title: Hippocampus, K9me3-P65ISC5_S14

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads were aligned to the rat reference genome (rn6) using HISAT2 (Kim et al., 2019).
MACS was utilized to assess sites of H3K9me3 histone modification (peaks).
diffReps (Shen et al., 2013) was run on the processed samples to find differential sites for the comparisons to the IS control group (ID, IDch, or ISch vs IS).
The atacseq.txt and chipseq.txt files are the annotation peak lists obtained from MACS software. The fold change for each peak is computed as the ratio of the read count in the peak to the maximum of the local and global lambda values.
Local Lambda: MACS2 computes a local lambda value for each peak, which is a measure of the local background noise around the peak.
Global Lambda: MACS2 also computes a global lambda value, which is a measure of the background noise across the entire genome.
Assembly: rn6
Supplementary files format and content: tab-delimited text peaks file

source_name: Brain

extract_protocol:
For ChIP-seq, chromatin was fixed with 1% formaldehyde solution, fragmented, and precipitated with H3K9me3 antibody. DNA was quantified using the PicoGreen dsDNA Assay Kit.
Library preparation for ChIP-seq was completed using ThruPLEX® DNA-Seq (Rubicon Genomics) kit. Libraries were assessed for quality using electrophoresis on an Agilent Bioanalyzer (Agilent) and size-selected for 200~800 bp fragments.

value: Brain

tag: tissue region

value: Hippocampus

tag: group

tag: maternal treatment

value: ISC

tag: offspring age

value: H3K9me3 (Diagenode, Cat.# C15410193)


title: Hippocampus, K9me3-P65ISC3_S13

status: Public on Mar 13 2024

type: SRA

city: New York

country: USA

library_source: genomic

molecule: genomic DNA

organism: Rattus norvegicus

tag: tissue

tag: chip antibody


title: Hippocampus, K9me3-P65ISC2_S5


title: Hippocampus, K9me3-P65IS6_S2

value: IS


title: Hippocampus, K9me3-P65ISC1_S12


title: Hippocampus, K9me3-P65IS7_S8


title: Hippocampus, K9me3-P65IDC2_S15

value: IDC


title: Hippocampus, K9me3-P65IS5_S1


title: PQN85_JK06_1hrauxin_L3_rep2 [HW48]

first: Jun

last: Kim

state: NY

address: 100 Washington Square East 1009 Silver Center

department: Biology

institute: NYU

description:
PQN85_JK06_1hrauxin_inputsubt_avg.bw
PQN85_JK06_1hrauxin_inputsubt_avg.bw
PQN85_JK06_1hrauxin_avg_chip_peaks.bed
PQN85_JK06_1hrauxin_avg_chip_summits.bed

data_processing:
Bowtie2 version 2.4.2 was used to align 75 bp single-end reads to WS220 with default parameters. Bam sorting and indexing was performed using samtools version 1.11. BamCompare tool in Deeptools version 3.5.0 was used to normalize for the sequencing depth using CPM and create ChIP-Input coverage with a bin size of 10 bp and 200 bp read extension. Only reads with a minimum mapping quality of 20 were used, and mitochondrial DNA, PCR duplicates, and blacklisted regions were removed. The average coverage data was generated by averaging ChIP-Input enrichment scores per 10 bp bins across the genome.  ChIP-seq peaks are identified using MACS2 version 2.1.1 (https://github.com/macs3-project/MACS). Peaks are called using both the individual replicates and combined bam files with minimum false discovery rate of 0.05. The peaks shown below average ChIP-seq tracks are peaks called using the combined bam files, whereas the peaks shown below individual replicates are peaks called using the corresponding replicate.
Assembly: WS220
Supplementary files format and content: bw file contains signal track, input subtracted enrichment at each binned genomic loci
Supplementary files format and content:bed file contains binarized chip enrichment across the genome

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Mixed developmental stage embryos were obtained by bleaching gravid adults. To isolate synchronized L2/L3 worms, gravid adults were bleached and embryos were hatched overnight in M9 buffer. The resulting starved L1s were grown for 24 hours at 22°C. L3 worms were kept on plates with or without auxin prior to collection.

extract_protocol:
ChIP-seq: L2/L3s and adult worms were dounce-homogenized in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) and sonicated in 0.1% sarkosyl to obtain chromatin fragments between 200 and 800 bp. 2 mg of protein extract and 3 to 10 ug of antibody was used per ChIP.
ChIP-seq: half of the ChIP DNA and 30 ng of input DNA were ligated to Illumina TruSeq adapters and amplified by PCR. Library DNA between 250 and 600 bp was gel purified.

treatment_protocol: collected worms were treated with auxin using NGM media containing 1 mM auxin. The worms were left on NGM plate to crawl around for an hour.

value: whole worms

tag: strain

tag: development stage

tag: genotype


title: SMC3_JK06_1hrauxin_L3_rep3 [HW47]

description:
SMC3_JK06_1hrauxin_inputsubt_rep3.bw
SMC3_JK06_1hrauxin_inputsubt_rep3.bw
SMC3_JK06_1hrauxin_rep3_chip_peaks.bed

value: SMC3 (SDIX,Q4469)


title: Hippocampus, K9me3-P65IDC1_S6


title: Hippocampus, K9me3-P65IDC13_S16


title: Hippocampus, K9me3-P65IS-pooled_S3


title: Hippocampus, K9me3-P65ID-pooled2_S11

value: ID


title: HFD_WT_1

status: Public on Mar 14 2024

city: Tainan

first: Siao Muk

last: Cheng

address: No. 367, Sheng-Li Rd., North District

country: Taiwan

institute: National Institutes of Cancer Research

library_source: transcriptomic

data_processing:
CLC genomic workbench 20.0.4 (CLC Bio)
Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic workbench
Trimmed sequence reads were mapped to Grcm39/mm10 using CLC genomic workbench
Read cound extraction and normalization were performed using CLC genomic workbench
Assembly: mm10
Supplementary files format and content: text file includes raw counts for each sample
Supplementary files format and content: text file includes RPKM/TPM/CPM for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: liver

growth_protocol: mice were housed (4–5 per cage) in a temperature- (temperature: 25 ± 2 °C; humidity: around 60-80%) and light-control environment under a 12:12 h light-dark cycle (lights on at 6:00 AM)

extract_protocol:
TRIzol reagent (Invitrogen)
cDNA libraries were prepared based on the MGIEasy RNA Directional Library Prep Kit Guide (MGI Tech, Cat. 1000006385).

treatment_protocol: High fat diet feeding

value: liver

tag: cell type

value: liver cells

value: WT

tag: treatment

value: high fat diet for 12 week


title: Hippocampus, K9me3-P65IDC14_S7


title: Hippocampus, K9me3-P65ID11B_S10


title: Hippocampus, K9me3-P65ID10_S9


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 034

type: genomic

city: Ribeirão Preto

first: Junier

middle: Marrero

last: Gutiérrez

state: São Paulo

address: Av Bandeirantes, 3900

department: Pediatric

country: Brazil

institute: Ribeirão Preto Medical School-University of São Paulo

hyb_protocol: Standard Illumina protocol

scan_protocol: Raw methylation data were obtained using the Illumina iScan system (RRID:SCR_016388) according to Illumina protocol.

data_processing: Minfi software program in R computing language (RRID:SCR_012830)

label: Cy5 and Cy3

organism: Homo sapiens

source_name: Adamantinomatous craniopharyngioma

label_protocol: Standard Illumina protocol

extract_protocol: DNA from microdissected, fresh frozen tumor samples was extracted using the QIAamp DNA Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer's instruction. DNA quantification was performed by fluorometry using the Qubit dsDNA BR Assay (Thermo Fisher Scientific, Waltham, MA), and the integrity was assessed by electrophoresis using the Tape Station 4200 System (Agilent, Santa Clara, CA). DNA integrity number (DIN) ≥ 6 was considered adequate.

