title: HFF-1, DUX4, CUT&Tag, HSV-1 GFP 4h.p.i., Replicate1

value: HSV-1 infection


title: HFF-1, DUX4, CUT&Tag, HSV-1 GFP 2h.p.i., Replicate1

status: Public on Jun 11 2023

type: SRA

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

library_source: genomic

data_processing:
For CUT&Tag, sequencing reads were mapped to the hg19 genome using bowtie2 (Langmead et al., 2012). The bigWig tracks were created by extending reads to 200, collapsing them into pileups, and normalizing to reads per million. Peaks were called using MACS2, using a cut off q-value<0.05, and IgG samples as control files. Filtering peaks using Bedtools to subtract peaks of 2h.p.i timepoint and subsequent filtering for peaks occuring in two or more consecutive timepoints.
For RNA-seq, Sequencing reads were aligned to hg19 and the HSV-1 strain 17 genome (the fasta file is part of this GEO entry) separately using hisat2 (Kim et al, 2015). Readcounts per gene were quantified using quasR (Gaidatzis et al, 2015) using a RefSeq gtf file for hg19, and the gtf file that is part of this GEO entry. For the HSV-1 gene counting, the bam and gtf files were both strand-separaed before counting.
Assembly: hg19, HSV1
Supplementary files format and content: bigwig, fasta, gtf, tsv
Library strategy: Cut & Tag

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: DMEM, 10% fetal bovine serum, 1mM GlutaMAX, 1mM HEPES and 1x penicillin/streptomycin. Cells were cultured at 37°C / 5% CO2.

extract_protocol:
For CUT&Tag, we used the CUT&Tag Assay Kit (Active Motif) using 2.5ug Dux4 antibody (E5-5 Abcam) or 2.5ug rabbit IgG antibody (Cell Signalling Technology)
For RNA-seq, cells were resuspended in Trizol LS (Thermo Fisher) and RNA isolated using the Zymo Clean and Concetrator Kit (Zymo).
PolyA enriched RNA-sequencing library were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Infections were done in PBS, 0.1% Glucose, 1% fetal bovine serum. After 1h remaining virus was washed away with low pH Wash buffer (40mM Citic acid, 10mM KCl, 135 mM NaCl, pH 3).

tag: cell line

tag: genotype

value: wt

tag: treatment

tag: timepoint


title: 20573

type: RNA

city: Heidelberg

first: Chang

last: Lu

address: Im Neuenheimer Feld 130

institute: Heidelberg University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.50.0).

molecule: total RNA

source_name: LPS stimulated momocytes from CAD patients

label_protocol: Standard Illumina protocol

extract_protocol: total RNA was isolated using Illumina TotalPrep RNA Amplification Kit (Illumina, San Diego, CA, USA) and cDNA was produced.Quality control was performed with GenomeStudio.

tag: cell type

value: monocytes

tag: Sex

value: male

tag: age


title: HFF-1, DUX4, CUT&Tag, HSV-1 GFP 12h.p.i., Replicate2


title: 20510


title: lymph node FFPE sample of Lung cancer [22M000080]

city: Shanghai

first: Leiqin

last: Liu

address: 320 Yueyang Road

country: China

institute: CAS Center for Excellence in Molecular Cell Science (CEMCS)

data_processing:
Approximately eight gigabases of RRBS data were obtained for each library. Adapter and inline barcode sequences were removed using Trim Galore (version 0.6.2).
The trimmed reads were mapped to the human genome version hg19 using BSMAP, with options “-q 20 -f 5 -r 0 -v 0.05 -s 16 -S 1”.
The resulting BAM files were converted to mHap files using the mHapTools.
CpG methylation metrics were extracted using the tool MethylDackel developed by Devon Ryan (https://github.com/dpryan79/MethylDackel).
We filtered out samples with low bisulfite conversion rates (< 99%), low mapping ratios (< 50%), and insufficient numbers of CpGs (< 0.8 million) at 10x coverage.
Assembly: hg19
Supplementary files format and content: The bedGraph contains the following 6 columns: 1) The chromosome. 2) The start coordinate. 3) The end coordinate. 4) The methylation percentage rounded to an integer. 5) The number of alignments/pairs reporting methylated bases. 6) The number of alignments/pairs reporting unmethylated bases.
Supplementary files format and content: The mhap contains the following 6 columns: 1) The chromosome. 2) The start coordinate, also the first CpG site position. 3) The end coordinate, also the last CpG site position. 4) The haplotype status with 1 for methylated sites, 0 for unmethylated ones. 5) Number of DNA methylation haplotypes. 6) Strand.

source_name: lymph node

extract_protocol:
Genomic DNA was isolated from FF tissues and FFPE sections using the TIANamp Genomic DNA kit (TIANGEN, Beijing, China) and TIAamp FFPE DNA kit (TIAGEN, Beijing, China), respectively, per the manufacture's recommendations.
Genomic DNA (10-50 ng) of FFPE samples was treated with shrimp alkaline phosphatase (New England Biolabs, USA), and the dephosphorylated DNA was used for subsequent MspI digestion, end-repair, and Illumina adapter ligation in "the same tube" without DNA purification. After sodium bisulfite conversion and PCR enrichment, the FFPE-RRBS libraries were subjected to 150 cycles of paired-end sequencing runs on a NovaSeq 6000 platform (Illumina, USA) with 15% of PhiX spike-in. For FF tissues, RRBS libraries were constructed utilizing 10-20 ng DNA without the SAP treatment, but the libraries were sequenced as described above.

tag: tissue

value: lymph node

tag: gender

value: M

tag: clinical prognosis

value: Lung cancer

tag: specimen type

value: Formalin fixed paraffin-embedded tissue

tag: dataset

value: Test set


title: lymph node FFPE sample of Head and neck neoplasm [22M000196]

value: Head and neck neoplasm


title: Pleura FFPE sample of Esophagus cancer [ST_HZ_20230215_9_16]

source_name: Pleura

value: Pleura

value: Esophagus cancer

value: wgbs


title: abdominal cavity FFPE sample of Stomach cancer [22M000075]

source_name: abdominal cavity

value: abdominal cavity

value: F

value: Stomach cancer


title: Ascites FFPE sample of Ovarian cancer [ST_HZ_20230215_7_19]

source_name: Ascites

value: Ascites

value: Ovarian cancer


title: FFPE sample of Breast cancer [ST_HZ_20230215_5_6]

source_name: Unknown

value: Unknown

value: Breast cancer


title: lymph node FFPE sample of Thyroid cancer [22M000072]

value: Thyroid cancer


title: lymph node FFPE sample of Ovarian cancer [22M000077]

value: lymph node


title: dorsum FFPE sample of Lung cancer [22M000082]

source_name: dorsum

value: dorsum

value: M


title: FFPE sample of Breast cancer [ST_HZ_20230215_5_5]

value: Formalin fixed paraffin-embedded tissue


title: liver FFPE sample of Lung cancer [22M000081]

source_name: liver

value: liver

value: unknown

value: Lung cancer

value: Test set


title: neck FFPE sample of Head and neck neoplasm [22M000200]

source_name: neck

value: neck

value: Head and neck neoplasm


title: lymph node FFPE sample of Head and neck neoplasm [22M000068]


title: lymph node FFPE sample of Stomach cancer [22M000194]

value: F


title: liver FFPE sample of Colon and rectum cancer [22M000062]

value: Colon and rectum cancer


title: liver FFPE sample of Liver and gallbladder [22M000064]

value: Liver and gallbladder


title: hydrothorax FFPE sample of Stomach cancer [22M000102]

source_name: hydrothorax

value: hydrothorax

value: Stomach cancer


title: dorsum FFPE sample of Thyroid cancer [22M000079]


title: lymph node FFPE sample of Lung cancer [22M000078]


title: lymph node FFPE sample of Head and neck neoplasm [22M000073]


title: abdominal cavity FFPE sample of Colon and rectum cancer [22M000063]

value: abdominal cavity


title: chest wall FFPE sample of Ovarian cancer [22M000058]

source_name: chest wall

value: chest wall

value: Ovarian cancer


title: abdominal cavity FFPE sample of Ovarian cancer [22M000074]


title: neck FFPE sample of Lung cancer [22M000076]


title: neck FFPE sample of Head and neck neoplasm [22M000061]


title: lymph node FFPE sample of Head and neck neoplasm [22M000071]

value: lymph node


title: ovary FFPE sample of Lung cancer [22M000048]

source_name: ovary

value: ovary


title: small intestine FFPE sample of Lung cancer [22M000049]

source_name: small intestine

value: small intestine

value: M

value: Formalin fixed paraffin-embedded tissue


title: lymph node FFPE sample of Head and neck neoplasm [22M000057]


title: liver FFPE sample of Colon and rectum cancer [22M000050]

value: liver


title: lung FFPE sample of Lung cancer [22M000044]

source_name: lung

value: lung

value: Lung cancer

value: Test set


title: lymph node FFPE sample of Stomach cancer [22M000054]


title: lymph node FFPE sample of Head and neck neoplasm [22M000055]

value: Head and neck neoplasm


title: lymph node FFPE sample of Cervix cancer [22M000052]

value: F

value: Cervix cancer


title: bone FFPE sample of Stomach cancer [22M000029]

source_name: bone

value: bone


title: lymph node FFPE sample of Colon and rectum cancer [22M000046]

value: Colon and rectum cancer


title: neck FFPE sample of Head and neck neoplasm [22M000056]

value: neck


title: neck FFPE sample of Head and neck neoplasm [22M000020]

value: unknown


title: liver FFPE sample of Liver and gallbladder [22M000025]

value: Liver and gallbladder


title: lymph node FFPE sample of Stomach cancer [22M000024]

value: lymph node

value: Stomach cancer


title: bone FFPE sample of Lung cancer [22M000032]


title: liver FFPE sample of Head and neck neoplasm [22M000043]


title: lymph node FFPE sample of Colon and rectum cancer [22M000008]


title: abdominal cavity FFPE sample of Lung cancer [22M000006]

value: abdominal cavity


title: bone FFPE sample of Ovarian cancer [22M000009]

value: Ovarian cancer


title: liver FFPE sample of Esophagus cancer [22M000014]

value: M

value: Esophagus cancer

value: Formalin fixed paraffin-embedded tissue


title: liver FFPE sample of Liver cancer [22M000030]

value: liver

value: Liver cancer


title: lymph node FFPE sample of Liver and gallbladder [22M000028]

value: Test set


title: lymph node FFPE sample of Head and neck neoplasm [22M000021]

value: Head and neck neoplasm


title: brain FFPE sample of Lung cancer [22M000018]

source_name: brain

value: brain

value: Lung cancer


title: liver FFPE sample of Liver and gallbladder [22M000016]


title: lung FFPE sample of Ovarian cancer [22M000017]

value: lung

value: F


title: brain FFPE sample of Thyroid cancer [22M000004]

value: Thyroid cancer


title: neck FFPE sample of Head and neck neoplasm [22M000015]

value: neck


title: left thigh FFPE sample of Lung cancer [22M000019]

source_name: left thigh

value: left thigh


title: lymph node FFPE sample of Head and neck neoplasm [22M000011]

value: lymph node


title: lymph node FFPE sample of Liver cancer [22A017687]


title: lung FFPE sample of Lung cancer [22T005880]


title: brain FFPE sample of Lung cancer [22A005867]


title: lymph node FFPE sample of Stomach cancer [21T012031]

value: Stomach cancer


title: lymph node FFPE sample of Head and neck neoplasm [22T003632]


title: lung FFPE sample of Lung cancer [21A016128]


title: 20590

source_name: LPS stimulated momocytes from CAD patients

value: monocytes

value: male


title: abdominal cavity FFPE sample of Stomach cancer [22M000005]

value: abdominal cavity

value: M


title: abdominal cavity FFPE sample of Lung cancer [21A000124]

value: Formalin fixed paraffin-embedded tissue


title: liver FFPE sample of Lung cancer [193144]

value: liver

value: unknown


title: lymph node FFPE sample of Lung cancer [22M000002]

source_name: lymph node

value: Test set


title: lymph node FFPE sample of Head and neck neoplasm [22M000003]

value: Head and neck neoplasm


title: ovary FFPE sample of Colon and rectum cancer [22A017521]

value: ovary

value: Colon and rectum cancer


title: neck FFPE sample of Head and neck neoplasm [21A003923]


title: liver FFPE sample of Colon and rectum cancer [193334A2]

value: F


title: Esophagus Squamous Cell Carcinoma [21T002990]

source_name: Lymphnode

value: Lymphnode

value: Esophagus cancer

tag: clinical stage

value: Ⅲ

tag: sample source

value: Affiliated Hangzhou First People's Hospital,Zhejiang University School of Medicine

tag: site label

value: Metastatic

value: Validation set


title: Esophagus Squamous Cell Carcinoma [18A006451]

value: Unknown


title: Esophagus Squamous Cell Carcinoma [21T002988]


