title: TF ChIP-seq from upper lobe of left lung (ENCLB409QHE)

description:
https://www.encodeproject.org/experiments/ENCSR224WWI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR224WWI
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR422TGJ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB409QHE
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens upper lobe of left lung tissue female adult (53 years)

value: CTCF

value: upper lobe of left lung

value: Bradley Bernstein, Broad

value: 53 year

value: female

value: ENCBS684YJH at ENCODE; https://www.encodeproject.org/ENCBS684YJH/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: Histone ChIP-seq from tibial artery (ENCLB373RPT)

status: Public on Jan 06 2020

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR187SVM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR187SVM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR819JOI
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB373RPT
fragmentation methods: sonication (generic)
size range: 200-600

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens male adult (54 years) tibial artery tissue

tag: antibody

value: tibial artery

value: tissue

tag: description

value: EnTEX:Artery - Tibial

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 54 year

tag: lab

tag: link

value: ENCBS646JZQ at ENCODE; https://www.encodeproject.org/ENCBS646JZQ/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from prostate gland (ENCLB623PVC)

description:
https://www.encodeproject.org/experiments/ENCSR133QBG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR133QBG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR113QDZ
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB623PVC
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) prostate gland tissue

value: prostate gland

tag: source

value: Kristin Ardlie

value: ENCBS619YXY at ENCODE; https://www.encodeproject.org/ENCBS619YXY/


title: Histone ChIP-seq from prostate gland (ENCLB112IBJ)

description:
https://www.encodeproject.org/experiments/ENCSR133QBG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR133QBG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR113QDZ
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB112IBJ
fragmentation methods: sonication (generic)
size range: 200-600

value: ENCBS633UTQ at ENCODE; https://www.encodeproject.org/ENCBS633UTQ/


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB333EOZ)

description:
https://www.encodeproject.org/experiments/ENCSR049FUB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR049FUB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR514EZP
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB333EOZ
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) esophagus squamous epithelium tissue

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa

value: 51 year

value: Bradley Bernstein, Broad

value: ENCBS821VGX at ENCODE; https://www.encodeproject.org/ENCBS821VGX/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: TF ChIP-seq from prostate gland (ENCLB601XIH)

description:
https://www.encodeproject.org/experiments/ENCSR230ORT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR230ORT
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR113QDZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB601XIH
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: tissue


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB003MHP)

description:
https://www.encodeproject.org/experiments/ENCSR049FUB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR049FUB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR514EZP
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB003MHP
fragmentation methods: sonication (generic)
size range: 200-600

value: female

value: ENCBS467KQD at ENCODE; https://www.encodeproject.org/ENCBS467KQD/


title: TF ChIP-seq from thyroid gland (ENCLB877HLO)

description:
https://www.encodeproject.org/experiments/ENCSR033KMZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR033KMZ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR164POT
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB877HLO
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) thyroid gland tissue

value: thyroid gland

value: male

value: adult

value: 54 year

value: ENCBS146XNZ at ENCODE; https://www.encodeproject.org/ENCBS146XNZ/


title: Histone ChIP-seq from tibial artery (ENCLB438ZLP)

description:
https://www.encodeproject.org/experiments/ENCSR187SVM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR187SVM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR819JOI
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB438ZLP
fragmentation methods: sonication (generic)
size range: 200-600

value: tibial artery

value: EnTEX:Artery - Tibial

value: ENCBS736PQK at ENCODE; https://www.encodeproject.org/ENCBS736PQK/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB715QEW)

description:
https://www.encodeproject.org/experiments/ENCSR030NGB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR030NGB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR777AJC
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB715QEW
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) esophagus muscularis mucosa tissue

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis

value: Kristin Ardlie

value: ENCBS390MKW at ENCODE; https://www.encodeproject.org/ENCBS390MKW/


title: Sample 21

status: Public on Dec 31 2019

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, for minimum quality threshold of 20. Reads were filtered for window (4 bases) based filtering with average quality lower than 15 and for minimum read length (25 bp).
Pre-processed reads were mapped to Bos taurus (UMD3.1) with STAR aligner including genome annotation (setting default parameters and allowing for maximum 5 mismatches).
Reads mapped to each gene (Ensembl Bos taurus release 87) were counted with HTSeq-count
Genome_build: Bos taurus (UMD3.1)
Supplementary_files_format_and_content: Text files (.txt) containing the Ensembl gene IDs and raw counts . One file for each sample (23 samples)

molecule: total RNA

organism: Bos taurus

source_name: endometrial biopsy

extract_protocol:
Endometrial biopsies were homogenized with Tissue Lyser LT.  RNA was isolated and purified with RNAeasy mini Kit.
Illumina TruSeq-stranded total RNA protocol

treatment_protocol: The biopsies were transferred in RNAlater (Qiagen). Each biopsy was divided into two replicates (each of 25-30 mg tissue) and stored at -80°C

tag: breed

value: Holstein

tag: tissue

value: endometrial biopsy

tag: pregnancy status

value: pregnant

tag: parity number

tag: days from last calving to embryo transfer


title: Sample 18


title: Sample 17


title: TF ChIP-seq from prostate gland (ENCLB140POX)

description:
https://www.encodeproject.org/experiments/ENCSR230ORT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR230ORT
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR113QDZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB140POX
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: prostate gland

value: tissue

value: Bradley Bernstein, Broad

value: ENCBS619YXY at ENCODE; https://www.encodeproject.org/ENCBS619YXY/


title: Histone ChIP-seq from ovary (ENCLB522KHW)

description:
https://www.encodeproject.org/experiments/ENCSR242AHB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR242AHB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR149EOW
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB522KHW
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) ovary tissue

value: ovary

value: female

value: adult

value: 51 year

value: ENCBS423EPK at ENCODE; https://www.encodeproject.org/ENCBS423EPK/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Sample 15


title: Sample 11


title: 4 mM fumarate, 1 % of oxygen_4

status: Public on Jan 02 2020

type: RNA

city: Braunschweig

first: Rebekka

last: Biedendieck

address: Rebenring 56

department: Institute of Microbiology

country: Germany

institute: Technische Universtität Braunschweig

hyb_protocol: 300 ng of Cy3-labeled RNA and 300 ng of Cy5-labeled RNA were mixed and fragmented, and hybridized to the microarray at 65 °C for 17 hours using the Agilent Hybridization Chamber according to the manufacturer’s instructions.

scan_protocol: The microarrays were scanned with the help of the Agilent C Scanner (Agilent Technologies, USA) using the software Agilent Scan Controll 8.4.1

data_processing: For feature extraction the software Feature Extraction 10.7.3.1 (Agilent Technologies, USA) was used, data processing was carried out using the Bioconducter – Linear Models for Microarray analysis (LIMMA) package of the R language (http://www.r-project.org).

organism: Geobacter sulfurreducens

source_name: G. sulfurreducens DSM12127_40 mM fumarate, anaerob

label_protocol: RNA samples were labelled with Cy3 or Cy5 using the ULS fluorescent labelling kit (Kreatech, Germany).

growth_protocol: Cells were grown in 500 mL minimal medium in a bioreactor system equipped with Rushton turbines set to 200 min-1 at 30 °C with a gas flow rate of 6 Lh-1. The medium contained the following components per liter of deionized water 0.31 g of NH4Cl, 0.13 g of KCl, 2.69 g of NaH2PO4 ∙ H2O, 4.33 g of Na2HPO4, 2 mM of L-cysteine, 12.5 mL of trace mineral solution (containing per litre: 1.5 g of nitrilotriacetic acid, 3 g of MgSO4 ∙ 7 H2O, 0.5 g of MnSO4 ∙ 2 H2O, 1 g of NaCl, 0.1 g of FeSO4 ∙ 7 H2O, 0.1 g of CoCl¬2, 0.1 g of CaCl2 ∙ 2 H2O, 0.13 g of ZnSO4, 0.1 g of CuSO4 ∙ H2O, 0.1 g of AlK(SO4)2, 0.1 g of H3BO3, 0.01 g of Na2MoO4 ∙ 2 H2O, 0.3 mg of Na2SeO3 ∙ 5 H2O and 0.03 g of NiCl2 ∙ 6 H2O) and 12.5 mL of vitamin solution (containing per litre: 2 mg of biotine, 2 mg of folic acid, 10 mg of pyridoxine hydrochloride, 5 mg of thiamine hydrochloride, 5 mg of riboflavin, 5 mg nicotinic acid, 5 mg DL-calcium pantothenate, 0.1 mg of vitamin B12, 5 mg of p-aminobenzoic acid and 5 mg of lipoic acid). 10 mM of acetate were added as carbon source. For anaerobic growth, 40 mM of fumarate were added as electron acceptor and inlet gas composition consisted of pure N2. For aerobic experiments, 4 mM of fumarate were added as electron acceptor in addition to 1, 3 or 5 % of oxygen provided in the gas inlet.

extract_protocol: Cell pellets were resuspended in 200 µL TE-buffer (10mM Tris HCl, 1 mM EDTA, pH 8) containing lysozyme from chicken egg white (Sigma Aldrich, St. Louis, Missouri, USA) at a concentration of 15 mgmL-1 and incubated for 30 min with regular mixing. Subsequently, glass beads (diameter 150-212µm) were added and cells were vortexed for 3 min for mechanical cell disruption. RNA was purified from the supernatant using the RNeasy Mini Kit (Quiagen, Hilden, Germany) according to the manufacturer’s instructions. Digestion of chromosomal DNA with DNAse (Quiagen, Hilden, Germany) was carried out twice.

treatment_protocol: Cells were harvested by centrifugation of 15 mL or 50 mL (in case of experiment performed with 5 % of oxygen) of cultivation broth in falcon tubes at 11.800 g and 4 °C for 10 min. After discarding the supernatant, cell pellets were immediately frozen in liquid nitrogen and stored at -80 °C until RNA purification.

tag: strain

tag: growth condition

value: 40 mM fumarate, anaerobic

source_name: G. sulfurreducens DSM12127_4 mM fumarate and 1 % oxygen in gas inlet

value: 4 mM fumarate, 1 % of oxygen


title: 4 mM fumarate, 5 % of oxygen_4

source_name: G. sulfurreducens DSM12127_4 mM fumarate and 5 % oxygen in gas inlet

value: 4 mM fumarate, 5 % of oxygen


title: 4 mM fumarate, 1 % of oxygen_1


title: 4 mM fumarate, 1 % of oxygen_3


title: 4 mM fumarate, 5 % of oxygen_1


title: Sample 8

value: Holstein


title: 4 mM fumarate, 3 % of oxygen_3

source_name: G. sulfurreducens DSM12127_4 mM fumarate and 3 % oxygen in gas inlet

value: 4 mM fumarate, 3 % of oxygen


title: Sample 10

value: endometrial biopsy

value: pregnant


title: Sample 23


title: Sample 7


title: 4 mM fumarate, 3 % of oxygen_1


title: 4 mM fumarate, 3 % of oxygen_2


title: Sample 5


title: Sample 22


title: Sample 16

value: non-pregnant


title: Sample 19


title: Sample 14


title: 4 mM fumarate, 5 % of oxygen_2


title: Sample 13


title: Sample 12


title: Sample 20


title: 4 mM fumarate, 1 % of oxygen_2


title: Sample 9


title: 4 mM fumarate, 3 % of oxygen_4

source_name: G. sulfurreducens DSM12127_40 mM fumarate, anaerobic


title: Sample 4


title: Sample 3


title: Sample 2


title: 4 mM fumarate, 5 % of oxygen_3


title: Sample 1


title: CD271_neg_4

city: Winnipeg

first: Tamra

last: Werbowetski-Ogilvie

state: Manitoba

address: 611-745 Bannatyne Avenue

department: Biochemistry & Medical Genetics

country: Canada

institute: University of Manitoba

data_processing:
Aligned reads to GRCh38 genome/GENCODE v23 transcript annotation using hisat2 v2.0.4
Assigned mapped reads to GENCODE v23 transcripts using featureCounts v1.4.6-p3
Performed differential expression analysis using DESeq2 v1.12.2 in R v3.3.1. Expression was compared in CD271+ vs CD271- samples, with replicate pairs included in the model formula
Generated table of differentially-expressed genes at a padj/FDR value of 0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: (1) Matrix of read counts in genes vs samples. (2) Table of differentially-expressed genes (DESeq2 results format with annotation of gene symbol and gene_biotype)
Supplementary_files_format_and_content: all_samples_unstranded_GENCODE.23.txt.gz: gene/read count matrix (featureCounts)
Supplementary_files_format_and_content: Meduloblastoma CD271- vs CD271+ 5rep.xlsx: Excel file of differentially-expressed genes (FDR <0.05) from DESeq2

source_name: Medulloblastoma

growth_protocol: UI226 tumorspheres were dissociated and counted using an automated cell counter.  Cells were stained with CD271 (BD Biosciences Cat#560326) and 7-Aminoactinomycin D (7AAD) viability dye (Beckman Coulter, Inc., Mississauga ON, Canada) and then FACS sorted on the basis of CD271+ and CD271- expression using a MoFlo XDP cell sorter (Beckman Coulter, Inc.) at the University of Manitoba. Analysis was performed using FlowJo software (Tree Star Inc., Ashland, OR, USA).