tag: sexo

value: Male

tag: age at diagnosis(years)

value: not available

tag: hypothalamic invasion

value: type 2

tag: tumor ctnnb1 mutation

value: Yes


title: BAC-Igf2_Igf2_dCTCFinICR~dIgf2~Sox2-BS15912A

first: Matthew

middle: T

last: Maurano

address: 435 East 30th Street

department: Institute for Systems Genetics

institute: NYU Grossman School of Medicine

data_processing:
Illumina libraries were sequenced in paired-end mode on an Illumina NextSeq 500 operated at the Institute for Systems Genetics. Reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing BC sequences.
All WGS and Capture-Seq data were processed using a uniform mapping and peak calling pipeline. Illumina sequencing adapters were trimmed with Trimmomatic v0.39. Sequencing reads were aligned using BWA v0.7.17 to a genome reference (GRCm38/mm10) including unscaffolded contigs and alternate references, as well as independently to custom references for relevant vectors and their payloads. PCR duplicates were marked using samblaster v0.1.24. Generation of per-base coverage depth tracks and quantification was performed using BEDOPS v2.4.35.
The sequencing processing pipeline is available at https://github.com/mauranolab/mapping .
Assembly: mm10
Supplementary files format and content: coverage bigwig files for captured genomic DNA libraries to genome reference (GRCm38/mm10)

organism: synthetic construct

source_name: BAC clone library

growth_protocol: mESCs were cultured on gelatin-coated plates coated in 80/20 medium comprising 80% 2i medium and 20% mESC medium and with 1% Pen-strep.

extract_protocol:
Cells were dissociated using TryPE-Select, spun-down and media aspirate. Pellets were either processed immediately or stored at -80 deg. Genomic DNA was extracted using the DNeasy Blood & Tissue kit (QIAGEN 69506).
Double-stranded DNA libraries were prepared from sheared genomic DNA. DNA fragments were end-repaired, A-tailed, and Illumina-compatible adapters were ligated to DNA ends.
Payload and Targeted sequencing (Capture-seq)

treatment_protocol: Cells were engineered with different landing pads and payloads as described and were selected combinatorially with puromycin, blasticidin, proaerolysin and ganciclovir as described in the manuscript.

tag: payload id

tag: seq method

value: payload sequencing


title: BAC-Sox2_Sox2_dDistalLCR~H19Enh~inverted-BS17635A


title: Hippocampus, K9me3-P65ID-pooled1_S4

value: Brain

tag: tissue region

value: Hippocampus


title: BAC-Igf2_Igf2_miICR~dIgf2~Sox2-BS16232A


title: BAC-Igf2_Igf2_inverted~dEnh~miICR-BS12529A


title: BAC-Igf2_Igf2_inverted~dEnh~dCTCFinICR-BS12675A


title: BAC-Sox2_Sox2_dDistalLCR~H19Enh-BS17632A


title: BAC-Igf2_Igf2_inverted~dCTCFinICR-BS14102A


title: BAC-Igf2_Igf2_Sox2DistalLCR~inverted~dCTCFinICR-BS11137A


title: BAC-Igf2_Igf2_Sox2DistalLCR~inverted~miICR-BS11131A


title: BAC-Igf2_Igf2_inverted~miICR-BS12671A


title: BAC-Igf2_Igf2_Sox2DistalLCR~dCTCFinICR-BS11128A


title: BAC-Igf2_Igf2_dCTCFinICR-BS09866A


title: BAC-Igf2_Igf2_dEnh~dCTCFinICR-BS09687A


title: BAC-Sox2_DistalLCR_H19enh~inverted-BS11098A


title: PQN85_JK06_1hrauxin_L3_rep1 [HW46]


title: BAC-Sox2_DistalLCR_H19enh-BS11097A


title: BAC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS08667A


title: BAC-Igf2_Igf2_miICR~Igf2SV-BS08664A


title: BAC-Igf2_Igf2_157kb~Igf2SV-BS08196A


title: co-culture

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

country: China

institute: Tsinghua University

library_source: transcriptomic single cell

data_processing:
Raw data were input to STARsolo pipeline (version:2.7.8a), which performed read mapping, cell demultiplexing, UMI counting and cell filtering. WT and co-culture samples are both mapped to mixed GRCh38 and Rnor_6.0 reference genome.
Assembly: GRCh38 and Rnor_6.0
Supplementary files format and content: cell barcode and gene UMI matrix files generated by STARsolo pipeline (version:2.7.8a)

organism:
Homo sapiens
Rattus norvegicus

source_name: rat choroid and cultured cells

growth_protocol: EC differentiation protocol was described in a published study Zhang et al., Biomaterials 2021 (doi.org/10.1016/j.biomaterials.2021.120713).

extract_protocol:
Freshly dissected rat choroid and rat choroid-hPSC-EC co-cultured for 48 hours were dissociated to single-cell suspension and used for scRNA-seq library preparation.
libraries were generated according to 10X genomics's instrument instructions.

treatment_protocol: For co-culture of rat choroid and hPSC-EC: rat eyeballs were dissected. A circumferential cut along the cornea released the aqueous humour and the intraocular tension. After removal of the iris, lens, and the aqueous humour, four incisions were made to the cup-shaped retina-sclera complex, leaving a flower-shaped flattened tissue. Under the microscope, the retina was carefully removed.  The choroid-sclera complex were cut into 2mm squares, and transferred to 24-well tissue culture plates. For co-culture, 0.2 million EC suspension was added onto the choroid-sclera complex in 24-well plate. Media was changed daily. After 48 hours of co-culture, the choroid-sclera complex was washed and dissociated for scRNA-seq analysis.

value: rat choroid and cultured cells

tag: cell line

value: pluripotent stem cell (hPSC) derived endothelial cells


title: BAC-Igf2_Igf2_Sox2DistalLCR~miICR-BS11125A


title: Illumina NovaSeq X liver, mRNA derived cDNA, 1000ng input, 6 PCR cycles

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description:
liver, mRNA derived cDNA, 1000ng input, 6 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4

data_processing:
Fastp was used for trimming and quality control
Reads were aligned with STAR to the GRCh38.p13 human reference genome (Gencode 42 release)
UMI_tools were used for deduplication
FeatureCounts were used to build a gene count matrix for the deduplicated and non-deduplicated data
Assembly: GRCh38.p13
Supplementary files format and content: FeatureCounts output files, before (*pre_deduplication.txt) and after deduplication (*post_deduplication.txt)

molecule: total RNA

extract_protocol:
Human Liver total RNA was bought from Thermofisher Scientific
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with Unique Dual Index UMI Adapters RNA Set1


title: Illumina NovaSeq X liver, mRNA derived cDNA, 500ng input, 11 PCR cycles

description:
liver, mRNA derived cDNA, 500ng input, 11 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 1000ng input, 10 PCR cycles

description:
liver, mRNA derived cDNA, 1000ng input, 10 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 032

value: Female


title: Illumina NovaSeq X liver, mRNA derived cDNA, 500ng input, 7 PCR cycles

description:
liver, mRNA derived cDNA, 500ng input, 7 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 500ng input, 9 PCR cycles

description:
liver, mRNA derived cDNA, 500ng input, 9 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 250ng input, 12 PCR cycles

description:
liver, mRNA derived cDNA, 250ng input, 12 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 001

value: No


title: Illumina NovaSeq X liver, mRNA derived cDNA, 125ng input, 9 PCR cycles

description:
liver, mRNA derived cDNA, 125ng input, 9 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 62ng input, 12 PCR cycles

description:
liver, mRNA derived cDNA, 62ng input, 12 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 62ng input, 14 PCR cycles

description:
liver, mRNA derived cDNA, 62ng input, 14 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 62ng input, 10 PCR cycles

