCC PBMC


title: P05 bulk TCR of B3 HNSCC PBMC


title: P01 bulk TCR of B3 HNSCC PBMC


title: P32 bulk TCR of B2 HNSCC PBMC


title: P31 bulk TCR of B2 HNSCC PBMC


title: P24 bulk TCR of B2 HNSCC PBMC


title: P26 bulk TCR of B2 HNSCC PBMC


title: P30 bulk TCR of B2 HNSCC PBMC


title: P04 bulk TCR of B3 HNSCC PBMC


title: P19 bulk TCR of B2 HNSCC PBMC


title: P20 bulk TCR of B2 HNSCC PBMC


title: P16 bulk TCR of B2 HNSCC PBMC


title: P15 bulk TCR of B2 HNSCC PBMC


title: P14 bulk TCR of B2 HNSCC PBMC


title: P13 bulk TCR of B2 HNSCC PBMC


title: P29 bulk TCR of B2 HNSCC PBMC


title: P22 bulk TCR of B2 HNSCC PBMC


title: P04 bulk TCR of B2 HNSCC PBMC


title: P07 bulk TCR of B2 HNSCC PBMC


title: P10 bulk TCR of B2 HNSCC PBMC


title: P09 bulk TCR of B2 HNSCC PBMC


title: P12 bulk TCR of B2 HNSCC PBMC


title: P08 bulk TCR of B2 HNSCC PBMC


title: P06 bulk TCR of B2 HNSCC PBMC


title: P02 bulk TCR of B2 HNSCC PBMC


title: P23 bulk TCR of B2 HNSCC PBMC


title: P28 bulk TCR of B2 HNSCC PBMC


title: P32 bulk TCR of B1 HNSCC PBMC


title: P01 bulk TCR of B2 HNSCC PBMC


title: P27 bulk TCR of B2 HNSCC PBMC


title: P30 bulk TCR of B1 HNSCC PBMC


title: P17 bulk TCR of B2 HNSCC PBMC


title: P28 bulk TCR of B1 HNSCC PBMC


title: P29 bulk TCR of B1 HNSCC PBMC


title: P26 bulk TCR of B1 HNSCC PBMC


title: P27 bulk TCR of B1 HNSCC PBMC


title: P20 bulk TCR of B1 HNSCC PBMC


title: P24 bulk TCR of B1 HNSCC PBMC


title: P17 bulk TCR of B1 HNSCC PBMC


title: P25 bulk TCR of B1 HNSCC PBMC


title: P18 bulk TCR of B1 HNSCC PBMC


title: P23 bulk TCR of B1 HNSCC PBMC


title: P22 bulk TCR of B1 HNSCC PBMC


title: P05 bulk TCR of B2 HNSCC PBMC


title: P19 bulk TCR of B1 HNSCC PBMC


title: P21 bulk TCR of B1 HNSCC PBMC


title: P15 bulk TCR of B1 HNSCC PBMC


title: P12 bulk TCR of B1 HNSCC PBMC


title: P14 bulk TCR of B1 HNSCC PBMC


title: P09 bulk TCR of B1 HNSCC PBMC


title: P31 bulk TCR of B1 HNSCC PBMC


title: P07 bulk TCR of B1 HNSCC PBMC


title: P16 bulk TCR of B1 HNSCC PBMC


title: P08 bulk TCR of B1 HNSCC PBMC


title: P13 bulk TCR of B1 HNSCC PBMC


title: P06 bulk TCR of B1 HNSCC PBMC


title: P05 bulk TCR of B1 HNSCC PBMC


title: P32 bulk TCR of post-Tx HNSCC tumor

source_name: HNSCC tumor

extract_protocol:
Bulk TCR sequencing was performed from DNA extracted from formalin-fixed paraffin embedded (FFPE) sections.
Illumina libraries were prepared using the Adaptive Biotechnologies ImmunoSeq deep TCR beta assay.

value: Post-Tx


title: P01 bulk TCR of B1 HNSCC PBMC


title: P31 bulk TCR of post-Tx HNSCC tumor


title: P02 bulk TCR of B1 HNSCC PBMC


title: P26 bulk TCR of post-Tx HNSCC tumor


title: P27 bulk TCR of post-Tx HNSCC tumor


title: P29 bulk TCR of post-Tx HNSCC tumor


title: P30 bulk TCR of post-Tx HNSCC tumor


title: P18 bulk TCR of post-Tx HNSCC tumor


title: P21 bulk TCR of post-Tx HNSCC tumor


title: P07 bulk TCR of post-Tx HNSCC tumor


title: P20 bulk TCR of post-Tx HNSCC tumor


title: P10 bulk TCR of post-Tx HNSCC tumor


title: P04 bulk TCR of post-Tx HNSCC tumor


title: P23 bulk TCR of post-Tx HNSCC tumor


title: P25 bulk TCR of post-Tx HNSCC tumor


title: P08 bulk TCR of post-Tx HNSCC tumor


title: P28 bulk TCR of post-Tx HNSCC tumor


title: P24 bulk TCR of post-Tx HNSCC tumor


title: P15 bulk TCR of post-Tx HNSCC tumor


title: P17 bulk TCR of post-Tx HNSCC tumor


title: P13 bulk TCR of post-Tx HNSCC tumor


title: P32 bulk TCR of pre-Tx HNSCC tumor

value: Pre-Tx


title: P29 bulk TCR of pre-Tx HNSCC tumor


title: P27 bulk TCR of pre-Tx HNSCC tumor


title: P22 bulk TCR of pre-Tx HNSCC tumor


title: P05 bulk TCR of post-Tx HNSCC tumor


title: P04 bulk TCR of B1 HNSCC PBMC


title: P12 bulk TCR of post-Tx HNSCC tumor


title: P19 bulk TCR of post-Tx HNSCC tumor


title: P15 bulk TCR of pre-Tx HNSCC tumor


title: P14 bulk TCR of pre-Tx HNSCC tumor


title: P06 bulk TCR of pre-Tx HNSCC tumor


title: P07 bulk TCR of pre-Tx HNSCC tumor


title: P31 bulk TCR of pre-Tx HNSCC tumor


title: P01 bulk TCR of pre-Tx HNSCC tumor


title: P10 bulk TCR of B1 HNSCC PBMC


title: P22 bulk TCR of post-Tx HNSCC tumor


title: P21 bulk TCR of pre-Tx HNSCC tumor


title: P30 bulk TCR of pre-Tx HNSCC tumor


title: P02 bulk TCR of post-Tx HNSCC tumor


title: P23 bulk TCR of pre-Tx HNSCC tumor


title: 6h 500 mOsm + Torin1 rep4 Ribosome profiling

city: Stockholm

first: Krzysztof

middle: Jan

last: Szkop

state: Solna

address: SciLifeLab, Tomtebodavägen 23

department: Department of Oncology and Pathology

country: Sweden

institute: Karolinska Institutet

data_processing:
Library strategy: Ribo-Seq
Ribosomal profiling data preparation: Cutadapt (ver 1.18) (-q 10 -e 0.15 -O 1 -n 4 -m 20) was used to trim reads for adapter sequence:  ‘CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC ’ and first 6 nucleotides of each read  (-u 6 -u -4 -m 20 ). Reads matching ribosomal RNA sequences obtained from RefSeq database were removed using BBmap (ver. 36.59). Resulting reads were aligned to hg38 genome using hisat2 (ver. 2.1.0). In order to extract the genuine ribosome footprints, reads with a length (22–29 inclusive) were used for further analysis. Subsequently the uniquely mapped reads were summarised using HTseq (ver 0.11.4).
RNA-seq data preparation: Reads were trimmed for Nextera adapters using BBmap (ver. 36.59) (k=13 ktrim=n useshortkmers=t mink=5 qtrim=t trimq=10 minlength=25) and subsequently aligned to hg38 genome using hisat2 (ver. 2.1.0) and summarised using HTseq (ver 0.11.4).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw gene counts for every gene and every sample

source_name: Corneal epithelial cells

growth_protocol: Immortalized human corneal epithelial cells (10.014 pRSV-T) were cultivated in Keratinocyte-SFM (Thermo Fisher Scientific) with 5 ng/mL epidermal growth factor, 0.05 mg/mL bovine pituitary extract, 0.005 mg/mL insulin, and 500 ng/mL hydrocortisone on dishes coated with fibronectin, type I bovine collagen, and BSA. eIF2α S51A mutant MEFs were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/mL penicillin, and 100 μg/mL streptomycin.