title: Esophagus Squamous Cell Carcinoma [18A006449]


title: Ovarian cancer(subtype unknown) [21T007766]

value: Ascites

value: Ovarian cancer

value: Ⅳ

value: Affiliated Hangzhou Cancer Hospital,Zhejiang University School of Medicine


title: Ovarian Serous Carcinoma [21T007762]

source_name: Abdominal cavity

value: Abdominal cavity

value: Formalin fixed paraffin-embedded tissue


title: Ovarian Serous Carcinoma [21T007764]

source_name: Ascites


title: Ovarian High-grade Serous Carcinoma [21T007752]

value: unknown


title: Ovarian Serous Carcinoma [21T007765]

source_name: Hydrothorax

value: Hydrothorax


title: Esophagus Squamous Cell Carcinoma [21T002985]


title: lymph node FFPE sample of Cervix cancer [20A040925]

value: lymph node

value: Cervix cancer

value: Test set


title: Ovarian High-grade Serous Carcinoma [21T007749]

value: Lymphnode

value: F


title: Esophagus Adenocarcinoma [21T007735]

value: Esophagus cancer

value: Ⅲ

value: Affiliated Hangzhou First People's Hospital,Zhejiang University School of Medicine


title: Ovarian cancer(subtype unknown) [21T007681]

source_name: Unknown

value: Unknown

value: Metastatic

value: Validation set


title: Esophagus Squamous Cell Carcinoma [21T007737]


title: Cervix Adenocarcinoma [21T007679]


title: Cervix Squamous Cell Carcinoma [21T007680]


title: Cervix Squamous Cell Carcinoma [21T007676]


title: Cervix Squamous Cell Carcinoma [21T007677]


title: Ovarian High-grade Serous Carcinoma [21T007665]

value: Ovarian cancer

value: Ⅳ


title: Cervix Squamous Cell Carcinoma [21T007671]


title: Ovarian High-grade Serous Carcinoma [21T007767]

value: Affiliated Hangzhou Cancer Hospital,Zhejiang University School of Medicine


title: Hypopharynx Squamous Cell Carcinoma [21T000239]

source_name: Underskin

value: Underskin

value: M

value: Head and neck neoplasm

value: Formalin fixed paraffin-embedded tissue


title: Ovarian Serous Carcinoma [21T000240]

source_name: Pelvic cavity

value: Pelvic cavity


title: Ovarian Serous Carcinoma [21T000233]

value: Abdominal cavity


title: Esophagus Squamous Cell Carcinoma [21T000232]

value: Lymphnode

value: unknown


title: Ovarian Serous Carcinoma [21T007666]

value: F


title: Esophagus Squamous Cell Carcinoma [21T000224]

source_name: Pleura

value: Pleura

value: Esophagus cancer


title: Esophagus Squamous Cell Carcinoma [21T000227]


title: Esophagus Squamous Cell Carcinoma [21T000223]

value: lung


title: Colon and rectum   Adenocarcinoma [21T000215]

value: Colon and rectum  cancer

value: Ⅲ

value: Metastatic


title: Colon and rectum   Adenocarcinoma [21T000214]

source_name: Stomach

value: Stomach

value: Validation set


title: Liver and gallbladder(subtype unknown) [21T000218]

source_name: Liver

value: Liver

value: Liver and gallbladder

value: Ⅳ

value: Affiliated Hangzhou Cancer Hospital,Zhejiang University School of Medicine


title: Nasopharyngeal Carcinoma [21T000216]

value: M

value: Head and neck neoplasm

value: Formalin fixed paraffin-embedded tissue


title: Colon and rectum   Adenocarcinoma [21T000212]


title: Colon and rectum   Adenocarcinoma [21T000213]

value: Abdominal cavity


title: Breast cancer (subtype unknown) [18A006509]

value: Lymphnode

value: F

value: unknown

value: Breast cancer

value: Affiliated Hangzhou First People's Hospital,Zhejiang University School of Medicine


title: Stomach Adenocarcinoma [21T000208]

value: Stomach cancer

value: Ⅲ


title: Stomach Adenocarcinoma [21T000209]

value: Metastatic


title: Lung Adenocarcinoma [21T000207]

value: Lung cancer

value: Validation set


title: Lung Adenocarcinoma [21T000206]


title: Colon and rectum   Adenocarcinoma [18A006510]

value: Liver

value: Colon and rectum  cancer


title: Cervix Squamous Cell Carcinoma [21T000237]

value: Cervix cancer

value: Ⅳ

value: Affiliated Hangzhou Cancer Hospital,Zhejiang University School of Medicine


title: Lung Adenocarcinoma [21T000204]

value: M

value: Formalin fixed paraffin-embedded tissue


title: Esophagus Squamous Cell Carcinoma [21T000235]

value: Esophagus cancer


title: Papillary Thyroid Carcinoma [21T000226]

value: Unknown

value: F

value: Thyroid cancer


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [21T000202]

source_name: Breast

value: Breast

value: Breast cancer

value: unknown


title: Papillary Thyroid Carcinoma [18A006641]

value: Lymphnode

value: Cancer Hospital of the University of Chinese Academy of Science,Zhejiang Cancer Hospital (ZJCH)

value: Metastatic


title: Papillary Thyroid Carcinoma [18A006643]

value: Validation set


title: Papillary Thyroid Carcinoma [18A006639]


title: Papillary Thyroid Carcinoma [18A006661]


title: Papillary Thyroid Carcinoma [18A006649]


title: Papillary Thyroid Carcinoma [18A006662]


title: Cervix Squamous Cell Carcinoma [21T000229]


title: Ovarian cancer(subtype unknown) [20A040775]

value: Hydrothorax

value: Ovarian cancer


title: Papillary Thyroid Carcinoma [18A006655]


title: Papillary Thyroid Carcinoma [18A006640]


title: Papillary Thyroid Carcinoma [18A006644]


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A040751]


title: Papillary Thyroid Carcinoma [18A006652]


title: Papillary Thyroid Carcinoma [18A006637]


title: Lung Adenocarcinoma [21T000205]

source_name: Left axilla

value: Left axilla

value: Lung cancer

value: Ⅳ


title: Stomach Adenocarcinoma [21T000210]

source_name: Skin

value: Skin

value: M

value: Stomach cancer

value: Affiliated Hangzhou Cancer Hospital,Zhejiang University School of Medicine

value: Formalin fixed paraffin-embedded tissue


title: Papillary Thyroid Carcinoma [18A006653]

value: F

value: Thyroid cancer


title: Esophagus Squamous Cell Carcinoma [20A040745]

source_name: Scalp

value: Scalp

value: Esophagus cancer


title: Esophagus Squamous Cell Carcinoma [20A040744]

value: Liver


title: Esophagus Squamous Cell Carcinoma [20A040763]

value: Metastatic


title: Stomach Adenocarcinoma [20A040788]

value: Validation set


title: Stomach Adenocarcinoma [20A040796]

value: Hydrothorax


title: Papillary Thyroid Carcinoma [18A006659]

value: Lymphnode

value: unknown

value: Cancer Hospital of the University of Chinese Academy of Science,Zhejiang Cancer Hospital (ZJCH)


title: Esophagus Adenocarcinoma [20A040783]

value: Ⅳ


title: Lung Squamous Cell Carcinoma [21T000203]

value: Lung cancer


title: Lung Adenocarcinoma [20A040770]

value: M


title: Colon and rectum  Neuroendocrine Carcinoma [20A040761]

source_name: Ileocecal junction

value: Ileocecal junction

value: Colon and rectum  cancer


title: Lung Adenocarcinoma [20A040762]

source_name: Hip

value: Hip

value: Affiliated Hangzhou Cancer Hospital,Zhejiang University School of Medicine

value: Formalin fixed paraffin-embedded tissue


title: Lung Adenocarcinoma [20A040792]

source_name: Lung

value: Lung


title: Lung Adenocarcinoma [20A040785]

source_name: Lymphnode


title: Lung Squamous Cell Carcinoma [20A040793]


title: Lung Adenocarcinoma [20A040794]


title: Lung Adenocarcinoma [20A040768]


title: Lung Adenocarcinoma [20A040765]

value: F


title: Lung Adenocarcinoma [20A040786]

value: Liver


title: Lung Adenocarcinoma [20A040789]

value: Pleura

value: Metastatic


title: HFF-1, DUX4, CUT&Tag, HSV-1 GFP 2h.p.i., Replicate2

value: wt

value: HSV-1 infection


title: Lung Adenocarcinoma [20A040790]

value: Lymphnode

value: Validation set


title: Lung Adenocarcinoma [20A040757]

value: Unknown

value: unknown


title: Breast Invasive Ductal Carcinoma [20A040772]

source_name: Chest wall

value: Chest wall

value: Breast cancer

value: Ⅳ


title: Lung Squamous Cell Carcinoma [20A040782]

value: Breast

value: M

value: Lung cancer


title: Lung cancer(subtype unknown) [20A040780]

value: Stomach

value: Affiliated Hangzhou Cancer Hospital,Zhejiang University School of Medicine

value: Formalin fixed paraffin-embedded tissue


title: Lung Squamous Cell Carcinoma [20A040771]

value: Lung


title: Breast Invasive Ductal Carcinoma [20A040750]

value: F

value: Ⅲ

value: Metastatic


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A040746]

value: Ⅱ


title: Breast Mucinous Carcinoma [20A040753]

value: Validation set


title: Breast Invasive Ductal Carcinoma [20A040767]

value: Unknown


title: Breast Invasive Ductal Carcinoma [20A040776]


title: Breast cancer (subtype unknown) [20A040747]

value: Lymphnode


title: Breast Invasive Ductal Carcinoma [20A040754]


title: Breast cancer (subtype unknown) [20A040787]


title: Breast Invasive Ductal Carcinoma [20A040749]


title: Breast Invasive Ductal Carcinoma [20A040764]


title: Breast Invasive Ductal Carcinoma [20A040791]


title: Breast Invasive Ductal Carcinoma [20A040756]


title: Breast cancer (subtype unknown) [20A040752]


title: Lung Adenocarcinoma [20A040781]

value: Liver


title: Breast Invasive Ductal Carcinoma [20A040760]

value: Breast cancer

value: unknown


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A040755]


title: Breast Invasive Ductal Carcinoma [20A040777]


title: Hepatocellular Carcinoma [20A040882]

source_name: Abdominal cavity

value: Abdominal cavity

value: Liver and gallbladder

value: Ⅳ


title: Ovarian Serous Carcinoma [20A040883]

value: Pelvic cavity

value: Ovarian cancer


title: Hepatocellular Carcinoma [20A040881]

value: Chest wall

value: M

value: Affiliated Hangzhou Cancer Hospital,Zhejiang University School of Medicine

value: Formalin fixed paraffin-embedded tissue


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A040774]

value: F

value: Ⅲ

value: Metastatic


title: Nasopharyngeal Carcinoma [20A040889]

source_name: Right subaxillary paraspecial mass

value: Right subaxillary paraspecial mass

value: Head and neck neoplasm

value: Validation set


title: Ovarian Serous Carcinoma [20A040885]

source_name: Abdominal wall

value: Abdominal wall


title: Cervix Squamous Cell Carcinoma [20A040887]

value: Lymphnode

value: Cervix cancer


title: Hypopharynx Squamous Cell Carcinoma [20A040891]


title: Nasopharyngeal Carcinoma [20A040890]


title: Cervix Squamous Cell Carcinoma [20A040888]

value: Pleura


title: Nasopharyngeal Carcinoma [20A040897]

value: Liver

value: Ⅳ


title: Hypopharynx Squamous Cell Carcinoma [20A040894]


title: Nasopharyngeal Carcinoma [20A040896]

source_name: Neck

value: Neck


title: Nasopharyngeal Carcinoma [20A040899]


title: Nasopharyngeal Carcinoma [20A040895]


title: Hypopharynx Squamous Cell Carcinoma [20A040898]


title: Nasopharyngeal Carcinoma [20A040900]

source_name: lung

value: lung


title: Colon and rectum   Adenocarcinoma [20A040902]

value: Colon and rectum  cancer


title: Colon and rectum   Adenocarcinoma [20A040901]

value: M

value: Affiliated Hangzhou Cancer Hospital,Zhejiang University School of Medicine


title: Colon and rectum   Adenocarcinoma [20A040903]

value: F

value: Formalin fixed paraffin-embedded tissue


title: Breast Invasive Ductal Carcinoma [20A040766]

source_name: Unknown

value: Unknown

value: Breast cancer

value: Metastatic


title: Colon and rectum   Adenocarcinoma [20A040906]

value: Validation set


title: Colon and rectum   Adenocarcinoma [20A040905]


title: Hepatocellular Carcinoma [20A040879]

value: Liver and gallbladder


title: Cholangiocarcinoma [20A040880]


title: Colon and rectum   Adenocarcinoma [20A040908]


title: Colon and rectum   Adenocarcinoma [20A040909]