description:
liver, mRNA derived cDNA, 62ng input, 10 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 31ng input, 13 PCR cycles

description:
liver, mRNA derived cDNA, 31ng input, 13 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 31ng input, 15 PCR cycles

description:
liver, mRNA derived cDNA, 31ng input, 15 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 024


title: Illumina NovaSeq X liver, mRNA derived cDNA, 1000ng input, 8 PCR cycles

description:
liver, mRNA derived cDNA, 1000ng input, 8 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 15ng input, 16 PCR cycles

description:
liver, mRNA derived cDNA, 15ng input, 16 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 125ng input, 11 PCR cycles

description:
liver, mRNA derived cDNA, 125ng input, 11 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 31ng input, 11 PCR cycles

description:
liver, mRNA derived cDNA, 31ng input, 11 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 250ng input, 10 PCR cycles

description:
liver, mRNA derived cDNA, 250ng input, 10 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 125ng input, 13 PCR cycles

description:
liver, mRNA derived cDNA, 125ng input, 13 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 027


title: Illumina NovaSeq X liver, mRNA derived cDNA, 250ng input, 8 PCR cycles

description:
liver, mRNA derived cDNA, 250ng input, 8 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 15ng input, 14 PCR cycles

description:
liver, mRNA derived cDNA, 15ng input, 14 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 028


title: Illumina NovaSeq X liver, mRNA derived cDNA, 15ng input, 12 PCR cycles

description:
liver, mRNA derived cDNA, 15ng input, 12 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 4ng input, 18 PCR cycles

description:
liver, mRNA derived cDNA, 4ng input, 18 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 7ng input, 17 PCR cycles

description:
liver, mRNA derived cDNA, 7ng input, 17 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 7ng input, 13 PCR cycles

description:
liver, mRNA derived cDNA, 7ng input, 13 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 4ng input, 16 PCR cycles

description:
liver, mRNA derived cDNA, 4ng input, 16 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 2ng input, 19 PCR cycles

description:
liver, mRNA derived cDNA, 2ng input, 19 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 4ng input, 14 PCR cycles

description:
liver, mRNA derived cDNA, 4ng input, 14 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 019


title: Illumina NovaSeq X liver, mRNA derived cDNA, 7ng input, 15 PCR cycles

description:
liver, mRNA derived cDNA, 7ng input, 15 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 1ng input, 18 PCR cycles

description:
liver, mRNA derived cDNA, 1ng input, 18 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 2ng input, 15 PCR cycles

description:
liver, mRNA derived cDNA, 2ng input, 15 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Viral FLIP expression

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: normalized log2 ratio(E8_Neo/C3H10T1_2)

hyb_protocol: Hybridized for 16 h at 37 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: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: APC

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Cells were cultured in the 10% FCS/DMEM medium.

extract_protocol: Total RNA extracted using Sepazol following manufacturer's instructions

treatment_protocol: To establish the stably-transfected cells, transfected cells were treated with the medium containing 1 mg/ml G418 for one week.

value: mouse mesenchymal stem cell (MSC)

value: parental

value: stably-transfected cells carrying both Flag-E8 and neomysin-resistant transgenes


title: Illumina NovaSeq X liver, mRNA derived cDNA, 0ng input, 21 PCR cycles

description:
liver, mRNA derived cDNA, 0ng input, 21 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4

value: liver


title: Illumina NovaSeq X liver, mRNA derived cDNA, 0ng input, 19 PCR cycles

description:
liver, mRNA derived cDNA, 0ng input, 19 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 1ng input, 20 PCR cycles

description:
liver, mRNA derived cDNA, 1ng input, 20 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 2ng input, 17 PCR cycles

description:
liver, mRNA derived cDNA, 2ng input, 17 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 015


title: Illumina NovaSeq X liver, mRNA derived cDNA, 0ng input, 17 PCR cycles

description:
liver, mRNA derived cDNA, 0ng input, 17 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 023


title: Element AVITI liver, mRNA derived cDNA, 1000ng input, 6 PCR cycles

description:
liver, mRNA derived cDNA, 1000ng input, 6 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 500ng input, 11 PCR cycles

description:
liver, mRNA derived cDNA, 500ng input, 11 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 1000ng input, 10 PCR cycles

description:
liver, mRNA derived cDNA, 1000ng input, 10 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 500ng input, 9 PCR cycles

description:
liver, mRNA derived cDNA, 500ng input, 9 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 500ng input, 7 PCR cycles

description:
liver, mRNA derived cDNA, 500ng input, 7 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 250ng input, 12 PCR cycles

description:
liver, mRNA derived cDNA, 250ng input, 12 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 250ng input, 10 PCR cycles

description:
liver, mRNA derived cDNA, 250ng input, 10 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 016


title: Element AVITI liver, mRNA derived cDNA, 250ng input, 8 PCR cycles

description:
liver, mRNA derived cDNA, 250ng input, 8 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 125ng input, 13 PCR cycles

description:
liver, mRNA derived cDNA, 125ng input, 13 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 125ng input, 9 PCR cycles

description:
liver, mRNA derived cDNA, 125ng input, 9 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 62ng input, 14 PCR cycles

description:
liver, mRNA derived cDNA, 62ng input, 14 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 62ng input, 10 PCR cycles

description:
liver, mRNA derived cDNA, 62ng input, 10 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 62ng input, 12 PCR cycles

description:
liver, mRNA derived cDNA, 62ng input, 12 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 125ng input, 11 PCR cycles

description:
liver, mRNA derived cDNA, 125ng input, 11 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq X liver, mRNA derived cDNA, 1ng input, 16 PCR cycles

description:
liver, mRNA derived cDNA, 1ng input, 16 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 31ng input, 15 PCR cycles

description:
liver, mRNA derived cDNA, 31ng input, 15 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 31ng input, 13 PCR cycles

description:
liver, mRNA derived cDNA, 31ng input, 13 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 15ng input, 14 PCR cycles

description:
liver, mRNA derived cDNA, 15ng input, 14 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 7ng input, 17 PCR cycles

description:
liver, mRNA derived cDNA, 7ng input, 17 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 15ng input, 16 PCR cycles

description:
liver, mRNA derived cDNA, 15ng input, 16 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 15ng input, 12 PCR cycles

description:
liver, mRNA derived cDNA, 15ng input, 12 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 7ng input, 15 PCR cycles

description:
liver, mRNA derived cDNA, 7ng input, 15 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 31ng input, 11 PCR cycles

description:
liver, mRNA derived cDNA, 31ng input, 11 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 1000ng input, 8 PCR cycles

description:
liver, mRNA derived cDNA, 1000ng input, 8 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 4ng input, 18 PCR cycles

description:
liver, mRNA derived cDNA, 4ng input, 18 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 7ng input, 13 PCR cycles

description:
liver, mRNA derived cDNA, 7ng input, 13 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 4ng input, 16 PCR cycles

description:
liver, mRNA derived cDNA, 4ng input, 16 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 4ng input, 14 PCR cycles

description:
liver, mRNA derived cDNA, 4ng input, 14 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 2ng input, 19 PCR cycles

description:
liver, mRNA derived cDNA, 2ng input, 19 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 2ng input, 17 PCR cycles

description:
liver, mRNA derived cDNA, 2ng input, 17 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 2ng input, 15 PCR cycles

description:
liver, mRNA derived cDNA, 2ng input, 15 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 1ng input, 20 PCR cycles

description:
liver, mRNA derived cDNA, 1ng input, 20 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 1ng input, 16 PCR cycles

description:
liver, mRNA derived cDNA, 1ng input, 16 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 0ng input, 19 PCR cycles

description:
liver, mRNA derived cDNA, 0ng input, 19 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 0ng input, 17 PCR cycles

description:
liver, mRNA derived cDNA, 0ng input, 17 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Element AVITI liver, mRNA derived cDNA, 1ng input, 18 PCR cycles

description:
liver, mRNA derived cDNA, 1ng input, 18 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: phiKZ_enriched