extract_protocol:
Ribosome profiling: Three 150 mm dishes of pRSV-T cells (80% confluency) were treated with hypertonic stress.  To avoid potential artifacts of pre-treating live cells with cycloheximide, it was added to the lysis buffer only after cells were harvested as previously described (PMID: 26657557, PMID: 30029003, PMID: 25056308, PMID: 31767846). After washing three times with ice-cold PBS, cells were scraped in 1 mL lysis buffer (10 mM HEPES pH 7.4, 5 mM MgCl2, 100 mM KCl, 1% Triton-X,100 μg/mL cycloheximide, 2 mM DTT, RNase inhibitor (1:100 dilution, NEB, M0314L), protease inhibitor (1 tablet per 10 mL, Roche, 04693159001). The lysate was passed four times through a 26G needle and centrifuged at 1300 x g for 10 min. Lysate (OD A260 = 10) was loaded on a linear 10%-50% sucrose gradient (gradient buffer is the same as the lysis buffer, lacking only Triton-X and Protease and RNase inhibitors) and centrifuged at 4°C at 31,000 rpm for 2.5 h using an SW 32 Ti rotor (Beckman Coulter, 369694). The gradients were fractionated using a Teledyne ISCO Density Gradient Fractionation System and 12 fractions were collected. The fractions from (including) the 80S peak to the bottom of the gradient were combined. 300 μL of the combined fractions was digested with 5 μL RNase I (Thermo Fisher Scientific, AM2295) for 1 h at 4°C (with slow rotation on a nutator). Immediately, Trizol LS (Thermo Fisher Scientific, 10296028) was added, and RNA isolated according to the manufacturer’s instructions.  10 μg of total RNA isolated from the combined fractions was resolved by 15% TBE-Urea gel (Thermo Fisher Scientific, EC6885BOX) and visualized with SYBR™ Gold Nucleic Acid Gel Stain (Thermo Fisher Scientific, S11494); the 28-30 nt region was excised from the gel. The RNA was eluted in 400 μL RNA elution buffer (EB) at 4°C overnight (RNA EB: 0.3M sodium acetate (NaOAc, pH 5.5), 1 mM EDTA, 0.4 U/μL RNase inhibitor). Gel debris was removed using Corning Costar Spin-X centrifuge tube filters (Sigma-Aldrich, CLS8160). RNA was precipitated with 4 µL GlycoBlue Coprecipitant (Thermo Fisher Scientific, AM9515), 40 µL sodium acetate, and 1 mL ethanol overnight at -80°C. Recovered footprints were dephosphorylated in a 15 µL reaction mixture (1 µL T4 PNK (NEB, M0201S), 10X T4 PNK buffer, 0.4 U/μL RNase inhibitor) at 37°C for 1 h followed by heat inactivation at 65°C for 10 min. Dephosphorylated RNA was precipitated as described above and recovered in 4 µL of water. Pre-adenylated DNA linker (DNA oligo purchase from IDT was adenylated using 5´ DNA Adenylation Kit (NEB, E2610S)) was ligated to the 3’-end of RNA in a 20 µL reaction (25% PEG8000, 1X T4 RNA ligase buffer, 1 mM DTT, 0.4 U/μL murine RNase inhibitor, 300 U T4 RNA ligase truncated KQ (NEB, M0373S), 1 µM pre-adenylated DNA linker) for 6 h at 25°C followed by overnight ethanol precipitation as described above. Ligated footprints were resolved by 10% TBE-Urea Gel (Thermo Fisher Scientific, EC6875BOX), purified, eluted in the RNA EB at 4°C overnight, precipitated at -80°C as described above and resuspended in 10.5 µL water. 1 µL of 2.5 µM RT primer was added and heated at 65°C for 5 min, cooled on ice and incubated in 20 µL RT mix (300 U Superscript III (Thermo Fisher Scientific, 18080044), 1X RT buffer, 500 µM dNTPs, 5 mM DTT) for 30 min at 55°C, then heat inactivated at 70°C for 15 min.  RT product was precipitated with ethanol as described above, resuspended in 10 µL water and resolved by 10% TBE-Urea gel. cDNA was isolated and eluted overnight in DNA elution buffer (DNA EB: 0.3 M NaCl, 1 mM EDTA), precipitated overnight, recovered and used for the 20 µL circularization reaction (100 U CircLigase ssDNA Ligase (Lucigen, CL4111K), 50 mM ATP, 2.5 mM MnCl2, 1X Circligase buffer) at 60°C for 2 h. rRNA depletion was performed according to Ingolia et al. (Ingolia et al., 2012). Circularized, rRNA-depleted cDNA was used in the PCR using NEBNext Ultra II Q5 Master Mix (NEB, M0544S) and NEBNext Multiplex Oligos for Illumina (NEB, E7335S). Half of the cDNA was used to determine the optimal PCR cycle number. The PCR products were resolved by 8% TBE gel (Thermo Fisher Scientific, EC6215BOX). The other half of the cDNA was amplified by the determined PCR cycle, resolved by 8% TBE gel, and PCR products were cut, eluted in DNA EB, precipitated as described above, and recovered in 15 µL water. The quality and quantity of libraries were confirmed using DNA High Sensitivity Bioanalyzer (Agilent). Equal amounts of libraries were mixed and sequenced using SE75, NextSeq 500 (Illumina) sequencing platform.    RNA-seq: RNA was isolated from the cytoplasmic lysate (input that was loaded on the sucrose gradients for the abovementioned ribosome profiling) using Trizol LS according to the manufacturer’s instructions, except that precipitation with isopropanol was conducted overnight at -80°C. 1 µg RNA was depleted from rRNA using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB, E6310L) and was used to make libraries with NEBNext Ultra™ II Directional RNA Library Prep (NEB, E7765S) according to the manufacturer’s instructions. The quality and quantity of libraries were confirmed using DNA High Sensitivity Bioanalyzer (Agilent) and sequenced using PE150, NovaSeq sequencing platform.
RNA libraries were prepared for sequencing using standard Illumina protocols (see also extract protocol)

treatment_protocol: hyperosmolarity was induced by adding 100 mM NaCl to growth media (500 mOsm), Cells were treated for 1 or 6h, torin 1 was used at 250 nM concentration, MeAIB was used at 5 mM concentration

value: 500 mOsm + Torin1  (for the last hour)

tag: time

value: 6 hours


title: P18 bulk TCR of pre-Tx HNSCC tumor


title: 6h 500 mOsm + Torin1 rep2 Ribosome profiling


title: P16 bulk TCR of pre-Tx HNSCC tumor


title: P13 bulk TCR of pre-Tx HNSCC tumor


title: 1h 500 mOsm rep3 Ribosome profiling

value: 500 mOsm

value: 1 hour


title: 6h 500 mOsm + MeAIB rep4 Ribosome profiling

value: 500 mOsm + MeAIB  (for the last hour)


title: 6h 500 mOsm + MeAIB rep3 Ribosome profiling


title: P20 bulk TCR of pre-Tx HNSCC tumor


title: Control rep2 Ribosome profiling

value: control


title: 6h 500 mOsm + Torin1 rep1 Ribosome profiling

value: 500 mOsm + Torin1 (for the last hour)


title: 6h 500 mOsm + MeAIB rep1 Ribosome profiling


title: P25 bulk TCR of pre-Tx HNSCC tumor


title: 6h 500 mOsm + Torin1 rep3 Ribosome profiling


title: P05 bulk TCR of pre-Tx HNSCC tumor


title: 6h 500 mOsm rep3 Ribosome profiling


title: 6h 500 mOsm rep4 Ribosome profiling


title: 6h 500 mOsm rep1 Ribosome profiling


title: 6h 500 mOsm + Torin1 rep1

data_processing:
Ribosomal profiling data preparation: Cutadapt (ver 1.18) (-q 10 -e 0.15 -O 1 -n 4 -m 20) was used to trim reads for adapter sequence:  ‘CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC ’ and first 6 nucleotides of each read  (-u 6 -u -4 -m 20 ). Reads matching ribosomal RNA sequences obtained from RefSeq database were removed using BBmap (ver. 36.59). Resulting reads were aligned to hg38 genome using hisat2 (ver. 2.1.0). In order to extract the genuine ribosome footprints, reads with a length (22–29 inclusive) were used for further analysis. Subsequently the uniquely mapped reads were summarised using HTseq (ver 0.11.4).
RNA-seq data preparation: Reads were trimmed for Nextera adapters using BBmap (ver. 36.59) (k=13 ktrim=n useshortkmers=t mink=5 qtrim=t trimq=10 minlength=25) and subsequently aligned to hg38 genome using hisat2 (ver. 2.1.0) and summarised using HTseq (ver 0.11.4).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw gene counts for every gene and every sample


title: 6h 500 mOsm + MeAIB rep1


title: 1h 500 mOsm rep4 Ribosome profiling


title: 6h 500 mOsm rep2 Ribosome profiling


title: 1h 500 mOsm rep1 Ribosome profiling


title: 1h 500 mOsm rep2 Ribosome profiling


title: Control rep4 Ribosome profiling


title: 6h 500 mOsm rep4


title: 6h 500 mOsm rep1


title: 6h 500 mOsm + MeAIB rep3


title: Control rep3 Ribosome profiling


title: 1h 500 mOsm rep3


title: 6h 500 mOsm + Torin1 rep3


title: 6h 500 mOsm + Torin1 rep2


title: Control rep1 Ribosome profiling


title: 6h 500 mOsm + MeAIB rep2


title: Control rep3


title: Control rep2


title: 1h 500 mOsm rep4


title: Control rep1


title: 1h 500 mOsm rep1


title: 1h 500 mOsm rep2


title: 6h 500 mOsm + Torin1 rep4


title: 6h 500 mOsm rep2


title: Control rep4


title: 6h 500 mOsm rep3


title: i14G1-12_Ti-seq_1 [OligodT cleaned RNA]