extract_protocol:
Sorted CD271+ and CD271- cells were collected and RNA was isolated using the Norgen RNA extraction kit (Norgen Biotek) according to manufacturer’s instructions for mammalian cultured cells.
Libraries were prepared from 500 ng of input total RNA with the Truseq RNA v2 library prep kit (Illumina).
DNA libraries were prepared with unique barcodes and pooled; 75 cycles of single-end sequencing were performed on a high output flowcell with the NextSeq 500 (Illumina).

tag: cell line

value: UI226 SHH Medulloblastoma tumorspheres

tag: cd271 sorting status


title: CD271_pos_2


title: CD271_neg_3


title: CD271_pos_5


title: Sample 6


title: CD271_neg_1


title: CD271_pos_3


title: CD271_pos_1


title: U2O_S7_R1_001

status: Public on Dec 19 2019

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

data_processing:
Runing STAR aligner in "Gene_counts" mode
Merging STAR output ("ReadPerGene.out" files) with Python into a single table
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw gene counts for each sample

source_name: human osteosarcoma

extract_protocol:
Cell line samples were stabilized in RNAlater (Qiagen, Germany) and stored at room temperature. RNA extraction was performed immediately before the preparation of sequencing libraries using QIAGEN RNeasy Kit (Qiagen) or Direct-zol RNA MiniPrep (Zymo Research, USA), followed by an additional purification step by TRI Reagent (MRC, USA) for cell lines in RNAlater and RecoverAll Total Nucleic Acid Isolation Kit (Invitrogen, USA) for FFPE, according to the manufacturers’ protocols. RNA was quantified using Nanodrop (Thermo Fisher Scientific, USA), ethanol-precipitated, and stored in liquid nitrogen until sequencing.
RNA Integrity Number (RIN) was measured using Agilent 2100 bioanalyzer (Agilent, USA). Agilent RNA 6000 Nano or Qubit RNA Assay (Thermo Fisher Scientific) kits were used to measure RNA concentration. KAPA RNA Hyper with RiboErase Kit (KAPA Biosystems, USA) was used for further depletion of ribosomal RNA and library preparation. Different adaptors were used for multiplexing samples in one sequencing run. Library concentration and quality were measured using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and Agilent TapeStation system (Agilent). Single-end RNA sequencing was performed using Illumina HiSeq 3000 system (Illumina, USA), 50 bp read length, for approx. 30 million raw reads per sample. Data quality check was conducted using Illumina SAV. De-multiplexing was performed with Illumina Bcl2fastq2 v 2.17 software.


title: CD271_pos_4


title: 8_S3_R1_001

source_name: neuroblastoma biopsy

value: neuroblastoma biopsy


title: U373_S5_R1_001

source_name: human glioma


title: HOS_S6_R1_001

value: HOS


title: T98g_S4_R1_001


title: 1MR-32_S1_R1_001

source_name: human neuroblastoma


title: SH-SY-Y5_S2_R1_001


title: mono 2

status: Public on Nov 27 2019

city: Newcastle upon Tyne

first: Anastasia

last: Resteu

address: M3.127, 3rd Floor Leech Building, Framlington Place

country: United Kingdom

institute: Newcastle University

data_processing:
trimmd with Trimmomatic v 0.36
aligned with STAR v 2.4.0 - bases with quality scores below Q10 (inferred base cell accuracy below 90%) were trimmed and reads shorter than 50bp were dropped
counts obtained with HTSEQ v 0.6.1

Genome_build: GRCh38.p7 (GENCODE release 25)
Supplementary_files_format_and_content: csv files containg HTSEQ counts

source_name: Peripheral blood

extract_protocol:
Flow Cytometric Sorting
Nextera XT

tag: day

value: blood

tag: cell type

value: monocyte


title: 9_S4_R1_001


title: mono 1


title: IC-PD1-12

status: Public on Nov 26 2019

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

description:
CRISPR Screen
Amplified sgRNA pools

data_processing:
The adaptor sequences were trimmed using cutadapt (v1.18) and the untrimmed reads were removed.
gRNAs were mapped to the annotation file and read count tables were made.
MAGeCK (0.5.8) was used to normalize the count table based on median normalization and fold changes and the significance of the changes in the conditions were calculated for genes and sgRNAs.
Genome_build: mm10
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include read counts.

organism: Mus musculus

source_name: KP allograft tumor

growth_protocol: KP-Cas9 cells were transfected with lentivirus pool (MOI=0.2), and selected by using 5ug/ml Blasticidin, and then cultured for 2 weeks for expanding. At week 2, harvested part of the cell pool as input ctrl, and subcutaneously injected cell pool into the B6 Rag1-/- mice and B6 WT mice to form tumors. Then performed 3 weeks' treatment and harvested tumors.

extract_protocol:
For Library, just used plasmid pool as PCR template; For input cell pool, extracted genomic DNA was used as PCR template; For tumor samples, homogenated tumor and extracted genomic DNA, and then used as PCR template.
For Library, just amplified sgRNA pool from the plasmid pool; For Input cell pool, amplified sgRNA pool from genomic DNA; For samples from treatment groups, amplified sgRNA pool from genomic DNAs.

treatment_protocol: ID-IgG group has 12 tumors, which were treated with IgG control; ID-PD1 group has 12 tumors, which were treated with anti-PD1; IC-IgG group has 12 tumors, which were treated with IgG control; IC-PD1 group has 12 tumors, which were treated with anti-PD1. Here ID means immunodeficient mice (B6 Rag1-/-), and IC means immunocompetent mice (B6 WT).

tag: strain/background

tag: mouse genotype/variation

value: WT

tag: treatment

value: Subcutaneously injected tumor

tag: group

value: Immunocompetent mouse + anti-PD1


title: IC-PD1-11

description:
CRISPR Screen
Amplified sgRNA pools


title: CD271_neg_5


title: IC-PD1-7

description:
CRISPR Screen
Amplified sgRNA pools


title: IC-PD1-9

description:
CRISPR Screen
Amplified sgRNA pools


title: IC-PD1-8

description:
CRISPR Screen
Amplified sgRNA pools


title: IC-PD1-10

description:
CRISPR Screen
Amplified sgRNA pools


title: CD271_neg_2


title: moLC 1

source_name: 3 day culture

growth_protocol: 3 days culture with GM-CSF and TGF-B on OP9-DLL4 feeder layer in RF10 Media (RPMI+10%FCS)

value: culture

value: monocyte-derived Langerhans cells


title: IC-PD1-6

description:
CRISPR Screen
Amplified sgRNA pools


title: 10_S5_R1_001


title: moLC 2


title: IC-IgG-12

description:
CRISPR Screen
Amplified sgRNA pools

value: IgG control

value: Immunocompetent mouse + IgG


title: IC-IgG-11

description:
CRISPR Screen
Amplified sgRNA pools


title: IC-PD1-2

description:
CRISPR Screen
Amplified sgRNA pools


title: IC-PD1-5

description:
CRISPR Screen
Amplified sgRNA pools


title: IC-PD1-4

description:
CRISPR Screen
Amplified sgRNA pools


title: IC-IgG-5

description:
CRISPR Screen
Amplified sgRNA pools


title: IC-PD1-3

description:
CRISPR Screen
Amplified sgRNA pools


title: IC-PD1-1

description:
CRISPR Screen
Amplified sgRNA pools


title: IC-IgG-6

description:
CRISPR Screen
Amplified sgRNA pools


title: IC-IgG-9

description:
CRISPR Screen
Amplified sgRNA pools


title: IC-IgG-10

description:
CRISPR Screen
Amplified sgRNA pools


title: IC-IgG-8

description:
CRISPR Screen
Amplified sgRNA pools


title: IC-IgG-2

description:
CRISPR Screen
Amplified sgRNA pools


title: IC-IgG-1

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-PD1-12

description:
CRISPR Screen
Amplified sgRNA pools

value: Immunodeficient mouse + anti-PD1


title: IC-IgG-3

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-PD1-11

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-PD1-10

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-PD1-9

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-PD1-8

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-PD1-6

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-PD1-5

description:
CRISPR Screen
Amplified sgRNA pools


title: IC-IgG-7

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-PD1-4

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-IgG-12

description:
CRISPR Screen
Amplified sgRNA pools

value: Immunodeficient mouse + IgG


title: IC-IgG-4

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-PD1-2

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-IgG-11

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-IgG-6

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-IgG-9

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-IgG-10

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-IgG-7

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-IgG-1

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-IgG-2

description:
CRISPR Screen
Amplified sgRNA pools


title: Input

description:
CRISPR Screen
Amplified sgRNA pools

source_name: KP cell pools

value: In vitro cultured KP-Cas9 cells

value: Input


title: ID-PD1-3

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-IgG-5

description:
CRISPR Screen
Amplified sgRNA pools


title: ID-IgG-8

description:
CRISPR Screen
Amplified sgRNA pools


title: A549-2 RIP-seq

status: Public on Sep 26 2019

city: guangzhou

first: Xingyang

last: Li

state: Guangdong

address: 195, dongfengxi road

department: Department of Temporomandibular Joint Surgery

country: China

institute: Affiliated Stomatology Hospital of Guangzhou Medical University

description: Lung epithelial cell

data_processing:
m6A-seq and RIP-seq reads were aligned to the hg38 genome assembly using STAR version 020201 with the "twopassMode"  configuration.
m6A peaks were called using MeTPeak version 1.0.0 with the default setting.
Genes expression estimate were calculated using RSEM.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using bedtools.
Genome_build: hg38
Supplementary_files_format_and_content: txt files were generated using RSEM and MeTPeak.

growth_protocol: A549 and A549 DDP cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
Eluted m6A-containing fragments (IP) and untreated input control fragments are converted to final cDNA library in accordance with a strand-specific library preparation by dUTP method. Then we performed the paired-end 2×150bp sequencing on an Illumina NovaseqTM 6000 platform at the LC-BIO Bio-tech ltd (Hangzhou, China) following the vendor's recommended protocol.

value: Lung cancer cell line

tag: passages

tag: rip antibody

value: YTHDF1(Proteintech, 17479-1-AP)


title: Library

description:
CRISPR Screen
Amplified sgRNA pools

molecule: other

organism: synthetic construct

source_name: Plasmid pools

value: Library


title: A549-1 RIP-seq

description: Lung epithelial cell


title: A549-2 input.