source_name: Left iliopsoas muscle

value: Left iliopsoas muscle


title: Colon and rectum   Adenocarcinoma [20A040910]

value: Lymphnode


title: Stomach Squamous Cell Carcinoma [20A040912]

source_name: Stomach

value: Stomach

value: Stomach cancer


title: Colon and rectum  Neuroendocrine Carcinoma [20A040911]

value: Ileocecal junction

value: Ⅳ


title: Hypopharynx Squamous Cell Carcinoma [20A040872]

source_name: Underjaw

value: Underjaw

value: Head and neck neoplasm


title: Stomach Adenocarcinoma [20A040920]

value: Abdominal cavity

value: M


title: Stomach Squamous Cell Carcinoma [20A040916]

source_name: Liver

value: Liver

value: Affiliated Hangzhou Cancer Hospital,Zhejiang University School of Medicine


title: Stomach Neuroendocrine carcinoma [20A040917]

value: Formalin fixed paraffin-embedded tissue


title: Stomach cancer（subtype unknown） [20A040915]

value: F


title: Stomach Adenocarcinoma [20A040919]

value: Metastatic


title: Stomach Adenocarcinoma [20A040918]

value: Abdominal wall

value: Validation set


title: Stomach Adenocarcinoma [20A040914]


title: Esophagus Squamous Cell Carcinoma [20A040922]

value: Unknown

value: Esophagus cancer


title: Hepatocellular Carcinoma [20A040921]

source_name: Adrenal gland

value: Adrenal gland

value: Liver and gallbladder


title: Colon and rectum   Adenocarcinoma [20A040867]

value: Colon and rectum  cancer

value: Ⅲ


title: Colon and rectum   Adenocarcinoma [20A040865]


title: Colon and rectum   Adenocarcinoma [20A040868]


title: Colon and rectum   Adenocarcinoma [20A040864]

source_name: Vagina

value: Vagina

value: Ⅳ


title: Colon and rectum   Adenocarcinoma [20A040866]


title: Colon and rectum   Adenocarcinoma [20A040862]


title: Colon and rectum   Adenocarcinoma [20A040863]


title: Colon and rectum   Adenocarcinoma [20A040859]


title: Colon and rectum   Adenocarcinoma [20A040860]

value: unknown


title: Colon and rectum   Adenocarcinoma [20A040858]

value: M


title: Colon and rectum   Adenocarcinoma [20A040857]


title: Colon and rectum   Adenocarcinoma [20A040861]


title: Colon and rectum   Adenocarcinoma [20A040856]


title: Colon and rectum   Adenocarcinoma [20A040855]


title: Stomach cancer（subtype unknown） [20A040853]

value: Lymphnode

value: Stomach cancer


title: Stomach Adenocarcinoma [20A040852]

value: Abdominal cavity

value: Affiliated Hangzhou Cancer Hospital,Zhejiang University School of Medicine

value: Formalin fixed paraffin-embedded tissue


title: Stomach Adenocarcinoma [20A040851]

value: F

value: Metastatic


title: Ovarian Serous Carcinoma [20A040924]

value: Ovarian cancer

value: Validation set


title: Colon and rectum   Adenocarcinoma [20A040869]

value: Unknown


title: Stomach Adenocarcinoma [20A040850]


title: Stomach Adenocarcinoma [20A040849]

value: Stomach


title: Stomach Adenocarcinoma [20A040842]


title: Stomach Adenocarcinoma [20A040847]


title: Stomach Adenocarcinoma [20A040846]


title: Colon and rectum   Adenocarcinoma [193115]

value: Colon and rectum  cancer


title: Breast cancer (subtype unknown) [193253]

source_name: Breast

value: Breast

value: Breast cancer


title: Hepatocellular Carcinoma [193583]

value: Liver and gallbladder

value: Ⅳ


title: Lung Adenocarcinoma [193145]

value: M

value: Lung cancer


title: Lung Adenocarcinoma [193437]

value: Lymphnode


title: Breast cancer (subtype unknown) [193586A2]

value: Liver


title: Papillary Thyroid Carcinoma [193036]

source_name: Thyroid

value: Thyroid

value: Thyroid cancer

value: Affiliated Hangzhou Cancer Hospital,Zhejiang University School of Medicine


title: Papillary Thyroid Carcinoma [20B011144]

value: F

value: unknown

value: Cancer Hospital of the University of Chinese Academy of Science,Zhejiang Cancer Hospital (ZJCH)

value: Metastatic

value: Formalin fixed paraffin-embedded tissue


title: Ovarian Serous Carcinoma [193176B1]

value: Ovarian cancer

value: Validation set


title: Papillary Thyroid Carcinoma [20B011143]


title: Stomach Adenocarcinoma [20A040854]

value: Stomach

value: Stomach cancer


title: Papillary Thyroid Carcinoma [20B011142]


title: Papillary Thyroid Carcinoma [20B011139]


title: Papillary Thyroid Carcinoma [20B011140]


title: Papillary Thyroid Carcinoma [20B011138]


title: Papillary Thyroid Carcinoma [20B011137]


title: Stomach Adenocarcinoma [20A040848]

value: Unknown

value: Ⅱ


title: Stomach Adenocarcinoma [20A040843]

value: M

value: Ⅲ


title: Stomach Adenocarcinoma [20A040841]


title: Papillary Thyroid Carcinoma [20B011130]

value: Lymphnode

value: Ⅳ


title: Papillary Thyroid Carcinoma [20B011132]

value: Thyroid cancer


title: Papillary Thyroid Carcinoma [20B011134]


title: Papillary Thyroid Carcinoma [20B011131]


title: Papillary Thyroid Carcinoma [20B011128]


title: Papillary Thyroid Carcinoma [20B011126]


title: Papillary Thyroid Carcinoma [20B011129]


title: Stomach Adenocarcinoma [193175]

value: Affiliated Hangzhou Cancer Hospital,Zhejiang University School of Medicine


title: Breast cancer (subtype unknown) [2019-4744]

value: Liver

value: F

value: Breast cancer


title: Gallbladder Carcinoma [2019-4546]

source_name: Annex on the right

value: Annex on the right

value: Liver and gallbladder

value: Metastatic


title: Liver and gallbladder(subtype unknown) [2019-4489]

source_name: Lymphnode

value: Formalin fixed paraffin-embedded tissue

value: Validation set


title: Papillary Thyroid Carcinoma [20B011127]

value: Cancer Hospital of the University of Chinese Academy of Science,Zhejiang Cancer Hospital (ZJCH)


title: Lung Adenocarcinoma [2019-3945]

value: Lung cancer


title: Stomach Adenocarcinoma [2019-4380]

value: Stomach cancer


title: Lung Adenocarcinoma [2019-3748]

source_name: Pleura

value: Pleura


title: Oral Squamous Cell Carcinoma [20A040468]

value: Neck

value: M

value: unknown

value: Head and neck neoplasm

value: Frozen tissue


title: Lung Adenocarcinoma [2019-3746]

value: Lymphnode

value: Ⅳ

value: Affiliated Hangzhou Cancer Hospital,Zhejiang University School of Medicine


title: Oral Squamous Cell Carcinoma [20A040470]

source_name: Oral cavity

value: Oral cavity

value: Ⅰ

value: Primary


title: Oral Squamous Cell Carcinoma [20A040471]

value: Metastatic


title: Papillary Thyroid Carcinoma [20B011136]

value: F

value: Thyroid cancer

value: Formalin fixed paraffin-embedded tissue

value: Validation set


title: Hypopharynx Squamous Cell Carcinoma [20A040469]

value: Cancer Hospital of the University of Chinese Academy of Science,Zhejiang Cancer Hospital (ZJCH)


title: Breast cancer (subtype unknown) [2019-4745]

value: Liver

value: Breast cancer


title: Head and neck neoplasm(subtype unknown) [20A040477]

value: unknown


title: Oral Squamous Cell Carcinoma [20A040472]

source_name: Tongue

value: Tongue

value: M

value: Head and neck neoplasm


title: Colon and rectum   Adenocarcinoma [20A042475]

source_name: Rectum

value: Rectum

value: Colon and rectum  cancer

value: Ⅱ

value: Affiliated Hangzhou First People's Hospital,Zhejiang University School of Medicine

value: Frozen tissue

value: Training set


title: Hypopharynx Squamous Cell Carcinoma [20A040474]

value: Lymphnode

value: Ⅲ

value: Metastatic


title: Colon and rectum   Adenocarcinoma [20A042365]

value: Primary


title: Colon and rectum   Adenocarcinoma [20A042346]

source_name: Colon

value: Colon


title: Stomach Adenocarcinoma [20A042245]

value: Stomach

value: Stomach cancer


title: Colon and rectum   Adenocarcinoma [20A042344]


title: Stomach Adenocarcinoma [20A042153]


title: Stomach Adenocarcinoma [20A042315]


title: Stomach Signet Ring Cell Carcinoma [20A042329]


title: Stomach Adenocarcinoma [2019-4383]

value: Ⅳ

value: Affiliated Hangzhou Cancer Hospital,Zhejiang University School of Medicine

value: Formalin fixed paraffin-embedded tissue

value: Validation set


title: Stomach Adenocarcinoma [20A040913]

source_name: Pelvic cavity

value: Pelvic cavity

value: F


title: Lung Adenocarcinoma [20A042163]

source_name: Lung

value: Lung

value: Lung cancer

value: Ⅰ


title: Lung Adenocarcinoma [20A042186]

value: Affiliated Hangzhou First People's Hospital,Zhejiang University School of Medicine

value: Frozen tissue

value: Training set


title: Colon and rectum   Adenocarcinoma [20A042301]

value: M

value: Colon and rectum  cancer

value: Ⅲ


title: Breast Invasive Carcinoma, NOS [20A042615]

value: Breast

value: Breast cancer

value: Ⅱ

value: Primary


title: Breast Invasive Carcinoma, NOS [20A042565]


title: Esophagus Squamous Cell Carcinoma [20A041620]

source_name: Esophagus

value: Esophagus

value: Esophagus cancer

value: Cancer Hospital of the University of Chinese Academy of Science,Zhejiang Cancer Hospital (ZJCH)


title: Esophagus Squamous Cell Carcinoma [20A041518]


title: Esophagus Squamous Cell Carcinoma [20A041622]


title: Esophagus Squamous Cell Carcinoma [20A041621]


title: Esophagus Squamous Cell Carcinoma [20A041531]

value: F


title: Esophagus Squamous Cell Carcinoma [20A041501]

value: Ⅳ


title: Esophagus Squamous Cell Carcinoma [20A041533]


title: Esophagus Squamous Cell Carcinoma [20A041503]


title: Esophagus Squamous Cell Carcinoma [20A041502]


title: Esophagus Squamous Cell Carcinoma [20A041499]


title: Esophagus Squamous Cell Carcinoma [20A041484]


title: Esophagus Squamous Cell Carcinoma [20A041538]


title: Esophagus Squamous Cell Carcinoma [20A041619]


title: Esophagus Squamous Cell Carcinoma [20A041481]


title: Esophagus Squamous Cell Carcinoma [20A041602]


title: Esophagus Squamous Cell Carcinoma [20A041532]


title: Esophagus Squamous Cell Carcinoma [20A041534]


title: Esophagus Squamous Cell Carcinoma [20A041507]


title: Esophagus Squamous Cell Carcinoma [20A041536]


title: Esophagus Squamous Cell Carcinoma [20A041516]


title: Lung Adenocarcinoma [20A042143]

value: Lung

value: Lung cancer


title: Esophagus Squamous Cell Carcinoma [20A041535]


title: Esophagus Squamous Cell Carcinoma [20A041504]


title: Esophagus Squamous Cell Carcinoma [20A041615]


title: Esophagus Squamous Cell Carcinoma [20A041513]


title: Esophagus Squamous Cell Carcinoma [20A041482]


title: Esophagus Squamous Cell Carcinoma [20A041483]


title: Esophagus Squamous Cell Carcinoma [20A041478]


title: Esophagus Squamous Cell Carcinoma [20A041500]


title: Esophagus Squamous Cell Carcinoma [20A041511]


title: Esophagus Squamous Cell Carcinoma [20A041514]


title: Esophagus Squamous Cell Carcinoma [20A041515]


title: Esophagus Adenosquamous Carcinoma [20A041537]


title: Esophagus Squamous Cell Carcinoma [20A041616]


title: Esophagus Squamous Cell Carcinoma [20A041497]


title: Esophagus Squamous Cell Carcinoma [20A041506]


title: Esophagus Squamous Cell Carcinoma [20A041505]


title: Esophagus Squamous Cell Carcinoma [20A041479]


title: Esophagus Squamous Cell Carcinoma [20A041614]


title: Esophagus Squamous Cell Carcinoma [20A041617]


title: Hepatocellular Carcinoma [20A041562]

value: Liver

value: Liver and gallbladder


title: Esophagus Squamous Cell Carcinoma [20A041517]