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

description:
OligodT cleaned RNA
i14G1-12_Ti-seq_1

data_processing:
Bcl files were converted into fastq by bcl2fastq v2.17.1.14. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).
All further analysis steps were done using UTAP pipeline. Namely, adapters and low quality bases were removed from the raw reads using cutadapt version 1.8.3 (parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{100}" -a "T{100}" --times 2 -q 20  -m 30 )
The remaining reads (raw data submitted)  were mapped to hg38(igenomes) using STAR.
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file (downloaded from igenomes), which was modified to contain a window surrounding the 3' UTR.
Genes were filtered out if thier sum counts   <=5 .  Normalization and differential expression analysis was performed using the DESeq2 R-package (Bioconductor, https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: hg38
Supplementary_files_format_and_content: Within this Excel  - sheet named  "mars-seq norm counts"  contains normalized DESeq2 counts (not UMI counts)

source_name: HEK293T cells

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

extract_protocol:
Cell lysates were thawed and messanger RNA was captured with 15ul of NEB oligo(dT) beads, and washed according to manufacture guidelines.
Purified messanger RNA was eluted at 70C with 60ul of 10mM Tris-Cl pH 7.5 and stored at -80C.For library preparation RNA was used for the bulk MARS-seq  protocol (Jaitin et al. 2014 Science.343:776-9). MARS-seq libraries were sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).

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: i14G1-10_Ti-seq_1 [OligodT cleaned RNA]

description:
OligodT cleaned RNA
i14G1-10_Ti-seq_1

value: DMSO


title: i14G1-12_Ribo-seq_2 [OligodT cleaned RNA]

description:
OligodT cleaned RNA
i14G1-12_Ribo-seq_2


title: i14G1-12_Ti-seq_2 [OligodT cleaned RNA]

description:
OligodT cleaned RNA
i14G1-12_Ti-seq_2


title: 6h 500 mOsm + MeAIB rep4


title: 6h 500 mOsm + MeAIB rep2 Ribosome profiling


title: i14G1-12_Ribo-seq_1 [OligodT cleaned RNA]

description:
OligodT cleaned RNA
i14G1-12_Ribo-seq_1


title: i14G1-10_Ribo-seq_1 [OligodT cleaned RNA]

description:
OligodT cleaned RNA
i14G1-10_Ribo-seq_1


title: i14G1-10_Ti-seq_2 [OligodT cleaned RNA]

description:
OligodT cleaned RNA
i14G1-10_Ti-seq_2


title: Control_Ribo-seq_1 [OligodT cleaned RNA]

description:
OligodT cleaned RNA
Control_Ribo-seq_1


title: Control_Ti-seq_2 [OligodT cleaned RNA]

description:
OligodT cleaned RNA
Control_Ti-seq_2


title: Control_Ribo-seq_2 [OligodT cleaned RNA]

description:
OligodT cleaned RNA
Control_Ribo-seq_2


title: Targeted RNA of patient CLB_95

city: Lyon

first: PIERRE

last: SAINTIGNY

address: 28 Rue Laennec

country: France

institute: Centre Léon Bérard

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.

source_name: tumor

extract_protocol:
sample preparation: 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.).

value: non-small cell lung cancer

tag: tissue

value: tumor

tag: age

tag: Sex

value: Male

tag: os (month)

tag: os (event)

tag: pfs (month)

tag: pfs (event)

tag: histology

value: SCC

tag: hot score

tag: hot phenotype

value: HOT


title: Targeted RNA of patient CLB_93

value: COLD


title: Targeted RNA of patient CLB_92


title: i14G1-10_Ribo-seq_2 [OligodT cleaned RNA]

description:
OligodT cleaned RNA
i14G1-10_Ribo-seq_2

tag: cell type

tag: treatment


title: Targeted RNA of patient CLB_90


title: Targeted RNA of patient CLB_84


title: Targeted RNA of patient CLB_86


title: Targeted RNA of patient CLB_88

value: Female


title: Targeted RNA of patient CLB_91


title: Targeted RNA of patient CLB_82


title: Targeted RNA of patient CLB_85


title: Targeted RNA of patient CLB_87


title: Targeted RNA of patient CLB_83


title: Control_Ti-seq_1 [OligodT cleaned RNA]

description:
OligodT cleaned RNA
Control_Ti-seq_1


title: Targeted RNA of patient CLB_77


title: Targeted RNA of patient CLB_79


title: Targeted RNA of patient CLB_81


title: Targeted RNA of patient CLB_76


title: Targeted RNA of patient CLB_78


title: Targeted RNA of patient CLB_80


title: Targeted RNA of patient CLB_94


title: Targeted RNA of patient CLB_72


title: Targeted RNA of patient CLB_75


title: Targeted RNA of patient CLB_96


title: Targeted RNA of patient CLB_74


title: Targeted RNA of patient CLB_70


title: Targeted RNA of patient CLB_89


title: Targeted RNA of patient CLB_71


title: Targeted RNA of patient CLB_69


title: Targeted RNA of patient CLB_68


title: Targeted RNA of patient CLB_67


title: Targeted RNA of patient CLB_66


title: Targeted RNA of patient CLB_61


title: Targeted RNA of patient CLB_60


title: Targeted RNA of patient CLB_59


title: Targeted RNA of patient CLB_65


title: Targeted RNA of patient CLB_58


title: Targeted RNA of patient CLB_56


title: Targeted RNA of patient CLB_64


title: Targeted RNA of patient CLB_55


title: Targeted RNA of patient CLB_63


title: Targeted RNA of patient CLB_54


title: Targeted RNA of patient CLB_57


title: Targeted RNA of patient CLB_51


title: Targeted RNA of patient CLB_53


title: Targeted RNA of patient CLB_48

value: ADK


title: Targeted RNA of patient CLB_47


title: Targeted RNA of patient CLB_50


title: Targeted RNA of patient CLB_49


title: Targeted RNA of patient CLB_46


title: Targeted RNA of patient CLB_73


title: Targeted RNA of patient CLB_44


title: Targeted RNA of patient CLB_45


title: Targeted RNA of patient CLB_42


title: Targeted RNA of patient CLB_41


title: Targeted RNA of patient CLB_43


title: Targeted RNA of patient CLB_40


title: Targeted RNA of patient CLB_37


title: Targeted RNA of patient CLB_36


title: Targeted RNA of patient CLB_38


title: Targeted RNA of patient CLB_31


title: Targeted RNA of patient CLB_33


title: Targeted RNA of patient CLB_34


title: Targeted RNA of patient CLB_32


title: Targeted RNA of patient CLB_52


title: Targeted RNA of patient CLB_30


title: Targeted RNA of patient CLB_29


title: Targeted RNA of patient CLB_26


title: Targeted RNA of patient CLB_22


title: Targeted RNA of patient CLB_24


title: Targeted RNA of patient CLB_23


title: Targeted RNA of patient CLB_25


title: Targeted RNA of patient CLB_39


title: Targeted RNA of patient CLB_18


title: Targeted RNA of patient CLB_17


title: Targeted RNA of patient CLB_16


title: Targeted RNA of patient CLB_21


title: Targeted RNA of patient CLB_14


title: Targeted RNA of patient CLB_15


title: Targeted RNA of patient CLB_8


title: Targeted RNA of patient CLB_11


title: Targeted RNA of patient CLB_12


title: Targeted RNA of patient CLB_10


title: Targeted RNA of patient CLB_13


title: Targeted RNA of patient CLB_9


title: Targeted RNA of patient CLB_6


title: Targeted RNA of patient CLB_20


title: Targeted RNA of patient CLB_5


title: Targeted RNA of patient CLB_4


title: Targeted RNA of patient CLB_1


title: Targeted RNA of patient CLB_2


title: Targeted RNA of patient CLB_19


title: Targeted RNA of patient CLB_7


title: Targeted RNA of NSCLC patient number 81

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.
Supplementary_files_format_and_content: Nivobio_log2cpm_data.csv

source_name: formalin-fixed paraffin embedded biopsies or archival surgically resected specimens collected prior to treatment initiation

extract_protocol:
[sample preparation]  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.).
Targeted RNASeq

tag: patient id

value: AD

tag: immunotherapy line

tag: best response on immunotherapy (recist)