description: Lung epithelial cell


title: GPR43KO ILC3-F

status: Public on Sep 16 2019

city: MA

first: Sena

last: Bae

address: Boston

institute: Harvard T.H. Chan School of Public Health

data_processing:
Low quality reads were filtered by using sickle version 1.33
Alignment to the NCBI GRCm38/mm10 mouse genome using the STAR aligner version 2.7 with default setting
Reads per gene counts using HTSeq version 0.11.1
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Entrez ID) in each sample

source_name: colon

extract_protocol:
Colonic ILC3s (CD45+Lin- CD90.2+ NK1.1- NKp46+/- KLRG1-) were sorted from Ffar2-/- mice and littermate control WT mice. Two independent RNA-seq experiments were performed. (i.e.  two biological replicates (sex-matched) for each group that contained RNA from pooled colonic ILC3s from 10 to 15 mice). Sorted ILC3s were collected in RNAlater (Sigma-Aldrich) and RNA was extracted with RNeasy Micro Kit (Qiagen).
RNA quality verification, library preparation, and sequencing were performed at BPF Next-Gen Sequencing Core Facility at Harvard Medical School. RNA samples showed an average 9.0 of RNA integrity number (RIN) and libraries were generated using SMART-seq v4 Ultra Low Input RNA kit (Takara Bio Inc.).

value: colon

tag: genotype/variation

tag: Sex

value: F


title: A549-1 input.

description: Lung epithelial cell


title: ID-PD1-7

description:
CRISPR Screen
Amplified sgRNA pools

tag: tissue


title: WT ILC3-F

value: Wild-Type


title: GPR43KO ILC3-M

value: M


title: WT ILC3-M


title: mm10_J2_WT_H3K27me2

status: Public on Sep 11 2019

city: Dublin 2

first: Craig

last: Monger

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

description: Note that this was previously incorrectly labelled as an me3 chip.

data_processing:
Align reads to reference genome (hg19) using bowite2 and the --very-sensitive-local parameter
Align reads to spike-in genome (mm9 or dm6) using bowtie2 and the --very-sensitive-local parameter
Convert sams to sorted bams using Samtools, and extract headers from both alignments for each of the 2 alignments (reference and spike-in)
Filter read ambiguosly aligned to both genomes using Picards FilterSamReads, mark duplicates using Picards MarkDuplicates and index the filtered, marked bam file with Samtools
The number of spike-in reads was used as a scale factor to generate normalised bigWigs using bamCoverage from the deeptools suite with a bin size of 10
Genome_build: hg19, mm9 & dm6
Supplementary_files_format_and_content: bigwig files of ChIP-Rx spike-in normalised tracks for each sample

organism:
Drosophila melanogaster
Mus musculus

source_name: Embryonic stem cell and S2 cell line

growth_protocol:
ESCs that have been maintained in a pluripotent state through culturing with LIF on gelatinised plates.ChIPs for certain histone modification ChIP samples include a 2% spike in of Drosophila S2 chromatin that were cultured according to established protocols. ChIPs for PRC2 components and H2AK119ub1 include a 10% spike in of human NT2 chroamtin that were cultured according to established protocols .
Embryonic stem cells (ESCs) were grown on gelatinised culture dishes in GMEM (sigma) supplemented with 10% ES cell qualified FBS (Millipore), 100 U/mL penicillin (Gibco), 100 U/mL streptomycin (Gibco), 50µM β-mercaptoethanol (sigma), 1:100 Glutamax (Gibco), 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco) and 1:500 homemade leukemia inhibitory factor (LIF). S2 cells were cultured in Schneider media supplemented with 10% Heat inactivated FBS

extract_protocol:
Embryonic stem cells were washed once with PBS before crosslinking for 10 minutes with PBS containing 1% formaldehyde (Sigma). Crosslinking was quenched with 0.125M Glycine for 5 minutes before two PBS washes. The crosslinked cells were lysed in 6mL of SDS-Lysis buffer (100mM NaCl, 50mM Tris pH8.1, 5mM EDTA pH 8.0, 0.02% NaN3, 0.5% SDS, 2μg/mL Aprotonin, 1μg/mL Leupeptin, 1mM PMSF). Chromatin was pelleted by centrifugation at 1200rpm for 5 minutes at room temperature. The supernatant was then discarded, and the chromatin was resuspended in 3mL of ChIP buffer (2:1 dilution of SDS-Lysis buffer: Triton dilution buffer [100mM Tris pH 8.6, 100mM NaCl, 5mM EDTA pH 8.0, 0.02% NaN3, 5% Triton X-100, 2μg/mL Aprotonin, 1μg/mL Leupeptin, 1mM PMSF]). Chromatin was sheared to approximately 200bp-600bp fragments by sonication on a Branson Sfx150 Sonifier for a total of 4min at 50% amplitude. Sonicated chromatin was incubated overnight with antibody while rotating at 4°C. Following clarification, the chromatin was incubated for 3 hours with 50µL of protein A or G Dyna beads (ThermoFisher) beads. After incubation, the beads were washed three times in Mixed Micelle Buffer (150mM NaCl, 20mM Tris pH 8.1, 5mM EDTA pH 8.0, 5.2% Sucrose, 0.02% NaN3, 1% Triton X-100, 0.2% SDS), twice with Buffer 500 (0.1% Sodium Deoxycholate, 1mM EDTA pH 8.0, 50mM HEPES pH7.5, 1% Triton X-100, 0.02% NaN3), twice with LiCl detergent wash (0.5% Sodium Deoxycholate, 1mM EDTA pH 8.0, 250mM LiCl, 0.5% NP-40, 10mM Tris pH 8.0, 0.02% NaN3) and finally one wash with TE. Immunoprecipitated material was eluted from the beads with Elution buffer (0.1M NaHCO3, 1% SDS) while shaking for 1 hour at 65°C. The supernatant was retained and incubated overnight at 65°C while shaking to reverse the crosslinks. The eluted complexes were then subject to RNase (Thermo Fisher) and Proteinase K (Sigma) treatment prior to DNA clean up (Qiagen Qiaquick PCR Purification Kit). ChIP enrichments were analysed by qPCR using the SYBR Green I detection chemistry (M3003E NEB) on an Applied Biosystems Quant Studio 3 platform.
Following the ChIP experiment, the precipitated DNA was quantified using the Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Q32854). A Total of 2-10 ng of DNA from each ChIP-Rx experiment was used for library preparation using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) and NEBNext Multiplex Oligos for Illumina (Set#1, NEB #7335). Following adaptor ligation, DNA was PCR amplified for 5-9 cycles, depending on amount of input DNA. DNA purification was then performed using NEBNext Sample Purification Beads (E7767S). The quality of DNA libraries was analysed on a High Senstivity D1000 Screen Tape (Agilent). The resulting libraries were then used for cluster generation and sequencing using an Illumina NextSeq 500 (ID: NB501524), with 75bp read length.

value: Embryonic stem cell and S2 cell line

tag: genotype

value: Wild type

tag: antibody


title: S4_MU1

status: Public on Sep 01 2019

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
Sequencing reads were trimmed for adapter contamination with Cutadapt
then aligned to fly genome with HISAT2
read counts were produced by using featureCounts
Genome_build: DM6
Supplementary_files_format_and_content: read counts

organism: Drosophila melanogaster

extract_protocol:
Ovaries were dissected on ice, and total RNA was harvested using Trizol reagent.
RNA libraries were generated with standard Illumina protocols

tag: age

value: 4-6 days

value: ovaries


title: mm10_J2_WT_H3K27me3

description: Note that this sample was previously incorrectly labelled as an me2 chip.


title: ID-IgG-4

description:
CRISPR Screen
Amplified sgRNA pools

value: IgG control

value: Subcutaneously injected tumor


title: S6_MU3


title: S5_MU2


title: ID-IgG-3

description:
CRISPR Screen
Amplified sgRNA pools


title: S3_WT3


title: S2_WT2


title: CRPC_17-043I1_LN

status: Public on Jul 17 2019

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: CRPC lymph node (LN) metastasis

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.X software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Reads were mapped to the hg38 human genome build using TopHat v2.X and bowtie2 v2.2.X.
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.1
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: CRPC lymph node (LN) metastasis

extract_protocol:
Total RNA was isolated from 98 CRPC metastases frozen in Optimal Cutting Temperature compound (OCT; Tissue-Tek) from 55 patients with RNA STAT-60 (Tel-Test). Using an H&E stained slide for each metastatic site for orientation, one millimeter core punches of tumor were obtained, or where appropriate multiple sections enriched for tumor were cut using a Leica CM3050S cryostat. Total RNA was isolated from flash frozen LuCaP xenograft tissue or cell lines with RNA STAT-60 (Tel-Test) followed by purification with RNeasy Mini Kit (Qiagen) utilizing the manufacturer’s recommended in solution DNase digestion (Qiagen).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol. Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50 bp paired end reads.

tag: gender

value: male

value: prostate cancer

tag: tumor site

value: lymph node (LN)

tag: patient

tag: molecular phenotype


title: CRPC_17-043J1_PERIRECTAL_OMENTAL

description: CRPC perirectal omental metastasis

source_name: CRPC perirectal omental metastasis

tag: cell type

value: perirectal omental


title: CRPC_17-042H2_BONE

description: CRPC bone metastasis

source_name: CRPC bone metastasis

value: bone


title: CRPC_17-036L3_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_17-036N6_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_17-033H7_TAIL_OF_PANCREAS

description: CRPC tail of pancreas metastasis

source_name: CRPC tail of pancreas metastasis

value: tail of pancreas


title: CRPC_17-036H10_LIVER

description: CRPC liver metastasis

source_name: CRPC liver metastasis

value: liver


title: CRPC_17-017N1_LUNG

description: CRPC lung metastasis

source_name: CRPC lung metastasis

value: lung


title: CRPC_17-007H1_LIVER

description: CRPC liver metastasis


title: CRPC_16-101N2_PARIETAL_DIAPHRAGM

description: CRPC parietal diaphragm metastasis

source_name: CRPC parietal diaphragm metastasis

value: parietal diaphragm


title: CRPC_17-022K1_LIVER

description: CRPC liver metastasis


title: CRPC_17-033J1_PANCREAS

description: CRPC pancreas metastasis

source_name: CRPC pancreas metastasis

value: pancreas


title: CRPC_17-017H8_LIVER

description: CRPC liver metastasis


title: CRPC_16-101J6_LIVER

description: CRPC liver metastasis


title: CRPC_16-071I2_LUNG

description: CRPC lung metastasis


title: CRPC_16-080L2_LIVER

description: CRPC liver metastasis


title: CRPC_16-071H10_LIVER

description: CRPC liver metastasis


title: CRPC_16-052K1_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_16-052H1_LIVER

description: CRPC liver metastasis


title: CRPC_17-043K1_PELVIC_PERITONEAL

description: CRPC pelvic peritoneal metastasis

source_name: CRPC pelvic peritoneal metastasis

value: pelvic peritoneal


title: CRPC_15-069P5_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_15-096FF1_BONE

description: CRPC bone metastasis


title: CRPC_15-090H1_LIVER

description: CRPC liver metastasis


title: CRPC_15-090KK1_BONE

description: CRPC bone metastasis


title: CRPC_15-069K1_LIVER

description: CRPC liver metastasis


title: S1_WT1


title: CRPC_15-096L2_PERIAORTIC

description: CRPC periaortic metastasis

source_name: CRPC periaortic metastasis

value: periaortic


title: CRPC_15-023AA1_BONE

description: CRPC bone metastasis


title: CRPC_15-023L2_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_15-010K4_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_15-023K2_SPLEEN