value: Frozen tissue

value: Training set


title: Cholangiocarcinoma [20A041569]


title: Cholangiocarcinoma [20A041555]

value: M

value: Ⅰ


title: Hepatocellular Carcinoma [20A041572]

value: Ⅲ


title: Esophagus Squamous Cell Carcinoma [20A041519]


title: Hepatocellular Carcinoma [20A041527]


title: Hepatocellular Carcinoma [20A041574]


title: Esophagus Squamous Cell Carcinoma [20A041480]


title: Hepatocellular Carcinoma [20A041560]


title: Hepatocellular Carcinoma [20A041577]


title: Esophagus Squamous Cell Carcinoma [20A041510]


title: Hepatocellular Carcinoma [20A041547]


title: Hepatocellular Carcinoma [20A041565]


title: Hepatocellular Carcinoma [20A041528]


title: Hepatocellular Carcinoma [20A041546]


title: Hepatocellular Carcinoma [20A041573]


title: Hepatocellular Carcinoma [20A041559]


title: Cholangiocarcinoma [20A041540]


title: Hepatocellular Carcinoma [20A041576]


title: Hepatocellular Carcinoma [20A041575]


title: Hepatocellular Carcinoma [20A041543]


title: Hepatocellular Carcinoma [20A041567]


title: Cholangiocarcinoma [20A041525]


title: Hepatocellular Carcinoma [20A041542]


title: Cholangiocarcinoma [20A041549]


title: Cholangiocarcinoma [20A041541]


title: Hepatocellular Carcinoma [20A041551]


title: Cholangiocarcinoma [20A041524]


title: Cholangiocarcinoma [20A041530]


title: Hepatocellular Carcinoma [20A041526]


title: Hepatocellular Carcinoma [20A041545]


title: Hepatocellular Carcinoma [20A041579]


title: Hepatocellular Carcinoma [20A041571]


title: Hepatocellular Carcinoma [20A041578]


title: Cholangiocarcinoma [20A041544]


title: Hepatocellular Carcinoma [20A041550]


title: Cholangiocarcinoma [20A041580]


title: Hepatocellular Carcinoma [20A041552]


title: Hepatocellular Carcinoma [20A041561]


title: Hepatocellular Carcinoma [20A041564]


title: Hepatocellular Carcinoma [20A041556]


title: Hepatocellular Carcinoma [20A041581]


title: Cholangiocarcinoma [20A041558]


title: Hepatocellular Carcinoma [20A041570]


title: Hepatocellular Carcinoma [20A041568]


title: Hepatocellular Carcinoma [20A041582]


title: Hepatocellular Carcinoma [20A041563]


title: Ovarian Mucinous Carcinoma [20A042283]

source_name: Ovary

value: Ovary

value: Ovarian cancer


title: Hepatocellular Carcinoma [20A041566]

value: Primary


title: Ovarian Serous Carcinoma [20A042468]


title: Ovarian Mucinous Carcinoma [20A042207]

value: Ⅱ


title: Ovarian Serous Carcinoma [20A042570]


title: Ovarian Serous Carcinoma [20A042455]


title: Ovarian Serous Carcinoma [20A042576]


title: Ovarian Serous Carcinoma [20A042461]


title: Ovarian Serous Carcinoma [20A042209]


title: Ovarian Serous Carcinoma with Clear cell adenocarcinoma [20A042281]


title: Ovarian Papillary Serous Cystadenocarcinomas with Clear cell adenocarcinoma [20A042297]


title: Ovarian Papillary Serous Cystadenocarcinomas [20A042428]


title: Ovarian Serous Carcinoma [20A042385]


title: Ovarian Serous Carcinoma [20A042454]


title: Hepatocellular Carcinoma [20A041557]


title: Ovarian High-grade Serous Carcinoma [20A042198]


title: Ovarian High-grade Serous Carcinoma [20A042206]


title: Ovarian Serous Carcinoma [20A042479]


title: Ovarian Serous Carcinoma [20A042269]


title: Ovarian High-grade Serous Carcinoma [20A042348]


title: Ovarian Serous Carcinoma with Clear cell adenocarcinoma [20A042167]


title: Ovarian Serous Carcinoma [20A042327]


title: Ovarian Papillary Serous Cystadenocarcinomas [20A042553]


title: Ovarian Serous Carcinoma [20A042314]


title: Ovarian Serous Carcinoma [20A042320]


title: Ovarian High-grade Serous Carcinoma [20A042323]


title: Ovarian Serous Carcinoma [20A042277]


title: Ovarian Clear cell adenocarcinoma [20A042275]


title: Ovarian Serous Carcinoma [20A042447]


title: Ovarian Serous Carcinoma [20A042389]


title: Ovarian Serous Carcinoma [20A042295]


title: Ovarian High-grade Serous Carcinoma [20A042310]


title: Ovarian Serous Carcinoma [20A042276]


title: Ovarian High-grade Serous Carcinoma [20A042274]


title: Ovarian Serous Carcinoma [20A042332]


title: Ovarian Serous Carcinoma with Endometrioid Carcinoma [20A042280]


title: Ovarian High-grade Serous Carcinoma [20A042175]


title: Ovarian Serous Carcinoma [20A042552]


title: Ovarian Clear cell adenocarcinoma [20A042178]


title: Ovarian Malignant mullerian duct mixed tumor [20A042328]


title: Ovarian Serous Carcinoma [20A042336]


title: Ovarian Serous Carcinoma [20A042337]


title: Ovarian Serous Carcinoma [20A042510]


title: Ovarian Serous Carcinoma [20A042401]


title: Ovarian Clear cell adenocarcinoma [20A042466]


title: Ovarian Serous Carcinoma [20A042216]


title: Cervix Squamous Cell Carcinoma [20A042305]

source_name: Cervix

value: Cervix

value: unknown

value: Cervix cancer


title: Cervix Squamous Cell Carcinoma [20A042511]

value: F

value: Ⅳ

value: Cancer Hospital of the University of Chinese Academy of Science,Zhejiang Cancer Hospital (ZJCH)


title: Ovarian Serous Carcinoma [20A042270]


title: Cervix Adenocarcinoma [20A042496]


title: Cervix Squamous Cell Carcinoma [20A042196]


title: Ovarian Serous Carcinoma [20A042463]


title: Ovarian Serous Carcinoma [20A042168]


title: Ovarian Endometrioid Carcinoma [20A042339]


title: Cervix Squamous Cell Carcinoma [20A042312]


title: Cervix Squamous Cell Carcinoma [20A042214]


title: Ovarian Serous Carcinoma [20A042284]


title: Cervix Adenocarcinoma [20A042575]


title: Cervix Squamous Cell Carcinoma [20A042303]


title: Cervix Small cell Neuroendocrine Carcinoma [20A042612]


title: Cervix Squamous Cell Carcinoma [20A042208]


title: Cervix Squamous Cell Carcinoma [20A042319]


title: Cervix Adenocarcinoma [20A042261]


title: Cervix Squamous Cell Carcinoma [20A042264]


title: Cervix Squamous Cell Carcinoma [20A042286]


title: Cervix Adenocarcinoma [20A042201]

source_name: Uterus

value: Uterus


title: Cervix Squamous Cell Carcinoma [20A042562]


title: Cervix Squamous Cell Carcinoma [20A042513]


title: Cervix Squamous Cell Carcinoma [20A042278]


title: Cervix Squamous Cell Carcinoma [20A042452]


title: Cervix Squamous Cell Carcinoma [20A042448]


title: Cervix Squamous Cell Carcinoma [20A042335]


title: Cervix Squamous Cell Carcinoma [20A042151]


title: Cervix Squamous Cell Carcinoma [20A042338]


title: Cervix Squamous Cell Carcinoma [20A042535]


title: Cervix Adenocarcinoma [20A042282]


title: Cervix Squamous Cell Carcinoma [20A042318]


title: Cervix Squamous Cell Carcinoma [20A042211]


title: Cervix Squamous Cell Carcinoma [20A042285]


title: Cervix Squamous Cell Carcinoma [20A042384]


title: Cervix Squamous Cell Carcinoma [20A042258]


title: Cervix Squamous Cell Carcinoma [20A042395]


title: Cervix Squamous Cell Carcinoma [20A042268]


title: Cervix Squamous Cell Carcinoma [20A042388]


title: Cervix Squamous Cell Carcinoma [20A042417]


title: Cervix Squamous Cell Carcinoma [20A042500]


title: Cervix Squamous Cell Carcinoma [20A042324]


title: Cervix Squamous Cell Carcinoma [20A042381]


title: Cervix Squamous Cell Carcinoma [20A042571]


title: Cervix Adenocarcinoma [20A042361]


title: Cervix Squamous Cell Carcinoma [20A042177]


title: Cervix Adenocarcinoma [20A042267]


title: Cervix Squamous Cell Carcinoma [20A042279]


title: Cervix Squamous Cell Carcinoma [20A042526]


title: Papillary Thyroid Carcinoma [20A042600]

value: Thyroid

value: Thyroid cancer


title: Cervix Small cell Neuroendocrine Carcinoma [20A042300]

value: Frozen tissue

value: Training set


title: Cervix Squamous Cell Carcinoma [20A042406]


title: Papillary Thyroid Carcinoma [20A042597]

value: M


title: Papillary Thyroid Carcinoma [20A042569]


title: Papillary Thyroid Carcinoma [20A042595]


title: Papillary Thyroid Carcinoma [20A042520]

value: Ⅰ


title: Papillary Thyroid Carcinoma [20A042601]


title: Papillary Thyroid Carcinoma [20A042423]


title: Papillary Thyroid Carcinoma [20A042547]


title: Medullary Thyroid Carcinoma [20A042546]


title: Papillary Thyroid Carcinoma [20A042398]


title: Papillary Thyroid Carcinoma [20A042400]


title: Papillary Thyroid Carcinoma [20A042396]


title: Papillary Thyroid Carcinoma [20A042457]


title: Follicular Thyroid Carcinoma [20A042540]

value: Ⅲ


title: Medullary Thyroid Carcinoma [20A042549]


title: Cervix Squamous Cell Carcinoma [20A042555]


title: Papillary Thyroid Carcinoma [20A042322]


title: Medullary Thyroid Carcinoma [20A042561]


title: Papillary Thyroid Carcinoma [20A042219]


title: Thyroid cancer(subtype unknown) [20A042287]

value: Metastatic


title: Papillary Thyroid Carcinoma [20A042420]

value: Primary


title: Papillary Thyroid Carcinoma [20A042316]


title: Papillary Thyroid Carcinoma [20A042252]


title: Papillary Thyroid Carcinoma [20A042580]


title: Medullary Thyroid Carcinoma [20A042191]


title: Papillary Thyroid Carcinoma [20A042517]


title: Papillary Thyroid Carcinoma [20A042183]


title: Papillary Thyroid Carcinoma [20A042590]


title: Papillary Thyroid Carcinoma [20A042273]


title: Medullary Thyroid Carcinoma [20A042532]


title: Medullary Thyroid Carcinoma [20A042288]


title: Papillary Thyroid Carcinoma [20A042456]


title: Papillary Thyroid Carcinoma [20A042325]


title: Medullary Thyroid Carcinoma [20A042497]


title: Medullary Thyroid Carcinoma [20A042485]


title: Medullary Thyroid Carcinoma [20A042199]


title: Papillary Thyroid Carcinoma [20A042568]


title: Papillary Thyroid Carcinoma [20A042213]

value: Ⅱ


title: Oral Squamous Cell Carcinoma [20A042512]

value: Tongue

value: Head and neck neoplasm


title: Papillary Thyroid Carcinoma [20A042554]

value: unknown


title: Mucinous Thyroid Carcinoma [20A042296]


title: Papillary Thyroid Carcinoma [20A042142]

value: F


title: Hypopharynx Squamous Cell Carcinoma [20A042541]

source_name: Hypopharynx

value: Hypopharynx

value: Ⅳ


title: Papillary Thyroid Carcinoma [20A042330]

value: Cancer Hospital of the University of Chinese Academy of Science,Zhejiang Cancer Hospital (ZJCH)


title: Oropharynxx Squamous Cell Carcinoma [20A042193]

source_name: Oropharynx

value: Oropharynx


title: Hypopharynx Squamous Cell Carcinoma [20A042559]

source_name: Sinuspiriformis

value: Sinuspiriformis


title: Oral Squamous Cell Carcinoma [20A042521]

value: Oral cavity

value: Frozen tissue


title: Oropharynxx Squamous Cell Carcinoma [20A042548]

value: M

value: Training set


title: Hypopharynx Squamous Cell Carcinoma [20A042429]

source_name: Throat

value: Throat

value: Ⅲ


title: Follicular Thyroid Carcinoma [20A042581]

source_name: Thyroid

value: Thyroid

value: Thyroid cancer

value: Ⅰ

value: Primary


title: Oral Squamous Cell Carcinoma [20A042200]