value: PR

tag: performance status

tag: Stage

value: IV


title: Targeted RNA of NSCLC patient number 126

value: CSARC


title: Targeted RNA of NSCLC patient number 69


title: Targeted RNA of NSCLC patient number 143

value: IIB


title: Targeted RNA of NSCLC patient number 89

value: SD

value: IIIB


title: Targeted RNA of NSCLC patient number 3

value: PD


title: Targeted RNA of NSCLC patient number 62


title: Targeted RNA of NSCLC patient number 22


title: Targeted RNA of NSCLC patient number 140


title: Targeted RNA of NSCLC patient number 155

value: NOS


title: Targeted RNA of NSCLC patient number 95

value: SC


title: Targeted RNA of NSCLC patient number 138


title: Targeted RNA of NSCLC patient number 123


title: Targeted RNA of NSCLC patient number 30


title: Targeted RNA of NSCLC patient number 125


title: Targeted RNA of patient CLB_3

tag: patient diagnosis

value: non-small cell lung cancer

tag: tissue

value: tumor


title: Targeted RNA of NSCLC patient number 133

tag: age

tag: Sex

value: Male


title: Targeted RNA of NSCLC patient number 129

tag: os (month)

tag: os (event)

value: HOT


title: Targeted RNA of NSCLC patient number 4

tag: pfs (month)


title: Targeted RNA of NSCLC patient number 66

tag: histology

value: IIIA

value: COLD


title: Targeted RNA of NSCLC patient number 76

value: CNEGC

value: IIA

tag: hot score


title: Targeted RNA of NSCLC patient number 106

value: AD

tag: hot phenotype


title: Targeted RNA of NSCLC patient number 88

value: Female


title: Targeted RNA of NSCLC patient number 55

value: IV


title: Targeted RNA of NSCLC patient number 96


title: Targeted RNA of NSCLC patient number 64

value: IB


title: Targeted RNA of NSCLC patient number 101

value: SD


title: Targeted RNA of NSCLC patient number 146

value: PR


title: Targeted RNA of NSCLC patient number 144


title: Targeted RNA of NSCLC patient number 105

value: CR

value: IIIB


title: Targeted RNA of NSCLC patient number 75

value: PD


title: Targeted RNA of NSCLC patient number 119


title: Targeted RNA of NSCLC patient number 127

value: NOS


title: Targeted RNA of NSCLC patient number 6


title: in-con-3

city: Wuhan

first: cao

last: lu

state: Hubei

address: 7 Donghu South Road

department: Chinese Academy   of Sciences

institute: Institute of Hydrobiology

data_processing:
Raw reads were produced by an Illumina Hiseq4000 instrument with 150 bp paired end reads by the BioMarker Biotechnology Co., Ltd (Beijing).
The trimming and quality controls of raw Illumina reads were performed using Sickle (https://github.com/najoshi/sickle) and SeqPrep (https://github.com/jstjohn/SeqPrep) with the default settings.
Raw data reads in fastq format were initially processed using in-house perl scripts.
Assembly: GCGD:Grass Carp Genome Database http://bioinfo.ihb.ac.cn/gcgd/php/index.php?page=download
Supplementary files format and content: tab-delimited text files include count and FPKM values for each Sample

organism: Ctenopharyngodon idella

source_name: intestine

growth_protocol: grass carp with a mean body mass of 20 g were obtained from wuhan, hubei province of China.

extract_protocol:
Total RNA was extracted using the TRIzol? Reagent (ThermoFisher Scientific, Massachusetts, USA) according to the manufacturer's protocol.
The mRNA-seq library construction was performed with the TruseqTM RNA sample prep Kit (Illumina, California, USA ) following the manufacturer's protocol.

treatment_protocol: Prior to the experiment, fish were reared in plastic tanks with fresh water and a normal diet for one week, and then the engineered S. cerevisiae expressing gcH2A-4 and gcH2A-11 on the grass carp via injection. Each experimental fish in 3 groups was infected with Flavobacterium columnare. The fish were not feed during the challenge experiment, with the water temperature at 28C."

value: intestine

value: injected with the engineered S. cerevisiae


title: in-con-2


title: in-con-1


title: in-7t-3

value: injected with the engineered S. cerevisiae expressing gcH2A-11


title: in-7t-1


title: Targeted RNA of NSCLC patient number 63

value: HOT


title: in-2t-2

value: injected with the engineered S. cerevisiae expressing gcH2A-4


title: Targeted RNA of NSCLC patient number 10

value: Male


title: Targeted RNA of NSCLC patient number 14


title: in-2t-3


title: Targeted RNA of NSCLC patient number 97


title: Targeted RNA of NSCLC patient number 27


title: Targeted RNA of NSCLC patient number 32

value: IIIA


title: Targeted RNA of NSCLC patient number 48

value: AD


title: Targeted RNA of NSCLC patient number 128

value: Female

value: COLD


title: Targeted RNA of NSCLC patient number 56

value: IV


title: TP53B1-1 [ribosome profiling]

city: La Jolla

first: Wun Kiat Justin

last: Tan

state: California

address: 9500 Gilman Drive #0412, PFBH 414

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

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

tag: induction concentration

value: 1mM Rhamnose

tag: induction od

tag: induction time


title: TP53B1-2 [ribosome profiling]


title: WT-2 [ribosome profiling]

source_name: WT

value: none (wild type)


title: ssDDC-2 [ribosome profiling]

source_name: ssDDC

value: ssDDC


title: Targeted RNA of NSCLC patient number 104

tag: patient id

tag: immunotherapy line

tag: best response on immunotherapy (recist)

value: SD

tag: performance status


title: Targeted RNA of NSCLC patient number 100

tag: age

tag: Stage


title: in-7t-2

tag: tissue

tag: treatment


title: WT-1 [ribosome profiling]


title: ssDDC-1 [ribosome profiling]


title: Targeted RNA of NSCLC patient number 85

value: SC

tag: Sex

value: PD

tag: os (month)

tag: os (event)

tag: pfs (month)


title: sgAANAT-D63G-2 [ribosome profiling]

tag: strain


title: Targeted RNA of NSCLC patient number 86

tag: histology

tag: hot score

tag: hot phenotype


title: sgAANAT-D63G-1 [ribosome profiling]

tag: gene expressed

tag: induction concentration

tag: induction od

tag: induction time


title: sfCOMT-1 [ribosome profiling]

source_name: sfCOMT

value: sfCOMT


title: sfCOMT-2 [ribosome profiling]


title: Targeted RNA of NSCLC patient number 29

tag: patient id

value: CSARC

tag: immunotherapy line

tag: best response on immunotherapy (recist)

value: PR

tag: performance status


title: in-2t-1

tag: tissue

value: intestine

tag: treatment


title: saCOMT-T2A-1 [ribosome profiling]


title: Targeted RNA of NSCLC patient number 148

tag: age

tag: Sex

tag: os (month)

tag: Stage


title: Targeted RNA of NSCLC patient number 71

tag: histology

tag: os (event)

tag: pfs (month)

value: HOT


title: saCOMT-T2A-2 [ribosome profiling]

tag: strain

tag: gene expressed


title: Targeted RNA of NSCLC patient number 74

value: Male

tag: hot score

tag: hot phenotype


title: rnTDC-trunc-2 [ribosome profiling]

source_name: rnTDC-trunc

value: rnTDC-trunc

tag: induction concentration

tag: induction od

tag: induction time


title: Targeted RNA of NSCLC patient number 73

tag: patient id

value: AD

tag: immunotherapy line

tag: best response on immunotherapy (recist)

tag: performance status


title: rnTDC-trunc-1 [ribosome profiling]


title: Targeted RNA of NSCLC patient number 149

tag: age

tag: Sex

value: IIIA


title: Targeted RNA of NSCLC patient number 153

tag: os (month)

tag: Stage

value: IIIB

value: COLD


title: rnTDC-2 [ribosome profiling]

source_name: rnTDC

value: rnTDC

value: 1mM Rhamnose


title: Targeted RNA of NSCLC patient number 107

tag: histology

tag: os (event)


title: Targeted RNA of NSCLC patient number 151

value: Female

tag: pfs (month)

value: IV


title: SNP-S

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: All samples were analyzed using an Agilent 2100 Bioanalyzer, and the 18S and 28S ribosomal RNA peaks were identified. The RNA integrities of the 2D- and 3D-SNP cells were 9.8 and 9.7, respectively.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

organism: Canis lupus familiaris

source_name: canine mammary gland tumor cells which was cultured under 3D condition

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: Adherent SNP cells (2D-SNP cells) were maintained as adherent monolayer cultures in Roswell Park Memorial Institute (RPMI)-1640 medium (Invitrogen; Thermo Fisher Scientific, Inc., Waltham, MA, USA). Subsequently, these cells were supplemented with 10% heat-inactivated fetal bovine serum (FBS; Nichirei Biosciences Inc., Tokyo, Japan) and antibiotics (5 mg/mL penicillin, 5 mg/mL streptomycin, and 10 mg/mL neomycin; Invitrogen; Thermo Fisher Scientific, Inc.) in an atmosphere containing 5% CO2 at 37°C.  We observed non-adherent SNP cells in the growth medium. SNP spheroids (3D-SNP cells) were established by selecting the non-adherent SNP cells and culturing them without the addition of basement membrane components and ECM-like biomaterials.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

treatment_protocol: The cells were harvested from near-confluent cultures by brief exposure to a solution containing 0.25% w/v trypsin-1 mmol/L ethylenediamine tetraacetic acid-4Na solution with phenol red (FUJIFILM Wako Pure Chemical, Ltd., Osaka, Japan). Trypsinization was stopped using RPMI-1640 medium supplemented with 10% FBS. Cells were concentrated by centrifugation at 300 × g for 5 min at 23°C.