description: CRPC spleen metastasis

source_name: CRPC spleen metastasis

value: spleen


title: CRPC_15-096M1_PERIAORTIC_DIAPHRAGM

description: CRPC periaortic diaphragm metastasis

source_name: CRPC periaortic diaphragm metastasis

value: periaortic diaphragm


title: CRPC_14-096J1_LEFT_POSTERIOR

description: CRPC left posterior metastasis

source_name: CRPC left posterior metastasis

value: left posterior


title: CRPC_14-077N15_LIVER

description: CRPC liver metastasis


title: CRPC_14-105J1_LIVER

description: CRPC liver metastasis


title: CRPC_14-091E1_LUNG

description: CRPC lung metastasis


title: CRPC_14-053H3_LIVER

description: CRPC liver metastasis


title: CRPC_14-053K7_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_14-053AA3_BONE

description: CRPC bone metastasis


title: CRPC_14-043H6_LIVER

description: CRPC liver metastasis


title: CRPC_15-003H1_LIVER

description: CRPC liver metastasis


title: CRPC_14-039K4_LIVER

description: CRPC liver metastasis


title: CRPC_14-043CC3_BONE

description: CRPC bone metastasis


title: CRPC_14-039E3_LUNG

description: CRPC lung metastasis


title: CRPC_13-117H7_LIVER

description: CRPC liver metastasis


title: CRPC_15-010H1_LIVER

description: CRPC liver metastasis


title: CRPC_14-031L2_PLEURAL

description: CRPC pleural metastasis

source_name: CRPC pleural metastasis

value: pleural


title: CRPC_13-122H1_PELVIC_MASS

description: CRPC pelvic mass metastasis

source_name: CRPC pelvic mass metastasis

value: pelvic mass


title: CRPC_14-031H2_LIVER

description: CRPC liver metastasis

value: male


title: CRPC_13-104I3_LN

description: CRPC lymph node (LN) metastasis

value: prostate cancer


title: CRPC_13-101H1_LN

description: CRPC lymph node (LN) metastasis

value: lymph node (LN)


title: CRPC_13-104K7_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_13-101K3_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_13-099H7_LIVER

description: CRPC liver metastasis


title: CRPC_13-104AA2_BONE

description: CRPC bone metastasis


title: CRPC_13-099J2_LUNG

description: CRPC lung metastasis


title: CRPC_13-042M3_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_13-084H5_LIVER

description: CRPC liver metastasis


title: CRPC_13-012L2_LIVER

description: CRPC liver metastasis


title: CRPC_12-021I1_LUNG

description: CRPC lung metastasis


title: CRPC_12-021H6_LIVER

description: CRPC liver metastasis


title: CRPC_12-005K3_RENAL

description: CRPC renal metastasis

source_name: CRPC renal metastasis

value: renal


title: CRPC_12-011I8_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_12-021FF6_BONE

description: CRPC bone metastasis

value: bone


title: CRPC_12-011J3_BLADDER

description: CRPC bladder metastasis

source_name: CRPC bladder metastasis

value: bladder


title: CRPC_12-005H6_LIVER

description: CRPC liver metastasis

value: liver


title: CRPC_12-005I5_LIVER

description: CRPC liver metastasis


title: CRPC_11-028L3_LUNG

description: CRPC lung metastasis

value: lung


title: CRPC_11-028H1_LIVER

description: CRPC liver metastasis


title: CRPC_10-056J1_LN

description: CRPC lymph node (LN) metastasis

source_name: CRPC lymph node (LN) metastasis


title: CRPC_10-056K1_LIVER

description: CRPC liver metastasis


title: CRPC_11-028G3_ADRENAL

description: CRPC adrenal metastasis

source_name: CRPC adrenal metastasis

value: adrenal


title: CRPC_10-039G1_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_10-013L2_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_10-013K4_DIAPHRAM

description: CRPC diaphram metastasis

source_name: CRPC diaphram metastasis

value: diaphram


title: CRPC_13-012M3_LUNG

description: CRPC lung metastasis


title: CRPC_08-093H3_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_07-042K2_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_06-127G3_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_07-042L3_ADRENAL

description: CRPC adrenal metastasis


title: CRPC_08-020I2_DIAPHRAM

description: CRPC diaphram metastasis


title: CRPC_06-131TT1_BONE

description: CRPC bone metastasis

source_name: CRPC bone metastasis


title: CRPC_08-020T1_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_05-217I3_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_05-165O1_ADRENAL

description: CRPC adrenal metastasis


title: CRPC_05-165K1_LUNG

description: CRPC lung metastasis


title: CRPC_05-144V3_ADRENAL

description: CRPC adrenal metastasis


title: CRPC_05-217F4_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_05-144E6_LIVER

description: CRPC liver metastasis

source_name: CRPC liver metastasis


title: CRPC_05-011D5_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_05-011G2_LUNG

description: CRPC lung metastasis

source_name: CRPC lung metastasis


title: CRPC_04-050P1_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_04-050S1_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_03-163S5_LIVER

description: CRPC liver metastasis


title: CRPC_03-139M5_RETROPERITONEAL

description: CRPC retroperitoneal metastasis

source_name: CRPC retroperitoneal metastasis

value: retroperitoneal


title: CRPC_03-192C3_LN

description: CRPC lymph node (LN) metastasis


title: CRPC_03-027P3_LIVER

description: CRPC liver metastasis


title: TTXwd ratHipp RNA_seq Grin3a knockdown Rep3

status: Public on Jul 08 2019

city: Durham

first: Anne

last: West

state: NC

address: 311 research drive

department: Neurobiology

institute: Duke University

description: 1µM TTX for 48 hrs plus 6 hrs TTX withdrawal

data_processing:
Hiseq 4000 reads were trimmed (Trimmomatic)
RNAseq were aligned to the rn5 genome by TopHat2
FPKM matrix was derived using Cufflinks suite using default settings,  and differential expression quantified using CuffDiff at p-FDR < 0.05.
Genome_build: rn5
Supplementary_files_format_and_content: bigwig

organism: Rattus norvegicus

source_name: Cultured hippocampal neurons

growth_protocol: Neuron-enriched cultures were generated from hippocampus of male and female E18.5 CD IGS rat embryos (Charles River Laboratories) and cultured in  neurobasal medium with B27 supplements on poly-d-lysine–coated dishes. Neurons were infected with lentiviruses at 1 day in vitro (DIV), they were treated with 1µM TTX at 5DIV and then either harvested on 7DIV or TTX was withdrawn for 6hr before RNA harvesting

extract_protocol:
RNA was harvested using Qiagen RNeasy Mini Kit (Cat# 74104).  Potential DNA contamination was removed on-column DNase’s digestion using Qiagen’s RNase-free DNase Set (Cat# 79254).
Stranded mRNA-seq was done by Duke Sequencing core facility using the Kapa Stranded mRNA-Seq library prep kit to make sequencing libraries, which are typically sequenced on Illumina instruments with a 50 bp single end reads length.

treatment_protocol: RNA interference, we used shRNAs targeting rat Grin3a  that were cloned in the lentiviral vector pLKO.1 (Thermo Scientific). Grin3a shRNA (TRCN0000100220): GCTCCATGACAAGTGGTACAA. Empty pLKO.1 vector was used as the control. Viral shRNAs were packaged as lentivirus in HEK293T cells (ATCC). Neurons in culture were infected with virus on DIV1. For each genetic condition (Ctrl or KD) there are two treatment conditions, either 1µm TTX added on DIV5 for 48 hours (TTX) or 1µM TTX for 48 hours followed by 6 hours of TTX withdrawal (TTXwd). All cells were harvested for RNA on DIV 7.

tag: strain

value: CD (Sprague Dawley) IGS Charles River Labs

tag: developmental stage

value: E18.5 plus 7 days in vitro

tag: shRNA

value: Grin3a shRNA knockdown

tag: agent

value: 1microM TTX for 48 hrs plus 6 hrs TTX withdrawal


title: TTXwd ratHipp RNA_seq Grin3a knockdown Rep2


title: TTXwd ratHipp RNA_seq Grin3a knockdown Rep1


title: TTXwd ratHipp RNA_seq Control Rep3

value: Ctrl


title: CRPC_05-214E2_LN

description: CRPC lymph node (LN) metastasis


title: TTX ratHipp RNA_seq Grin3a knockdown Rep3

description: 1µM TTX for 48 hrs

value: 1microM TTX for 48 hrs


title: TTX ratHipp RNA_seq Grin3a knockdown Rep1

description: 1µM TTX for 48 hrs


title: TTX ratHipp RNA_seq Control Rep1

description: 1µM TTX for 48 hrs


title: TTX ratHipp RNA_seq Grin3a knockdown Rep2

description: 1µM TTX for 48 hrs


title: TTX ratHipp RNA_seq Control Rep2

description: 1µM TTX for 48 hrs


title: OE_Input

city: Tainjin

first: Weiyu

last: Zhang

address: No.38 Tongyan Road, Jinnan District

institute: Nankai University

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutadapt with parameters " -q 5 -m 30 -n 4 -O 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", then sequence reads were mapped to mm10 genome using Bowtie2 with parameters "-5 1 --very-sensitive -p 20 -I 0 -X 1000 --no-mixed --no-discordant --un-conc-gz".
Zscan4 peak bed file was called by macs2 with parameters "-f BAMPE -g mm -q 0.1 --keep-dup auto".
Zscan4 enrichment bigwig file was generated by bamCompare from Deeptools with parameter "--scaleFactorsMethod readCount -e --minMappingQuality 1 --samFlagExclude 256 --pseudocount -1 --operation ratio"
Genome_build: mm10
Supplementary_files_format_and_content: bed file of Zscan4 peaks and bigwig file of Zscan4 enrichment.

source_name: Embryonic stem cell

growth_protocol: Mouse J1 embryonic stem cells (ESCs) were cultured under 5% CO2 at 37℃ on well plate coated with 0.2% gelatin(Sigma),in medium(Hyclone) that supplement with15% FBS（Hyclone）,10ng/ml mLIF (GeneScript)，1% Penicillin-Streptomycin (Solarbio)，1% GlutaMAX(Solarbio), 1% nonessential amino acids(Gibco), 0.1 mM β-mercaptoethanol (Sigma). .

extract_protocol:
Cells were lysed and chromatin was extracted. Anti-FLAG antibody was used to immunoprecipiate FLAG-Zscan4 in mESCs. Proteins on chromatin associated with Zscan4 was digested and chromatin was decrosslinked at 65 degree overnight. DNA was extracted in phenol-chloroform.
For ChIP-seq, 5ng of Zscan4-assocated chromatin DNA was used in ChIP-seq library preparation.  Libraries were prepared according to Illumina protocols and library fragments of ~250 bp were used for sequencing.

treatment_protocol: The CDS region of Zscan4c was cloned into pCMV-FLAG vector.WT mESCs were transfected with 1000ng pCMV-tag2 vector.After transfection for 24h,the cells were treated with 500ug/ml G418 for 10days and the medium were changed every 24h, then we picked monoclonal cells.

tag: cell line

value: Zscan4 overexpression


title: TTXwd ratHipp RNA_seq Control Rep1


title: ID-PD1-1

description:
CRISPR Screen
Amplified sgRNA pools

source_name: KP allograft tumor

tag: strain/background

tag: mouse genotype/variation

tag: treatment

value: Subcutaneously injected tumor

tag: group

value: Immunodeficient mouse + anti-PD1


title: CRPC_03-139E5_RETROPERITONEAL

description: CRPC retroperitoneal metastasis

value: male

value: prostate cancer


title: TTXwd ratHipp RNA_seq Control Rep2


title: T02

status: Public on Apr 25 2019

city: Zhenjiang

first: Qiru

address: Xiangshan street

institute: Jiangsu University

description: processed data file: all.gene_fpkm.txt

data_processing:
Raw reads were pre-processed to obtain the clean reads by removing reads containing poly-N, reads containing adapter and low-quality reads from raw data were filtered with FASTQ-Quality-Filter tool.
HISAT2 generate a database of splice junctions based on the gene model annotation ﬁle, which was used to align the paired-end clean reads to the reference genome of Pyrus_bretschneideri_chromosome_V121121.fa.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. Then, the number of fragments per kilobase of transcript per Million fragments mapped (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Pyrus_bretschneideri_chromosome_V121121.fa
Supplementary_files_format_and_content: *.t_data.ctab.txt and all.gene_fpkm.xls files include FPKM values.