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

country: Belgium

institute: KU Leuven

data_processing:
Live basecalling and demultiplexing by promethION 24 device
Identification and orientation of full-length reads using Pychopper (v2.5.0)
Read trimming using Cutadapt (v2.7)
Mapping reads against reference genomes of P. aeruginosa host strain and phages using minimap2
Peak calling using termseq-peaks scripts
Assembly: PAO1 (NC_002516.2); PAK (LR657304.1); Li010 (CP124600); LUZ19 (NC_010326.1); LUZ24 (NC_010325.1); YuA (NC_010116.1); 14-1 (NC_011703.1); phiKZ (NC_004629.1); PAK_P3 (NC_022970.1)
Supplementary files format and content: Narrowpeak files generated by peak calling

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa PAO1, Pseudomonas virus phiKZ

growth_protocol: P. aeruginosa cells (PAO1/PAK/Li010) were grown to exponential phase in LB medium and infected with the appropriate phage (LUZ19, LUZ24, YuA, PAK_P3, 14-1 or phiKZ). Culture samples were taken at multiple timepoints during infection. The number of samples and the timepoints were decided depending on the duration of the phage infection cycle.

extract_protocol:
All samples, aside from 0 min, were pooled together and homogenized (sample tφ). The resulting samples t0 (uninfected) and tφ (phage infected) were subjected to hot phenol treatment and ethanol precipitation to extract and purify  the RNATotal RNA was extracted using hot-phenol extraction, followed by DNAse treatment.
Total RNA was enriched for primary transcripts using the ONT-cappable-seq enrichment protocol. In parallel, control samples were subjected to similar environmental conditions. The RNA was reverse transcribed, PCR amplified and barcoded accoriding to Oxford Nanopore Technology cDNA-PCR protocol (SQK-PCB109)
Total RNA was enriched for primary transcripts using the ONT-cappable-seq enrichment protocol. In parallel, control samples were subjected to similar environmental conditions. The RNA was reverse transcribed, PCR amplified and barcoded accoriding to Oxford Nanopore Technology cDNA-PCR protocol (SQK-PCB109). The amplified cDNA samples were pooled together in a final library.

treatment_protocol: Total RNA was extracted using hot-phenol extraction, followed by DNAse treatment. For each phage, the samples from different timepoints were pooled in equal amounts before starting the library prepartion. The enriched samples were subjected to an enrichment procedure based on streptavidin beads to enrich for primary transcripts. For the control samples the enrichment steps were omitted.

value: bacterial cell

value: enriched for primary RNAs

tag: agent

value: Pseudomonas virus phiKZ

tag: infection stage

value: infected with phage (samples from different timepoints during infection pooled)


title: 14-1_enriched

source_name: Pseudomonas aeruginosa PAO1, Pseudomonas virus 14-1

value: Pseudomonas virus 14-1


title: PAKP3_enriched

source_name: Pseudomonas aeruginosa PAK, Pseudomonas virus PAKP3

value: PAK

value: Pseudomonas virus PAKP3


title: YuA_enriched

source_name: Pseudomonas aeruginosa PAO1, Pseudomonas virus YuA

value: Pseudomonas virus YuA


title: phiKZ_control

value: no enrichment


title: YuA_control


title: LUZ24_enriched

source_name: Pseudomonas aeruginosa Li010, Pseudomonas virus LUZ24

value: Pseudomonas virus LUZ24


title: LUZ19_control

source_name: Pseudomonas aeruginosa PAO1, Pseudomonas virus LUZ19

value: Pseudomonas virus LUZ19


title: LUZ24_control


title: LUZ19_enriched


title: Element AVITI liver, mRNA derived cDNA, 0ng input, 21 PCR cycles

description:
liver, mRNA derived cDNA, 0ng input, 21 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4

tag: tissue


title: rhTCR BOB9084_2

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
BOB9084_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR

data_processing:
Demultiplexing of raw sequencing data
Separation of TCR alpha and beta reads using BLAST
Assembly and annotation of reads using MiXCR
Quality control and error correction
Quantification of T cell clonotypes
Assembly: GRCh38
Supplementary files format and content: excel files include T cell clonotype count values for each Sample

source_name: Peripheral Blood

extract_protocol:
Total RNA of peripheral blood was extracted from 400 μl of each blood sample using Quick-DNA/RNA miniprep plus kit
Bulk TCR-sequencing was performed with 200 ng of total RNA by the Dana-Farber Cancer Institute Translational Immunogenomics Laboratory following the protocol of RNase H-dependent PCR enabled T-cell receptor sequencing

value: blood


title: rhTCR BOB9475_2

description:
BOB9475_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB9109_2

description:
BOB9109_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB9472_2

description:
BOB9472_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB9205_2

description:
BOB9205_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB9262_2

description:
BOB9262_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB9480_2

description:
BOB9480_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB9135_3

description:
BOB9135_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB9080_2

description:
BOB9080_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB9259_2

description:
BOB9259_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB9069_3

description:
BOB9069_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB8928_3

description:
BOB8928_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB8927_2

description:
BOB8927_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB8916_3

description:
BOB8916_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: PAKP3_control


title: rhTCR BOB8903_5

description:
BOB8903_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB8905_2

description:
BOB8905_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB8902_2

description:
BOB8902_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB8886_3

description:
BOB8886_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB8867_2

description:
BOB8867_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB8907_3

description:
BOB8907_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: 14-1_control


title: rhTCR BOB9481_2

description:
BOB9481_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB7553WB_1

description:
BOB7553WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB7473WB_1

description:
BOB7473WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB7501WB_1

description:
BOB7501WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB9211_3

description:
BOB9211_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB9027_2

description:
BOB9027_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB6934WB_1

description:
BOB6934WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB6902WB_1

description:
BOB6902WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB6817WB_1

description:
BOB6817WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB6231WB_1

description:
BOB6231WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB5536WB_1

description:
BOB5536WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB5841WB_1

description:
BOB5841WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB6741WB_1

description:
BOB6741WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB6900WB_1

description:
BOB6900WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB6452WB_1

description:
BOB6452WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB6867WB_1

description:
BOB6867WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB6828WB_1

description:
BOB6828WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB5356WB_1

description:
BOB5356WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB5397WB_1

description:
BOB5397WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB5810WB_1

description:
BOB5810WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB6091WB_1

description:
BOB6091WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB5158WB_2

description:
BOB5158WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB5530WB_1

description:
BOB5530WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB4986_3

description:
BOB4986_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB7104WB_1

description:
BOB7104WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB4725WB_1

description:
BOB4725WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB4851WB_1

description:
BOB4851WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB44687WB_1

description:
BOB44687WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB4620WB_1

description:
BOB4620WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB5134WB_1

description:
BOB5134WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB4447WB_1

description:
BOB4447WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB4427WB_1

description:
BOB4427WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB44317WB_1

description:
BOB44317WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB43872WB_1

description:
BOB43872WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB43855WB_1

description:
BOB43855WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB4345_3

description:
BOB4345_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB4313WB_1

description:
BOB4313WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB42959BC_1

description:
BOB42959BC_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOb42319WB_1

description:
BOb42319WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB43089BC_1

description:
BOB43089BC_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB4120WB_1

description:
BOB4120WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB40993WB_1

description:
BOB40993WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB4133WB_1

description:
BOB4133WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB41246WB_1

description:
BOB41246WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB41824WB_1

description:
BOB41824WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB39130WB_1

description:
BOB39130WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB4022WB_1

description:
BOB4022WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB40630WB_1

description:
BOB40630WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB35599WB_1

description:
BOB35599WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB40959WB_1

description:
BOB40959WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB39934WB_1

description:
BOB39934WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB35602WB_2

description:
BOB35602WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB40921WB_1