tag: sample type

value: spheroid


title: Epithelial-Endometrial_Tam+Alp_mouse1

first: Rinath

last: Jeselsohn

state: MD

address: 450 Brookline Ave, D728

department: Medical Oncology

institute: DFCI

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to hg19 using Bowtie
Cufflinks was used to assemble transcripts and obtain normalized read counts per gene.
Genome_build: hg19
Supplementary_files_format_and_content: Processed counts

source_name: C57BL/6 ovarectomized female mouse treated with tamoxifen and alpelisib

growth_protocol: Eighteen C57BL/6 female mice (Jackson Laboratories) were oophorectomized after they reached puberty (6-7 weeks).

extract_protocol:
Total RNA isolation was performed using the RNeasy Mini Kit (Qiagen). DNA was degraded on columns with DNase I (Qiagen).
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) adapted for use on the Sciclone (Perkin-Elmer) liquid handler.

treatment_protocol: Mice were randomized (N=6 per arm) to Vehicle (ED), tamoxifen (Sigma, in peanut oil, 0.5mg/day, S.Q.), or tamoxifen plus alpelisib (Selleck, in 30% PEG400+0.5% Tween80+5% Propylene glycol, 30mg/kg/day, O.S.) for 28 days. Two mice were treated with low dose of estrogen (E2, 0.01mg/pellet, 60 days release) for 28 days. At the end of the study, mice were euthanized and uterine horns were collected.

tag: strain

value: female

tag: cell type

value: mouse epithelial endometrial cells


title: rnTDC-1 [ribosome profiling]

tag: gene expressed

tag: induction concentration


title: Targeted RNA of NSCLC patient number 24

value: SC

value: SD

tag: hot score

tag: hot phenotype


title: Targeted RNA of NSCLC patient number 61

tag: patient id

tag: immunotherapy line

value: PD


title: rnPNMT-2 [ribosome profiling]

source_name: rnPNMT

value: rnPNMT

tag: induction od

tag: induction time


title: rnPNMT-1 [ribosome profiling]


title: Targeted RNA of NSCLC patient number 60

tag: age

tag: Sex

tag: best response on immunotherapy (recist)

tag: performance status


title: SNP-A

source_name: canine mammary gland tumor cells which was cultured under 2D condition

value: monolayer


title: Targeted RNA of NSCLC patient number 58

tag: histology

value: CNEGC

value: Male

tag: os (month)

tag: os (event)

tag: Stage


title: Targeted RNA of NSCLC patient number 47

tag: pfs (month)


title: Epithelial-Endometrial_Tam_mouse1

source_name: C57BL/6 ovarectomized female mouse treated with tamoxifen

tag: strain

tag: cell type


title: Targeted RNA of NSCLC patient number 57

value: AD

tag: hot score


title: Targeted RNA of NSCLC patient number 13

tag: hot phenotype


title: rnCOMT_sol-1 [ribosome profiling]

tag: gene expressed

tag: induction concentration


title: Epithelial-Endometrial_ED

description: ED

source_name: C57BL/6 ovarectomized female mouse


title: rnCOMT_sol-2 [ribosome profiling]

tag: induction od


title: Targeted RNA of NSCLC patient number 137

tag: patient id

tag: immunotherapy line

value: IB

value: HOT


title: Targeted RNA of NSCLC patient number 80

value: ADSC

tag: age

tag: Sex

value: COLD


title: Targeted RNA of NSCLC patient number 23

tag: best response on immunotherapy (recist)

tag: performance status


title: RFC-2 [ribosome profiling]

source_name: RFC

value: RFC

value: 1mM Rhamnose

tag: induction time


title: Epithelial-Endometrial_E2_mouse2

source_name: C57BL/6 ovarectomized female mouse treated with E2


title: Epithelial-Endometrial_Tam+Alp_mouse2


title: Targeted RNA of NSCLC patient number 117

tag: histology

value: Female

tag: os (month)

tag: os (event)

value: IV


title: RFC-1 [ribosome profiling]

tag: strain


title: Epithelial-Endometrial_E2_mouse1

value: female

tag: cell type

value: mouse epithelial endometrial cells


title: Epithelial-Endometrial_Tam_mouse2


title: Targeted RNA of NSCLC patient number 122

value: SC

tag: pfs (month)

tag: Stage

tag: hot score


title: P18 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)

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: Targeted RNA of NSCLC patient number 67

tag: patient id

value: AD

tag: age

tag: Sex

tag: immunotherapy line

value: PD

value: IIB

tag: hot phenotype


title: Targeted RNA of NSCLC patient number 82

tag: histology

value: Male

tag: best response on immunotherapy (recist)

tag: os (month)

tag: performance status


title: Targeted RNA of NSCLC patient number 139

tag: os (event)

tag: pfs (month)

value: COLD


title: Targeted RNA of NSCLC patient number 124

tag: Stage

value: IIIB

tag: hot score


title: Targeted RNA of NSCLC patient number 37


title: RFC_v2-2 [ribosome profiling]

tag: strain

tag: gene expressed

tag: induction concentration

value: 1mM Rhamnose

tag: induction od

tag: induction time


title: RFC_v3-1 [ribosome profiling]


title: P15 single cell TCR of post-Tx HNSCC tumor

tag: cell marker

tag: single cell or bulk

tag: state

tag: patient diagnosis

tag: molecule


title: Targeted RNA of NSCLC patient number 21

tag: patient id

tag: histology

tag: age

tag: Sex

tag: immunotherapy line

tag: best response on immunotherapy (recist)

tag: hot phenotype


title: P14 single cell TCR of post-Tx HNSCC tumor


title: Targeted RNA of NSCLC patient number 154

value: SD

tag: os (month)

tag: os (event)

tag: pfs (month)

tag: performance status

tag: Stage

value: IA

tag: hot score


title: Targeted RNA of NSCLC patient number 42

value: IV


title: Targeted RNA of NSCLC patient number 150

value: HOT


title: RFC_v2-1 [ribosome profiling]

tag: strain

tag: gene expressed

tag: induction concentration

tag: induction od

tag: induction time


title: P18 single cell TCR of pre-Tx HNSCC tumor

tag: cell marker

tag: single cell or bulk

tag: state

value: Pre-Tx

tag: patient diagnosis

tag: molecule


title: RFC_v1-2 [ribosome profiling]


title: Targeted RNA of NSCLC patient number 44

tag: patient id

tag: histology

tag: age

tag: Sex

tag: immunotherapy line

tag: best response on immunotherapy (recist)

value: PR

tag: hot phenotype


title: Targeted RNA of NSCLC patient number 142

value: SC

tag: os (month)

tag: os (event)

tag: pfs (month)

tag: performance status

tag: Stage

tag: hot score


title: Targeted RNA of NSCLC patient number 152


title: Targeted RNA of NSCLC patient number 65


title: Targeted RNA of NSCLC patient number 134

value: Female


title: RFC_v1-1 [ribosome profiling]

tag: strain

tag: gene expressed

tag: induction concentration

tag: induction od

tag: induction time


title: pmTPH-2 [ribosome profiling]

source_name: pmTPH

value: pmTPH


title: cord blood E3447 -750knsp

type: genomic

city: Fuzhou

first: Xiaoqing

last: Wu

address: 18 daoshan road, Gulou district

institute: Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University

description: Hybridized to 750K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (ChAS 4.0). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
primary data description:
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: cord blood E3447

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from uncultured amniotic fluid, fetal cord blood using a QIAGEN kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

tag: cell type

value: cord blood

tag: ultrasound abnormality classification

value: Isolated GITO

tag: obstruction level classification

value: Jejunal or ileal atresia/stenosis


title: amniotic fluid P5128-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P5128

value: amniotic fluid

value: Esophageal atresia/stenosis


title: RFC_v3-2 [ribosome profiling]


title: amniotic fluid P7128-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P7128

value: Non-isolated GITO


title: pmTPH-1 [ribosome profiling]


title: Targeted RNA of NSCLC patient number 17

source_name: formalin-fixed paraffin embedded biopsies or archival surgically resected specimens collected prior to treatment initiation

tag: patient id

tag: histology

value: AD

tag: age

tag: Sex

value: Male

tag: immunotherapy line

value: PD

value: COLD


title: Targeted RNA of surgical resection for patient number 40 [108-18C16381_1]

source_name: gingivomandibular

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: sample nature

value: surgical resection

tag: site

value: gingivomandibular

tag: pt

tag: pn

tag: hot phenotype


title: amniotic fluid P4291-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P4291

value: Duodenal atresia/stenosis


title: Targeted RNA of surgical resection for patient number 42 [102-17C24933_1]

value: retromolar trigone

tag: hot score


title: amniotic fluid R3442-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R3442


title: amniotic fluid P2462-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P2462


title: Targeted RNA of surgical resection for patient number 33 [102-18C00753_1]