organism: Pyrus pyrifolia

source_name: tissues in wound

growth_protocol: Incubator 28℃, 95% RH.

extract_protocol:
The sample was ground in liquid nitrogen. RNA of pears was extracted with UNlQ-10 Column Trizol Total RNA Extraction Reagent (Sangon Biotech, Shanghai, China) according to the instruction of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 30 μL of Wickerhamomyces anomalus suspension was pipetted into each wound (T02), and 30 μL of sterilized water was used as the control (T01).

tag: cultivar

tag: tissue

value: pear

value: Wickerhamomyces anomalus

tag: treatment duration

value: 3 days


title: T01

description: processed data file: all.gene_fpkm.txt

value: Sterilized water


title: OE_Zscan4

tag: genotype


title: TTX ratHipp RNA_seq Control Rep3

description: 1µM TTX for 48 hrs


title: MRC5 Control Replicate 2 [miRNA-seq]

status: Public on Apr 10 2019

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
MRC5 cells not treated (replicate 2)
Processed data file: tablecounts.txt

data_processing:
Illumina adaptor trimming with cutadapt-1.2.1 (--adapter=TGGAATTCTCGGGTGCCAAGG).
Discard reads of size under 15 bases.
Bowtie2 mapping versus hg19 (--local --very-sensitive-local -k 24).
Annotation versus gff miRBase v21, Ensembl ncrna rel73, tRNAs and piRNA clusters from piRNAclusterDB.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: tablecount.txt: Tab-delimited text file indicating for each feature, the name, the feature type, a description, a genomic coordinate and the number of reads associated to this feature in each sample.

source_name: MRC5 human lung fibroblasts, control

extract_protocol:
Total RNAs were extracted from MRC5 cells using TRIzol reagent (Invitrogen).
500ng of total RNA were ligated, reverse transcribed and amplified (18 cycles) with the reagents from the NextFlex small RNAseq kit V3 (Bioo Scientific). Amplified libraries were quantified with the Bioanalyzer High Sensitivity DNA Kit (Agilent), pooled and size-selected from 140 nt to 170 nt with the LabChip XT DNA 300 Assay Kit (Caliper Lifesciences). Libraries were then sequenced on an Illumina Nextseq 500 Mid Flowcell with 75bp reads.

treatment_protocol: Human MRC5 pulmonary fibroblasts (CCL-171) were exposed to TGF-β at 10 ng/mL. RNA samples were harvested 24 hours after TGF-β exposition.

tag: age

value: pulmonary fibroblast cell line

tag: concentration sample (ng/nl)

tag: rin number


title: DMSO_treatment_3 as ctrl for Ban Ex

status: Public on Jun 30 2019

city: Tsukuba

first: Kazumi

last: Hirano

state: Ibaraki

address: 1-1-1 Higashi

department: Biomedical

country: Japan

institute: AIST

description:
AR-2955_03
Gene expression after 2 days in DMSO treated hfNSCs.

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted by using TRIZOL reagent.

treatment_protocol: hfNSCs were treated by 10ng/ml Bangle extract and 10μM cis-Banglene for two days in neuronal differentiated medium (neurobasal medium containing 2% B27 supplement and 0.5 mM L-glutamine).

tag: cell type

value: hfNSCs

value: DMSO

tag: time

value: 2 days


title: DMSO_treatment_2 as ctrl for cBan

description:
AR-2955-02_02
Gene expression after 2 days in DMSO treated hfNSCs.


title: MRC5 TGF-β Replicate 3 [RNA-seq]

description:
MRC5 cells exposed to TGF-β during 24h (replicate 3).
Processed data file: tablecounts.txt

data_processing:
Mapping with STAR_2.4.0a versus hg19 with default parameters.
Gene counting with featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1" options.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: tablecounts.txt: Tab-delimited text file includes counts values of each gene in each sample.

source_name: MRC5 human lung fibroblasts, TGF-β

extract_protocol:
Total RNAs were extracted from MRC5 cells using TRIzol reagent (Invitrogen).
Libraries were generated from 500ng of total RNAs using TruSeq Stranded Total RNA kit (Illumina). Libraries were then quantified with KAPA library quantification kit (Kapa biosystems) and pooled. 4nM of this pool were loaded on a high output flowcell and sequenced on a NextSeq 500 platform (Illumina) with 2x75bp paired-end chemistry.

treatment_protocol: Human MRC5 pulmonary fibroblasts (CCL-171) were exposed or not to TGF-β at 10 ng/mL. RNA samples were harvested 24 hours after TGF-β exposition.

tag: strain

value: TGF-beta


title: MRC5 Control Replicate 1 [miRNA-seq]

description:
MRC5 cells not treated (replicate 1)
Processed data file: tablecounts.txt


title: Bangle_extract_treatment_2

description:
AR-2955_05
Gene expression after 2 days in Bangle extract treated hfNSCs.

value: Bangle extract


title: DMSO_treatment_2 as ctrl for Ban Ex

description:
AR-2955_02
Gene expression after 2 days in DMSO treated hfNSCs.


title: Bangle_extract_treatment_1

description:
AR-2955_04
Gene expression after 2 days in Bangle extract treated hfNSCs.


title: DMSO_treatment_1 as ctrl for cBan

description:
AR-2955-02_01
Gene expression after 2 days in DMSO treated hfNSCs.


title: MRC5 Control Replicate 3 [miRNA-seq]

description:
MRC5 cells not treated (replicate 3)
Processed data file: tablecounts.txt


title: MRC5 TGF-β Replicate 3 [miRNA-seq]

description:
MRC5 cells exposed to TGF-β during 24h (replicate 3)
Processed data file: tablecounts.txt


title: Bangle_extract_treatment_3

description:
AR-2955_06
Gene expression after 2 days in Bangle extract treated hfNSCs.


title: KO cytopasm_infected_4h

status: Public on Apr 17 2019

city: Tianjin

first: Wang

last: Lei

address: Weijin Road 94

description: A2B1 KO cytoplasm-3

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Affymetrix Mouse Gene 1.0 ST Array in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: Expression data were generated by Affymetrix Expression Console software and normalized by the RMA (Robust Multi-chip Average) method.

label: biotin

source_name: cytoplasm of peritoneal macrophages from Hnrnpa2b1fl/flLyz2-Cre+ mice, infected with HSV-1, 4 h

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit.

growth_protocol: Cells were maintained in DMEM (Hyclone) with 10% (vol/vol) FBS (Gibco).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Peritoneal macrophages were infected with HSV-1 (MOI, 10) for 4 h.

tag: genotype/variation

value: Peritoneal macrophages

tag: cell fraction

value: Cytoplasm

value: HSV-1 infection


title: KO nucleus_infected_4h

description: A2B1 KO nucleus-4

source_name: nucleus of peritoneal macrophages from Hnrnpa2b1fl/flLyz2Cre+ mice, infected with HSV-1, 4 h

value: Nucleus


title: MRC5 TGF-β Replicate 1 [miRNA-seq]

description:
MRC5 cells exposed to TGF-β during 24h (replicate 1)
Processed data file: tablecounts.txt

tag: cell line


title: MRC5 TGF-β Replicate 2 [miRNA-seq]

description:
MRC5 cells exposed to TGF-β during 24h (replicate 2)
Processed data file: tablecounts.txt


title: DMSO_treatment_3 as ctrl for cBan

description:
AR-2955-02_03
Gene expression after 2 days in DMSO treated hfNSCs.


title: wt nucleus_infected_4h

description: Wild-type nucleus-2

source_name: nucleus of peritoneal macrophages from wild-type mice, infected with HSV-1, 4 h

value: Wild-type


title: cBan_treatment_1

description:
AR-2956-02_02
Gene expression after 2 days in cis-Banglene treated hfNSCs.

value: cis-Banglene


title: cBan_treatment_2

description:
AR-2956-02_03
Gene expression after 2 days in cis-Banglene treated hfNSCs.


title: DMSO_treatment_1 as ctrl for Ban Ex

description:
AR-2955_01
Gene expression after 2 days in DMSO treated hfNSCs.


title: MRC5 TGF-β Replicate 2 [RNA-seq]

description:
MRC5 cells exposed to TGF-β during 24h (replicate 2).
Processed data file: tablecounts.txt


title: wt cytopasm_infected_4h

description: Wild-type cytoplasm-1

source_name: cytoplasm of peritoneal macrophages from wild-type mice, infected with HSV-1, 4 h


title: 52 hpf CHT cells

status: Public on Apr 23 2019

city: Shanghai

first: Denghui

last: Liu

state: Shanghai

address: ShengLi Building, 320 Yueyang Road

institute: CAS-MPG Partner Institute for Computational Biology (PICB)

data_processing:
UMI-tools was used to analysis our single cell data. Firstly, in “whitelist” step we set 5000 as cell number and check quality plots.
The R1 fastq file is the technical read including barcode and UMI, and R2 is biological sequencing.
Then in “extract” step we filter some low-quality reads and non-UMI reads with recommend parameters, so that we can use STAR to map to the reference genome.
Finally, in “count” step we generate a gene expression matrix for following analysis.
Genome_build: GRCz10
Supplementary_files_format_and_content: Contains the expression level of all samples, measured by UMI counts

organism: Danio rerio

source_name: zebrafish embryos

extract_protocol:
The single cells were sorted by FACS and cell suspensions (300-1000 living cells per microliter determined by trypan blue staining) were loaded on a Chromium Single Cell Controller (10x Genomics) to generate single-cell gel beads in emulsion (GEMs) by using Single Cell 3' Library and Gel Bead Kit V2 (10x Genomics, 120237). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs (Zheng et al., 2017). Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads (Invitrogen, 37002D).
Single-cell RNA-seq libraries were prepared using Single Cell 3' Library Gel Bead Kit V2 (10x Genomics, 120237) following the manufacture’s introduction.

tag: region

value: CHT

tag: cells

value: endothelial cells+hematopoietic cells+ double negative niche cells

tag: Stage

value: 52 hpf


title: MRC5 TGF-β Replicate 1 [RNA-seq]

description:
MRC5 cells exposed to TGF-β during 24h (replicate 1).
Processed data file: tablecounts.txt

tag: treatment


title: MRC5 Control Replicate 2 [RNA-seq]

description:
MRC5 cells not treated (replicate 2).
Processed data file: tablecounts.txt


title: MRC5 Control Replicate 1 [RNA-seq]

description:
MRC5 cells not treated (replicate 1).
Processed data file: tablecounts.txt


title: MRC5 Control Replicate 3 [RNA-seq]

description:
MRC5 cells not treated (replicate 3).
Processed data file: tablecounts.txt


title: Bleo_GP DNM3OS-3_Sample3

description: RNA extracted from whole lung after anti-Dnm3os gapmer 3 transfection and Bleomycin treatment (Sample 3)

hyb_protocol: Agilent : 200.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and differential analysis using Limma package in R / Bioconductor.