description:
BOB40921WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB3855WB_1

description:
BOB3855WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB4093WB_1

description:
BOB4093WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB3894WB_1

description:
BOB3894WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB38997WB_1

description:
BOB38997WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB35332WB_1

description:
BOB35332WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB40920WB_1

description:
BOB40920WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB4006WB_1

description:
BOB4006WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB4743WB_1

description:
BOB4743WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB35203WB_1

description:
BOB35203WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB35321WB_1

description:
BOB35321WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB3518WB_1

description:
BOB3518WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB43251WB_1

description:
BOB43251WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB35019WB_1

description:
BOB35019WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB35122WB_1

description:
BOB35122WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB3706WB_1

description:
BOB3706WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB3579WB_1

description:
BOB3579WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB3480WB_1

description:
BOB3480WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB34852WB_1

description:
BOB34852WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB34423WB_1

description:
BOB34423WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB34313WB_1

description:
BOB34313WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB34341WB_1

description:
BOB34341WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB34308WB_1

description:
BOB34308WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB34157WB_1

description:
BOB34157WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB33521WB_2

description:
BOB33521WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB34067WB_1

description:
BOB34067WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB34175WB_1

description:
BOB34175WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB33328WB_1

description:
BOB33328WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB33060WB_1

description:
BOB33060WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB3294_3

description:
BOB3294_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB3224WB_1

description:
BOB3224WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB34993WB_1

description:
BOB34993WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB32221WB_1

description:
BOB32221WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB34190WB_1

description:
BOB34190WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB34185WB_1

description:
BOB34185WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB3244WB_1

description:
BOB3244WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB3334WB_1

description:
BOB3334WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB3179_1_2

description:
BOB3179_1_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB34520WB_1

description:
BOB34520WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB34570WB_3

description:
BOB34570WB_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB32167WB_1

description:
BOB32167WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB32044WB_1

description:
BOB32044WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB32111WB_1

description:
BOB32111WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB31217WB_1

description:
BOB31217WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB34158WB_1

description:
BOB34158WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB3369WB_1

description:
BOB3369WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB3115WB_1

description:
BOB3115WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB31243BC

description:
BOB31243BC
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB31097WB_1

description:
BOB31097WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB30969WB_1

description:
BOB30969WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB31080WB_1

description:
BOB31080WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB30773WB_1

description:
BOB30773WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB30398WB_2

description:
BOB30398WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB30321WB_2

description:
BOB30321WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB3015WB_1

description:
BOB3015WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB30257WB_1

description:
BOB30257WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB29880WB_2

description:
BOB29880WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB2965WB_1

description:
BOB2965WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB29734WB_1

description:
BOB29734WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB2997WB_1

description:
BOB2997WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB29608WB_1

description:
BOB29608WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB29158WB_1

description:
BOB29158WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB29473WB_1

description:
BOB29473WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB29024WB_1

description:
BOB29024WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB28881WB_1

description:
BOB28881WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB2888_1_2

description:
BOB2888_1_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB28859WB_2

description:
BOB28859WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB28998WB_2

description:
BOB28998WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB28843WB_1

description:
BOB28843WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB28803WB_2

description:
BOB28803WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB30911WB_1

description:
BOB30911WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB28790WB_2

description:
BOB28790WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB30859WB_1

description:
BOB30859WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB30853WB_2

description:
BOB30853WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB28557WB_1

description:
BOB28557WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB28421WB_1

description:
BOB28421WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB28439WB_2

description:
BOB28439WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB30547WB_1

description:
BOB30547WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB28465WB_1

description:
BOB28465WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB30277WB_1

description:
BOB30277WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB28392WB_1

description:
BOB28392WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB28312WB_1

description:
BOB28312WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB27974WB_2

description:
BOB27974WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB28342WB_1

description:
BOB28342WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB28270WB_1

description:
BOB28270WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB28258WB_1

description:
BOB28258WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB27783WB_2

description:
BOB27783WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB27720WB_2

description:
BOB27720WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB27621WB_1

description:
BOB27621WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB2757WB_1

description:
BOB2757WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB27455WB_1

description:
BOB27455WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB27509WB_2

description:
BOB27509WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB28442WB_2

description:
BOB28442WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB27302WB_1

description:
BOB27302WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26981WB_2

description:
BOB26981WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB27212WB_1

description:
BOB27212WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26976WB_2

description:
BOB26976WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB2674WB_1

description:
BOB2674WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26956WB_2

description:
BOB26956WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB2691WB_1

description:
BOB2691WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26783WB_2

description:
BOB26783WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26574WB_1

description:
BOB26574WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26583WB_2

description:
BOB26583WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26804WB_1

description:
BOB26804WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26524WB_1

description:
BOB26524WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26502WB_1

description:
BOB26502WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26526WB_2

description:
BOB26526WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB2650_1

description:
BOB2650_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB27778WB_1

description:
BOB27778WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26005WB_1

description:
BOB26005WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26234WB_2

description:
BOB26234WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26230WB_2

description:
BOB26230WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26033WB_2

description:
BOB26033WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26159WB_1

description:
BOB26159WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26081WB_1

description:
BOB26081WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB27710WB_1

description:
BOB27710WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB26044WB_1

description:
BOB26044WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB2580_1

description:
BOB2580_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB2739WB_1

description:
BOB2739WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB2595_1

description:
BOB2595_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB25994WB_3

description:
BOB25994WB_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB25601WB_1

description:
BOB25601WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB25709WB_1

description:
BOB25709WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB25569WB_1

description:
BOB25569WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB2560_1

description:
BOB2560_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB25461WB_2

description:
BOB25461WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB25183WB_1

description:
BOB25183WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB25153WB_1

description:
BOB25153WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB25159WB_1

description:
BOB25159WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB25232WB_1

description:
BOB25232WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB2506WB_1

description:
BOB2506WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB24984WB_1

description:
BOB24984WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB24827WB_4

description:
BOB24827WB_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB24819WB_1

description:
BOB24819WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB24591WB_1

description:
BOB24591WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB24523WB_1

description:
BOB24523WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB24513WB_2

description:
BOB24513WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB23984WB_1

description:
BOB23984WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB2411WB_1

description:
BOB2411WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: AmB/LNP sample 3 [H6]

city: West Lafayette

first: Tony

last: Hazbun

state: Indiana

address: 201 South University Street

department: Borch Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

data_processing:
150-bp paired-end DNA samples were sequenced using an Illumina NovaSeq6000. Fastp  was used to quality-trim reads and eliminate Illumina TruSeq adaptor sequences. Reads were aligned to the C. auris NCBI reference genome version B11221 using STAR aligner (v2.7.10a) The read counts mapped to each gene were counted using FeatureCounts  (v2.1). The EdgeR  Bioconductor package (v3.16.5) was used to perform the differential expression analysis. The Benjamini-Hochberg method was used to adjust the P-values for multiple testing. The cutoff for the significant differential expression was chosen at a FDR of 0.05. DEGs were annotated by blasting the sequences of identified DEGs versus C. albicans SC5314 Genome Database with an e-value cutoff of 0.01. Cluster Profiler Bioconductor  package (v2.4.3) was used to perform Gene Ontology analysis of DEGs. The length of each gene in the related annotation GTF file and the number of reads mapped to each gene were used to generate FPKM values for each gene.
Assembly: C. auris NCBI reference genome version B11221

organism: Candidozyma auris

source_name: Candida cells

growth_protocol: C. auris was grown on YPD broth

extract_protocol:
Exponential C. auris AR0390 in RPMI 1640 medium were treated with DMSO (control), AmB (0.5 µg/ml), LNP (32 µg/ml), or the combination of AmB/LNP in triplicates for 3 hr at 35 °C. Candida cells were collected, washed three times with PBS, and the total RNA was extracted using a RiboPureTM-Yeast Kit (AmBion, AM1926, MA, USA) as per the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Candida cells were treated with the tested drugs in RPMI media