source_name: mobile tongue

value: mobile tongue

value: HOT


title: Targeted RNA of surgical resection for patient number 34 [103-18C06349_1]

value: Female


title: Targeted RNA of surgical resection for patient number 39 [108-18C14839_1]


title: osTDC-L360V-1 [ribosome profiling]

tag: strain

tag: gene expressed

tag: induction concentration

value: 1mM Rhamnose


title: Targeted RNA of surgical resection for patient number 36 [102-18C04492_1]

source_name: gingivomaxillar

value: gingivomaxillar


title: Targeted RNA of surgical resection for patient number 37 [103-18C08041_1]

value: floor of mouth


title: osTDC-K374Q-2 [ribosome profiling]

tag: induction od

tag: induction time


title: osTDC-K374L-2 [ribosome profiling]


title: osTDC-K374Q-1 [ribosome profiling]


title: Targeted RNA of surgical resection for patient number 28 [102-17C24663_1]


title: osTDC-K374L-1 [ribosome profiling]


title: Targeted RNA of surgical resection for patient number 25 [108-18C14486_1]

source_name: floor of mouth

value: NX


title: Targeted RNA of surgical resection for patient number 31 [103-18C09028_1]


title: Targeted RNA of surgical resection for patient number 16 [108-18C15148_1]


title: amniotic fluid R2995-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R2995

tag: cell type

value: amniotic fluid

tag: ultrasound abnormality classification

value: Isolated GITO

tag: obstruction level classification


title: Targeted RNA of surgical resection for patient number 14 [103-18C09549_1]

tag: patient id

tag: age


title: osTDC-L360V-2 [ribosome profiling]


title: amniotic fluid R4089-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R4089

value: Non-isolated GITO

value: Jejunal or ileal atresia/stenosis


title: amniotic fluid S24-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid S24


title: Targeted RNA of surgical resection for patient number 20 [108-18C14801_1]

tag: Sex


title: osTDC-K374H-2 [ribosome profiling]


title: amniotic fluid R1267-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R1267

value: Esophageal atresia/stenosis


title: ocAANAT-2 [ribosome profiling]

source_name: ocAANAT

value: ocAANAT


title: amniotic fluid S60-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid S60


title: Targeted RNA of surgical resection for patient number 12 [102-18C04929_1]

tag: sample nature

value: surgical resection

value: Male


title: Targeted RNA of surgical resection for patient number 23 [102-17C24912_1]

tag: site


title: Targeted RNA of surgical resection for patient number 30 [109-18C12383_1]

tag: pt


title: Targeted RNA of surgical resection for patient number 9 [108-18C11733_1]

source_name: tongue

value: tongue

tag: pn


title: amniotic fluid R3714-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R3714


title: Targeted RNA of surgical resection for patient number 22 [103-18C09827_1]

source_name: buccal mucosa

value: buccal mucosa

tag: hot phenotype


title: Targeted RNA of surgical resection for patient number 13 [102-18C02127_1]

value: mobile tongue

tag: hot score

value: COLD


title: Targeted RNA of surgical resection for patient number 10 [102-18C02867_1]

value: Female

value: HOT


title: amniotic fluid Z18-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid Z18

value: Anal atresia


title: Targeted RNA of surgical resection for patient number 8 [109-18C15858_1]

source_name: gingivomandibular

value: gingivomandibular


title: ocAANAT-1 [ribosome profiling]

tag: strain

value: 1mM Rhamnose


title: Targeted RNA of surgical resection for patient number 6 [103-18C06933_1]

value: gingivomaxillar


title: amniotic fluid P8151-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P8151

value: amniotic fluid

value: Isolated GITO

value: Duodenal atresia/stenosis


title: amniotic fluid R1050-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R1050


title: msCOMT-1 [ribosome profiling]

source_name: msCOMT

tag: gene expressed

value: msCOMT


title: Targeted RNA of surgical resection for patient number 3 [108-18C18663_1]


title: Targeted RNA of surgical resection for patient number 2 [103-18C06506_1]

source_name: mobile tongue

value: floor of mouth


title: msCOMT-2 [ribosome profiling]

tag: induction concentration


title: Targeted RNA of surgical resection for patient number 1 [103-18C07689_1]

value: surgical resection


title: Targeted RNA of surgical resection for patient number 5 [103-18C07186_1]

source_name: hard palate

value: hard palate


title: amniotic fluid R801-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R801

value: Non-isolated GITO


title: Targeted RNA of perendoscopic biopsy for patient number 40 [109-18C14784_1]

value: perendoscopic biopsy


title: Targeted RNA of perendoscopic biopsy for patient number 42 [102-17C21408_1]

value: retromolar trigone

value: Male


title: MBP-2 [ribosome profiling]

source_name: MBP

value: MBP

tag: induction od


title: amniotic fluid P7522-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P7522


title: Targeted RNA of surgical resection for patient number 11 [102-18C04180_1]

value: COLD


title: amniotic fluid P8664-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P8664

value: Esophageal atresia/stenosis


title: MBP-1 [ribosome profiling]

tag: induction time


title: Targeted RNA of perendoscopic biopsy for patient number 39 [109-18C11940_1]

value: gingivomandibular

value: HOT


title: osTDC-K374H-1 [ribosome profiling]

value: 1mM Rhamnose


title: hsTPH-E2K-N91I-P99C-1 [ribosome profiling]


title: amniotic fluid P8869-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P8869

tag: cell type

value: amniotic fluid

value: Jejunal or ileal atresia/stenosis


title: Targeted RNA of perendoscopic biopsy for patient number 37 [102-18C04939_1]

value: mobile tongue


title: hsTPH-E2K-N91I-P99C-2 [ribosome profiling]


title: Targeted RNA of perendoscopic biopsy for patient number 36 [102-18C01846_1]

source_name: gingivomaxillar

value: gingivomaxillar


title: Targeted RNA of perendoscopic biopsy for patient number 31 [103-18C06948_1]


title: hsTPH-2 [ribosome profiling]

source_name: hsTPH

value: hsTPH


title: amniotic fluid P7041-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P7041

tag: ultrasound abnormality classification

value: Isolated GITO

value: Duodenal atresia/stenosis


title: Targeted RNA of perendoscopic biopsy for patient number 33 [102-17C24914_1]


title: cord blood E3675 -750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E3675

value: cord blood

value: Non-isolated GITO

tag: obstruction level classification


title: Targeted RNA of perendoscopic biopsy for patient number 28 [102-17C21848_1]

tag: patient id

value: perendoscopic biopsy

value: Female


title: Targeted RNA of perendoscopic biopsy for patient number 30 [108-18C10331_1]

source_name: floor of mouth

value: floor of mouth

tag: age


title: Targeted RNA of perendoscopic biopsy for patient number 25 [109-18C12779_01_1]

tag: Sex

value: Male

value: NX

value: COLD


title: cord blood E3021-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E3021


title: hsTPH1-2 [ribosome profiling]


title: Targeted RNA of perendoscopic biopsy for patient number 23 [102-17C23400_1]

tag: sample nature

value: HOT


title: Targeted RNA of perendoscopic biopsy for patient number 22 [103-18C07064_1]

source_name: buccal mucosa

tag: site

value: buccal mucosa


title: cord blood E2647-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E2647


title: Targeted RNA of perendoscopic biopsy for patient number 34 [102-18C03402_1]

source_name: gingivomandibular

value: gingivomandibular

tag: pt


title: hsTPH1-1 [ribosome profiling]

value: 1mM Rhamnose


title: Targeted RNA of perendoscopic biopsy for patient number 20 [109-18C12761_1]

tag: pn


title: cord blood E2322-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E2322

value: Jejunal or ileal atresia/stenosis


title: Targeted RNA of perendoscopic biopsy for patient number 16 [109-18C13652_1]

tag: hot phenotype


title: Targeted RNA of perendoscopic biopsy for patient number 12 [102-18C03144_1]

value: gingivomaxillar

tag: hot score


title: hsTPH-1 [ribosome profiling]

tag: strain

value: hsTPH


title: hsTPH_Ntermtrunc-2 [ribosome profiling]

tag: gene expressed


title: Targeted RNA of perendoscopic biopsy for patient number 11 [102-18C00893_1]


title: hsTPH_Ntermtrunc-1 [ribosome profiling]

tag: induction concentration


title: Targeted RNA of perendoscopic biopsy for patient number 14 [103-18C08398_1]

source_name: mobile tongue

value: mobile tongue


title: hsTPH_N174trunc-1 [ribosome profiling]

tag: induction od


title: amniotic fluid P4964-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P4964

value: amniotic fluid

value: Isolated GITO

value: Duodenal atresia/stenosis


title: Targeted RNA of perendoscopic biopsy for patient number 10 [102-18C00686_1]

value: perendoscopic biopsy


title: Targeted RNA of perendoscopic biopsy for patient number 6 [103-18C05705_1]

value: Female


title: Targeted RNA of perendoscopic biopsy for patient number 9 [109-18C09986_1]

source_name: tongue

value: tongue


title: Targeted RNA of perendoscopic biopsy for patient number 5 [102-18C04515_1]