source_name: Lip

value: Lip

value: unknown

value: Head and neck neoplasm

value: Ⅱ


title: Medullary Thyroid Carcinoma [20A042567]

value: Cancer Hospital of the University of Chinese Academy of Science,Zhejiang Cancer Hospital (ZJCH)


title: Oral Squamous Cell Carcinoma [20A042190]

value: Tongue

value: Ⅳ


title: Oral Squamous Cell Carcinoma [20A042583]

value: Oral cavity

value: F


title: Hypopharynx Squamous Cell Carcinoma [20A042415]

value: Hypopharynx

value: M

value: Frozen tissue


title: Hypopharynx Squamous Cell Carcinoma [20A042272]

value: Sinuspiriformis

value: Training set


title: Papillary Thyroid Carcinoma [20A042621]

value: Thyroid

value: Thyroid cancer


title: Oral Squamous Cell Carcinoma [20A042603]

value: Primary


title: Oropharynxx Squamous Cell Carcinoma [20A042146]

value: Ⅲ


title: Hypopharynx Squamous Cell Carcinoma [20A042607]

value: unknown


title: Oral Squamous Cell Carcinoma [20A042550]

value: Head and neck neoplasm


title: Oropharynxx Squamous Cell Carcinoma [20A042165]

value: Oropharynx

value: Ⅰ


title: Hypopharynx Squamous Cell Carcinoma [20A042203]

value: Cancer Hospital of the University of Chinese Academy of Science,Zhejiang Cancer Hospital (ZJCH)


title: Hypopharynx Squamous Cell Carcinoma [20A042253]

value: Ⅳ


title: Hypopharynx Squamous Cell Carcinoma [20A042263]

value: Throat


title: Hypopharynx Squamous Cell Carcinoma [20A042247]


title: Oral Squamous Cell Carcinoma [20A042150]

value: Tongue


title: Oropharynxx Squamous Cell Carcinoma [20A042387]

value: F


title: Hypopharynx Squamous Cell Carcinoma [20A042471]

value: Hypopharynx

value: M


title: Oropharynxx Squamous Cell Carcinoma [20A042309]

value: Frozen tissue


title: Oral Squamous Cell Carcinoma [20A042188]

value: Oral cavity

value: Ⅱ

value: Training set


title: Oral Squamous Cell Carcinoma [20A042515]

value: Primary


title: Hypopharynx Squamous Cell Carcinoma [20A042489]

value: Sinuspiriformis

value: Ⅲ


title: Oropharynxx Squamous Cell Carcinoma [20A042470]

value: unknown

value: Head and neck neoplasm


title: Esophagus Squamous Cell Carcinoma [20A042197]

value: Esophagus cancer


title: Oral Squamous Cell Carcinoma [20A042333]

value: Oropharynx

value: Ⅰ

value: Cancer Hospital of the University of Chinese Academy of Science,Zhejiang Cancer Hospital (ZJCH)


title: Oral Squamous Cell Carcinoma [20A042145]


title: Oral Squamous Cell Carcinoma [20A042514]

value: Ⅳ


title: Hypopharynx Squamous Cell Carcinoma [20A042584]


title: Hypopharynx Squamous Cell Carcinoma [20A042592]


title: Oropharynxx Squamous Cell Carcinoma [20A042192]

value: F


title: Hypopharynx Squamous Cell Carcinoma [20A042528]

value: Hypopharynx


title: Oral Squamous Cell Carcinoma [20A042453]

value: M


title: Hypopharynx Squamous Cell Carcinoma [20A042149]

value: Frozen tissue


title: Hypopharynx Squamous Cell Carcinoma [20A042148]


title: Hypopharynx Squamous Cell Carcinoma [20A042307]


title: Hypopharynx Squamous Cell Carcinoma [20A042404]


title: Oral Squamous Cell Carcinoma [20A042230]

value: Tongue


title: Hypopharynx Squamous Cell Carcinoma [20A042585]


title: Hypopharynx Squamous Cell Carcinoma [20A042135]


title: Colon and rectum  Serous carcinoma [20A042126]

value: Rectum

value: Colon and rectum  cancer

value: Affiliated Hangzhou First People's Hospital,Zhejiang University School of Medicine


title: Colon and rectum   Adenocarcinoma [20A042380]

value: Primary

value: Training set


title: Oropharynxx Squamous Cell Carcinoma [20A042557]

value: unknown


title: Oral Squamous Cell Carcinoma [20A042144]

value: Oral cavity

value: Head and neck neoplasm


title: Colon and rectum   Adenocarcinoma [20A042171]

value: Ⅱ


title: Colon and rectum   Adenocarcinoma [20A042128]


title: Colon and rectum   Adenocarcinoma [20A042184]


title: Colon and rectum   Adenocarcinoma [20A042390]

value: Ⅲ


title: Colon and rectum   Adenocarcinoma with Mucinous Carcinoma [20A042426]


title: Colon and rectum   Adenocarcinoma with Mucinous Carcinoma [20A042386]


title: Hypopharynx Squamous Cell Carcinoma [20A042566]

value: Oropharynx

value: Cancer Hospital of the University of Chinese Academy of Science,Zhejiang Cancer Hospital (ZJCH)


title: Oropharynxx Squamous Cell Carcinoma [20A042467]


title: Colon and rectum   Adenocarcinoma with Mucinous Carcinoma [20A042458]

value: F


title: Colon and rectum   Adenocarcinoma [20A042205]


title: Colon and rectum   Adenocarcinoma [20A042425]


title: Colon and rectum   Adenocarcinoma [20A042441]


title: Colon and rectum  Mucinous Carcinoma with Signet Ring Cell Carcinoma [20A042383]


title: Colon and rectum   Adenocarcinoma [20A042378]

value: Ⅰ


title: Colon and rectum   Adenocarcinoma [20A042613]


title: Colon and rectum   Adenocarcinoma [20A042481]


title: Colon and rectum   Adenocarcinoma [20A042478]

value: M


title: Colon and rectum   Adenocarcinoma [20A042445]

value: Frozen tissue


title: Colon and rectum   Adenocarcinoma [20A042321]


title: Colon and rectum   Adenocarcinoma [20A042486]


title: Colon and rectum   Adenocarcinoma [20A042382]


title: Colon and rectum   Adenocarcinoma [20A042451]


title: Colon and rectum   Adenocarcinoma with Mucinous Carcinoma [20A042427]


title: Colon and rectum   Adenocarcinoma [20A042443]


title: Colon and rectum   Adenocarcinoma [20A042166]


title: Colon and rectum   Adenocarcinoma [20A042170]

value: Colon


title: Colon and rectum   Adenocarcinoma [20A042179]


title: Colon and rectum   Adenocarcinoma [20A042308]


title: Colon and rectum   Adenocarcinoma [20A042432]


title: Colon and rectum   Adenocarcinoma [20A042545]

value: Rectum


title: Colon and rectum   Adenocarcinoma [20A042536]

value: Colon and rectum  cancer


title: Colon and rectum   Adenocarcinoma with Mucinous Carcinoma [20A042439]

value: Affiliated Hangzhou First People's Hospital,Zhejiang University School of Medicine


title: Colon and rectum   Adenocarcinoma [20A042409]

value: Primary


title: Colon and rectum   Adenocarcinoma [20A042544]

value: Training set


title: Colon and rectum   Adenocarcinoma [20A042588]


title: Colon and rectum   Adenocarcinoma [20A042509]


title: Colon and rectum   Adenocarcinoma [20A042464]


title: Colon and rectum   Adenocarcinoma [20A042174]


title: Colon and rectum   Adenocarcinoma [20A042589]


title: Colon and rectum   Adenocarcinoma [20A042498]


title: Colon and rectum   Adenocarcinoma [20A042405]


title: Colon and rectum   Adenocarcinoma [20A042306]


title: Colon and rectum   Adenocarcinoma [20A042504]


title: Colon and rectum   Adenocarcinoma with Mucinous Carcinoma [20A042483]


title: Colon and rectum   Adenocarcinoma [20A042490]


title: Colon and rectum   Adenocarcinoma [20A042334]


title: Colon and rectum   Adenocarcinoma with Mucinous Carcinoma [20A042362]

value: Ⅳ


title: Colon and rectum   Adenocarcinoma [20A042433]


title: Stomach Adenocarcinoma [20A042488]

source_name: Stomach

value: Stomach

value: Stomach cancer


title: Stomach Adenocarcinoma [20A042345]

value: Ⅱ


title: Stomach Adenocarcinoma [20A042473]


title: Colon and rectum   Adenocarcinoma [20A042302]

value: Ⅲ


title: Colon and rectum   Adenocarcinoma with Mucinous Carcinoma [20A042169]


title: Stomach Adenocarcinoma [20A042217]


title: Stomach Adenocarcinoma [20A042502]


title: Stomach Adenocarcinoma [20A042172]


title: Stomach Adenocarcinoma [20A042435]


title: Stomach Adenocarcinoma [20A042255]


title: Stomach Adenocarcinoma [20A042260]


title: Stomach Adenocarcinoma [20A042317]


title: Stomach Adenocarcinoma [20A042313]


title: Stomach Adenocarcinoma [20A042523]


title: Stomach Adenocarcinoma [20A042531]


title: Stomach Adenocarcinoma [20A042472]


title: Stomach Neuroendocrine carcinoma [20A042244]


title: Stomach Adenocarcinoma [20A042543]


title: Stomach Adenocarcinoma [20A042411]


title: Stomach Adenocarcinoma [20A042331]


title: Stomach Adenocarcinoma [20A042292]


title: Stomach Adenocarcinoma [20A042438]


title: Stomach Adenocarcinoma [20A042494]


title: Stomach Signet Ring Cell Carcinoma [20A042304]


title: Stomach Adenocarcinoma [20A042507]


title: Stomach Adenocarcinoma [20A042505]


title: Stomach Adenocarcinoma [20A042242]


title: Stomach Adenocarcinoma [20A042340]


title: Stomach Adenocarcinoma [20A042606]


title: Stomach Adenocarcinoma [20A042158]


title: Stomach Adenocarcinoma [20A042391]


title: Stomach Adenocarcinoma [20A042132]


title: Stomach Adenocarcinoma [20A042508]


title: Stomach Adenocarcinoma [20A042377]


title: Stomach Adenocarcinoma [20A042421]


title: Stomach Adenocarcinoma [20A042133]


title: Stomach Adenocarcinoma [20A042125]


title: Stomach Adenocarcinoma [20A042579]


title: Stomach Adenocarcinoma [20A042551]


title: Stomach Adenocarcinoma [20A042147]


title: Stomach Adenocarcinoma [20A042136]


title: Stomach Adenocarcinoma [20A042130]


title: Lung Squamous Cell Carcinoma [20A042139]

value: Lung

value: Lung cancer


title: Stomach Adenocarcinoma [20A042137]


title: Lung Squamous Cell Carcinoma [20A042558]


title: Stomach Adenocarcinoma [20A042123]


title: Lung Squamous Cell Carcinoma [20A042440]


title: Lung Squamous Cell Carcinoma [20A042239]


title: Lung Squamous Cell Carcinoma [20A042259]


title: Stomach Adenocarcinoma [20A042124]


title: Lung Squamous Cell Carcinoma [20A042223]


title: Lung Squamous Cell Carcinoma [20A042605]


title: Lung Squamous Cell Carcinoma [20A042222]


title: Lung Squamous Cell Carcinoma [20A042237]


title: Lung Squamous Cell Carcinoma [20A042154]


title: Lung Squamous Cell Carcinoma [20A042227]


title: Lung Squamous Cell Carcinoma [20A042195]


title: Lung Adenocarcinoma [20A042574]


title: Lung Squamous Cell Carcinoma [20A042221]

value: F


title: Lung Adenocarcinoma [20A042299]


title: Lung Squamous Cell Carcinoma [20A042363]


title: Stomach Adenocarcinoma [20A042602]

value: Ⅰ


title: Lung Adenocarcinoma [20A042218]

value: M


title: Lung Adenocarcinoma [20A042156]

value: Frozen tissue


title: Lung Adenocarcinoma [20A042155]


title: Lung Adenocarcinoma [20A042487]


title: Lung Adenocarcinoma [20A042418]


title: Lung Adenocarcinoma [20A042527]


title: Lung Adenocarcinoma [20A042294]


title: Lung Adenocarcinoma [20A042413]

value: unknown


title: Lung Adenocarcinoma [20A042180]


title: Lung Squamous Cell Carcinoma [20A042162]


title: Lung Squamous Cell Carcinoma [20A042210]


title: Lung Adenocarcinoma [20A042289]


title: Lung Squamous Cell Carcinoma [20A042215]


title: Lung Squamous Cell Carcinoma [20A042226]


title: Lung Adenocarcinoma [20A042182]


title: Lung Adenocarcinoma [20A042298]


title: Lung Adenocarcinoma [20A042529]


title: Lung Adenocarcinoma [20A042501]


title: Lung Squamous Cell Carcinoma [20A042474]


title: Lung Squamous Cell Carcinoma [20A042194]


title: Lung Adenocarcinoma [20A042129]


title: Lung Adenocarcinoma [20A042618]


title: Lung Adenocarcinoma [20A042202]


title: Lung Adenocarcinoma [20A042624]


title: Lung Adenocarcinoma [20A042469]


title: Lung Squamous Cell Carcinoma [20A042160]


title: Lung Adenocarcinoma [20A042187]


title: Lung Adenocarcinoma [20A042516]


title: Lung Adenosquamous Carcinoma [20A042534]


title: Lung Adenocarcinoma [20A042161]


title: Lung Adenocarcinoma [20A042271]


title: Lung Squamous Cell Carcinoma [20A042159]


title: Lung Squamous Cell Carcinoma [20A042176]


title: Lung Adenocarcinoma [20A042185]


title: Lung Squamous Cell Carcinoma [20A042164]


title: Lung Squamous Cell Carcinoma [20A042131]