value: Candida cells

value: Amphotericin 0.5 + Lansoprazole 30 ug/mL

tag: ng/ul

tag: total volume

value: 40 ul


title: rhTCR BOB23952WB_1

description:
BOB23952WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB24000WB_1

description:
BOB24000WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: AmB/LNP sample 2 [H5]

tag: strain


title: rhTCR BOB24060WB_1

description:
BOB24060WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB23936WB_1

description:
BOB23936WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: LNP sample 3 [E6]

value: Lansoprazole 30 ug/mL


title: rhTCR BOB25995WB_1

description:
BOB25995WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: AmB/LNP sample 1 [H4]


title: rhTCR BOB23854WB_1

description:
BOB23854WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB23838WB_1

description:
BOB23838WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: LNP sample 1 [E4]


title: AmB sample 3 [B6]

value: Amphotericin 0.5 ug/mL


title: rhTCR BOB23735WB_1

description:
BOB23735WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB2538WB_1

description:
BOB2538WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: AmB sample 2 [B4]


title: AmB sample 1 [B3]


title: rhTCR BOB23622WB_1

description:
BOB23622WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB23438WB_1

description:
BOB23438WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB2335WB_1

description:
BOB2335WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB23467WB_2

description:
BOB23467WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB23351WB_2

description:
BOB23351WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB23249WB_2

description:
BOB23249WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: LNP sample 2 [E5]


title: rhTCR BOB22919WB_2

description:
BOB22919WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB23865WB_1

description:
BOB23865WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB22745WB_1

description:
BOB22745WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB22646WB_1

description:
BOB22646WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: E3H150m_rep6_MGF_leaf

city: Yokohama

first: motoaki

last: seki

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

institute: RIKEN

data_processing:
base-calling:RTA and bcl2fastq
adapter trim: trimmomatic
alignment: HISAT2
aligned reads count: featureCounts
normalize: DESeq2
Assembly: ITAG4.0
Supplementary files format and content: Tab-delimited text files includes raw counts for each sample
Supplementary files format and content: Tab-delimited text files include normalized count values for each sample

organism: Solanum lycopersicum

source_name: leaf

growth_protocol: Seeds of a tomato (Solanum lycopersicum L.) cultivar, “Micro-Tom” were grown in pots containing horticultural cray granule soil at 22 °C with a 16 h light (110 to 140 µmol m-2 s-1 photon flux density) / 8 h dark cycle.

extract_protocol:
Total RNAs were extracted using purelink Plant RNA  Reagent (Thermo Fisher Scientifc Inc., Waltham, MA,  USA).
The sequencing library was prepared using the Lasy-Seq method (Kamitani et al. 2019). Specifically, 200 ng of total RNA was used per sample.

treatment_protocol: Sixteen-day-old plants grown in pots were used for ethanol pretreatment. The bottoms of the pots were dipped into 20 mM ethanol solution and kept for 3 days. After ethanol pretreatment, the pots were placed in an air incubator set at 50 °C and maintained for the indicated time periods as heat stress treatment. During the heat stress treatment, the pots were electrically rotated in the air incubator to avoid the local effect. After the heat stress treatment, the pots were returned to the growth room and maintained for the indicated time periods.

value: leaf


title: rhTCR BOB22644WB_1

description:
BOB22644WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB22606WB_1

description:
BOB22606WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: E3H150m_rep3_MGF_leaf


title: E3H150m_rep2_MGF_leaf


title: rhTCR BOB2288WB_1

description:
BOB2288WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB22600WB_1

description:
BOB22600WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: E3H150m_rep4_MGF_leaf


title: rhTCR BOB2254WB_1

description:
BOB2254WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB22543WB_2

description:
BOB22543WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: E3H150m_rep1_MGF_leaf


title: rhTCR BOB22492WB_1

description:
BOB22492WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB22461WB_1

description:
BOB22461WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: E3H150m_rep5_MGF_leaf


title: W3H150m_rep6_MGF_leaf


title: rhTCR BOB22394WB_2

description:
BOB22394WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: W3H150m_rep5_MGF_leaf


title: W3H150m_rep4_MGF_leaf


title: W3H150m_rep3_MGF_leaf


title: rhTCR BOB22386WB_2

description:
BOB22386WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB22190WB_1

description:
BOB22190WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: CAF3

city: Shijiazhuang

first: yan

last: zhao

address: Jiankang Road No.12

institute: The Fourth Hospital of Hebei Medical University

description: Gene expression with cancer

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4*180k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CAF

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: cancer-associated fibroblasts

tag: patient diagnosis

value: lung adenocacinoma


title: CAF2

description: Gene expression with cancer

tag: cell type


title: NF1

description: Gene expression with non-cancer

source_name: fibroblasts from paired normal tissue

value: fibroblasts


title: rhTCR BOB21945WB_2

description:
BOB21945WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: E3H150m_rep5_MGF

source_name: fruit

value: fruit

tag: treatment


title: rhTCR BOB21741WB_1

description:
BOB21741WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: W3H150m_rep2_MGF_leaf


title: rhTCR BOB22081WB_1

description:
BOB22081WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: W3H150m_rep1_MGF_leaf


title: CAF1

description: Gene expression with cancer


title: rhTCR BOB22048WB_1

description:
BOB22048WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: E3H150m_rep2_MGF


title: NF3

description: Gene expression with non-cancer


title: E3H150m_rep4_MGF


title: NF2

description: Gene expression with non-cancer


title: E3H150m_rep1_MGF


title: rhTCR BOB21594WB_1

description:
BOB21594WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: E3H150m_rep3_MGF


title: rhTCR BOB21695WB_1

description:
BOB21695WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: W3H150m_rep6_MGF


title: rhTCR BOB21735WB_3

description:
BOB21735WB_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB21401WB_1

description:
BOB21401WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB21539WB_2

description:
BOB21539WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB21370WB_2

description:
BOB21370WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: W3H150m_rep3_MGF


title: W3H150m_rep4_MGF


title: rhTCR BOB21581WB_1

description:
BOB21581WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB21321WB_2

description:
BOB21321WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: W3H150m_rep5_MGF


title: W3H150m_rep2_MGF


title: rhTCR BOB21287WB_1

description:
BOB21287WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: W3H150m_rep1_MGF


title: Whole brain, 24m, rep 2 [ONT]

city: Göttingen

first: Nisha

last: Hemandhar Kumar

address: Humboldtallee 23

department: Institute for Neuro and Sensory Physiology

country: Germany

institute: University Medical Center Goettingen

data_processing:
RNA-seq reads were aligned to the GRCm39.103 genome assembly using minimap2 v2.24
Assembly: GRCm39.103

source_name: Whole brain

extract_protocol:
RNA was extracted from a total of 8 biological samples, corresponding to 4 young-adult samples (6-month, brain hemisphere, from 4 males), 4 aged (24-month, brain hemisphere, from 4 males). Raw data were procured from MiniON  sequencing
NEBNext Ultra II directional polyA+

value: Whole brain

tag: Sex

value: Male

tag: age

value: 24 months


title: Whole brain, 24m, rep 4 [ONT]


title: Whole brain, 24m, rep 3 [ONT]


title: rhTCR BOB21073WB_2

description:
BOB21073WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB21250WB_1

description:
BOB21250WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB21135WB_1

description:
BOB21135WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: Whole brain, 6m, rep 4 [ONT]

value: 6 months


title: Whole brain, 24m, rep 1 [ONT]


title: Whole brain, 6m, rep 2 [ONT]


title: rhTCR BOB21107WB_2

description:
BOB21107WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: Whole brain, 6m, rep 1  [ONT]


title: rhTCR BOB2101WB_1

description:
BOB2101WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB21034WB_1

description:
BOB21034WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: Whole brain, 6m, rep 3 [ONT]


title: rhTCR BOB21033BC

description:
BOB21033BC
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: 143B model treated with B6H12

city: Stanford

first: Yiyun

last: Chen

state: California

address: 265 Campus Dr Room G2105

department: Stanford Cancer Institute

institute: Stanford University

data_processing:
Reads were aligned and quantified with Cell Ranger (10x GENOMICS) using the standard workflow, with the reference transcriptomes GRCh38 for human and mm10 for mouse.
The Cell Ranger output was imported into R using Seurat 4.2.0. The following filters were applied using the subset function to select for live cells: nFeature_RNA > 200 & nFeature_RNA < 5000; percent mitochondrial reads < 5%.
The data matrix was normalized with NormalizeData and scaled with Seurat.
Differential expression analysis, clustering, and UMAP dimensionality reduction analysis were performed on the resulting data matrix using Seurat.
Assembly: hg38+mm10
Supplementary files format and content: Gene expression matrix in h5 format.
Supplementary files format and content: Seurat objects of all single cells passing QC, T cell and macrophage subsets.