source_name: hard palate

value: hard palate


title: hsTPH_N158trunc-2 [ribosome profiling]

tag: induction time


title: amniotic fluid P4963-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P4963

tag: cell type


title: hsTPH_N174trunc-2 [ribosome profiling]


title: Targeted RNA of perendoscopic biopsy for patient number 2 [102-18C04852_1]

value: floor of mouth

value: Male


title: cord blood E3264-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E3264

value: cord blood

tag: ultrasound abnormality classification


title: Targeted RNA of perendoscopic biopsy for patient number 3 [109-18C16390_1]

value: HOT


title: amniotic fluid P6332-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P6332

tag: obstruction level classification


title: cord blood E2275-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E2275


title: Targeted RNA of perendoscopic biopsy for patient number 13 [102-18C00110_1]

tag: patient id

value: COLD


title: Targeted RNA of perendoscopic biopsy for patient number 1 [103-18C05265_1]

value: gingivomandibular

tag: age


title: hsTPH_E2K-2 [ribosome profiling]

value: 1mM Rhamnose


title: cord blood E2240-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E2240

value: Non-isolated GITO


title: Targeted RNA of patient number 102

source_name: Oral cavity

value: Oral cavity

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: PD

tag: os (month)

tag: os (event)

tag: pfs (month)

tag: pfs (event)


title: hsTPH_E2K-1 [ribosome profiling]

tag: strain

tag: gene expressed

tag: induction concentration

tag: induction od


title: Targeted RNA of patient number 99

source_name: Hypopharynx

tag: site

value: Hypopharynx

value: SD

tag: hot phenotype

tag: hot score


title: Targeted RNA of patient number 98

source_name: Oropharynx

value: Oropharynx

tag: age

tag: Sex

value: PR


title: cord blood E2147-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E2147

tag: cell type

tag: ultrasound abnormality classification

value: Isolated GITO

tag: obstruction level classification

value: Jejunal or ileal atresia/stenosis


title: Targeted RNA of perendoscopic biopsy for patient number 8 [108-18C13821_1]

tag: patient id

tag: sample nature

value: perendoscopic biopsy

value: Female

tag: pt

tag: pn


title: cord blood E1851-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E1851

value: cord blood

value: Duodenal atresia/stenosis


title: Targeted RNA of patient number 97

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: os (event)

tag: pfs (month)

tag: pfs (event)

value: HOT


title: Targeted RNA of patient number 95

tag: site

tag: age

tag: Sex

tag: hot phenotype

tag: hot score

value: COLD


title: Targeted RNA of patient number 100

source_name: Larynx

value: Larynx


title: hsPNMT-mb-1 [ribosome profiling]

source_name: hsPNMT-mb

tag: strain

tag: gene expressed

value: hsPNMT-mb

tag: induction concentration

value: 1mM Rhamnose

tag: induction od

tag: induction time


title: hsTPH_N158trunc-1 [ribosome profiling]


title: hsASMT-1 [ribosome profiling]

source_name: hsASMT

value: hsASMT


title: Targeted RNA of patient number 96

value: Oral cavity

value: M

tag: tobacco status

tag: alcohol status

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

value: PD


title: Day 6 nph4-1 arf19-1 replicate 2

city: Tsurumi-ku, Yokohama

first: Yuki

last: Sakamoto

address: 1-7-22, Suehiro-cho

department: CSRS

institute: RIKEN

data_processing:
Raw data files (bcl format) were converted to fastq files by bcl2fastq (Illumina).
Reads were mapped to the Arabidopsis reference using Bowtie 0.12.9.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited data with transcript tag counts and the number of total mapped reads for each sample

organism: Arabidopsis thaliana

source_name: Cultured mesophyll protoplasts

growth_protocol: Plants were grown at 22℃ constant temperature under continuous light (30 to 40 μmol/m2/sec) on half-strength MS medium containing MS vitamins, 1 % sucrose, 0.05 % MES and 0.8 % Gelzan CM-Gelrite

extract_protocol:
Total RNA was extracted using Rneasy Plant Mini Kit (QIAGEN) according to manufacturer's instructions, including on-column Dnase digeston
Isolated RNA was subjected to library preparation using the Kapa stranded mRNA sequencing kit (Kapa Biosystems) with NEBNext Multiplex Oligos for Illumina (New England Biolabs) as adapters and Agencourt AMPure XP (Beckman Coulter) beads instead of KAPA Pure Beads.

treatment_protocol: Protoplasts were isolated from 1st to 5th rosette leaves of 23-DAS  plants, embedded into 0.75 % sodium alginate/ D(-)-mannitol gels and incubated in liquid Gamborg B5 medium containing B5 vitamins, 2 % D(+)-glucose, 0.05 % MES, 0.4 M D(-)-mannitol, 1 mg/L 2,4-D and 176 μg/L thidiazuron funder dark condition.

tag: ecotype

tag: genotype

tag: tissue

value: protoplasts

value: 6 days after incubation

tag: treatment

value: yucasin


title: hsPNMT-mb-2 [ribosome profiling]


title: Day 6 nph4-1 arf19-1 replicate 1


title: hsASMT-2 [ribosome profiling]


title: Day 6 nph4-1 arf19-1 replicate 3


title: Targeted RNA of patient number 94

tag: site

value: Oropharynx

tag: immunotherapy line

tag: best response on immunotherapy (recist)

value: PR

tag: os (month)

tag: os (event)

tag: pfs (month)

tag: pfs (event)


title: Targeted RNA of patient number 93

tag: age

tag: Sex

value: SD

tag: hot phenotype

tag: hot score


title: Targeted RNA of patient number 101

value: F

tag: tobacco status

tag: alcohol status


title: Day 6 WT replicate 3

tag: ecotype

value: WT

value: control


title: Targeted RNA of patient number 89

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

value: COLD


title: hsAANAT-2 [ribosome profiling]

source_name: hsAANAT

tag: strain

tag: gene expressed

value: hsAANAT

tag: induction concentration

tag: induction od

tag: induction time


title: Targeted RNA of patient number 90

tag: site

tag: immunotherapy line

tag: best response on immunotherapy (recist)

tag: os (month)

value: HOT


title: Targeted RNA of patient number 88

tag: age

tag: os (event)

tag: pfs (month)

tag: pfs (event)


title: Targeted RNA of patient number 87

tag: Sex

tag: tobacco status

value: CR

tag: hot phenotype

tag: hot score


title: Day 6 WT replicate 2

tag: ecotype

tag: genotype

tag: tissue

tag: treatment


title: hsAANAT-1 [ribosome profiling]

tag: strain

tag: gene expressed

tag: induction concentration

value: 1mM Rhamnose

tag: induction od

tag: induction time


title: Targeted RNA of patient number 86

tag: site

tag: age

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)


title: Day 6 WT replicate 1


title: Targeted RNA of patient number 85

value: Hypopharynx

tag: Sex

tag: tobacco status

tag: os (event)

tag: pfs (month)

tag: pfs (event)

tag: hot phenotype

tag: hot score


title: Day 4 nph4-1 arf19-1 replicate 3

tag: ecotype

tag: genotype

tag: tissue

value: 4 days after incubation

tag: treatment


title: Targeted RNA of patient number 84

tag: site

value: Oral cavity

tag: age

value: PD


title: ggTPH-2 [ribosome profiling]

source_name: ggTPH

tag: strain

tag: gene expressed

value: ggTPH

tag: induction concentration

tag: induction od

tag: induction time


title: Targeted RNA of patient number 82

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)

tag: os (month)


title: ggAANAT-2 [ribosome profiling]

source_name: ggAANAT

value: ggAANAT


title: Targeted RNA of patient number 92

value: Oropharynx

tag: os (event)

tag: pfs (month)

tag: pfs (event)

tag: hot phenotype

tag: hot score


title: Targeted RNA of patient number 83

tag: site

tag: age


title: Day 4 nph4-1 arf19-1 replicate 2

tag: ecotype

tag: genotype

tag: tissue

value: protoplasts

tag: treatment


title: Targeted RNA of patient number 81

tag: Sex

tag: tobacco status


title: Targeted RNA of patient number 79

tag: alcohol status

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


title: Day 4 nph4-1 arf19-1 replicate 1


title: ggAANAT-1 [ribosome profiling]

tag: strain

tag: gene expressed

tag: induction concentration

tag: induction od

tag: induction time


title: Day 4 WT replicate 3


title: ggTPH-1 [ribosome profiling]


title: Targeted RNA of patient number 80

value: Larynx

tag: immunotherapy line

tag: best response on immunotherapy (recist)

tag: os (month)

tag: os (event)

tag: pfs (month)

tag: pfs (event)

tag: hot phenotype


title: Targeted RNA of patient number 76

tag: site

tag: age

tag: hot score


title: Day 4 WT replicate 2

tag: ecotype

tag: genotype

value: WT

tag: tissue

tag: treatment


title: Targeted RNA of patient number 77

tag: Sex

value: F

tag: tobacco status

tag: alcohol status

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


title: Day 4 WT replicate 1

value: control


title: Targeted RNA of patient number 73

tag: immunotherapy line

tag: best response on immunotherapy (recist)