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A042506]

source_name: Breast

value: Breast

value: Breast cancer


title: Breast Ductal Carcinoma In Situ [20A042343]

value: Affiliated Hangzhou First People's Hospital,Zhejiang University School of Medicine


title: Breast Invasive Carcinoma, NOS [20A042596]

value: Primary


title: Breast Solid Papillary Carcinoma with Invasion [20A042238]

value: Training set


title: Breast Invasive Carcinoma, NOS [20A042370]


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A042353]


title: Breast Invasive Carcinoma, NOS [20A042367]


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A042236]


title: Breast Invasive Carcinoma, NOS [20A042369]


title: Breast Ductal Carcinoma with Mucinous Carcinoma [20A042250]


title: Breast Invasive Carcinoma, NOS [20A042627]


title: Breast Invasive Carcinoma, NOS [20A042241]


title: Breast Invasive Carcinoma, NOS [20A042351]


title: Breast Invasive Carcinoma, NOS [20A042358]


title: Breast Invasive Carcinoma, NOS [20A042619]


title: Breast Invasive Carcinoma, NOS [20A042248]


title: Breast Ductal Carcinoma In Situ [20A042625]


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A042368]


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A042243]


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A042257]


title: Lung Squamous Cell Carcinoma [20A042181]


title: Breast Invasive Carcinoma, NOS [20A042350]


title: Breast Ductal Carcinoma In Situ [20A042609]


title: Breast Invasive Carcinoma, NOS [20A042349]


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A042422]


title: Breast Invasive Carcinoma, NOS [20A042604]


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A042249]


title: Breast cancer (subtype unknown) [20A042598]


title: Breast Ductal Carcinoma with Mucinous Carcinoma [20A042229]


title: Breast Invasive Carcinoma, NOS [20A042224]


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A042364]


title: Breast Invasive Carcinoma, NOS [20A042356]


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A042360]


title: Breast Ductal Carcinoma with Microinvasion [20A042359]


title: Lung Squamous Cell Carcinoma [20A042138]


title: Breast Neuroendocrine Carcinoma [20A042431]


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A042342]


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A042352]


title: Breast Invasive Carcinoma, NOS [20A042341]


title: Breast cancer (subtype unknown) [20A042347]


title: OG2 MEF

city: Guangzhou

first: Lining

last: Liang

address: 190,Kaiyuan Ave.

institute: Guangzhou Institute of Biomedicine and Health,Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: mm10
Supplementary_files_format_and_content: TPM

organism: Mus musculus

source_name: day 13.5 embryos

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain


title: Breast Invasive Carcinoma, NOS [20A042371]


title: Breast Invasive Carcinoma, NOS [20A042376]


title: Breast Ductal Carcinoma In Situ [20A042235]


title: glia

source_name: brain


title: Breast Neuroendocrine Carcinoma [20A042366]


title: Breast Invasive Carcinoma, NOS [20A042228]


title: Breast Invasive Carcinoma, NOS [20A042374]


title: Breast Invasive Carcinoma with Ductal Carcinoma in Situ [20A042232]


title: cortex

source_name: cortex


title: Breast Invasive Carcinoma, NOS [20A042225]


title: neuron


title: cerebellum

source_name: cerebellum


title: Breast Invasive Carcinoma, NOS [20A042233]


title: Breast Invasive Carcinoma, NOS [20A042492]


title: Breast Invasive Carcinoma, NOS [20A042533]


title: stem, Bn13-3

city: Changsha

first: Touming

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

data_processing:
cDNA library was carried out a paired-end sequencing using a HiSeq PE Cluster Kit v4 cBot (Illumina, San Diego, CA, USA) on the Illumina sequencing platform, following the manufacturer’s instructions.
After filtering the low-quality reads, the clean reads were aligned with the garlic genome (GenBank accession: GCA_014155895.2) using hisat2 software
Then, gene expression level was quantified by estimating fragments per kilobase per million reads (FPKM)
Supplementary files format and content: the excel file contain the gene name and RPKM value,

organism: Arabidopsis thaliana

source_name: stem

growth_protocol: Wild and Bnt07G011994-overexpressed Arabidopsis were grown in a greenhouse at 22°C under a 15 h light/ 9 h dark cycle. When the stems reached to about 10 cm-length, stems of each individual were collected as a sample,

extract_protocol:
Total RNAs of each sample were extracted using an E.Z.N.A. Plant RNA Kit (OMEGA Bio-Tek, Norcross, GA, USA) according to the protocol of manufacturer.
these RNAs were individually used for performing the construction of cDNA libraries, with a fragment length of 300 bp (± 150 bp), using a NEBNext UltraTM RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA) according to the manufacturer’s instructions.

treatment_protocol: The stems of each individual were separated manually, and then stored immediately at －80 °C until use.

tag: ecotype

value: Columbia

value: stem

tag: developmental stage

value: stems reached to about 10 cm-length


title: stem, Bn13-1

tag: genotype


title: A-3_IgG

city: Indianapolis

first: Lei

last: Yang

state: Indiana

address: 1044 W. Walnut St.

department: Department of Pediatrics

country: USA

institute: Indiana University School of Medicine

description:
50
genomic DNA

data_processing:
Base calling and quality scoring were performed in Illumina NextSeq/HiSeq
The reads were mapped to the human genome (UCSC hg38) using Bowtie2 (v2.3.2), PICARD (v2.10.7) function MarkDuplicates was used to identify duplicate reads
MACS2 (v 2.1.2) were used to call peaks using rabbit IgG as control at FDR cut off of less than 1e-2
The signal at each base was normalized by per 10 million reads
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig file showing the normalized read signal, narrowpeak file showing the peaks

source_name: hESCs H9 cells

growth_protocol: H9 hESCs were routinely cultured in mTesR medium (typically 1× 106 - 1×107 cells in a matrigel-coated P10 plate).

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.

treatment_protocol: Briefly, hESCs were fixed with methanol-free formaldehyde provided by truChIP™ Chromatin Shearing Kit (Covaris, PN 520154). Chromatin of cell lysis was sheared using truChIP™ Chromatin Shearing Kit according its manual by ME220 Focused-ultrasonicator (Covaris). The sheared chromatin was then incubated with anti-ARID1A antibody and purified by using EZ-Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (Millipore, 17-10086). Chromatin DNAs quality was assessed by 2100 Bioanalyzer (Agilent Technologies)

tag: cell line

value: hESCs

tag: antibody

value: Rabbit (DA1E) mAb IgG XP® Isotype Control #3900, Cell signaling technology


title: Breast Invasive Carcinoma, NOS [20A042477]

value: Ⅱ


title: Breast Invasive Carcinoma, NOS [20A042629]


title: R1 ESCs

source_name: inner cell mass


title: stem, WT3

value: WT


title: Breast Invasive Carcinoma, NOS [20A042594]

value: F


title: stem, Bn13-2


title: Breast Invasive Carcinoma with Mucinous Carcinoma [20A042231]


title: ICR MEF

value: ICR


title: Breast Invasive Carcinoma, NOS [20A042622]


title: Breast Invasive Carcinoma, NOS [20A042355]


title: stem, WT2


title: dcl_m6A MeRIP-seq_rep3

city: Xuzhou

first: Tao

last: Xu

state: Jiangsu

address: Shanghai Road 101

institute: Jiangsu Normal University

data_processing:
The reads with adapters, repetitive sequences, and low-quality sequences were removed using fastp software (https://github.com/OpenGene/fastp), and the resulting clean data were mapped to the A. thaliana genome (Version TAIR10) using HISAT2 (http://daehwankimlab.github.io/hisat2).
The R package exomePeak (https://bioconductor.org/packages/exomePeak) was used for peak calling and difference peak analysis.
ChIPseeker (https://bioconductor.org/packages/ChIPseeker) was used to annotate called peaks, and MEME2 (http://meme-suite.org) and HOMER (http://homer.ucsd.edu/homer/motif) were used to detect conserved sequence motifs.
StringTie (https://ccb.jhu.edu/software/stringtie) was used to analyze the expression level of all mRNAs from input libraries by calculating the FPKM [total exon fragments /mapped reads (millions) × exon length (kB)].
Differentially expressed genes were analyzed using R package edgeR (https://bioconductor.org/packages/edgeR) based on fold change > 1.5 and p-value < 0.05.
Assembly: The genome of A. thaliana was used as the reference genome (https://www.arabidopsis.org/download/index-auto.jsp?dir=/download_files/Sequences)

source_name: Leaf

growth_protocol: The plants were grown at 23±2°C with relative humidity of 70% under 16-h-light / 8-h-dark photocycle at the light intensity of 100 µmol m-2 s-1. The plants were also grown in soil (2.5:1:1 mixture of vermiculite, peat moss, and perlite) under 16-h-light / 8-h-dark photocycle.

extract_protocol:
Total RNA was extracted from Arabidopsis seedlings using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instruction. Poly(A) mRNA was extracted from total RNA using a Dynabeads Oligo (dT)25 kit (Thermo Fisher, Waltham, MA, USA).
The RNA was then fragmented into oligonucleotides using a Magnesium RNA Fragmentation Module (NEB), the fragmented RNA was incubated with m6A-specific antibody (Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl, and 0.5% Igepal CA-630), and the bound RNA was recovered. The RNA from IP fraction and input control fraction was converted to a cDNA library, and the paired-end libraries with an average insert size of approximate 100±50 base pair were subjected to sequencing

treatment_protocol: The plants  were grown under normal growth condition without any special treatment.

value: Leaf

value: dcl1 mutant


title: hippocampus

source_name: hippocampus


title: Breast Invasive Carcinoma, NOS [20A042611]

value: Frozen tissue


title: Breast Invasive Carcinoma, NOS [20A042617]

value: Breast


title: dcl_m6A MeRIP-seq_rep2


title: Breast Ductal Carcinoma In Situ [20A042560]

value: Breast cancer


title: stem, WT1


title: Breast Invasive Carcinoma, NOS [20A042397]

value: Affiliated Hangzhou First People's Hospital,Zhejiang University School of Medicine


title: dcl_m6A MeRIP-seq_rep1


title: hEE Day6

city: New Haven

first: Berna

last: Sozen

state: CT

address: 333 Cedar St

department: Department of Genetics

institute: Yale School of Medicine

description: Chromium Next GEM Single Cell 3ʹ platform (10x Genomics)

library_source: transcriptomic single cell

data_processing:
Prior to more detailed analyses, the overall runs were validated according to the initial CellRanger outputs, including ~30,000 mean transcripts per cell and 3,800 median genes per cell.  The overall fraction of transcripts represented by mitochondrial genes was less than 5%. A total of 22,054 cells were obtained for day 4 and day 6 aggregates. Day 4 consisted of 10,826 cells, and Day 6 aggregates comprised 11,228 cells.
After initial validation of the library quality, preliminary clustering and filtering steps were taken to identify and eliminate library preparation and sequencing artifacts. These include the removal of cells with >10% mitochondrial transcript counts to discard nonviable cells (1493 cells, 6.7% of total), >27500 transcript counts to remove likely doublets (1069 cells, 4.8% of total), and <3430 transcripts to remove low-quality cells (2013 cells, 9.0% of total). A total of 19,247 cells were preserved at this stage, corresponding to 85.8% of total cells.  Data for days 4 and 6 were processed separately using the Seurat v.4.0.1 package pipeline in R v.4.0.3.
Processing steps include library log normalization, data scaling, and linear dimensionality reduction through principal component analysis (PCA) using the most highly variable genes in the sample, found with a variance stabilizing transformation. We then applied the UMAP algorithm for non-linear dimensionality reduction into two dimensions. Cell cycle scores were also calculated for single cells based on the expression of canonical proliferation markers for S and G2M phases, using Seurat’s CellCycleScoring function. These scores were used in a regression model to reduce variance derived from cell cycle differences during data scaling, and subsequent dimensionality reduction steps were re-performed. All processing steps were performed with default parameters unless specified. We observed a high degree of separation between day 4 and day 6 samples in the low-dimensionality projection, suggesting a possible batch effect. We performed data integration using reciprocal PCA to correct technical variance while conservatively accounting for timepoint-specific transcriptional states. Integrated data were re-scaled and reduced to 30 principal components, then further reduced with UMAP for visualization in two dimensions, with default parameters
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

growth_protocol: Prior to generation of hEEs, ESI017 cells were cultured in 37 °C in 5% CO2 on inactivated CF-1 MEFs in human expanded potential complete media (hEP media) as descired in Yang et al., 2017

extract_protocol:
The extra-embryoids that exhibited an inner and outer compartment organization under brightfield are collected on day 4 and day 6 for single-cell isolation. Roughly 200 aggregates per time-points were serially washed with 0.1% BSA in PBS and briefly washed before incubation in 200 mL TrypLE (GIBCO) and incubation at 37ºC.  At five-minute intervals, structures were dissociated by pipetting under a stereomicroscope and returned to incubation until confirmed to be predominantly single-cell suspension.  Although the epithelial cells of the internal compartment dissociated readily, additional time was required to fully dissociate cells in the outside layer due to the appearance of a more extensive extracellular matrix.  Once dissociated, cells were collected in a total of 1 mL 0.1% BSA in PBS and filtered using a FlowMi™ cell strainer (40 mM, Scienceware®) and centrifuged for 5 min at 1,000 rpm.  After two washes, single-cell suspensions were resuspended at a set volume, counted using a standard hemocytometer, and adjusted to 1,000 cells per μL.
16,500 single cells for each time point were loaded onto a Chromium Controller (10x genomics) to generate single-cell transcriptomes using the Chromium Next GEM Single Cell 3ʹ platform according to the manufacturer’s protocol (10x Genomics).

treatment_protocol: AggreWell plate is prepared as described in our previously established methods (Sozen et a. 2018 and 2019). The hPSCs were dissociated into single cells with accutase (Thermo Fisher Scientific) incubation at 37 °C for 3 to 4 minutes. Cells were pelleted by centrifugation for 3 minutes at 1,000 r.p.m. and resuspended in hEP media from Yang et al., 2017. MEFs depleted on gelatin coated plates at 37 °C in 5% CO2 on gelatinized tissue-culture-grade plates. Single cells resuspended in SDM were added dropwise to the AggreWell.

tag: cell type

value: Human Pluripotent Stem Cells

value: Wild type

tag: treatment

tag: time point

value: Day 6 in vitro


title: dcl_RNA-seq_rep3

tag: tissue

tag: age


title: hEE Day4

value: Day 4 in vitro


title: day5_admission

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: fifth day of admission

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform in a 101+101-base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.1.1 in combination with Bowtie2.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: whole blood

extract_protocol:
Total RNA was isolated from the whole blood using the PAXgeneTM Blood RNA System (BD Biosciences, Franklin Lakes, NJ, USA). The collection tubes containing the blood samples were stored at -30°C until analysis.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

tag: disease state

value: methemoglobinemia

value: whole blood

tag: time

value: fifth day of admission


title: day3_admission

description: third day of admission

value: third day of admission


title: day1_admission

description: first day of admission

value: first day of admission


title: Rip2;IMP2

city: Boston

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome mm10 using STAR
Transcript abundance was calculated using Htseq
Genome_build: mm10

source_name: islets

extract_protocol:
Islets were isolated and flash frozen in liquid N2. RNA was harvested using Trizol reagent.
RNA libraries were prepared using standard Illumina sequencing protocols

value: islet


title: IMP2-RIP seq

value: WT


title: dcl_RNA-seq_rep1

value: Leaf


title: WT_m6A MeRIP-seq_rep3


title: dcl_RNA-seq_rep2

value: dcl1 mutant


title: M2_GW

city: Solna

first: Paulo

last: Czarnewski

address: Tomtebodavägen 23b

country: Sweden

institute: KTH

data_processing:
Basecalling was performed using Illumina Casava v.1.7 software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequences.
Read quality was accessed using FASTQC.
Read counts were estimated at the transcript level using kallisto: kallisto quant -i /$input_directory/transcripts.idx -o /$output_directory/$sample_name -b 100 -t 6 --single -l 180 -s 20 $sample_name
Genome_build: mm10
Supplementary_files_format_and_content: We provided individual tab-separated text files containing Kallisto estimated counts (est_counts) and transcript per million (tpm) for each Sample. We also included a matrix contating rounded estimated counts (kallisto_counts.csv) and a log2-normalized counts (cpm, log2_counts_per_million.csv), summarized at the gene level.

growth_protocol: Small intestinal crypts were isolated from two C57BL/6J male mice and seeded in vitro in Matrigel and organoids growth media. DMSO (vehicle) or GW3965 (2uM) was added in the overlaying media. Crypts from each mouse were stimulated with both vehicle and GW3965 (n=2 in each experimental group). After 6 hours, organoids were collected and RNA extracted and submitted for RNAseq analysis.

extract_protocol:
Colon samples were stored in RNAlater (Ambion) at -80˚C until further use. Colonic samples were homogenized using bead-beating system (Precellys) for total RNA purification using RNAeasy kit (Qiagen) following manufacturers recommendations. RNA purity and quantity was measured by NanoDrop spectrophotometer (ThermoFisher). All samples were screened for RNA integrity check and presented RIN values above 8 on 2100 Bioanalyzer instrument (Agilent).
Samples were submitted to Novogene for library preparation using TruSeq Stranded mRNA Library Prep Kit (poly-A selection) and sequencing using HiSeq-2500 platform (Illumina). Samples were sequenced using single-end 50bp sequencing, aiming a minimum coverage of 20M reads.

treatment_protocol: C57BL/6J mice were obtained from ScanBur (Charles River, Germany) and housed in environmentally enriched ventilated cages under specific pathogen free conditions (SPF) at Astrid Fagræus laboratory (AFL, Karolinska Institutet) under 12h light cycle and receiving water and ration ad libitum (RM1(P), Special Diet Services).

tag: group

value: Small intestine organoid

tag: Sex

value: Male

value: 9 weeks old


title: control

value: control


title: shCAPG_+Dox_2

first: yingying

last: zhao

state: State...

address: Tianhe District, Guangzhou, Guangdong Province

institute: Sun Yat-Sen University

data_processing:
SOAPnuke(v1.5.6) software used for basecalling
raw data obtained by sequencing was filtered using SOAPnuke (v1.5.6) to filter out reads containing 1) joints (joint contamination). 2) reads with unknown base N content greater than 5%; 3) clean data were obtained from low-quality reads (reads with a mass value of less than 15 bases accounting for more than 20% of the total base number of the reads).
The main methods for matching reads to genome include Bowtie, BWA, STAR, etc.
The method of converting reads into FPKM generally includes the following steps: 1) reads is aligned to the reference genome using comparison software; 2) Using software such as Cufflinks for transcription reconstruction and quantification; 3) Using software such as RSEM and Kallisto to estimate gene expression; 4) Use the formula to calculate the FPKM value; 5) Convert the FPKM value into a representation matrix.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Rectum

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37.

extract_protocol:
Total RNA was extracted using TRIzol Reagent. Total RNA of each sample was quantified and qualified by Nanodrop. Next generation sequencing library preparations were constructed according to the manufacturers protocol.
The RNA library of RNA-SeQ was prepared by BGI.

treatment_protocol: shCAPG transfected HCT116 cells and induced with 100ng/ul doxycycline for 3 days.

value: Rectum

value: Human colon cancer cell

value: CAPG Knockdown

value: Dox inducing three days


title: WT_m6A MeRIP-seq_rep2


title: PY60 treated control – Biological replicate 2

city: La Jolla

first: Edyta

last: Grzelak

state: CA

address: 10550 N. Torrey Pines Road, SR202

department: Chemistry

institute: The Scripps Research Institute

data_processing:
Basecalling was performed by the sequencing core at the Scripps Research Institute
Transcript abundance was estimated using Kallisto
Assembly: Genome_build: GRCh37.p13 human genome reference assembly
Supplementary files format and content: tab-delimited text file includes raw file for each Sample
Supplementary files format and content: tab-delimited text file includes tpm values for each Sample

source_name: Skin; Epidermis

growth_protocol: HEKa were cultured in dermal cell basal medium supplemented with a Keratinocyte Growth Kit (PCS-200-030 and PCS-200-040 from ATCC) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
After 24-hour treatment with compound, the cells were washed once with PBS and then trypsinized with 500 µL of TrypLE Express dissociation reagent (Gibco) and neutralized with the addition of 500 µL of growth medium. After pelleting cells with centrifugation (300g) for 3 minutes in 1.5 mL microfuge tubes, total RNA was isolated using a RNeasy kit (Qiagen).
Three biological replicates were submitted for library preparation and sequencing on an Illumina HiSeq Platform (~58 million paired end reads per sample)

treatment_protocol: Cells were treated with DMSO or PY-60 for 24 hr.

value: Skin; Epidermis

value: HEKa

value: keratinocyte

value: PY60 treatment


title: shCAPG_+Dox_3


title: PY60 treated control – Biological replicate 3


title: M2_DMSO

value: DMSO


title: shCAPG_+Dox_1


title: PY60 treated control – Biological replicate 1


title: WT_m6A MeRIP-seq_rep1


title: IgG

value: islet


title: WT_RNA-seq_rep3

value: WT


title: shCAPG_-Dox_3

value: Untreated


title: DMSO treated control – Biological replicate 2

value: DMSO treatment


title: DMSO treated control – Biological replicate 3


title: M1_DMSO

value: Small intestine organoid


title: shCAPG_-Dox_2


title: WT_RNA-seq_rep2

value: Leaf


title: 6-ARID1A-rc_ARID1A_ChIPSeq

description:
50
genomic DNA

value: hESCs

value: ARID1A/BAF250A (D2A8U) Rabbit mAb, Cat# 12354, Cell signaling technology


title: shCAPG_-Dox_1

value: Rectum


title: WT_RNA-seq_rep1


title: M2222-M4

status: Public on Jun 10 2023

city: Kurume-city

first: Fumiko

last: Arakawa

address: Asahi-machi  67

department: Department of Pathology

institute: Kurume University, School of Medicine

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: hg38
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

source_name: male,ICTS,SSCT

extract_protocol:
SSCTs were removed, stored in RNAlater at 4℃ for more than overnight, and total RNA was isolated using Rneasy Plus Universal Mini Kit.
RNA libraries were prepared for sequencing using MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set  according protocols

tag: gender

value: male

value: SSCT


title: M1_GW

value: Male

value: 9 weeks old


title: HUVEC_PIK3CA-wt_rep4

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

country: Finland

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

data_processing:
Base-calling was perform during the sequencing run by RTA version 2.11.3 running under NextSeq Control Software version 2.2.0.4.
The RNA-Seq reads were processed using the nf-core RNA-Seq pipeline (version 3.0; Ewels et al. 2020) with the GRCh37 genome and the default quantification workflow (STAR aligner for read mapping followed by Salmon for gene quantification).
Genome_build: GRCh37
Supplementary_files_format_and_content: raw count matrix

source_name: umbilical vein

growth_protocol: HUVECs were isolated from human umbilical cords with collagenase type IV (Worthington) treatment and maintained in Endothelial Cell Growth medium (Cambrex Biosciences, East Rutherford, NJ, USA).

extract_protocol:
Cells were harvested with Buffer RLT (Qiagen, Hilden, Germany) and total RNA of was isolated using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.
RNA-Seq libraries were prepared from total RNA using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) according to the manufacturer’s instructions.

treatment_protocol: Lentivirus vectors pHAGE-PIK3CA (encoding PIK3CA wild-type; Addgene plasmid #116771) and pHAGE-PIK3CA-H1047R (encoding PIK3CA with pathological point mutation on p.H1047R; Addgene plasmid #116500) were received as gifts from Gordon Mills & Kenneth Scott. Third generation lentiviruses were produced in National Virus Vector Laboratories (NVVL, UEF, Kuopio, Finland). HUVECs were seeded onto 6-well plates at a density of 125,000 cells/well and allowed to adhere for 4 hours. Cells were transduced in fresh media with lentivirus vectors expressing PIK3CA WT or PIK3CA p.H1047R with multiplicity of infection (MOI) of 7.5-10. After culturing the cells for 16 h, cells were washed with PBS (Thermo Fisher Scientific) and fresh growth medium was added. After 72 h cells were passaged onto new 6-well plates and culturing was continued for additional 72 h.

value: endothelial cell

tag: lentivirus transduction

value: PIK3CA wild type

tag: replicate


title: HUVEC_UT_rep3

value: none (untransduced)


title: HUVEC_UT_rep4


title: 5S-005Hb

first: Ionita

middle: Calin

last: Ghiran

state: MA

address: 3 Blackfan Circle

department: Medicine

institute: Beth Israel Deaconess Medical Center

description: Healthy Subject

data_processing:
Non-normalized were obtained from raw CT values
Normalized were obtained from substracting the mean of raw CT values by 25
ExpressionSuite Software v1.3

source_name: Serum

label_protocol: As per TaqMan Advanced miRNA Assays protocol

extract_protocol: RNA was extracted from serum/plasma using Qiagen miRNeasy Serum/Plasma Advanced Kit

value: Female

tag: anticoagulant

value: S

tag: anatomical location

value: Entire cardiovascular system

tag: sample collection method

value: Peripheral venous cannula insertion - forearm


title: 5H-5Hb

description: Healthy Subject

source_name: Plasma

value: H


title: HUVEC_UT_rep2


title: M2422-M1


title: 5S-5Hb

description: Healthy Subject


title: HUVEC_PIK3CA-wt_rep3


title: 5H-0Hb

description: Healthy Subject


title: 5H-05Hb

description: Healthy Subject


title: 5S-0Hb

description: Healthy Subject


title: M1322-M3


title: HUVEC_PIK3CA-wt_rep1


title: M1222-M6


title: HUVEC_PIK3CA-wt_rep2


title: HUVEC_PIK3CA-mut_rep4

value: PIK3CA mutant p.H1047R


title: HUVEC_PIK3CA-mut_rep3


title: M0421-M2


title: DMSO treated control – Biological replicate 1

value: Skin; Epidermis

tag: cell line

value: HEKa

value: keratinocyte

value: DMSO treatment


title: 5H-005Hb

description: Healthy Subject


title: HUVEC_PIK3CA-mut_rep2


title: 5E-5Hb

description: Healthy Subject

value: E


title: HUVEC_PIK3CA-mut_rep1


title: HUVEC_UT_rep1


title: 5E-0Hb

description: Healthy Subject


title: 5S-05Hb

description: Healthy Subject


title: M0221-M5

value: male

value: SSCT


title: Squamous cell carcinoma of the tongue-CuB treated SCC9-rep3

city: ChangChun

first: Boqiang

last: Tao

address: Xi'an Road

institute: Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: Count
Supplementary_files_format_and_content: TPM
Supplementary_files_format_and_content: FPKM

source_name: Squamous cell carcinoma of the tongue

growth_protocol: SCC9 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Gaithersburg, MD, USA), high glucose or DMEM/F12. The culture media was supplemented with 10% fetal bovine serum and 100 U/mL penicillin/streptomycin (Gibco). The cells were cultured in a 5% CO2 incubator at 37°C.

extract_protocol:
total RNA was extracted from SCC9 cells through the use of a TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Ribosomal RNA was removed and purified using the Ribo Zero Magnetic Gold Kit (Sangon Biotech, Shanghai, China). RNA-seq was performed using the Sequencing and Non-Coding RNA Program (Sangon Biotech, Shanghai, China). Next, the reads were aligned to the genome. Then, the reads were compared to known genes, and the raw counts were generated and calculated using various algorithms, including HISAT2, RSeQC, BEDTools and Qualimap.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One replicate was CuB treated for 24 hours.

value: CuB


title: F2922-F3

source_name: female,ICTS,SSCT

value: female


title: Squamous cell carcinoma of the tongue-CuB treated SCC9-rep1


title: F2822-F5


title: F2722-F4


title: Squamous cell carcinoma of the tongue-SCC9-rep2

value: PBS


title: Squamous cell carcinoma of the tongue-SCC9-rep1


title: 5E-05Hb

description: Healthy Subject


title: SO4_NM2

city: Dijon

first: Pierre-Emmanuel

last: COURTY

address: 17 rue Sully

country: France

institute: INRAE Dijon

data_processing:
CLC genomics work bench 12.0.4
Sequences were trimmed for adaptator/lowquality sequence using CLC genomics benchwork (parameter - qualitit limit 0,05)
Trimmed sequence reads were mapped to vitis vinifera genome ( Vvinifera_457_v2.1 from phytozome (https://phytozome-next.jgi.doe.goc/info/Vvinifera_2_1) using CLC genomics benchwork (parameters - mismatch cost: 2 insertion cost: 3 deletion cost:3 length fraction 0.8 similarity fraction : 0.8)
Read counts extraction and normalization were performed using CLC genomics bench work
Assembly: Vvinifera_457_v2.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Vitis vinifera

source_name: grapevine rootstock SO4

growth_protocol: Rootstocks of seven hybrids (110 Richter, 140 Ruggeri, 1103 Paulsen, Selection Oppenheim4, 420A Millardet et de Grasset, 41B Millardet et de Grasset and 101.14 Millardet et de Grasset) and some of their parentals (V. riparia, V. rupestris and V. berlandieri) were chosen. Hybrids were chosen according to (i) their parentals, (ii) their use at the French vineyard scale, (iii) their tolerance to drought, active limestone and the chlorosis power index (CPI), and the vigor conferred to the scion (Figure 1, Table 1). Herbaceous cuttings of rootstocks were dipped into water-saturated clumps of peat (Jiffy) and grown in a mini greenhouse at 25 °C for 4 weeks. Well-rooted plants with homogenous growth were transplanted individually in 1L pots filled with clay beads at their bottom and a mix of sterile sand/zeolite (1:1). From the first week on, 20 mL of modified Hoagland solution (Gamborg et al. 1976) were applied weekly.

extract_protocol:
RNA was extracted using protocol from sportes et al 2022
genewiz

treatment_protocol: Plantlets were watered twice a week. After two weeks of growth, about 200 spores of the AMF strain R. irregularis (Ri) DAOM197198 (spore suspension, Premier tech, Canada) were added directly in contact with the root system of half of the plants. inoculation was repeated one times, a month after the first inoculation. The plants were grown in a glasshouse with day - night temperatures of ca. 24 - 18 °C. Sixty pots were prepared.

value: grapevine root

tag: genotype

value: rootstock SO4

value: control


title: 5E-005Hb

description: Healthy Subject

value: Female

value: Entire cardiovascular system


title: SO4_NM3


title: SO4_NM1


title: SO4_M3


title: SO4_M1


title: SO4_M2


title: 4S-05Hb

description: Healthy Subject

value: S

value: Peripheral venous cannula insertion - forearm


title: F1122-F6


title: 4S-005Hb

description: Healthy Subject


title: Rupestris_NM3

source_name: grapevine rootstock Rupestris

value: rootstock Rupestris


title: Rupestris_NM2


title: 4H-5Hb

description: Healthy Subject

value: H


title: Rupestris_NM1


title: Squamous cell carcinoma of the tongue-CuB treated SCC9-rep2


title: Squamous cell carcinoma of the tongue-SCC9-rep3


title: F1722-F2


title: Rupestris_M3

value: Mycorrhization with rhizophagus irregularis


title: 4S-0Hb

description: Healthy Subject


title: 4S-5Hb

description: Healthy Subject


title: F1422-F1


title: Rupestris_M2


title: Rupestris_M1


title: 4H-05Hb

description: Healthy Subject


title: Riparia_NM2

source_name: grapevine rootstock Riparia

value: rootstock Riparia


title: Riparia_NM1


title: 4H-005Hb

description: Healthy Subject


title: Riparia_M3


title: Riparia_M1


title: MDA_Pt5-Ov

city: Houston

first: Linghua

last: Wang

address: 1881 East Road,

institute: MD Anderson Cancer Center

description:
10x Genomics
MDA_Pt5-Ov

data_processing: Sequence data was put through the 10X genomic cell ranger 3.0 pipeline. QC and Fastq files were obtained and checked for data quality, and Fastq files were used to do further analysis.

source_name: Ovarian metastases

extract_protocol:
the fresh tissues were stored in the tissue storage solution (MACS Media) and dissociated into single cell suspensions for scRNA-seq. The ascites were spun down for 10 minutes at 1500 rpm, then pelleted cells were collected and stored in Bambanker (Nippon Genetics, no.392014681) for scRNA-seq. PBMCs were separated from peripheral blood according to standardized procedure. Red blood cells were lysed and singlets were counted by Trypan Blue Exclusion before loading on 10X Chromium microfluidic chips.  All sample were processed using the same protocol and by the same research assistant.
The scRNA-seq libraries were constructed using the Chromium Single Cell 5ʹ Library & Gel Bead Kit (PN: 220112, 10 Genomics). The single-cell GEMs were used to generate 10 Barcoded cDNA through reverse-transcription PCR and the cDNA was purified using Dynabeads MyOne SILANE magnetic beads (PN: 2000048, 10 Genomics). The Amplification Master Mix kit (PN: 220125, 10 Genomics) was used for cDNA amplification, and the Beckman Coulter SPRIselect reagent was used for cDNA purification and target enrichment. The Agilent Bioanalyzer High Sensitivity kit was used for determination of concentrations of cDNA libraries as well as the quality control of libraries. 50 ng of each sample library in 20 uL were mixed with 30 uL Fragmentation Mix (PN: 220108, 220107/220130, 10 Genomics) for pooling. The barcoded libraries were sequenced on the NovaSeq 6000 (Illumina) platform using S2 flow cell (100 cycles) in a 26 (read 1) × 8 (index) × 91 (read 2) configuration.

value: Ovarian metastases

value: Treatment Naive


title: MDA_Pt5-PBMC

description:
10x Genomics
MDA_Pt5-PBMC

source_name: PBMC

value: PBMC


title: MDA_Pt5-Ca

description:
10x Genomics
MDA_Pt5-Ca

source_name: Gastric tissue

value: Gastric tissue


title: MDA_Pt9-Li

description:
10x Genomics
MDA_Pt9-Li

source_name: Liver metastases

value: Liver metastases


title: MDA_Pt9-Ad

description:
10x Genomics
MDA_Pt9-Ad


title: MDA_Pt9-Ca

description:
10x Genomics
MDA_Pt9-Ca


title: Berlandieri_NM3

source_name: grapevine rootstock Berlandieri

value: rootstock Berlandieri


title: 4E-0Hb

description: Healthy Subject

value: E


title: MDA_Pt5-As

description:
10x Genomics
MDA_Pt5-As

source_name: Ascites

value: Ascites


title: 4E-5Hb

description: Healthy Subject


title: 4E-05Hb

description: Healthy Subject


title: Berlandieri_NM2

value: grapevine root

value: control


title: Berlandieri_M3


title: Berlandieri_NM1


title: MDA_Pt5-Ad

description:
10x Genomics
MDA_Pt5-Ad


title: Riparia_NM3


title: MDA_Pt4-Ca

description:
10x Genomics
MDA_Pt4-Ca


title: 4E-005Hb

description: Healthy Subject

value: Female

value: Entire cardiovascular system


title: Berlandieri_M2


title: 4H-0Hb

description: Healthy Subject

value: Peripheral venous cannula insertion - forearm


title: Berlandieri_M1


title: 10114_NM3

source_name: grapevine rootstock 10114

value: rootstock 10114


title: 10114_NM2


title: 3S-5Hb

description: Healthy Subject

value: Male

value: S


title: 10114_NM1


title: Riparia_M2

value: rootstock Riparia

value: Mycorrhization with rhizophagus irregularis


title: 3S-0Hb

description: Healthy Subject


title: 10114_M3


title: MDA_Pt3-As

description:
10x Genomics
MDA_Pt3-As

value: Treatment Naive


title: MDA_Pt3-Ca

description:
10x Genomics
MDA_Pt3-Ca


title: 10114_M2


title: 3S-05Hb

description: Healthy Subject


title: 10114_M1

source_name: grapevine rootstock 1103P


title: 1103P_NM3

value: rootstock 1103P


title: 1103P_NM2


title: 3H-5Hb

description: Healthy Subject

value: H


title: 3S-005Hb

description: Healthy Subject


title: MDA_Pt2-PB

description:
10x Genomics
MDA_Pt2-PB

source_name: PB

value: PB


title: MDA_Pt2-Ca

description:
10x Genomics
MDA_Pt2-Ca

value: Gastric tissue


title: 1103P_NM1


title: MDA_Pt2-As

description:
10x Genomics
MDA_Pt2-As


title: 1103P_M3


title: 1103P_M1


title: 1103P_M2


title: MDA_Pt1-Ca

description:
10x Genomics
MDA_Pt1-Ca


title: MDA_Pt4-As

description:
10x Genomics
MDA_Pt4-As


title: 3H-0Hb

description: Healthy Subject


title: 420A_NM1

source_name: grapevine rootstock 420A

value: rootstock 420A


title: 420A_NM3


title: 3H-005Hb

description: Healthy Subject


title: 420A_NM2


title: MDA_Pt1-Ad

description:
10x Genomics
MDA_Pt1-Ad


title: 3H-05Hb

description: Healthy Subject


title: 420A_M3


title: 420A_M2


title: 3E-0Hb

description: Healthy Subject

value: E


title: 420A_M1

value: grapevine root


title: 140Ru_NM3

source_name: grapevine rootstock 140Ru

value: rootstock 140Ru

value: control


title: 3E-05Hb

description: Healthy Subject

source_name: Plasma

value: Entire cardiovascular system