organism:
Homo sapiens
Mus musculus

source_name: NOD/SCID/IL2rγ-/- (NSG) mice; no T cells

growth_protocol: 1x10^6 143B human osteosarcoma cells were engrafted into the tibia periosteum of NSG mice. Tumors were harvested after 21 days of growth.

extract_protocol:
Pooled like-treated dissociated tumor single-cell suspensions from the 143B osteosarcoma model described above were sorted for live cells using a Live/Dead stain at the Stanford Shared FACS facility.
Single-cell RNAseq libraries were prepared using the Chromium Next GEM Single Cell 5' v2 platform (10x GENOMICS). Libraries were sent to Novogene for sequencing on a NovoSeq S4 lane (PE150) with approximately 30,000 mean reads per cell.

treatment_protocol: Mice were injected intravenously with no T cells or 4x10^6 human mock T cells, 47WT-Her2.BBz, or 47E-Her2.BBz CAR T cells on day 13 of tumor growth. Mice were then injected intraperitoneally with either PBS (control) or B6H12 (anti-CD47; 250 ug/dose) on days 15 and 19 of tumor growth. Tumors were harvested and dissocaited into single-cell suspensions on day 21 of tumor growth. Each of the 8 treatment arms consisted of n=3 mice. After tumor dissociation, like-treated samples were pooled for downstream processing and sequencing.

value: tumor

value: human tumor, human T cell, mouse myeloid

value: No T cells + B6H12


title: 143B model treated with PBS

value: No T cells + PBS


title: rhTCR BOB20978WB_2

description:
BOB20978WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR

value: blood


title: 143B model treated with 47WT-Her2.BBz CAR T cells + B6H12

source_name: NOD/SCID/IL2rγ-/- (NSG) mice; 47TW-Her2.BBz human T cells

value: 47WT-Her2.BBz CAR T cells + B6H12


title: rhTCR BOB20948WB_3

description:
BOB20948WB_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB20995WB_2

description:
BOB20995WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB21170WB_1

description:
BOB21170WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB20884WB_1

description:
BOB20884WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: 143B model treated with 47WT-Her2.BBz CAR T cells + PBS

source_name: NOD/SCID/IL2rγ-/- (NSG) mice; 47WT-Her2.BBz human T cells

value: 47WT-Her2.BBz CAR T cells + PBS


title: E3H150m_rep6_MGF


title: 143B model treated with 47E-Her2.BBz CAR T cells + PBS

source_name: NOD/SCID/IL2rγ-/- (NSG) mice; 47E-Her2.BBz human T cells

value: 47E-Her2.BBz CAR T cells + PBS


title: rhTCR BOB20862WB_1

description:
BOB20862WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: 143B model treated with 47E-Her2.BBz CAR T cells + B6H12

value: 47E-Her2.BBz CAR T + B6H12


title: rhTCR BOB21204WB_2

description:
BOB21204WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB20877WB_1

description:
BOB20877WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB20812WB_1

description:
BOB20812WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB20837WB_1

description:
BOB20837WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB20817WB_1

description:
BOB20817WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: Vector_RiboSeq

city: Guangzhou

first: Shuibin

last: Lin

state: China

address: Zhongshan 2nd road, Guangzhou

department: Clincial for Translational Medicine

institute: The First Affliliated Hospital, Sun Yat-sen University

description:
small RNA
Ribo-seq_reads.txt

data_processing:
Library strategy: Ribo-seq
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Fragments per kilo base per million mapped reads (FPKM) using edgeR.
For Ribo-Seq data analysis, adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases, respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the human reference genome (hg38) using bowtie with a maximum one mismatch allowed.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015). The read counts of tRNA are normalized as reads per million (RPM) by the total number of small RNA reads that are matched to tRNAs in each sample.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Polyribosome_mRNA_expression.txt: Text file of RNA-seq includes the FPKM values for every gene.
Supplementary_files_format_and_content: Ribo-seq_reads.txt: Text file of Ribo-seq includes the FPKM values for every gene.
Supplementary_files_format_and_content: TRAC-seq_expression.txt: Text file of TRAC-seq represents the ratio and cleavage score for every tRNA in each sample.

source_name: Nasopharyngeal carcinoma 5-8F cells

growth_protocol: Human 5-8F cells were maintained in RPMI-1640 (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco, USA). Cells were grown in a 5% CO2 cell culture incubator at 37℃.

extract_protocol:
RNA was extracted according to TRIzol protocol. Small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set.

treatment_protocol: METTL1 was knocked out by sgRNA.

value: Nasopharyngeal carcinoma cell line

tag: genotype

value: Wild type

tag: sample type

value: Ribo-seq


title: 143B model treated with mock T cells + PBS

source_name: NOD/SCID/IL2rγ-/- (NSG) mice; mock human T cells

value: Mock T cells + PBS


title: rhTCR BOB20842WB_1

description:
BOB20842WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB20810WB_1

description:
BOB20810WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: Vector_Input_for_RiboSeq

description:
PolyA mRNA+lncRNA
Ribo-seq_reads.txt


title: 143B model treated with mock T cells + B6H12

value: Mock T cells + B6H12


title: Knockout_Input_for_RiboSeq

description:
PolyA mRNA+lncRNA
Ribo-seq_reads.txt

value: METTL1 knockout


title: Knockout_RiboSeq

description:
small RNA
Ribo-seq_reads.txt


title: rhTCR BOB20758WB_2

description:
BOB20758WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB20722WB_2

description:
BOB20722WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB20761WB_2

description:
BOB20761WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB20694WB_1

description:
BOB20694WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB23664WB_2

description:
BOB23664WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB20701WB_1

description:
BOB20701WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: Melanocyte Stem Cells (Sample 1)

city: Birmingham

first: Melissa

middle: L

last: Harris

state: AL

address: 1720 University Blvd

institute: University of Alabama at Birmingham

data_processing:
All sequencing files were aligned to the mm10 transcriptome using Cell Ranger (v5.0.1). on the UAB high-performance cluster computer (Cheaha).
Assembly: mm10
Supplementary files format and content: filtered bc matrix

source_name: Skin (Dermis)

extract_protocol:
Flow Sorted Kit+/Cd45- (McSCS) and single cell suspension for dermis sample
Cell suspension, 10x barcoded gel beads, and oil (all were included in 10xGenomics Chromium Next GEM Single Cell 3' Kit v3.1 PN 1000268)were loaded into 10x Chromium™ Single Cell Chip to capture single cells into nanoliter-scale oil droplets by 10xChromium™ Controller and generate Gel Bead-In-EMulsions (GEMs). cDNA from single cells were synthesized and barcoded by incubation of the GEMs in a thermocycler machine, and then purified from GEMs by DynaBeads (10xGenomics PN 2000048). cDNA was pre-amplified by PCR to generate sufficient mass for sequencing library construction. The single cell cDNA libraries were constructed by following 10xGenomics 3’ NextGem 3.1 version kit instruction, briefly by following steps of cDNA fragmentation, end repair & A-tailing, and size selection by SPRIselect beads (Beckman Coulter, PN B23318),adaptor ligation, and sample index PCR amplification, and then SPRIselect beads size selection again. The final constructed 3’-biased single cell libraries were sequenced by Illumina Nextseq500 machine, targeting 20,000 read pairs/cell. and the sequencing cycles consisted of 28bp for read 1, 91bp for read 2 and 10bp for i7 and i5