title: cobPNMT-2 [ribosome profiling]

source_name: cobPNMT

tag: strain

tag: gene expressed

value: cobPNMT

tag: induction concentration

tag: induction od

tag: induction time


title: Targeted RNA of patient number 74

tag: site

tag: age

tag: os (month)

tag: os (event)

tag: pfs (month)

tag: pfs (event)

tag: hot phenotype

value: COLD


title: cvPhhB-1 [ribosome profiling]

source_name: cvPhhB

value: cvPhhB


title: Day 0 nph4-1 arf19-1 replicate 3

source_name: Freshly isolated mesophyll protoplasts

tag: ecotype

tag: genotype

tag: tissue

value: 0 day after incubation

tag: treatment

value: fresh


title: Targeted RNA of patient number 72

tag: Sex

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: hot score

value: HOT


title: Day 0 nph4-1 arf19-1 replicate 2

tag: age


title: cobPNMT-1 [ribosome profiling]

tag: strain

tag: gene expressed

tag: induction concentration

value: 1mM Rhamnose

tag: induction od

tag: induction time


title: Targeted RNA of patient number 69

tag: site

value: SD

tag: os (month)

tag: os (event)

tag: pfs (month)

tag: pfs (event)

tag: hot phenotype


title: Day 0 nph4-1 arf19-1 replicate 1

tag: ecotype

tag: genotype

tag: tissue

tag: treatment


title: CNTF_belt-1 [ribosome profiling]


title: CNTF_belt-2 [ribosome profiling]


title: ckDDC-2 [ribosome profiling]

source_name: ckDDC

value: ckDDC


title: Targeted RNA of patient number 71

value: Oral cavity

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: CR

tag: hot score


title: Targeted RNA of patient number 67

tag: site

tag: age

value: PD


title: Targeted RNA of patient number 68

value: Oropharynx

tag: os (month)

tag: os (event)


title: Targeted RNA of patient number 65

value: Larynx

tag: pfs (month)

tag: pfs (event)


title: Targeted RNA of patient number 75

tag: hot phenotype


title: cvPhhB-2 [ribosome profiling]

tag: strain

tag: gene expressed

tag: induction concentration

tag: induction od

tag: induction time


title: Targeted RNA of patient number 78

tag: Sex

tag: tobacco status

tag: alcohol status


title: Day 0 WT replicate 2

tag: ecotype

tag: genotype

value: WT

tag: tissue

value: protoplasts

tag: treatment


title: Day 0 WT replicate 3

tag: age


title: Targeted RNA of patient number 66

tag: site

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)

tag: hot score


title: ckDDC-1 [ribosome profiling]

tag: strain

tag: gene expressed

tag: induction concentration

tag: induction od


title: Day 0 WT replicate 1


title: ccCOMT-2 [ribosome profiling]

source_name: ccCOMT

value: ccCOMT

tag: induction time


title: Targeted RNA of patient number 60

value: Hypopharynx

tag: Sex

tag: tobacco status

tag: alcohol status

tag: pfs (month)

tag: pfs (event)

tag: hot phenotype

value: COLD


title: Targeted RNA of patient number 64

source_name: Oral cavity

tag: site

tag: age

value: F

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


title: Targeted RNA of patient number 63

tag: immunotherapy line

tag: best response on immunotherapy (recist)

tag: os (month)


title: Targeted RNA of patient number 62

tag: os (event)

tag: hot score


title: Targeted RNA of patient number 61


title: Targeted RNA of patient number 70

source_name: Hypopharynx


title: Targeted RNA of patient number 58


title: BMSC-derived exosomes, Sham 2

city: Shenzhen

first: Guohua

last: Lai

state: Guangdong

address: NO.1333,Xinhu Road,Baoan District

institute: Shenzhen Hospital,Southern Medical University

data_processing:
miRNA sequencing was performed on the Illumina HiSeq 2500 platform from LC Sciences (Hangzhou, China)
The raw reads of each sample were internally programmed by ACGT101-miR, and clean reads were obtained by removing the adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, and snoRNA), and repetition.
unique sequences of 18–26 nucleotides were mapped to the precursors of Rattus norvegicus in miRBase 22.0 to identify the known and novel miRNAs. L/R ± n indicated that the detected miRNA sequence was n bases more/less than the known miRNAs on the left/right side. The read counts corresponding to tags per million counts (TPM) ratio was used to normalize the expression levels of miRNAs.
Differentially expressed miRNAs (DE-miRNAs) were identified by a fold-change ≥2 or a fold-change ≤0.5 and P≤0.05.
Supplementary_files_format_and_content: Table5_All_Expressed_miRNA.xlsx
Table9_Pre-miRNA_clusters.xlsx
Table11.1_Seed-based-families.xlsx
Table11.2_miFam-based-families.xlsx

organism: Rattus norvegicus

source_name: Sham-Exo

growth_protocol: When passage 3 BMSCs reached a confluency of 80–90%, the culture medium without exosomes was replaced, and the supernatant was collected after 2 days. The exosomes in the supernatant of BMSCs were extracted by differential ultracentrifugation. Briefly, the supernatant was collected by centrifugation at 300, 2000, and 10000 ×g for 10, 10, and 30 min, respectively, to remove the cells and cell debris. Next, the protein contamination was removed by ultracentrifugation of the supernatant at 110000 ×g for 70 min twice, and the precipitate was resuspended in PBS. Finally, the exosomes in the precipitate were resuspended in 100 μL PBS and stored at −80 °C.

extract_protocol:
Total RNA was extracted from BMSC-derived exosomes of OVX and Sham rats using TRIzol (Thermo Fisher Scientific, Waltham, MA, USA). The integrity of total RNAs was analyzed by Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and the RNA integrity number (RIN) > 7 was used for NGS. The concentration of total RNAs was detected by NanoDrop™ 2000.
MiRNA sequencing was performed on the Illumina Hiseq2500 platform from LC Sciences (Hangzhou, China). The raw reads of each sample were internally programmed by ACGT101-miR, and clean reads were obtained by removing the adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, and snoRNA), and repetition. Then, unique sequences of 18–26 nucleotides were mapped to the precursors of Rattus norvegicus in miRBase 22.0 to identify the known and novel miRNAs. L/R ± n indicated that the detected miRNA sequence was more/fewer n bases than the known miRNA on the left/right side. The read counts to tags per million counts (TPM) ratio was used to normalize the expression levels of miRNAs. The differentially expressed exosomal miRNAs (DE-miRNAs) were identified by fold-change ≥2 or fold-change ≤0.5 and P≤0.05.

treatment_protocol: The animals were anesthetized by an intraperitoneal injection of 2% 2,2,2-Tribromoethanol. Then, the bilateral ovaries were removed in the OVX group, while the peripheral ovarian fat was removed in the Sham group.

tag: strain

value: Sprague-Dawley

tag: cell type

value: Bone marrow mesenchymal stem cells (BMSCs)

tag: treatment

value: sham-operated

tag: sample type

value: BMSC-derived exosomes


title: Targeted RNA of patient number 54

tag: Sex

tag: tobacco status

value: HOT


title: Targeted RNA of patient number 55

source_name: Oropharynx

tag: alcohol status

tag: pfs (month)


title: Targeted RNA of patient number 91

value: Oral cavity

value: SD

tag: pfs (event)

tag: hot phenotype


title: btASMT-2 [ribosome profiling]

source_name: btASMT

tag: gene expressed

value: btASMT

tag: induction concentration

value: 1mM Rhamnose

tag: induction od

tag: induction time


title: CC1-2 [ribosome profiling]


title: BMSC-derived exosomes, OVX 1

source_name: OVX-Exo

value: ovariectomized


title: Targeted RNA of patient number 57

tag: site

value: Oropharynx

tag: age

value: M

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

tag: immunotherapy line

tag: best response on immunotherapy (recist)

tag: os (month)


title: BMSC-derived exosomes, Sham 1

tag: strain

tag: cell type

tag: treatment

tag: sample type


title: Targeted RNA of patient number 52

tag: Sex

tag: tobacco status

tag: alcohol status

value: PD

tag: os (event)

tag: pfs (month)

tag: hot score


title: Targeted RNA of patient number 51

tag: pfs (event)

tag: hot phenotype


title: BMSC-derived exosomes, Sham 3


title: Targeted RNA of patient number 50

source_name: Larynx

tag: site

value: Larynx

tag: age

value: PR


title: BMSC-derived exosomes, OVX 2


title: Targeted RNA of patient number 53

source_name: AUP

value: AUP

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

tag: immunotherapy line

value: COLD


title: ccCOMT-1 [ribosome profiling]

tag: gene expressed

value: ccCOMT

tag: induction concentration

tag: induction od

tag: induction time


title: btAANAT-2 [ribosome profiling]

source_name: btAANAT

tag: strain

value: btAANAT


title: Targeted RNA of patient number 49

tag: Sex

tag: best response on immunotherapy (recist)

tag: os (month)