source_name: Bleo_GP DNM3OS-3_Sample3

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Total RNAs were extracted using TRIzol reagent (Invitrogen)

value: Lung

tag: condition

value: GP DNM3OS-3 + Bleo


title: Bleo_GP DNM3OS-1_Sample5

description: RNA extracted from whole lung after anti-Dnm3os gapmer 1 transfection and Bleomycin treatment (Sample 5)

source_name: Bleo_GP DNM3OS-1_Sample5

tag: tissue

value: GP DNM3OS-1 + Bleo


title: Bleo_GP DNM3OS-3_Sample5

description: RNA extracted from whole lung after anti-Dnm3os gapmer 3 transfection and Bleomycin treatment (Sample 5)

source_name: Bleo_GP DNM3OS-3_Sample5


title: PBS_GP DNM3OS-1_Sample3

description: RNA extracted from whole lung after anti-Dnm3os gapmer 1 transfection and PBS treatment (Sample 3)

source_name: PBS_GP DNM3OS-1_Sample3

value: GP DNM3OS-1 + PBS


title: PBS_GP DNM3OS-3_Sample3

description: RNA extracted from whole lung after anti-Dnm3os gapmer 3 transfection and PBS treatment (Sample 3)

source_name: PBS_GP DNM3OS-3_Sample3

value: GP DNM3OS-3 + PBS


title: PBS_GP Ctrl_Sample2

description: RNA extracted from whole lung after control gapmer transfection and PBS treatment (Sample 2)

source_name: PBS_GP Ctrl_Sample2

value: GP Ctrl + PBS


title: Bleo_GP DNM3OS-3_Sample4

description: RNA extracted from whole lung after anti-Dnm3os gapmer 3 transfection and Bleomycin treatment (Sample 4)

source_name: Bleo_GP DNM3OS-3_Sample4


title: Bleo_GP DNM3OS-3_Sample2

description: RNA extracted from whole lung after anti-Dnm3os gapmer 3 transfection and Bleomycin treatment (Sample 2)

source_name: Bleo_GP DNM3OS-3_Sample2


title: PBS_GP Ctrl_Sample3

description: RNA extracted from whole lung after control gapmer transfection and PBS treatment (Sample 3)

source_name: PBS_GP Ctrl_Sample3


title: PBS_GP DNM3OS-3_Sample2

description: RNA extracted from whole lung after anti-Dnm3os gapmer 3 transfection and PBS treatment (Sample 2)

source_name: PBS_GP DNM3OS-3_Sample2


title: PBS_GP DNM3OS-3_Sample1

description: RNA extracted from whole lung after anti-Dnm3os gapmer 3 transfection and PBS treatment (Sample 1)

source_name: PBS_GP DNM3OS-3_Sample1


title: Bleo_GP Ctrl_Sample3

description: RNA extracted from whole lung after control gapmer transfection and Bleomycin treatment (Sample 3)

source_name: Bleo_GP Ctrl_Sample3

value: GP Ctrl + Bleo


title: Bleo_GP DNM3OS-3_Sample1

description: RNA extracted from whole lung after anti-Dnm3os gapmer 3 transfection and Bleomycin treatment (Sample 1)

source_name: Bleo_GP DNM3OS-3_Sample1


title: Bleo_GP Ctrl_Sample1

description: RNA extracted from whole lung after control gapmer transfection and Bleomycin treatment (Sample 1)

source_name: Bleo_GP Ctrl_Sample1


title: Bleo_GP DNM3OS-1_Sample3

description: RNA extracted from whole lung after anti-Dnm3os gapmer 1 transfection and Bleomycin treatment (Sample 3)

source_name: Bleo_GP DNM3OS-1_Sample3


title: Bleo_GP Ctrl_Sample5

description: RNA extracted from whole lung after control gapmer transfection and Bleomycin treatment (Sample 5)

source_name: Bleo_GP Ctrl_Sample5


title: PBS + Control TSB rep2

description: RNA extracted from whole lung after Control TSB and PBS treatment (Replicate 2).

hyb_protocol: Agilent : 200.0 ng at 65 degree_C during 17 hours.

source_name: Lung, PBS-ControlTSB

label_protocol: Agilent - Low RNA input QuickAmp.

extract_protocol: Total RNAs were extracted using TRIzol reagent (Invitrogen).

treatment_protocol: CAV1 TSB (5mg/kg) or control formulated for in vivo delivery (Control TSB) was instilled intratracheally 4 days and 2 days before intratracheal administration of bleomycin (1 unit/kg) or PBS as well as 4 days after bleomycin or PBS treatment.

tag: tbs

value: Control

value: PBS

tag: amount in (ug)


title: PBS_GP DNM3OS-1_Sample1

description: RNA extracted from whole lung after anti-Dnm3os gapmer 1 transfection and PBS treatment (Sample 1)

source_name: PBS_GP DNM3OS-1_Sample1

tag: age


title: Bleo_GP DNM3OS-1_Sample2

description: RNA extracted from whole lung after anti-Dnm3os gapmer 1transfection and Bleomycin treatment (Sample 2)

source_name: Bleo_GP DNM3OS-1_Sample2


title: Bleomycin + Control TSB rep4

description: RNA extracted from whole lung after Control TSB and Bleomycin treatment (Replicate 4).

source_name: Lung, Bleo-ControlTSB

value: Bleo


title: Bleo_GP DNM3OS-1_Sample1

description: RNA extracted from whole lung after anti-Dnm3os gapmer 1 transfection and Bleomycin treatment (Sample 1)

source_name: Bleo_GP DNM3OS-1_Sample1


title: Bleo_GP Ctrl_Sample2

description: RNA extracted from whole lung after control gapmer transfection and Bleomycin treatment (Sample 2)

source_name: Bleo_GP Ctrl_Sample2


title: PBS + CAV1 TSB rep2

description: RNA extracted from whole lung after CAV1 TSB and PBS treatment (Replicate 2).

source_name: Lung, PBS-CAV1TSB


title: Bleo_GP Ctrl_Sample4

description: RNA extracted from whole lung after control gapmer transfection and Bleomycin treatment (Sample 4)

source_name: Bleo_GP Ctrl_Sample4


title: Bleomycin + Control TSB rep5

description: RNA extracted from whole lung after Control TSB and Bleomycin treatment (Replicate 5).


title: Bleo_GP DNM3OS-1_Sample4

description: RNA extracted from whole lung after anti-Dnm3os gapmer 1 transfection and Bleomycin treatment (Sample 4)

source_name: Bleo_GP DNM3OS-1_Sample4


title: Bleomycin + CAV1 TSB rep5

description: RNA extracted from whole lung after CAV1 TSB and Bleomycin treatment (Replicate 5).

source_name: Lung, Bleo-CAV1TSB


title: Bleomycin + Control TSB rep6

description: RNA extracted from whole lung after Control TSB and Bleomycin treatment (Replicate 6).


title: PBS_GP Ctrl_Sample1

description: RNA extracted from whole lung after control gapmer transfection and PBS treatment (Sample 1)

source_name: PBS_GP Ctrl_Sample1


title: PBS_GP DNM3OS-1_Sample2

description: RNA extracted from whole lung after anti-Dnm3os gapmer 1 transfection and PBS treatment (Sample 2)

source_name: PBS_GP DNM3OS-1_Sample2


title: Bleomycin + CAV1 TSB rep4

description: RNA extracted from whole lung after CAV1 TSB and Bleomycin treatment (Replicate 4).


title: Bleomycin + CAV1 TSB rep1

description: RNA extracted from whole lung after CAV1 TSB and Bleomycin treatment (Replicate 1).


title: Bleomycin + CAV1 TSB rep6

description: RNA extracted from whole lung after CAV1 TSB and Bleomycin treatment (Replicate 6).


title: Bleomycin + CAV1 TSB rep2

description: RNA extracted from whole lung after CAV1 TSB and Bleomycin treatment (Replicate 2).


title: E8.75_anterior_Rep1

first: Manu

last: Setty

address: 1100 Fairview Ave N

department: Basic Sciences Division

data_processing:
scRNA-seq data was processed from raw fastq files to count matrices with SEQC v0.2.1 (see https://github.com/ambrosejcarr/seqc.git)
Cells with > 0.2 fraction of mitochondrial molecules were filtered out
Barcodes with fewer than 5,600 molecules for E3.5, E4.5 and E5.5 and 10,000 molecules for E6.5, E7.5 and E8.75 timepoints were filtered out.
Genome_build: mm38
Supplementary_files_format_and_content: Cell x gene unnormalized count matrices in gzipped csv format

molecule: polyA RNA

source_name: E8.75_Anterior gut

growth_protocol: Mice were maintained under a 12 hr light-dark cycle and checked for vaginal plugs in the morning. All embryos for this study were obtained by natural matings of virgins 6-8 weeks of age. Embryos at noon on the day of detecting copulation plugs were estimated at E0.5. Pre-implantation stage embryos were collected by flushing uterine horns of pregnant females at embryonic day (E) 3.5 and E4.5. Uteri were flushed with flushing and holding medium (FHM, Millipore) as previously described 5, and zona pellucida was removed from E3.5 blastocysts by incubation in acidic Tyrode’s solution (Millipore) at 37°C for 2-3 min. Embryos were subsequently washed in 2-3 drops of FHM and kept in drops of FHM covered with mineral oil (Sigma) on ice prior to single-cell dissociation. Post-implantation embryos were dissected in DMEM/F12 (Life Technologies)/5% Newborn calf serum (Life Technologies) and staged according to Downs and Davies 6 or by somite number.

extract_protocol:
13ss (E8.75) embryos were used as the terminal end point of this study since this is the latest time one can confidently assign cells in the gut tube with a VE-vs.-DE identity using either the Afp-GFP reporter 1,10 or the Ttr-Cre 3,10 driver crossed to a Cre reporter, since by 18-20ss (E9.0) both Afp and Ttr genes, and cis-regulatory elements used in the respective transgenic lines of mice, become activated in gut endoderm derivatives including the emergent liver. To obtain single cells from 13ss gut tubes, Afp-GFPTG/+ embryos were dissected out of the uterus, and extra- embryonic membranes and heads were removed. Torsos washed in three drops of DMEM/F12 on ice and subjected to Pancreatin/Trypsin treatment (2.5% Pancreatin / 0.5% Trypsin in PBS) for 5 min (exact time was batch dependent and empirically tested) on ice and then washed in three drops of DMEM/F12, 10% Newborn calf serum on ice. Gut tubes were dissected out using Tungsten needles (FST Cat No. 10130-10) and washed in cold DMEM/F12. Gut tubes were then incubated for 20 min at 37°C in Accutase/0.25% Trypsin (1:2) for the dissociation of single cells. To obtain single cells from definitive and visceral endoderm cell from stages E7.5 and visceral endoderm cells from E6.5, embryos were washed in three drops of DMEM/F12 on ice and subjected to Pancreatin/Trypsin treatment (2.5% Pancreatin / 0.25% Trypsin in PBS) for 3 min (E7.5) and 45s (E6.5) on ice and then washed in three drops of DMEM/F12, 10% Newborn calf serum on ice. The endoderm layer was removed from the rest of the tissue using Tungsten needles and subsequently washed in cold DMEM/F12 and incubated for 20 min at 37°C in Accutase/0.25% Trypsin (1:2). For E5.5 (defined as the stage when the DVE/AVE was distally positioned, observed as a thickening of the emVE epithelium), whole embryos were collected, and Reichert’s membrane removed with Tungsten needles. Embryos were washed in cold DMEM/F12 and then incubated in 0.25% Trypsin for 5 min at 37°C. To dissociate the tissue into a single cell suspension, DMEM/F12, 20% Newborn calf serum, 4mM EDTA were added in 1:1 ratio. Cell clumps were dissociated into single cells using a mouth pipet and 75mm glass capillaries. Subsequently, the single cell suspension was filtered through a FlowMI cell strainer (40μm) to remove debris. Single cells were spun down at 450g for 4 min at room temperature and then cell numbers were determined using a Neubauer hemocytometer. For pre-implantation embryo dissociations, embryos were incubated in 0.5% Trypsin-EDTA (Invitrogen) at 37°C for 3 minutes before transferring to PBS supplemented with 0.5mM EDTA (Invitrogen) and 4% BSA (Sigma) for mechanical dissociations. Trypsin-treated embryos were dissociated by repeated pipetting (trituration) using pulled capillaries (Sutter Instruments) attached to a mouth pipet. Dissociated cells were stored in FHM on ice until loading on the Chromium System (10X Genomics).
Prior to analysis, cells were counted and diluted to the final concentration in (DMEM/F12, 10% Fetal bovine Serum (FBS). Cells were mixed with single cell master mix and the resulting cellular suspensions were loaded on a Chromium System 11 to target cell number loading ranging from 2,500 to 10,000 cells, depending on the tissue type and the embryo stage, in duplicate, to generate single-cell single cell 3’ RNA-seq libraries. Single cell 3’ RNA-seq libraries were generated following manufacturer’s instructions (Chromium single cell 3’ reagents kits v2 user guide)

tag: developmental stage

value: Anterior gut

tag: sorting


title: E8.75_GFP-_Rep2

source_name: E8.75_Definitive endoderm

value: Definitive endoderm

value: GFP-


title: E8.75_posterior_Rep1

source_name: E8.75_Posterior gut

value: Posterior gut


title: E8.75_anterior_Rep2


title: Bleomycin + Control TSB rep3

description: RNA extracted from whole lung after Control TSB and Bleomycin treatment (Replicate 3).

tag: rin number


title: Bleomycin + Control TSB rep2

description: RNA extracted from whole lung after Control TSB and Bleomycin treatment (Replicate 2).


title: E8.75_posterior_Rep2


title: E8.75_GFP-_Rep1


title: PBS + Control TSB rep1

description: RNA extracted from whole lung after Control TSB and PBS treatment (Replicate 1).


title: Bleomycin + LNA-miR-199a-5p rep1

description: RNA extracted from whole lung after LNA-miR-199a-5p and Bleomycin treatment (Replicate 1).

source_name: Lung, Bleo-LNA-miR-199a-5p

treatment_protocol: LNA-miR-199a-5p (5mg/kg) or control formulated for in vivo delivery was instilled intratracheally 4 days and 2 days before intratracheal administration of bleomycin (1 unit/kg) or PBS as well as 4 days after bleomycin or PBS treatment.

tag: lna

value: Bleomycin


title: E8.75_GFP+_Rep2

source_name: E8.75_Visceral endoderm

tag: strain

value: Visceral endoderm

value: GFP+


title: PBS + CAV1 TSB rep1

description: RNA extracted from whole lung after CAV1 TSB and PBS treatment (Replicate 1).

value: Lung


title: Bleomycin + LNA-miR-199a-5p rep3

description: RNA extracted from whole lung after LNA-miR-199a-5p and Bleomycin treatment (Replicate 3).


title: Bleomycin + CAV1 TSB rep3

description: RNA extracted from whole lung after CAV1 TSB and Bleomycin treatment (Replicate 3).


title: Bleomycin + LNA-control rep1

description: RNA extracted from whole lung after LNA-control and Bleomycin treatment (Replicate 1).

source_name: Lung, Bleo-LNA-control

value: control


title: PBS + LNA-miR-199a-5p rep1

description: RNA extracted from whole lung after LNA-miR-199a-5p and PBS treatment (Replicate 1).

source_name: Lung, PBS-LNA-miR-199a-5p


title: PBS + LNA-control rep1

description: RNA extracted from whole lung after LNA-control and PBS treatment (Replicate 1).

source_name: Lung, PBS-LNA-control


title: PBS + LNA-miR-199a-5p rep2

description: RNA extracted from whole lung after LNA-miR-199a-5p and PBS treatment (Replicate 2).


title: Bleomycin + Control TSB rep1

description: RNA extracted from whole lung after Control TSB and Bleomycin treatment (Replicate 1).

source_name: Lung, Bleo-ControlTSB


title: E8.75_GFP+_Rep1


title: PBS + LNA-control rep3

description: RNA extracted from whole lung after LNA-control and PBS treatment (Replicate 3).


title: Bleomycin + LNA-miR-199a-5p rep5

description: RNA extracted from whole lung after LNA-miR-199a-5p and Bleomycin treatment (Replicate 5).


title: Bleomycin + LNA-miR-199a-5p rep4

description: RNA extracted from whole lung after LNA-miR-199a-5p and Bleomycin treatment (Replicate 4).


title: PBS + LNA-control rep2

description: RNA extracted from whole lung after LNA-control and PBS treatment (Replicate 2).


title: Bleomycin + LNA-control rep2

description: RNA extracted from whole lung after LNA-control and Bleomycin treatment (Replicate 2).


title: Bleomycin + LNA-miR-199a-5p rep2

description: RNA extracted from whole lung after LNA-miR-199a-5p and Bleomycin treatment (Replicate 2).


title: Bleomycin + LNA-control rep5

description: RNA extracted from whole lung after LNA-control and Bleomycin treatment (Replicate 5).


title: E8.75_YsE_Rep1

source_name: E8.75_Yolk sac endoderm

value: Yolk sac endoderm


title: E7.5_GFP-_Rep1

source_name: E7.5_Definitive endoderm


title: E7.5_GFP-_Rep3


title: E7.5_GFP-_Rep2


title: E8.75_ParE_Rep2

source_name: E8.75_Parietal endoderm

value: Parietal endoderm


title: E7.5_GFP+_Rep1

source_name: E7.5_Visceral endoderm


title: E8.75_ParE_Rep1


title: E7.5_GFP+_Rep3


title: E7.5_GFP+_Rep2


title: E8.75_YsE_Rep2


title: E6.5_Rep1

source_name: E6.5_Visceral and parietal endoderm

value: Visceral and parietal endoderm


title: E6.5_Rep2


title: Bleomycin + LNA-control rep4

description: RNA extracted from whole lung after LNA-control and Bleomycin treatment (Replicate 4).


title: E7.5_ParE_Rep2

source_name: E7.5_Parietal endoderm


title: E7.5_ParE_Rep1


title: E5.5_Rep3

source_name: E5.5_Whole embryo

value: Whole embryo


title: E5.5_Rep2


title: Bleomycin + LNA-control rep3

description: RNA extracted from whole lung after LNA-control and Bleomycin treatment (Replicate 3).


title: PBS + LNA-miR-199a-5p rep3

description: RNA extracted from whole lung after LNA-miR-199a-5p and PBS treatment (Replicate 3).


title: E3.5_Rep1

source_name: E3.5_Whole embryo


title: E3.5_Rep2


title: E5.5_Rep1


title: E4.5_Rep1

source_name: E4.5_Whole embryo


title: MRC5 + TGF-β rep1

description:
TGF_rep1
RNA extracted from human pulmonary fibroblasts after TGF-β exposition during 24h (Replicate 1).

source_name: MRC5 + TGF-β

tag: cell type

value: pulmonary fibroblast cell line

value: TGF-beta


title: MRC5 control rep1

description:
Control_rep1
RNA extracted from human pulmonary fibroblasts control (Replicate 1).

source_name: MRC5 control


title: MRC5 control rep2

description:
Control_rep2
RNA extracted from human pulmonary fibroblasts control (Replicate 2).


title: E4.5_Rep2


title: pre-miR-214-3p_rep3

description: RNA extracted from human lung fibroblasts after 48h of synthetic pre-miR-214-3p transfection (Replicate 3).

source_name: MRC5, pre-miR-214-3p

treatment_protocol: We overexpressed miR-Neg, miR-199-5p, miR-199a-3p, and miR-214-3p in human MRC5 pulmonary fibroblasts (CCL-171) using synthetic pre-miRNAs or a synthetic “negative” pre-miRNA control (miR-Neg). RNA samples were harvested 48 hours post-transfection.

value: lung fibroblast cell line

tag: miRNA


title: MRC5 + TGF-β rep2

description:
TGF_rep2
RNA extracted from human pulmonary fibroblasts after TGF-β exposition during 24h (Replicate 2).

tag: cell line


title: pre-miR-199-5p_rep1

description: RNA extracted from human lung fibroblasts after 48h of synthetic pre-miR-199-5p transfection (Replicate 1).

source_name: MRC5, pre-miR-199-5p


title: pre-miR-199a-3p_rep1

description: RNA extracted from human lung fibroblasts after 48h of synthetic pre-miR-199a-3p transfection (Replicate 1).

source_name: MRC5, pre-miR-199a-3p


title: pre-miR-199-5p_rep3

description: RNA extracted from human lung fibroblasts after 48h of synthetic pre-miR-199-5p transfection (Replicate 3).


title: pre-miR-Neg_rep3

description: RNA extracted from human lung fibroblasts after 48h of synthetic “negative” pre-miRNA control transfection (Replicate 3).

source_name: MRC5, pre-miR-Neg

value: pre-miR-Neg


title: pre-miR-214-3p_rep2

description: RNA extracted from human lung fibroblasts after 48h of synthetic pre-miR-214-3p transfection (Replicate 2).


title: Gapmer_anti-DNM3OS_rep1

description: RNA extracted from human lung fibroblasts after 48h of gapmer anti-DNM3OS transfection (Replicate 1).

source_name: MRC5, Gapmer_anti-DNM3OS

treatment_protocol: We transfected in human MRC5 pulmonary fibroblasts (CCL-171) a gapmer designed against DNM3OS for 48h and then exposed these cells to TGF- β (10 ng/mL). RNA samples were harvested 24 hours after TGF-β exposition.

tag: gapmer


title: pre-miR-199-5p_rep2

description: RNA extracted from human lung fibroblasts after 48h of synthetic pre-miR-199-5p transfection (Replicate 2).


title: Gapmer_control+TGFb_rep1

description: RNA extracted from human lung fibroblasts after 48h of gapmer control transfection and 24h of TGF-β transfection (Replicate 1).

source_name: MRC5, Gapmer_control+TGFb

value: TGFb


title: pre-miR-199a-3p_rep2

description: RNA extracted from human lung fibroblasts after 48h of synthetic pre-miR-199a-3p transfection (Replicate 2).


title: Gapmer_anti-DNM3OS_rep2

description: RNA extracted from human lung fibroblasts after 48h of gapmer anti-DNM3OS transfection (Replicate 2).


title: pre-miR-214-3p_rep1

description: RNA extracted from human lung fibroblasts after 48h of synthetic pre-miR-214-3p transfection (Replicate 1).


title: pre-miR-Neg_rep1

description: RNA extracted from human lung fibroblasts after 48h of synthetic “negative” pre-miRNA control transfection (Replicate 1).


title: Gapmer_control_rep2

description: RNA extracted from human lung fibroblasts after 48h of gapmer control transfection (Replicate 2).

source_name: MRC5, Gapmer_control


title: pre-miR-199a-3p_rep3

description: RNA extracted from human lung fibroblasts after 48h of synthetic pre-miR-199a-3p transfection (Replicate 3).


title: pre-miR-Neg_rep2

description: RNA extracted from human lung fibroblasts after 48h of synthetic “negative” pre-miRNA control transfection (Replicate 2).


title: Gapmer_anti-DNM3OS+TGFb_rep2

description: RNA extracted from human lung fibroblasts after 48h of gapmer anti-DNM3OS transfection and 24h of TGF-β transfection (Replicate 2).

source_name: MRC5, Gapmer_anti-DNM3OS+TGFb


title: Gapmer_control_rep1

description: RNA extracted from human lung fibroblasts after 48h of gapmer control transfection (Replicate 1).


title: Gapmer_anti-DNM3OS+TGFb_rep1

description: RNA extracted from human lung fibroblasts after 48h of gapmer anti-DNM3OS transfection and 24h of TGF-β transfection (Replicate 1).


title: Gapmer_control+TGFb_rep2

description: RNA extracted from human lung fibroblasts after 48h of gapmer control transfection and 24h of TGF-β transfection (Replicate 2).


title: treatment naive adenocarcinoma DJANGO_148

status: Public on Mar 01 2019

city: Oxford

first: Jan

last: Bornschein

address: John Radcliffe Hospital, Headley Way

department: Translational Gastroenterology Unit

institute: Oxford University

hyb_protocol: Standard Illumina Direct Hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw intensity data from the array scanner was processed using the BASH and HULK algorithms as implemented in the beadarray package. Log2 transformation and quantile normalization of the data were performed across all sample groups.

source_name: adenocarcinoma

label_protocol: Biotinylated cRNA were prepared with the Illumina Total Prep RNA Amplification kit from Ambion

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN AllPrep DNA/RNA mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: sample type

value: endoscopic biopsy

tag: Sex

value: Male

tag: siewert type

tag: tumour location

value: GOJ

tag: grading

tag: uicc stage

tag: t-stage

tag: n-stage

tag: m-stage


title: treatment naive adenocarcinoma DJANGO_137

tag: age


title: treatment naive adenocarcinoma DJANGO_135


title: treatment naive adenocarcinoma DJANGO_119

value: surgical resection specimen

value: ANTRUM


title: treatment naive adenocarcinoma DJANGO_144


title: treatment naive adenocarcinoma DJANGO_131

value: Female


title: treatment naive adenocarcinoma DJANGO_127


title: treatment naive adenocarcinoma DJANGO_133


title: duodenal non-cancer control DJANGO_111

source_name: control

value: Duodenum


title: treatment naive adenocarcinoma DJANGO_141


title: gastric non-cancer control DJANGO_102

value: Gastric/Antrum


title: treatment naive adenocarcinoma DJANGO_139


title: treatment naive adenocarcinoma DJANGO_156


title: treatment naive adenocarcinoma DJANGO_125


title: treatment naive adenocarcinoma DJANGO_128


title: treatment naive adenocarcinoma DJANGO_123


title: treatment naive adenocarcinoma DJANGO_136


title: gastric non-cancer control DJANGO_103

value: Gastric/Body


title: treatment naive adenocarcinoma DJANGO_140


title: treatment naive adenocarcinoma DJANGO_154

value: BODY (dist.)


title: treatment naive adenocarcinoma DJANGO_114


title: treatment naive adenocarcinoma DJANGO_160


title: treatment naive adenocarcinoma DJANGO_158


title: gastric non-cancer control DJANGO_107

value: Gastric/Cardia


title: treatment naive adenocarcinoma DJANGO_149


title: treatment naive adenocarcinoma DJANGO_155


title: gastric non-cancer control DJANGO_104


title: treatment naive adenocarcinoma DJANGO_150


title: treatment naive adenocarcinoma DJANGO_153


title: treatment naive adenocarcinoma DJANGO_129


title: treatment naive adenocarcinoma DJANGO_142


title: treatment naive adenocarcinoma DJANGO_152


title: treatment naive adenocarcinoma DJANGO_116


title: duodenal non-cancer control DJANGO_110


title: gastric non-cancer control DJANGO_106


title: treatment naive adenocarcinoma DJANGO_138


title: treatment naive adenocarcinoma DJANGO_130


title: treatment naive adenocarcinoma DJANGO_146


title: treatment naive adenocarcinoma DJANGO_132


title: duodenal non-cancer control DJANGO_109


title: treatment naive adenocarcinoma DJANGO_120


title: treatment naive adenocarcinoma DJANGO_112


title: treatment naive adenocarcinoma DJANGO_113


title: treatment naive adenocarcinoma DJANGO_157


title: treatment naive adenocarcinoma DJANGO_143


title: treatment naive adenocarcinoma DJANGO_117


title: treatment naive adenocarcinoma DJANGO_121


title: duodenal non-cancer control DJANGO_108


title: treatment naive adenocarcinoma DJANGO_159


title: treatment naive adenocarcinoma DJANGO_145


title: treatment naive adenocarcinoma DJANGO_82

hyb_protocol: Standard Illumina hybridization protocol

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

value: F


title: treatment naive adenocarcinoma DJANGO_122


title: treatment naive adenocarcinoma DJANGO_134


title: treatment naive adenocarcinoma DJANGO_118


title: gastric non-cancer control DJANGO_105


title: treatment naive adenocarcinoma DJANGO_151


title: gastric non-cancer control DJANGO_101


title: treatment naive adenocarcinoma DJANGO_27

value: M

value: x


title: treatment naive adenocarcinoma DJANGO_11


title: treatment naive adenocarcinoma DJANGO_115


title: treatment naive adenocarcinoma DJANGO_74

value: BODY (prox./fundus)


title: treatment naive adenocarcinoma DJANGO_8


title: treatment naive adenocarcinoma DJANGO_58


title: treatment naive adenocarcinoma DJANGO_18


title: treatment naive adenocarcinoma DJANGO_10


title: treatment naive adenocarcinoma DJANGO_15


title: treatment naive adenocarcinoma DJANGO_65


title: treatment naive adenocarcinoma DJANGO_28


title: treatment naive adenocarcinoma DJANGO_62


title: treatment naive adenocarcinoma DJANGO_17


title: treatment naive adenocarcinoma DJANGO_77


title: treatment naive adenocarcinoma DJANGO_35


title: treatment naive adenocarcinoma DJANGO_30


title: treatment naive adenocarcinoma DJANGO_31


title: treatment naive adenocarcinoma DJANGO_83


title: treatment naive adenocarcinoma DJANGO_56


title: treatment naive adenocarcinoma DJANGO_80


title: treatment naive adenocarcinoma DJANGO_39


title: treatment naive adenocarcinoma DJANGO_60


title: treatment naive adenocarcinoma DJANGO_126


title: treatment naive adenocarcinoma DJANGO_54


title: treatment naive adenocarcinoma DJANGO_9


title: treatment naive adenocarcinoma DJANGO_12


title: treatment naive adenocarcinoma DJANGO_59


title: treatment naive adenocarcinoma DJANGO_63


title: treatment naive adenocarcinoma DJANGO_37


title: treatment naive adenocarcinoma DJANGO_45


title: treatment naive adenocarcinoma DJANGO_124


title: treatment naive adenocarcinoma DJANGO_66


title: treatment naive adenocarcinoma DJANGO_36


title: treatment naive adenocarcinoma DJANGO_21


title: treatment naive adenocarcinoma DJANGO_79


title: treatment naive adenocarcinoma DJANGO_14


title: treatment naive adenocarcinoma DJANGO_53


title: treatment naive adenocarcinoma DJANGO_32


title: treatment naive adenocarcinoma DJANGO_13


title: treatment naive adenocarcinoma DJANGO_50


title: treatment naive adenocarcinoma DJANGO_61


title: treatment naive adenocarcinoma DJANGO_49


title: treatment naive adenocarcinoma DJANGO_72


title: treatment naive adenocarcinoma DJANGO_76


title: treatment naive adenocarcinoma DJANGO_20


title: treatment naive adenocarcinoma DJANGO_6


title: treatment naive adenocarcinoma DJANGO_19


title: treatment naive adenocarcinoma DJANGO_5


title: treatment naive adenocarcinoma DJANGO_22


title: treatment naive adenocarcinoma DJANGO_46


title: treatment naive adenocarcinoma DJANGO_52


title: treatment naive adenocarcinoma DJANGO_24


title: treatment naive adenocarcinoma DJANGO_47


title: treatment naive adenocarcinoma DJANGO_68


title: treatment naive adenocarcinoma DJANGO_43


title: treatment naive adenocarcinoma DJANGO_2


title: treatment naive adenocarcinoma DJANGO_42


title: treatment naive adenocarcinoma DJANGO_7


title: treatment naive adenocarcinoma DJANGO_44


title: treatment naive adenocarcinoma DJANGO_57


title: treatment naive adenocarcinoma DJANGO_4


title: treatment naive adenocarcinoma DJANGO_41


title: treatment naive adenocarcinoma DJANGO_51


title: treatment naive adenocarcinoma DJANGO_26


title: treatment naive adenocarcinoma DJANGO_67


title: treatment naive adenocarcinoma DJANGO_64


title: treatment naive adenocarcinoma DJANGO_70


title: treatment naive adenocarcinoma DJANGO_23


title: treatment naive adenocarcinoma DJANGO_55


title: treatment naive adenocarcinoma DJANGO_40


title: treatment naive adenocarcinoma DJANGO_25


title: treatment naive adenocarcinoma DJANGO_48


title: treatment naive adenocarcinoma DJANGO_3


title: treatment naive adenocarcinoma DJANGO_147


title: treatment naive adenocarcinoma DJANGO_75


title: Circulating clonal plasma cells (CTC) from patient 25

status: Public on Feb 26 2019

city: New York

first: Juan-Jose

last: Garces

state: New York

address: 321 E 61st St

institute: Memorial Sloan Kettering Cancer Center

description: Gene expression data from circulating clonal plasma cells (ctc)

hyb_protocol: Hybridizations was performed according to protocols from Affymetrix in a GeneChip Hybridization Oven 645.

scan_protocol: Scanning were performed using the GeneChip Scanner 7G.

data_processing: The processing and normalization steps were performed using the Robust Multi-array Average (RMA) procedure from limma.

source_name: Circulating clonal plasma cells (CTC) newly-diagnosed patient

label_protocol: Labelling and washing were performed according to protocols from Affymetrix: 50 ng of total RNA were amplified and labeled using the WT Pico reagent kit (Affymetrix), washing was carried out in a GeneChip Fluidics Station 450.

extract_protocol: RNA was extracted using the AllPrep DNA/RNA micro kit (Qiagen) according to manufacturer's indications.

tag: tissue

value: Circulating clonal plasma cells (CTC)

tag: gender

value: male

tag: cell number

tag: disease stage

value: newly-diagnosed

tag: disease state

value: Multiple Myeloma


title: Bone marrow clonal plasma cells from patient 20

description: Gene expression data from bone marrow clonal plasma cells

source_name: Bone marrow clonal plasma cells from newly-diagnosed patient

value: Bone marrow clonal plasma cells


title: Bone marrow clonal plasma cells from patient 27


title: Circulating clonal plasma cells (CTC) from patient 27


title: Circulating clonal plasma cells (CTC) from patient 26

source_name: Circulating clonal plasma cells (CTC) relapse patient

value: relapse


title: Bone marrow clonal plasma cells from patient 21

source_name: Bone marrow clonal plasma cells from relapse patient

value: female


title: Circulating clonal plasma cells (CTC) from patient 20


title: Bone marrow clonal plasma cells from patient 24


title: Bone marrow clonal plasma cells from patient 26


title: Circulating clonal plasma cells (CTC) from patient 24


title: Circulating clonal plasma cells (CTC) from patient 19

source_name: Circulating clonal plasma cells (CTC) MGUS (high risk) patient

value: MGUS (high risk)

value: MGUS


title: Bone marrow clonal plasma cells from patient 22


title: Bone marrow clonal plasma cells from patient 23


title: Circulating clonal plasma cells (CTC) from patient 22

source_name: Circulating clonal plasma cells (CTC) relapse2 patient


title: Circulating clonal plasma cells (CTC) from patient 21


title: Circulating clonal plasma cells (CTC) from patient 23


title: Bone marrow clonal plasma cells from patient 19

source_name: Bone marrow clonal plasma cells from MGUS (high risk) patient


title: Bone marrow clonal plasma cells from patient 25


title: Bone marrow clonal plasma cells from patient 18


title: Circulating clonal plasma cells (CTC) from patient 15


title: Bone marrow clonal plasma cells from patient 12


title: Circulating clonal plasma cells (CTC) from patient 14


title: Bone marrow clonal plasma cells from patient 14


title: Bone marrow clonal plasma cells from patient 16


title: Circulating clonal plasma cells (CTC) from patient 16


title: Bone marrow clonal plasma cells from patient 17


title: Circulating clonal plasma cells (CTC) from patient 18


title: Circulating clonal plasma cells (CTC) from patient 17


title: Bone marrow clonal plasma cells from patient 15


title: Circulating clonal plasma cells (CTC) from patient 12