value: Skin (Dermis)

tag: mouse strain

value: Melanocyte Stem Cells

value: 9 weeks

value: WT

value: Female


title: rhTCR BOB20540WB_2

description:
BOB20540WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: Melanocyte Stem Cells (Sample 3)


title: Melanocyte Stem Cells (Sample 2)


title: Dermal Cells


title: LI_m331_TCR

city: Aachen

first: Hieu

middle: Trong

last: Nguyen

address: Pauwelstrasse 30

department: Institut für Molekulare Medizin

institute: RWTH Aachen University Hospital

description: adaptive T cell co transfer (Tregs and Tnaive) in Rag2 KO, Tregs were generated in vitro before injection, replicate 2, TCR

library_source: genomic single cell

data_processing:
The hashtag library was demultiplexed using CellRanger software (version 7.1.0). Raw data was demultiplexed with cellranger mkfastq (10x Genomics v7.1.0) to generate fastq files. The fastq files were then analyzed by the cellranger multi with default parameters using refdata-gex-mm10-2020-A as reference. Subsequent data analysis was conducted by our custom pipeline written in R (v4.2.1). We used Seurat (v4.1.1) to perform quality controls, data scaling and normalization, cell filtering, cell cycle scoring, PCA /UMAP dimension reductions and data integration. Briefly, any cells whose nCount_RNA < 100 or nFeature_RNA < 50 were excluded. Gene expression matrices were scaled and normalized to remove technical cell-specific variation. Doublet detection was done by DoubletFinder (v.2.0.3, PMID: 30954475) with default parameters and prior estimate percentage of doublets provided by 10X Genomics. Cell cycle was scored by default built-in function of Seurat, however, we did not perform cell cycle regression since the effect was negligible. For dimensional reductions, gene expression matrices were transformed to top-25 principal components. These principal components were subsequently used to transformed to 2D UMAP coordinates. Cells were clustered by Seurat’s built-in algorithm with a resolution of 0.5. Differential gene expression between clusters were conducted by Wilcoxon test and Benjamin-Hochberg correction to remove false discovery rate.Cell type annotation was done manually based on the differentially expressed genes of each cluster, and we kept only clusters of interest for further analysis.
Assembly: mm10
Supplementary files format and content: CSV
Supplementary files format and content: H5

source_name: large intestine

extract_protocol:
T cells were sorted from LI 7 to 8 weeks after adoptive T cell transfer as CD45+TCRβ+CD45.2+Foxp3/GFP+ or CD45+TCRβ+CD45.1+Foxp3/hCD2 Tregs, or CD45+TCRβ+CD45.1+ Teff with FACSAria II (Becton Dickenson). Sorted cells were encapsulated into droplets with the ChromiumTM Controller (10x Genomics) and processed following manufacturer’s specifications. Transcripts captured in all the cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 10 bp unique molecular identifier (UMI).
cDNA libraries were generated using the Chromium™ Next GEM Single Cell 5’ Reagent Kit v1 or v2 (10x Genomics) following the detailed protocol provided by the manufacturer. Libraries were quantified by Quantus (Promega) and quality was checked using TapeStatoin 4200 with High Sensitivity DNA kit (Agilent). Libraries were sequenced with NextSeq 500 platform (NextSeq 500/550 Mid Output Kit v2.5 (150 cycles), Illumina)  with paired-end mode or NovaSeq 6000 platform (SP Reagent Kit v1.5, Illumina) in 50 bp paired-end mode.

value: large intestine


title: rhTCR BOB20533WB_2

description:
BOB20533WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR

value: blood


title: rhTCR BOB20461WB_2

description:
BOB20461WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: LI_GFP_m3_VDJ

description: adaptive T cell co transfer (Tregs and Tnaive) in Rag2 KO, in vitro expansion of Tregs before injection, replicate 3, TCR


title: LI_m330_TCR

description: adaptive T cell co transfer (Tregs and Tnaive) in Rag2 KO, Tregs were generated in vitro before injection, replicate 1, TCR


title: rhTCR BOB20432WB_2

description:
BOB20432WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: LI_GFP_m3_GEX

description: adaptive T cell co transfer (Tregs and Tnaive) in Rag2 KO, in vitro expansion of Tregs before injection, replicate 3, GEX


title: rhTCR BOB20414WB_1

description:
BOB20414WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: LI_GFP_m2_GEX

description: adaptive T cell co transfer (Tregs and Tnaive) in Rag2 KO, in vitro expansion of Tregs before injection, replicate 2, GEX


title: LI_GFP_m2_VDJ

description: adaptive T cell co transfer (Tregs and Tnaive) in Rag2 KO, in vitro expansion of Tregs before injection, replicate 2, TCR


title: LI_GFP_m1_GEX

description: adaptive T cell co transfer (Tregs and Tnaive) in Rag2 KO, in vitro expansion of Tregs before injection, replicate 1, GEX


title: rhTCR BOB20035_2

description:
BOB20035_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB20353WB_1

description:
BOB20353WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: LI_GFP_m1_VDJ

description: adaptive T cell co transfer (Tregs and Tnaive) in Rag2 KO, in vitro expansion of Tregs before injection, replicate 1, TCR


title: ZIF-8, rep2

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
Illumina NextSeq 500 using v3 chemistry. NextSeq Software: Control v4.0.2.7, RTA 2.4.11. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Paired-end RNA-seq data was used to quantify transcripts from the mm10 mouse assembly with the Ensembl version 101 annotation using Salmon version 1.3.0 Gene level summaries were prepared using tximport version 1.20.0 running under R version 4.1.0
Assembly: mm10 with ensembl version 101 annotation
Supplementary files format and content: seban_intCt.txt.gz is a tab delimited text file of integer count data
Supplementary files format and content: seban_l2tpm.txt.gz is a tab delimited text file of log 2 tpm with a plus1 offset

source_name: brachial lymph node

extract_protocol:
RNA MiniPrep Kit (QIAGEN)
RNAseq libraries were created from 400ng of total RNA using the NEBNext UltraII Directional RNA Library Prep kit (New England Biolabs) using half volume reagents and 17 cycles of PCR. Illumina library quality was confirmed using the Fragment Analyzer and qPCR

treatment_protocol: Mice were injected with RBD-trimer (3 ug), ZIF-8 or GR-ZIF (containing 0.9  ug of RBD-trimer) at week 0, 3 and 6. RNA was extracted from harvested brachial lymph node (3 biological replicate/condition) at week 5, after the first booster dose.

value: brachial lymph node

value: ZIF-8 immunization


title: rhTCR BOB20066_2

description:
BOB20066_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: ZIF-8, rep3


title: rhTCR BOB20101_4

description:
BOB20101_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB20029_2

description:
BOB20029_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: LI_m331_GEX

description: adaptive T cell co transfer (Tregs and Tnaive) in Rag2 KO, Tregs were generated in vitro before injection, replicate 2, GEX


title: rhTCR BOB200148_2

description:
BOB200148_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: PBS, rep2

value: PBS immunization


title: PBS, rep3


title: PBS, rep1


title: rhTCR BOB20016_4

description:
BOB20016_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB200136_3

description:
BOB200136_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB20510WB_2

description:
BOB20510WB_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR