title: si-iASPP_p53_HCT116

extract_protocol:
ChIP was performed using the ChIP-IT High Sensitivity (HS) Kit (Active Motif 53040) according to the manufacturer’s recommended protocol with the following modifications as briefly described. Cells were cross-linked with 1% formaldehyde in DMEM culture medium for 10 min at room temperature, and quenched in 0.125 M glycine for 5 min. Cells were then washed twice with phosphate-buffered saline (PBS) followed by 3 times with lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40, 1 mM PMSF), and resuspended in ChIP Buffer (Active Motif 37516) supplemented with 1 mM PMSF and a proteinase inhibitor cocktail (Sigma-Aldrich P2714-1BTL). Chromatin was sheared by sonication (30 s alternated with 30-s cooling for 25 cycles) using a Bioruptor Pico ultrasonicator (Diagenode). Solubilised chromatin was used for immunoprecipitation by incubation overnight at 4 °C with 5 μg of the polyclonal antibody FL-393 against human p53 (Santa Cruz Biotechnology sc-6243). The immunoprecipitation reactions were transferred to Protein G Agarose Columns (Active Motif 53039) and incubated for 2 h at 4 °C. Then, each column was washed 4 times with 900 μl Wash Buffer AM1. The ChIPed samples were eluted using 100 μl Elution Buffer AM4 at 37 °C. Cross-linking was reversed by adding 5 μl Proteinase K (New England Biolabs P8107S) and incubated overnight at 65 °C. Input and ChIPed DNA were purified using the DNA purification columns.
ChIP-seq libraries were prepared using MicroPlex Library Preparation Kit v2 (Diagenode C05010014) and the Agencourt AMPure XP system (Beckman Coulter A63880) was used to select 350–550 bp libraries. Sequencing was carried out on the Illumina MiSeq and HiSeq platforms.

tag: cell line

tag: chip antibody

value: siRNA against iASSP transfected


title: 34-12days-Kainate-technical-replicate-a

status: Public on Sep 23 2019

type: SRA

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

library_source: transcriptomic

data_processing:
Illumina Bcl2fastq 2.17.1.14 software was used for basecalling.
The analyses were performed using the Eoulsan pipeline version 2.0-beta3, including read filtering, mapping, alignment filtering, read quantification, normalisation and differential analysis: Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Mus musculus genome from Ensembl version 81 using STAR (version 2.4.0k). Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression, Mus musculus GFF3 genome annotation version 81 from Ensembl database was used. All overlapping regions between alignments and referenced genes were counted using HTSeq-count 0.5.3. The sample counts were normalized using DESeq2 1.8.1 [5]. Statistical treatments and differential analyses were also performed using DESeq2 1.8.1.
Genome_build: mm10 (Ensembl 81)
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: Hippocampus CA1 area

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA XS kit (Macherey-Nagel). For each sample 10 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech).  Afterwards an average of 180 ng of amplified cDNA was used to prepare libraries.
Libraries were prepared using the Nextera XT DNA kit (Illumina)

tag: genetic background

tag: time

value: 12 days

tag: treatment

value: Kainate


title: PBS 1.5hr treatment, PAEC line 3

type: RNA

city: Cambridge

first: Wei

last: Li

address: Hills Road

department: Medicine

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Plate arrays were processed on the GeneTitan instrument (Affymetrix) using the GeneTitan Hybridization, Wash and Stain kit (Affymetrix). Samples were hybridized to the array, washed, stained and scanned using the array specific parameters provided by Affymetrix.

scan_protocol: Automated protocol from the GeneTitan, according to the automated settings provided for the array

data_processing: The processing of the data was carried out in R, using the package Oligo and the normalisation method used is RMA (Robust Multichip Analysis). The comparisons were performed using the limma package

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: pulmonary artery endothelial cells

label_protocol: 100 ng total RNA was amplified along with inline PolyA spike in control RNA, using the WT PLUS amplification kit (Affymetrix). Successfully amplified samples were labelled using the GeneChip WT terminal labelling kit (Affymetrix) Using the in line hybridization controls.

growth_protocol: PAECs were seeded in 6-well plates and grown in EGM-2 with 10% FBS to 90% confluency. Cells were then put into EGM-2 with 0.1% FBS for 16-18 hours before the treatments applied.

extract_protocol: RNeasy Mini Kit from Qiagen following manufacturer's instruction

treatment_protocol: All ligands (at a final concentration of 0.4 ng/ml growth factor concentration) were added to the serum-starved cells. The 6-well plates were returned into CO2 incubator at 37 ºC for 1.5 hours before cells were harvested for RNA extraction.

tag: gender

value: male

tag: age

tag: cell type

value: PAEC

value: PBS 1.5hr


title: PBS 1.5hr treatment, PAEC line 4


title: pro-BMP9 1.5hr treatment, PAEC line 3

value: pro-BMP9 1.5hr


title: pro-BMP9 1.5hr treatment, PAEC line 1


title: sENG(M):BMP9 1.5hr treatment, PAEC line 3

value: sENG(M):BMP9 1.5hr


title: PBS 1.5hr treatment, PAEC line 2


title: sENG(M):BMP9 1.5hr treatment, PAEC line 4


title: PBS 1.5hr treatment, PAEC line 1


title: pro-BMP9 1.5hr treatment, PAEC line 4


title: 33-12days-NACl-technical-replicate-c

value: NaCl


title: 34-12days-Kainate-technical-replicate-b


title: 33-12days-NACl-technical-replicate-d


title: sENG(M):BMP9 1.5hr treatment, PAEC line 1


title: sENG(M):BMP9 1.5hr treatment, PAEC line 2


title: 33-12days-NACl-technical-replicate-b


title: 32-12days-NACl-technical-replicate-d


title: 31-12days-NACl-technical-replicate-d


title: 32-12days-NACl-technical-replicate-a


title: 31-12days-NACl-technical-replicate-c


title: 34-12days-Kainate-technical-replicate-c


title: NC_p53_HCT116

city: Shanghai

first: Yun

last: Tan

state: Shanghai

address: Room 1109, Building 11, 197 Ruijin Er Rd

department: Shanghai Institute of Hematology

country: China

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

library_source: genomic

data_processing:
All ChIP-seq reads were aligned to the hg38 reference human genome by Bowtie 2 (version 2.2.9)
Enriched p53 occupancies relative to a background input were called using MACS (version 1.4)6 with default settings.
Genomic regions with a P value < 1 × 10−10 were retained and these enriched regions were annotated using the annotatePeaks package from the HOMER suite
The bedgraph files were generated by MACS2 with the -B -trackline settings.
Genome_build: hg38
Supplementary_files_format_and_content: Genomic binding signal of p53 were illustrated as bedGraph files

molecule: genomic DNA

growth_protocol: HCT116 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM; Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS; Gibco), L-glutamine, and appropriate antibiotics. Cell cultures were maintained in a 5% CO2 humidified incubator at 37℃.

treatment_protocol: HCT116 cells were treated with siRNA against iASPP, none-targeting siRNA for 3 days. And HCT116 cells were treated with Nutlin for 12 hours.

value: Negative control siRNA transfected


title: 33-12days-NACl-technical-replicate-a


title: MEF_Het_2

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing:
Quantification using RSEM
Alignment to the mm9 mouse genome using STAR2
Preparation of bigWig files using wigToBigWIg
Genome_build: mm10
Supplementary_files_format_and_content: RSEM quantification files and bigWig read coverage

source_name: mEF

growth_protocol: The study was conducted in accordance with the guidelines of the Weizmann Institutional Animal Care and Use Committee (IACUC). C57black6 Ola HSD male mice were purchased from Harlan Laboratories (Rehovot, Israel). All other mouse strains were bred and maintained at the Veterinary Resources Department of the Weizmann Institute. Cell lines were routinely cultured in DMEM containing 10% fetal bovine serum and 100 U penicillin/0.1 mg ml-1 streptomycin at 37˚ C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted from different cell lines and mice tissues, using the TRIREAGENT (MRC) according to the manufacturer’s protocol.
Lexogen SENSE mRNA-seq kit

tag: tissue

value: mEF


title: pro-BMP9 1.5hr treatment, PAEC line 2


title: 31-12days-NACl-technical-replicate-b


title: 30-6days-Kainate-technical-replicate-d

value: 6 days


title: 30-6days-Kainate-technical-replicate-c


title: 30-6days-Kainate-technical-replicate-b


title: 32-12days-NACl-technical-replicate-b


title: 30-6days-Kainate-technical-replicate-a


title: 29-6days-Kainate-technical-replicate-d


title: 29-6days-Kainate-technical-replicate-b


title: 29-6days-Kainate-technical-replicate-c


title: 28-6days-Kainate-technical-replicate-d


title: 29-6days-Kainate-technical-replicate-a


title: 28-6days-Kainate-technical-replicate-a


title: 27-6days-NACl-technical-replicate-d


title: 27-6days-NACl-technical-replicate-b


title: 31-12days-NACl-technical-replicate-a


title: 27-6days-NACl-technical-replicate-a


title: E9.5_Het_1

source_name: E9.5 embryo

extract_protocol:
Total RNA was extracted from different cell lines and mice tissues, using the TRIREAGENT (MRC) according to the manufacturer’s protocol.
TruSeq stranded mRNA kit

value: E9.5 embryo


title: 26-6days-NACl-technical-replicate-c


title: 26-6days-NACl-technical-replicate-a


title: 25-6days-NACl-technical-replicate-d


title: 25-6days-NACl-technical-replicate-b


title: 25-6days-NACl-technical-replicate-c


title: 26-6days-NACl-technical-replicate-b


title: A549 TK1 A10 (shRNA#2), replicate 2

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: University of Alabama at Birmingham

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Signal intensities of probes were log2-transformed and Quantile normalized (beadarray package in R/Bioconductor).

source_name: A549 cell line, TK1 shRNA

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

growth_protocol: A549 TK1 shRNAs cell lines were grown in DMEM media with 10% fetal bovine serum and Penicilline and Streptomycin at 37 C under 5% CO2 condition.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacturer and then purified using RNeasy mini columns (Qiagen) as per the manufacturer's instruction.

treatment_protocol: A549 cells that expressed shRNA targeting TK1 (#1, #2) were used for preparing the total RNA and to perform gene expression array.

tag: shRNA

value: TK1 A10 (shRNA#2)


title: inputEBWT

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
RNA-seq raw data were aligned to the mouse genome mm10 using STAR_2.6.0a.  ChIP-seq reads were aligned to the mouse genome (mm10) using the Bowtie2 software.
For RNA-seq mapped reads, raw read count for gene expression was calculated by HTseq based on gene annotations from Ensembl. FPKM values for gene expression are calculated using cufflinks v2.2.1.
Differential expressed genes are calculated by DEseq2.
Quantification of ChIP-seq data is: RPKM calculation from raw read count within the promoters of genes.
Genome_build: mm10

source_name: EB

growth_protocol: TL1 mouse ES cells were grown in standard ES culture medium supplemented with 15% of FBS and LIF. Ebs was cultured with ES culture medium without LIF.

extract_protocol:
Cells for ChIP-seq were cross-linked with 1% formaldehyde for 10 min at RT and quenched with 125 mM glycine for 5 min. Cells were collected and washed once with cold TBS. EBs were digested by 0.25% trypsin (Gibco, Gaithersburg, Maryland) at 37°C before fixation using 1% formaldehyde for 10 min at RT. Fixed cells were re-suspended in lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% IGEPAL-CA630) and incubated on ice for 10 min. After centrifugation, the cell pellet was washed once with MNase digestion buffer (20 mM Tris-HCl, pH7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2). After re-suspended in 250 µl MNase digestion buffer with proteinase inhibitors, 2000 units per 4x106 cells MNase (M0247S; New England Biolabs, Ipswitch, Massachusetts) was added. After incubation at 37°C for 20 min, 250 µl of STOP buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate) was added. Lysates were sonicated for 15 cycles (30 sec on and 30 sec off) in Bioruptor (Diagenode, Inc., Danville, New Jersey) and centrifuged at 21,130 x g for 10min. the supernatant was collected after centrifugation and chromatin content was estimated by the Qubit assay (Invitrogen). The chromatin was incubated with 5 µg anti-H3K27me3 antibody (Cell Signaling, Cat.# 9733),  2 µg anti-H3K4me3 antibody (Abcam, ab8580) at 4°C overnight on a rotator. 30 µl Protein-G Mag Sepharose beads (GE Healthcare, Little Chalfont, United Kingdom) was added and incubated for additional 3 hours at 4°C. Beads were washed with ChIP buffer (50 mM Tris-HCl, pH8.0, 10 mM EDTA, 100 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), high salt buffer (ChIP buffer with 500 mM NaCl), LiCl buffer (10 mM Tris-HCl, pH8.0, 0.25 M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and TE buffer. Chromatin on beads was eluted and reverse-crosslinked at 65°C overnight and was purified by PCR purification kit (Qiagen) after the treatment of RNase A and proteinase K.
ChIP-seq libraries were prepared from 10 ng ChIP and input DNA using the Ovation ultralow DR Multiplex kit (NuGEN). The ChIP-seq libraries were sequenced at single end on an Illumina HiSeq 2000 instrument.

tag: genotype

value: WT

tag: class

value: Input


title: inputEBKO

value: KO


title: A549 TK1 A10 (shRNA#2), replicate 1


title: 25-6days-NACl-technical-replicate-a


title: 12-1day-Kainate-technical-replicate-d

value: 1 day


title: 12-1day-Kainate-technical-replicate-b


title: 12-1day-Kainate-technical-replicate-c


title: 28-6days-Kainate-technical-replicate-b


title: inputESKO

source_name: ES


title: A549 TK1 A7 (shRNA#1), replicate 2

value: TK1 A7 (shRNA#1)


title: 28-6days-Kainate-technical-replicate-c

value: Kainate


title: A549 TK1 A7 (shRNA#1), replicate 1


title: 32-12days-NACl-technical-replicate-c

value: 12 days


title: inputESWT


title: 11-1day-Kainate-technical-replicate-d


title: 12-1day-Kainate-technical-replicate-a


title: H3K4Me37EBKO


title: 11-1day-Kainate-technical-replicate-c


title: 11-1day-Kainate-technical-replicate-b


title: DCOD 4 Mem day 4 PBMC

city: Bethesda

first: Douglas Scott

last: Merrell

state: MD

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

institute: Uniformed Services University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95213.gif

hyb_protocol: not provided

scan_protocol: scanner model: G2505C

data_processing: VALUE is Log RED/GREEN

organism: Macaca mulatta

source_name: 825 ng of amplified monkey DCOD 4 Mem day 0 cDNA

label_protocol: not provided

extract_protocol: not provided

tag: tissue type

value: PBMC

value: memory CD4 T cells

source_name: 825 ng of amplified monkey DCOD 4 Mem day 4 cDNA

value: 4 d

tag: individual

value: DCOD

tag: Sex

value: male


title: H3K4Me37EBWT


title: H3K27Me37EBKO


title: 10-1day-Kainate-technical-replicate-d


title: 10-1day-Kainate-technical-replicate-c


title: H3K4Me3ESKO


title: 11-1day-Kainate-technical-replicate-a


title: 10-1day-Kainate-technical-replicate-b


title: H3K27Me37EBWT


title: H3K27Me3ESWT


title: 9-1day-NACl-technical-replicate-c

value: NaCl


title: F72 4 Mem day 10 PBMC

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95225.gif

source_name: 825 ng of amplified monkey F72 4 Mem day 0 cDNA

source_name: 825 ng of amplified monkey F72 4 Mem day 10 cDNA

value: female


title: EB_KO2

extract_protocol:
total RNA was extracted by the Rneasy Plus Kit (Qiagen).
RNA-seq libraries and deep sequencing were conducted by Novogene mRNA next-generation sequencing services. Two replicates for each sample were sequenced.

value: mRNA


title: DBXC 4 Mem day 4 PBMC

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95216.gif

source_name: 825 ng of amplified monkey DBXC 4 Mem day 0 cDNA

source_name: 825 ng of amplified monkey DBXC 4 Mem day 4 cDNA

value: DBXC


title: H3K27Me3ESKO


title: DBXC 4 Mem day 10 PBMC

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95217.gif

source_name: 825 ng of amplified monkey DBXC 4 Mem day 10 cDNA


title: 9-1day-NACl-technical-replicate-d


title: F03 4 Mem day 4 PBMC

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95218.gif

source_name: 825 ng of amplified monkey F03 4 Mem day 0 cDNA

source_name: 825 ng of amplified monkey F03 4 Mem day 4 cDNA


title: F72 4 Mem day 4 PBMC

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95224.gif

source_name: 825 ng of amplified monkey F72 4 Mem day 4 cDNA


title: EB_KO

description: EBKO


title: FML 4 Mem day 4 PBMC

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95220.gif

source_name: 825 ng of amplified monkey FML 4 Mem day 0 cDNA

source_name: 825 ng of amplified monkey FML 4 Mem day 4 cDNA

value: FML


title: F03 4 Mem day 10 PBMC

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95219.gif

source_name: 825 ng of amplified monkey F03 4 Mem day 10 cDNA


title: 8-1day-NACl-technical-replicate-d

source_name: Hippocampus CA1 area


title: 9-1day-NACl-technical-replicate-a


title: 9-1day-NACl-technical-replicate-b


title: 26-6days-NACl-technical-replicate-d

value: 6 days


title: ES_KO

description: ES


title: F61 4 Mem day 4 PBMC

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95222.gif

source_name: 825 ng of amplified monkey F61 4 Mem day 0 cDNA

source_name: 825 ng of amplified monkey F61 4 Mem day 4 cDNA


title: EB_WT2

source_name: EB

value: WT


title: 8-1day-NACl-technical-replicate-c


title: DCOC 4 Mem day 10 PBMC

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95212.gif

source_name: 825 ng of amplified monkey DCOC 4 Mem day 0 cDNA

source_name: 825 ng of amplified monkey DCOC 4 Mem day 10 cDNA

value: DCOC


title: DCOC 4 Mem day 4 PBMC

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95211.gif

source_name: 825 ng of amplified monkey DCOC 4 Mem day 4 cDNA


title: EB_WT

description: EBWT


title: FML 4 Mem day 10 PBMC

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95221.gif

source_name: 825 ng of amplified monkey FML 4 Mem day 10 cDNA


title: DCOR 4 Mem day 10 PBMC

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-11/95406.gif

source_name: 825 ng of amplified monkey DCOR 4 Mem day 0 cDNA

source_name: 825 ng of amplified monkey DCOR 4 Mem day 10 cDNA

value: DCOR


title: F61 4 Mem day 10 PBMC

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95223.gif

source_name: 825 ng of amplified monkey F61 4 Mem day 10 cDNA


title: 8-1day-NACl-technical-replicate-b

value: 1 day


title: ES_WT2

source_name: ES


title: 27-6days-NACl-technical-replicate-c


title: DCOD 4 Mem day 10 PBMC

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95214.gif

source_name: 825 ng of amplified monkey DCOD 4 Mem day 0 cDNA

source_name: 825 ng of amplified monkey DCOD 4 Mem day 10 cDNA


title: 8-1day-NACl-technical-replicate-a


title: ES_WT

description: ES


title: Fst-KO rep3

city: London

first: Paul

middle: T.

last: Sharpe

state: Please select one below:

address: Guy's hospitial

department: Centre for Craniofacial and Regenerative Biology

institute: King's College London

data_processing:
Partek Flow software was used for RNA-seq data analysis
Raw FASTQ files generated by Illumina Hiseq platform were trimmed based on End min quality level (Phred) and aligned BAM files were analysed by BWA 0.7.12 and mapped to the mouse mm10 reference genome.
Aligned reads were then quantified to the annotation mode (mm10; Ensembl Transcripts release 83) and the raw gene counts were normalized.
Differential gene expression was identified by Partek Gene-specific analysis.
False discovery rate (FDR) correction with difault p-value <=0.05 considered statistically significant.
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts (normalized) and differential expression

source_name: mouse tongue

extract_protocol:
Mouse tongue intermolar eminence (IE) tissues were freshly dissected and homogenized with TRIzol (Invitrogen). Total RNA was extracted using RNeasy MINI kit (Qiagen 74104) and RNA quantity was assessed by an Agilent Bioanalyzer (Agilent RNA 6000 nano). 1ug of each good quality (RIN > 7) RNA sample was used for RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: tongue epithelium

value: Fst-KO


title: 7-1day-NACl-technical-replicate-d


title: 7-1day-NACl-technical-replicate-b


title: 7-1day-NACl-technical-replicate-c


title: ES_KO2

value: KO


title: DCOR 4 Mem day 4 PBMC

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95215.gif

value: PBMC

value: memory CD4 T cells

source_name: 825 ng of amplified monkey DCOR 4 Mem day 4 cDNA


title: 7-1day-NACl-technical-replicate-a


title: Fst-KO rep1


title: WT rep3


title: Fst-KO rep2


title: WT rep2


title: 24-4days-Kainate-technical-replicate-d

value: 4 days

value: Kainate


title: 24-4days-Kainate-technical-replicate-c


title: 23-4days-Kainate-technical-replicate-c


title: 23-4days-Kainate-technical-replicate-d


title: 24-4days-Kainate-technical-replicate-a


title: 24-4days-Kainate-technical-replicate-b


title: PIPseq (cluster3_6)

city: Saint Louis

first: Donghoon

last: Lee

state: MO

address: 660 S Euclid Ave, PO 8108

department: Neuroscience

institute: Washington University In St. Louis

description: Control cells: 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47; Photo-tagged cells: 1 2 3 4 5 6 7 8

data_processing:
We used Cel-seq2 analysis pipeline (Hashimshony et al., 2016; https://github.com/yanailab/celseq2). See below for a brief description of each step:
Sequencing reads were demultiplexed by Cel-seq2 software.
The 26 bp read is the technical read and includes UMI from bp 1-6 and a 6 bp barcode starting at basepair position 7.
The 98 bp read is the biological read.
Sequencing reads were aligned to the mouse reference genome by STAR aligner (ver 2.6.0a; Dobin et al., 2013); Default parameters were used except for -sjdbOverhang, which was set to be 97; In the GTF file, the model of a gene, vmn1r237, was modified.
The number of UMI for each gene was extracted by Htseq-count (ver 0.8.0; Anders et al., 2015). Default parameters were used.
Genome_build: GRCm38
Supplementary_files_format_and_content: UMI counts in tab delimited csv files.  Column headers are formatted as BC-##-nnnnnn where ## is the cell number referenced in the 'description' field (for control vs phototagged status) and nnnnnn is the cell barcode.  Processed data contain cells that do not belong to either control or phototagged cells. These "unidentified" cells should be discarded in subsequent analysis. Please note that NNNNNN is a cell barcode.

source_name: Vomeronasal sensory epithelium

extract_protocol:
Single cells were collected by FACS into a 96-well PCR plate containing 1.4 μl of lysis buffer in each well; the lysis buffer consisted of 0.096% Triton X-100, 0.08 U RNase inhibitor (Promega, N2615), 1 nmol dNTP and 0.2 pmol of reverse transcription primer.
Libraries were prepared for RNA sequencing by Cel-seq2 protocol (Hashimshony et al., 2016) with minor modifications in the extract protocol (see above). Single cell RNA sequencing library with in vitro transcription amplification. UMIs were attached at 3’ ends of mRNA molecules.

value: GCaMP5g-P2A-PAmCherry transgenic mouse

value: Vomeronasal sensory epithelium

value: post natal day 80 - 160


title: PIPseq (cluster3_7)

description: Control cells: 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23; Photo-tagged cells: 25 26 27 28 29 31 32 33

value: female


title: PIPseq (cluster3_4)

description: Control cells: 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23; Photo-tagged cells: 25 27 28


title: 23-4days-Kainate-technical-replicate-a

source_name: Hippocampus CA1 area


title: 23-4days-Kainate-technical-replicate-b


title: PIPseq (cluster19_3)

description: Control cells: 7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23; Photo-tagged cells: 1  2  3  4  5  6 25 26 27 28 29 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48


title: PIPseq (cluster19_2)

description: Control cells: 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23; Photo-tagged cells: 25 26 27 28 29 30 31 32 33 34 36 41 42 43 45 46 47 48


title: 22-4days-Kainate-technical-replicate-d


title: PIPseq (cluster19_1)

description: Control cells: 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 17 18 19 20 21 22 23; Photo-tagged cells: 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 43 44 45 47 48


title: PIPseq (cluster3_3)

description: Control cells:  2  4  8 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47; Photo-tagged cells: 1 3 5 6 7


title: 22-4days-Kainate-technical-replicate-b


title: PIPseq (cluster2_2)

description: Control cells: 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47; Photo-tagged cells: 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24


title: 22-4days-Kainate-technical-replicate-a


title: 21-4days-NACl-technical-replicate-d

value: NaCl


title: PIPseq (cluster2_1)

description: Control cells: 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23; Photo-tagged cells: 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48


title: H3K4Me3ESWT


title: WT rep1


title: 21-4days-NACl-technical-replicate-c


title: PIPseq (cluster3_5)

description: Control cells: 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 20 21 22 23; Photo-tagged cells: 25 26 27 28 29 30 31 32 33 34 35 41 42 43 44 45 47


title: 21-4days-NACl-technical-replicate-a


title: PIPseq (cluster3_1)

description: Control cells: 1  5  7  9 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47; Photo-tagged cells: 2 4 6 8


title: 21-4days-NACl-technical-replicate-b


title: 20-4days-NACl-technical-replicate-d


title: 20-4days-NACl-technical-replicate-c


title: 20-4days-NACl-technical-replicate-a


title: PIPseq (cluster1_3)

description: Control cells: 1  2  3  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 22 23; Photo-tagged cells: 25 26 27 28 30 31 32 33 34 35 36 38 39 40 41 42 43 44 45 46 47


title: 20-4days-NACl-technical-replicate-b


title: 22-4days-Kainate-technical-replicate-c


title: 19-4days-NACl-technical-replicate-d


title: PIPseq (cluster6_1)

description: Control cells: 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47; Photo-tagged cells: 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 23 24


title: 19-4days-NACl-technical-replicate-c


title: PIPseq (cluster1_2)

description: Control cells: 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23; Photo-tagged cells: 25 26 27 28 29 30 31 32 33 34 35 36 40 41 42 43 44 45 46 47 48


title: PIPseq (cluster3_2)

description: Control cells: 1  3  7  8  9 10 17 18 20 23 25 26 27 28 29 30 31 32 34 35 36 37 38 39 40 41 42 43 44 45 46 47; Photo-tagged cells: 4  6 11 12 13 14 16 19 21 22 24


title: 19-4days-NACl-technical-replicate-a


title: 19-4days-NACl-technical-replicate-b


title: PIPseq (cluster1_1)

description: Control cells: 2  3  4  5  6  7  8  9 11 12 14 15 16 17 18 19 20 21 22; Photo-tagged cells: 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48

value: male


title: 18-2days-Kainate-technical-replicate-d

value: 2 days


title: LN3

city: HangZhou

first: Di

last: Wang

state: ZheJiang

address: No.866, Yuhangtang Road, Xihu District, Hangzhou

institute: ZheJiang university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat2
Reads Per Kilo bases per Million reads (RPKM) were calculated using a protocol from Mortazavi et al., Nat. Methods, 2008. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10

extract_protocol:
Bone marrow cells were flushed from tibias and femurs with cold Dulbecco’s modified Eagle’s medium (DMEM) and were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, and 10 ng/ml macrophage colony-stimulating factor (M-CSF, PeproTech) for 6 days to generate BMDMs. Then treated with LPS and phgdh inbibitor for 6 hours.And total RNA were extracted for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For sample C, BMDMs were cultured in complete DMEM medium for 6 hours. For sample L, BMDMs were cultured in complete DMEM medium for 6 hours in the presence of 500 ng/ml LPS.  For sample LN, BMDMs were cultured in complete DMEM medium for 6 hours in the presence of LPS (500 ng/ml) and NCT503 (50 μM).

value: Bone-marrow-derived macrophage (BMDM)

value: post natal week 8


title: PIPseq (cluster6_2)

description: Control cells: 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47; Photo-tagged cells: 2  3  4  5  6  7  8  9 10 11 12 18 19 20 21 22 23 24


title: LN2

source_name: BMDMs were cultured in complete DMEM medium for 6 hours in the presence of LPS (500 ng/ml) and NCT503 (50 μM)


title: 18-2days-Kainate-technical-replicate-c


title: 17-2days-Kainate-technical-replicate-d


title: 18-2days-Kainate-technical-replicate-a


title: 18-2days-Kainate-technical-replicate-b


title: 17-2days-Kainate-technical-replicate-c


title: LN1


title: 17-2days-Kainate-technical-replicate-a


title: L3

source_name: BMDMs were cultured in complete DMEM medium for 6 hours in the presence of 500 ng/ml LPS


title: 17-2days-Kainate-technical-replicate-b


title: 16-2days-Kainate-technical-replicate-d


title: 16-2days-Kainate-technical-replicate-c


title: L2


title: 16-2days-Kainate-technical-replicate-b


title: 10-1day-Kainate-technical-replicate-a

value: 1 day


title: 16-2days-Kainate-technical-replicate-a


title: L1


title: 15-2days-NACl-technical-replicate-d


title: C3

source_name: BMDMs were cultured in complete DMEM medium for 6 hours


title: 15-2days-NACl-technical-replicate-c


title: 15-2days-NACl-technical-replicate-a


title: C2


title: Control subjects 30 [CTL_240]

type: genomic

city: Kyoto

first: Ryo

last: Kimura

address: Yoshida-Konoe-cho

department: Anatomy and Developmental Biology

country: Japan

institute: Kyoto University Graduate School of Medicine

hyb_protocol: Sandard Illumina protocol using bisulfite converted genomic DNA

scan_protocol: Standard protocol using the Illumina iScan system

data_processing: ChAMP analysis pipeline [ Y.Tian et al.,  Bioinformatics (2017)]

label: Cy3 and Cy5

source_name: Control subject_peripheral blood

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from peripheral blood samples using the QIAamp DNA blood midi kit

tag: group

value: Control

value: Male

value: whole blood


title: 14-2days-NACl-technical-replicate-d


title: 14-2days-NACl-technical-replicate-c


title: C1


title: Control subjects 29 [CTL_233]

value: Female


title: 14-2days-NACl-technical-replicate-b


title: 15-2days-NACl-technical-replicate-b


title: Wildtype  3

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description:
Control 3
WT-7895_S6

data_processing:
ELAND aligner from Illumina in the CASAVA 1.8.2 package with the default parameter settings is used to align the fastq to the reference genome
Data was analyzed using the default parameter settings on Genomatix
Genome_build: mm9
Supplementary_files_format_and_content: RPKM

source_name: Wildtype

extract_protocol:
Bone marrow cells collected from 3 OgaVav-Cre and 3 wildtype female mice were sorted for Lin-Sca+Kit+ cells using a BD FACSAria Fusion Flow cytometer and the following antibodies: Lineage Cocktail FITC (R&D Biosystems), Sca-1(D7)APC (ebiosciences), c-Kit (2B8)PE (ebiosciences), FVD (ebiosciences). At least 2x10^4 cells were collected for each sample. RNA was extracted using RNeasy plus micro kit (Qiagen) following manufacturers protocol
RNA libraries were prepped using NEBNext Ultra RNA Library Prep Kit for Illumina and the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).

tag: strain background

value: Wildtype

value: ~12 weeks

value: Lin-Sca+Kit+ Bone marrow cells


title: 13-2days-NACl-technical-replicate-c


title: 13-2days-NACl-technical-replicate-d


title: Wildtype  2

description:
Control 2
WT-7894_S4


title: Control subjects 28 [CTL_232]


title: Control subjects 31 [CTL_241]


title: Control subjects 26 [CTL_220]


title: 13-2days-NACl-technical-replicate-a


title: 13-2days-NACl-technical-replicate-b


title: 6-6h-Kainate-technical-replicate-d

value: 6 hours

value: Kainate


title: Control subjects 23 [CTL_166]


title: 6-6h-Kainate-technical-replicate-b


title: Control subjects 22 [CTL_162]


title: Oga(Vav-Cre)  2

description:
Treatment 2
KO-7885_S5

source_name: Oga(Vav-Cre)

value: Oga(Vav-Cre)


title: 6-6h-Kainate-technical-replicate-a


title: Oga(Vav-Cre)  1

description:
Treatment 1
KO-7886_S1

value: female


title: Wildtype  1

description:
Control 1
WT-7896_S2


title: 6-6h-Kainate-technical-replicate-c


title: APOBEC1_2

city: D

first: Kate

last: Meyer

state: NC

address: 307 Research Drive Box 3711

department: Biochemistry

institute: Duke University School of Medicine

data_processing:
Barcodes used were: CGGAAT (APOBEC1YTH 1), CTAGCT (APOBEC1YTH 2), CTATAC (APOBEC1YTH 3), CTAGCT (Low input1),  GTGATC (APOBEC1YTHmut 1),GACGAC (APOBEC1YTHmut 2), TACAGC (APOBEC1YTHmut 3), CGGAAT (APOBEC1 1), CTAGCT (APOBEC1 2)
Alignment to hg19 was performed using novoalign
Genome_build: hg19
Supplementary_files_format_and_content: For global m6A profiling with DART-Seq, modified sites were identified from single reads using the CIMS program (C2T transitions, p=0.1) from the CLIP ToolKit (CTK) package. Metagene profiles were performed using hg19 genomic annotations.

growth_protocol: Cells were grown in standard growth media for each cell line

extract_protocol:
Total RNA was extracted using TRIzol reagent. RNA was then subjected to DNAseI treatment to remove any contaminating DNA.
Library construction was performed using NEB low input RNA-Seq kit (Low input1 sample) or the NEBNEXT Ultra II Directional RNA-Seq kit (all other samples)

treatment_protocol: Cells were transfected with APOBEC1YTH-containing plasmid (APOBEC1YTH 1,2,3, low input), APOBEC1YTHmut-containing plasmid (APOBEC1YTHmut 1,2,3), or APOBEC1 alone (APOBEC1 1,2) using lipofection and RNA was isolated 24h later.

tag: cell line

value: human embryonic kidney cells

tag: genotype/variation


title: Control subjects 25 [CTL_171]


title: Control subjects 24 [CTL_169]


title: Oga(Vav-Cre) 3

description:
Treatment 3
KO-7883_S3


title: Control subjects 19 [CTL_158]


title: Control subjects 17 [CTL_155]


title: PTL-Her2-CAR-T

city: Guangzhou

first: Lijuan

last: Lu

address: 74 Zhongshan 2nd Rd

institute: Sun Yat-sen University

description: Gene expression of CAR-T cells after 28 days injection to mice

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. Then hybridized arrays were washed and fixed.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (part number G2505C) using one color scan setting.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 1 out of 2 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

source_name: tumor infiltrating PTL-CAR-T cells

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated with TRIZOL reagent (Life Technologies) according to the manufacturer's instructions.RNA quantity and quality using a NanoDrop-1000 spectrophotometer.RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: T cells

value: Her2 with knockdown of PD-1, Tim-3 and Lag-3

tag: mouse host

value: SKOV3-bearing NSG


title: COX7RP-MCF7_hypoxia

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

description: Gene expression data from COX7RP-transfected MCF7 cells cultured in hypoxia

hyb_protocol: Following fragmentation, 4 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip (Human Gene 1.0 ST Array). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software (build.1.2.1.20) using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

growth_protocol: COX7RP-MCF7 and vector-MCF7 cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted using ISOGEN reagent (Nippon Gene, Japan).

treatment_protocol: Cells were cultured in normoxic (20% oxygen) or hypoxic (1% oxygen) condition.


title: 5-6h-Kainate-technical-replicate-c

tag: genetic background

tag: time

tag: treatment


title: Control subjects 18 [CTL_157]

tag: gender


title: APOBEC1_1

tag: cell type


title: 5-6h-Kainate-technical-replicate-b


title: APOBEC1YTHmut2


title: 5-6h-Kainate-technical-replicate-a


title: APOBEC1YTHmut3


title: APOBEC1YTHmut1


title: Control subjects 20 [CTL_159]

tag: tissue


title: Control subjects 12 [CTL_056]


title: Control subjects 16 [CTL_063]


title: COX7RP-MCF7_normoxia

description: Gene expression data from COX7RP-transfected MCF7 cells cultured in normoxia


title: Her2-CAR-T

source_name: tumor infiltrating CAR-T cells

tag: genotype


title: Low input1

description: Low input1

source_name: HEK293T_Low input1


title: 4-6h-Kainate-technical-replicate-c


title: APOBEC1YTH3


title: Control subjects 21 [CTL_161]


title: Control subjects 14 [CTL_060]


title: vector-MCF7_hypoxia

description: Gene expression data from vector-transfected MCF7 cells cultured in hypoxia


title: vector-MCF7_normoxia

description: Gene expression data from vector-transfected MCF7 cells cultured in normoxia


title: 14-2days-NACl-technical-replicate-a

value: 2 days

value: NaCl


title: APOBEC1YTH2


title: Control subjects 11 [CTL_051]

value: Control


title: APOBEC1YTH1


title: 4-6h-Kainate-technical-replicate-a


title: 129X1/SvJ strain CD4 splenocyte at T0, biological rep4

city: Sydney

first: Hugh

middle: John

last: French

state: New South Wales

address: UNSW

country: Australia

institute: UNSW

description:
Gene expression data from 129X1/SvJ strain unstimulated CD4 splenocytes
HF_S4B

hyb_protocol: Standard Affymetrix protocols followed. Hybridisation performed by The Ramaciotti Centre at The University of New South Wales (Sydney, Australia).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 high resolution scanner. Scanning performed by The Ramaciotti Centre at The University of New South Wales (Sydney, Australia).

data_processing: The data was RMA normalised with Affymetrix Powertools.

source_name: 129X1/SvJ strain_CD4 splenocyte at T0

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA. Labelling performed by The Ramaciotti Centre at The University of New South Wales (Sydney, Australia).

growth_protocol: Splenocytes where extracted and sorted using AutoMACS (Miltenyi Biotech) CD4 Beads (LT34 Miltenyi Biotech) and maintained in MLC supplemented with 10% fetal calf serum (CSL, Parkville, Victoria, Australia) 4 mM L--glutamine, 1 mM sodium pyruvate, 10 mM HEPES, 50 uM beta-mercaptoethanol, penicillin, streptomycin and neomycin.

extract_protocol: Trizol extraction of total RNA was performed followed by clean ups with RNeasy Mini Kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: These cells were divided into non-stimulated or phorbol 12-myristate 13-acetate (10 ng ml-1), Boeringer Mannheim) and ionomycin (1uM, Sigma-Aldrich, Missouri)--stimulated (PMA/I) groups and cultured at 37◦C and 5% CO2 for 4 hours.

tag: age

value: 8 weeks

value: CD4+ splenocytes

tag: time point

value: basal state_untreated (T0)


title: Control subjects 13 [CTL_057]

value: Male

value: whole blood


title: 129X1/SvJ strain CD4 splenocyte at T1, biological rep4

description:
Gene expression data from 129X1/SvJ strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_S4S

source_name: 129X1/SvJ strain_CD4 splenocyte at T1

value: 4hr after PMA/I stimulation (T1)


title: Control subjects 9 [CTL_046]

value: Female


title: 129X1/SvJ strain CD4 splenocyte at T1, biological rep2

description:
Gene expression data from 129X1/SvJ strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_S2S


title: 3-6h-NACl-technical-replicate-d

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA XS kit (Macherey-Nagel). For each sample 10 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech).  Afterwards an average of 180 ng of amplified cDNA was used to prepare libraries.
Libraries were prepared using the Nextera XT DNA kit (Illumina)

value: 6 hours


title: 3-6h-NACl-technical-replicate-c


title: 3-6h-NACl-technical-replicate-b


title: 5-6h-Kainate-technical-replicate-d

value: Kainate


title: 3-6h-NACl-technical-replicate-a


title: Control subjects 8 [CTL_044]


title: 129X1/SvJ CD4 splenocyte at T0, biological rep2

description:
Gene expression data from 129X1/SvJ strain unstimulated CD4 splenocytes
HF_S2B

value: female


title: 129X1/SvJ CD4 splenocyte at T1, biological rep1

description:
Gene expression data from 129X1/SvJ strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_S1S


title: Control subjects 15 [CTL_062]


title: 2-6h-NACl-technical-replicate-c


title: 2-6h-NACl-technical-replicate-d


title: Control subjects 27 [CTL_231]


title: Control subjects 7 [CTL_042]


title: 4-6h-Kainate-technical-replicate-b


title: 2-6h-NACl-technical-replicate-b


title: DBA/2J strain CD4 splenocyte at T1, biological rep4

description:
Gene expression data from DBA/2J strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_D4S

source_name: DBA/2J strain_CD4 splenocyte at T1


title: 2-6h-NACl-technical-replicate-a


title: 129X1/SvJ CD4 splenocyte at T0, biological rep1

description:
Gene expression data from 129X1/SvJ strain unstimulated CD4 splenocytes
HF_S1B


title: Control subjects 6 [CTL_038]


title: DBA/2J strain CD4 splenocyte at T0, biological rep3

description:
Gene expression data from DBA/2J strain unstimulated CD4 splenocytes
HF_D3B

source_name: DBA/2J strain_CD4 splenocyte at T0


title: DBA/2J strain CD4 splenocyte at T1, biological rep2

description:
Gene expression data from DBA/2J strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_D2S


title: DBA/2J strain CD4 splenocyte at T0, biological rep4

description:
Gene expression data from DBA/2J strain unstimulated CD4 splenocytes
HF_D4B


title: 1-6h-NACl-technical-replicate-d


title: DBA/2J strain CD4 splenocyte at T1, biological rep3

description:
Gene expression data from DBA/2J strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_D3S


title: 1-6h-NACl-technical-replicate-c


title: 1-6h-NACl-technical-replicate-b


title: DBA/2J strain CD4 splenocyte at T0, biological rep2

description:
Gene expression data from DBA/2J strain unstimulated CD4 splenocytes
HF_D2B


title: Control subjects 3 [CTL_028]


title: 1-6h-NACl-technical-replicate-a


title: 4-6h-Kainate-technical-replicate-d


title: Control subjects 4 [CTL_029]


title: Control subjects 5 [CTL_036]


title: Control subjects 2 [CTL_015]


title: Control subjects 1 [CTL_013]


title: Control subjects 10 [CTL_047]


title: C57BL/6J strain CD4 splenocyte at T0, biological rep3

description:
Gene expression data from C57BL/6J strain unstimulated CD4 splenocytes
HF_C3B

source_name: C57BL/6J strain_CD4 splenocyte at T0


title: C57BL/6J strain CD4 splenocyte at T1, biological rep4

description:
Gene expression data from C57BL/6J strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_C4S

source_name: C57BL/6J strain_CD4 splenocyte at T1


title: Macula retina 24hr Seq-Well read 1

city: New Haven

first: Brian

last: Hafler

state: Connecticut

address: 300 George Street

institute: Yale School of Medicine

description:
sample_annotations.tsv
counts.mtx
gene_names.txt

data_processing:
Raw sequencing runs were converted to demultiplexed FASTQ files using bcl2fastq2 based on the Nextera N700 indices.
FASTQ files were then aligned to the hg19 genome using standard settings for the Drop-Seq alignment on the Galaxy portal (Broad Institute) using the STAR aligner.
Genome_build: hg19
Supplementary_files_format_and_content: text files contain the count matrix, gene names and the sample annotations for the dataset

source_name: Retina

extract_protocol:
Trephine punches (6mm) were used to isolate samples from (1) the macula in the central retina and (2) a region of mid-peripheral retina. Retinal samples were processed using a single-use papain dissociation system (Worthington, Catalog No. LK003150).
Libraries were constructed using 800 pg of pooled cDNA product and the Nextera XT Library kit.

value: Macula retina

tag: cell types

value: neuronal, glial and vascular cells

tag: sequencing platform

value: Seq-well Illumina Next-Seq 500


title: Peripheral retina 8hr Seq-Well

value: Peripheral retina


title: Macula retina 8hr Seq-Well


title: C57BL/6J strain CD4 splenocyte at T1, biological rep3

description:
Gene expression data from C57BL/6J strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_C3S

tag: strain


title: C57BL/6J strain CD4 splenocyte at T0, biological rep4

description:
Gene expression data from C57BL/6J strain unstimulated CD4 splenocytes
HF_C4B


title: C57BL/6J strain CD4 splenocyte at T0, biological rep2

description:
Gene expression data from C57BL/6J strain unstimulated CD4 splenocytes
HF_C2B


title: C57BL/6J strain CD4 splenocyte at T1, biological rep2

description:
Gene expression data from C57BL/6J strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_C2S


title: Peripheral retina 6hr Seq-Well


title: ASD patients 38 [ASD_223]

source_name: ASD patient_peripheral blood

tag: group

value: ASD


title: ASD patients 34 [ASD_194]


title: Macula retina 6hr Seq-Well


title: ASD patients 35 [ASD_200]


title: C57BL/6J strain CD4 splenocyte at T1, biological rep1

description:
Gene expression data from C57BL/6J strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_C1S


title: ASD patients 37 [ASD_221]


title: MiaPaCa2 Parental napabucasin - rep 3

city: Cold Spring Harbor

first: David

middle: A.

last: Tuveson

address: 1 Bungtown Rd.

department: Cancer Center

institute: Cold Spring Harbor Laboratory

data_processing:
The quality of the RNA-seq reads was first confirmed using FastQC version 0.11.5 (Babraham Bioinformatics).
Reads were then mapped to transcripts from GENCODE release 30 on human GRCh38.p12 genome using STAR alignment software version 2.6.0c.
RSEM version 1.3.1 was used to calculate expression estimates per gene and per isoform.
Genome_build: human NCBI genome build 38.p12
Supplementary_files_format_and_content: The gene.results files are tab-delimited text files that include expected counts, TPM and FKPM values per gene for each sample as generated by RSEM. The isoforms.results files are tab-delimited text files that include expected counts, TPM and FKPM values per isoform for each sample as generated by RSEM.

source_name: Pancreas, epithelial cell carcinoma

growth_protocol: DMEM + 10% FCS

extract_protocol:
TRIzol Reagent (15596-018; Thermo Fisher Scientific); RNA extraction with a PureLink RNA mini kit (12183018A; Thermo Fisher Scientific)
KAPA mRNA HyperPrep Kit for Illumina sequencing (KR1352 – v4.17) was used with library preparation according to manufacturer's protocol.

treatment_protocol: 500 nM napabucasin or DMSO for 2 hours

value: Pancreatic cancer cell line

tag: sgrna

tag: agent

value: 500 nM napabucasin

value: 2 hours


title: MiaPaCa2 Parental DMSO - rep 3

tag: cell line

value: Vehicle control (DMSO)


title: MiaPaCa2 Parental napabucasin - rep 2


title: ASD patients 36 [ASD_219]


title: MiaPaCa2 Parental DMSO - rep 2


title: C57BL/6J strain CD4 splenocyte at T0, biological rep1

description:
Gene expression data from C57BL/6J strain unstimulated CD4 splenocytes
HF_C1B

value: 8 weeks

value: CD4+ splenocytes

value: basal state_untreated (T0)


title: MiaPaCa2 Parental napabucasin - rep 1


title: Balb/c strain CD4 splenocyte at T1, biological rep4

description:
Gene expression data from Balb/c strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_B4S

source_name: Balb/c strain_CD4 splenocyte at T1

value: Balb/c

value: 4hr after PMA/I stimulation (T1)


title: ASD patients 33 [ASD_193]

value: Female

value: whole blood


title: Balb/c strain CD4 splenocyte at T0, biological rep4

description:
Gene expression data from Balb/c strain unstimulated CD4 splenocytes
HF_B4B

source_name: Balb/c strain_CD4 splenocyte at T0

value: female


title: Balb/c strain CD4 splenocyte at T1, biological rep2

description:
Gene expression data from Balb/c strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_B2S


title: ASD patients 30 [ASD_188]

value: Male


title: ASD patients 31 [ASD_190]


title: MiaPaCa2 NQO1-163 napabucasin - rep 3

value: Cas9-expressing pancreatic cancer cell line

value: NQO1-163 (GAATGACATTCATGTCCCCG)


title: Balb/c strain CD4 splenocyte at T0, biological rep2

description:
Gene expression data from Balb/c strain unstimulated CD4 splenocytes
HF_B2B


title: MiaPaCa2 NQO1-163 napabucasin - rep 2


title: MiaPaCa2 Parental DMSO - rep 1


title: ASD patients 29 [ASD_185]


title: ASD patients 28 [ASD_177]


title: Balb/c strain CD4 splenocyte at T1, biological rep1

description:
Gene expression data from Balb/c strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_B1S


title: Balb/c strain CD4 splenocyte at T0, biological rep1

description:
Gene expression data from Balb/c strain unstimulated CD4 splenocytes
HF_B1B


title: A/J strain CD4 splenocyte at T1, biological rep5

description:
Gene expression data from A/J strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_A5S

source_name: A/J strain_CD4 splenocyte at T1

value: A/J


title: ASD patients 32 [ASD_191]

value: ASD


title: A/J strain CD4 splenocyte at T1, biological rep4

description:
Gene expression data from A/J strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_A4S


title: ASD patients 25 [ASD_174]


title: ASD patients 26 [ASD_175]


title: MiaPaCa2 NQO1-163 DMSO - rep 2


title: MiaPaCa2 NQO1-71 napabucasin - rep 3

value: NQO1-71 (TAAGCCAGAACAGACTCGGC)


title: MiaPaCa2 NQO1-71 napabucasin - rep 2

value: 500 nM napabucasin


title: ASD patients 23 [ASD_151]


title: MiaPaCa2 NQO1-163 DMSO - rep 1

value: 2 hours


title: ASD patients 20 [ASD_131]


title: ASD patients 27 [ASD_176]


title: ASD patients 22 [ASD_140]


title: ASD patients 24 [ASD_170]


title: A/J strain CD4 splenocyte at T0, biological rep4

description:
Gene expression data from A/J strain unstimulated CD4 splenocytes
HF_A4B

source_name: A/J strain_CD4 splenocyte at T0


title: A/J strain CD4 splenocyte at T0, biological rep2

description:
Gene expression data from A/J strain unstimulated CD4 splenocytes
HF_A2B


title: A/J strain CD4 splenocyte at T1, biological rep2

description:
Gene expression data from A/J strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_A2S


title: NOD strain CD4 splenocyte at T1, biological rep3

description:
HF_N3S
Gene expression data from NOD strain stimulated(PMA/I,4hr) Cd4 splenocytes.

data_processing:
The data was RMA normalised with Affymetrix Powertools. Probes potentially
containing SNPs were excluded (25690) using the '--kill-list' tag. Annotation
files were downloaded from the Affymetrix website. The command used
was "apt-probeset-summarize
-a rma -p MoGene-1_0-st-v1.r4.pgf -c MoGene-1_0-st-v1.r4.clf -m
MoGene-1_0-st-v1.r4.mps -b MoGene-1_0-st-v1.r4.bgp --qc-probesets
MoGene-1_0-st-v1.r4.qcc --kill-list". The version of apt-probeset-summarize
used was version 1.15.1.

source_name: NOD strain_CD4 splenocyte at T1

value: NOD

tag: genotype/variation

value: NODk

value: 8 Weeks

value: CD4+ splenocytes.


title: MiaPaCa2 NQO1-71 napabucasin - rep 1


title: ASD patients 19 [ASD_120]


title: A/J strain CD4 splenocyte at T1, biological rep1

description:
Gene expression data from A/J strain stimulated (PMA/I,4hr) CD4 splenocytes
HF_A1S

value: 8 weeks

value: CD4+ splenocytes


title: ASD patients 18 [ASD_075]


title: MiaPaCa2 NQO1-71 DMSO - rep 2

value: Vehicle control (DMSO)


title: ASD patients 17 [ASD_068]

value: whole blood


title: ASD patients 14 [ASD_058]

value: Female


title: MiaPaCa2 NQO1-71 DMSO - rep 3


title: MiaPaCa2 Rosa26 napabucasin - rep 3


title: NOD strain CD4 splenocyte at T1, biological rep2

description:
HF_N2S
Gene expression data from NOD strain stimulated(PMA/I,4hr) Cd4 splenocytes.

value: female

value: 4hr after PMA/I stimulation (T1)


title: NOD strain CD4 splenocyte at T0, biological rep3

description:
HF_N3N
Gene expression data from NOD strain unstimulated Cd4 splenocytes.

source_name: NOD strain_CD4 splenocyte at T0

value: basal state (T0)


title: NOD strain CD4 splenocyte at T0, biological rep1

description:
HF_N1N
Gene expression data from NOD strain unstimulated Cd4 splenocytes.


title: MiaPaCa2 NQO1-163 DMSO - rep 3

value: Cas9-expressing pancreatic cancer cell line

value: NQO1-163 (GAATGACATTCATGTCCCCG)


title: ASD patients 13 [ASD_055]

value: ASD


title: ASD patients 10 [ASD_050]


title: ASD patients 16 [ASD_066]

value: Male


title: MiaPaCa2 NQO1-163 napabucasin - rep 1

value: 500 nM napabucasin

value: 2 hours


title: NOD strain CD4 splenocyte at T0, biological rep2

description:
HF_N2N
Gene expression data from NOD strain unstimulated Cd4 splenocytes.

value: NOD

value: NODk


title: ASD patients 21 [ASD_133]


title: MiaPaCa2 NQO1-71 DMSO - rep 1

value: NQO1-71 (TAAGCCAGAACAGACTCGGC)


title: ASD patients 15 [ASD_059]


title: MiaPaCa2 Rosa26 napabucasin - rep 2


title: A/J strain CD4 splenocyte at T0, biological rep1

description:
Gene expression data from A/J strain unstimulated CD4 splenocytes
HF_A1B

value: A/J

value: 8 weeks

value: basal state_untreated (T0)


title: MiaPaCa2 Rosa26 napabucasin - rep 1


title: ASD patients 12 [ASD_054]

value: whole blood


title: PTU_T3_WT_H3K4me1_rep2

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
RNA-seq and ChIP-seq sequencing data was aligned to mm9 using STAR
Differential RNA expression, H3K27Ac and H3K9Ac were analysed by DESeq2
Bedgraph files were generated using HOMER
Nomilized tag counts were optained using HOMER
H3K27Ac and H3K9Ac domains were indentified using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraphs, peak bed file and text file with RPKM

source_name: liver

extract_protocol:
Crosslinked sonicated chromatin was IP'ed antibody and protein A/G agarose beads. DNA was extracted by phenol/choloroform.
ChIP-seq were constructed using the NEBNext Library prep kit according to manufacturer´s (NEB) instructions.

value: liver

value: WT

tag: chip antibody

value: H3K4me1 (Abcam, ab8895)


title: A/J strain CD4 splenocyte at T0, biological rep5

description:
Gene expression data from A/J strain unstimulated CD4 splenocytes
HF_A5B

value: female

value: CD4+ splenocytes


title: ASD patients 9 [ASD_049]

value: Female


title: ASD patients 7 [ASD_033]

value: ASD


title: B10 strain CD4 splenocyte at T0, biological rep3

description:
HF_B3N
Gene expression data from B10 strain unstimulated Cd4 splenocytes.

source_name: B10 strain_CD4 splenocyte at T0

value: 8 Weeks

value: CD4+ splenocytes.

value: basal state (T0)


title: B10 strain CD4 splenocyte at T1, biological rep3

description:
HF_B3S
Gene expression data from B10 strain stimulated(PMA/I,4hr) Cd4 splenocytes.

source_name: B10 strain_CD4 splenocyte at T1

value: 4hr after PMA/I stimulation (T1)


title: ASD patients 4 [ASD_030]

value: Male


title: MiaPaCa2 Rosa26 DMSO - rep 2

value: Cas9-expressing pancreatic cancer cell line

value: Vehicle control (DMSO)

value: 2 hours


title: Dox 72h, biological rep3

city: Tianjin

first: Hui

last: Cheng

address: 288 Nanjing road

institute: Institute of Hematology

description: Gene expression data from Dox inducible 72h leukemia cells

hyb_protocol: Following fragmentation,  Labeled cRNA was hybridized to Mouse Gene 2.0 ST GeneChip® arrays (Affymetrix, America).

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

data_processing: Raw data (CEL files) were normalized at transcript level using MAS5.0

source_name: Leukemia cells (MLL-AF9) after Dox induction 72h

label_protocol: RNA was labeled using the GeneChip® WT Terminal Labeling and Controls Kit combined with the Ambion® WT Expression Kit.

growth_protocol: leukemia cells were sorted by FACS from control groups and Dox inducible groups at different time points

extract_protocol: Total RNA was isolated with TRIzol reagent (Invitrogen, Canada) and purified using RNeasy Mini Kit (Qiagen, German)

treatment_protocol: After sorting, cells were centrifuged at 1400rpm and Trizol were added into the tube

value: leukemia cells (MLL-AF9)

tag: protocol

value: Dox induction 72h

value: spleen


title: B10 strain CD4 splenocyte at T1, biological rep2

description:
HF_B2S
Gene expression data from B10 strain stimulated(PMA/I,4hr) Cd4 splenocytes.


title: MiaPaCa2 Rosa26 DMSO - rep 1


title: ASD patients 11 [ASD_053]

value: whole blood


title: R1-AP-FF_Biological_replicate_1

city: Bonn

first: Tsige

last: Hailay

address: Endenicher Allee 15

department: Animal Breeding and Husbandry

country: Germany

institute: University of Bonn

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.). The FASTQ data were checked using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Trimming was done using Cutadapt (1.11) to extract information of adapter and UMI in raw reads. The output from cutadapt was used to remove adapter sequences and to collapse reads by UMI with inhouse script.
For mapping of the reads, Bowtie2 (2.2.2) software was used.
For the differential expression analysis, the EdgeR statistical (Bioconductor, http://bioconductor.org/) software package was used.
For normalization, the trimmed mean of M-values method based on log-fold and absolute gene-wise changes in expression levels between samples (TMM normalization) was used.
Genome_build: UMD3.1
Supplementary_files_format_and_content: CSV with average read count of each microRNA.

organism: Bos taurus

source_name: Follicular fluid

extract_protocol:
Extracellular vesicle isolation was performed using ultracentrifugation. Isolation of EV total RNA enriched for miRNA was done using an exosomal RNA isolation kit (Norgen Biotek Thorold, Canada).
The library preparation was done using the QIAseq miRNA Library Kit (QIAGEN Genomic Services, Hilden, Germany).

tag: condition

value: Postpartum

value: Follicular fluid extracellular vesicles

tag: metabolic status

value: Always positive

tag: weeks of postpartum

value: Week 5-6


title: R2-heifers-FF_Biological_replicate_2

tag: gender

value: Female

value: Heifers

tag: tissue

value: Positive


title: R1-heifers-FF_Biological_replicate_1


title: ASD patients 8 [ASD_037]

value: ASD


title: B10 strain CD4 splenocyte at T0, biological rep2

description:
HF_B2N
Gene expression data from B10 strain unstimulated Cd4 splenocytes.

tag: age

value: 8 Weeks

value: female

value: CD4+ splenocytes.

value: basal state (T0)


title: R2-AP-FF_Biological_replicate_2


title: R2-ANE-FF_Biological_replicate_2

value: Always negative


title: PTU_T3_WT_CBP_rep2

value: liver

tag: genotype

value: WT

tag: treatment

value: CBP (Santa Cruz, sc-369)


title: R1-ANE-FF_Biological_replicate_1


title: R3-LP-FF_Biological_replicate_3

value: Late positive

value: Week 9-10


title: PTU_WT_H3K4me1_rep2

value: PTU

value: H3K4me1 (Abcam, ab8895)


title: PTU_WT_CBP_rep2


title: B10 strain CD4 splenocyte at T0, biological rep1

description:
HF_B1N
Gene expression data from B10 strain unstimulated Cd4 splenocytes.

tag: time point


title: PTU_WT_NCOR1_rep2

value: NCOR1 (Abcam, ab24552)


title: R3-heifers-FF_Biological_replicate_3

value: Female

value: Follicular fluid extracellular vesicles


title: R2-LP-FF_Biological_replicate_2

value: Postpartum


title: R1-LP-FF_Biological_replicate_1


title: PTU_T3_WT_NCOR1_rep2


title: ASD patients 5 [ASD_031]

value: ASD

value: Male

value: whole blood


title: ASD patients 3 [ASD_012]


title: BL_48hr_rep3

city: Durham

first: Jian-Liang

last: Li

address: 111 TW Alexander Dr

institute: NIEHS

description:
BL48-3
Gene expression after 48hr in Botrytis cinerea-infected leaf tissues.
Replicate 3
This Sample represents one channel of a dual-channel array.
Raw data file: MZ13361_4.txt

hyb_protocol: For each array, 1,650 ng of Cy3- or Cy5-labeled copy RNA was fragmented and hybridized with rotation at 65°C for 17 hours. Samples were hybridized to Arabidopsis 4 x 44k arrays (Agilent Technologies). The arrays were washed according to the manufacturer's protocol.

scan_protocol: The arrays were scanned on a G2505B scanner (Agilent Technologies).

data_processing: Data were extracted using Feature Extraction 10.1.1.1 software (Agilent Technologies). The mean signals were background corrected within the samples, and then quartile normalized between the samples using limma package.

organism: Arabidopsis thaliana

source_name: Leaves, drl1 mutant, B. cinerea infection, 48hr

label_protocol: Complementary DNA (cDNA) was synthesized from 200 ng of the total RNA and used as a template for in vitro transcription in the presence of T7 RNA Polymerase and cyanine-labeled CTPs using the Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's protocol. The ampliﬁed, labeled copy RNA was puriﬁed using the RNeasy Minikit (Qiagen).

growth_protocol: Arabidopsis seeds were sown on autoclaved soil (Metro-Mix200, Grace-Sierra, http://www.sungro.com) and vernalized at 4°C for 3 days. Plants were germinated and grown at approximately 23°C under a 16-hlight/8-h dark regime.

extract_protocol: Total RNA was extracted from leaf tissues collected at each time point after B. cinerea inoculation. RNA concentration was determined on a NanoDrop Spectrophotometer (Thermo Fisher Scientiﬁc), and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: The B. cinerea strain B05 was used in this study. B. cinerea was grown on BD Difco Potato Dextrose Agar (Becton, Dickinson and Company, Sparks, MD) for about 10 days at 24°C. Spores were harvested, resuspended in BD Difco Potato Dextrose Broth (Becton, Dickinson and Company) at a density of 1-5x10^5 spores per mL, and incubated for 2 hours prior to inoculation. Five-µL spore suspensions were dropped on the adaxial surface of rosette leaves (one drop on each leaf) where the leaves were gently wounded with a needle.

tag: ecotype/background

value: Columbia

value: drl1 mutant

value: Leaves

value: Botrytis cinerea strain B05 infection

tag: time point (post-inoculation)


title: ASD patients 2 [ASD_011]

tag: group


title: BL_48hr_rep2

description:
BL48-2
Gene expression after 48hr in Botrytis cinerea-infected leaf tissues.
Replicate 2
This Sample represents one channel of a dual-channel array.
Raw data file: MZ13361_2.txt


title: ASD patients 6 [ASD_032]


title: BL_48hr_rep1

description:
BL48-1
Gene expression after 48hr in Botrytis cinerea-infected leaf tissues.
Replicate 1
This Sample represents one channel of a dual-channel array.
Raw data file: MZ13361_4.txt


title: Dox 72h, biological rep1

tag: cell type

value: leukemia cells (MLL-AF9)

value: Dox induction 72h

value: spleen


title: BW_48hr_rep3

description:
BW48-3
Gene expression after 48hr in Botrytis cinerea-infected leaf tissues.
Replicate 3
This Sample represents one channel of a dual-channel array.
Raw data file: MZ13361_3.txt

source_name: Leaves, wild-type, B. cinerea infection, 48hr

value: Wild-type


title: BW_48hr_rep2

description:
BW48-2
Gene expression after 48hr in Botrytis cinerea-infected leaf tissues.
Replicate 2
This Sample represents one channel of a dual-channel array.
Raw data file: MZ13361_1.txt


title: Dox 48h, biological rep2

description: Gene expression data from Dox inducible 48h leukemia cells

source_name: Leukemia cells (MLL-AF9) after Dox induction 48h

value: Dox induction 48h


title: Dox 48h, biological rep3


title: R3-EN-FF_Biological_replicate_3

value: Early negative

value: Week 5-6


title: Dox 72h, biological rep2


title: R2-EN-FF_Biological_replicate_2

value: Female


title: Control, biological rep3

description: Gene expression data from control leukemia cells

source_name: Leukemia cells (MLL-AF9) of control group

value: control mice


title: Dox 48h, biological rep1


title: PU1_Stag2WT_AAN6_SP

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 with default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to bigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

source_name: mouse

extract_protocol: ChIP-seq libraries were constructed with the NEBNext ChIP-seq library prep kit following the manufacturer’s recommended protocol (New England Biolabs, Ipswich, MA, USA).

treatment_protocol: The cells were sorted from murine bone marrow and spleen in Stag2 wild type and knockout mice

value: Stag2 WT

value: Santa Cruz sc-352


title: βgal

city: Harbin

first: Zheng

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensemble_GRCm38.96 whole genome using tophat2  with parameters  -p 8 -N 2 --read-edit-dist 2
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then   F  PKM   of each gene was calculated based on the length of the gene and reads count mapped   to this   gene.  F  PKM,   expected  number  of  Fragment  s  Per  Kilobase  of  transcript  sequence  per   Millions  base  pairs  sequenced  ,  considers  the  effect  of  sequencing  depth  and  gene  length   for the reads count at the same time, and is currently the most commonly used method for   estimating gene expression  levels (  Tr  apnell, Cole, et al., 2010  )
Genome_build: Ensemble_GRCm38.96

source_name: primary hepatocytes

growth_protocol: Primary hepatocytes were isolated from C57BL/6 mice by liver-perfusion with type II collagenase (Worthington Biochem, Lakewood, NJ) and cultured at 37°C and 5% CO2 in DMEM medium supplemented with 5% FBS.

extract_protocol:
Total RNAs were extracted using TriPure Isolation Reagent (Roche, Mannheim, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For Purβ-overexpressing experiments, the cells were infected with βgal and Purβ adenoviruses overnight. For Purβ-knocking down experiments, the cells were infected with Scramble and shPurβ1 or shPurβ2 adenoviruses for 30 h.

value: primary hepatocytes

value: beta-gal overexpression

tag: strain


title: Control, biological rep2


title: PurβKD

value: pur-beta knockdown


title: Control, biological rep1


title: Ope2: MuSCs in overloaded plantaris muscle

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

data_processing:
The barcodes and unique-molecular-identifiers in the reads were extracted using UMI-tools (version 1.0.0) with the command: umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern=NNNNNNCCCCCC --read2-stdout.
The reads were mapped by the aligning software HISAT2 (version 2.1.0) to the reference genome (GRCm38).
Read counts per gene was performed with featureCounts (version 1.6.4) and UMI-tools with the command: umi_tools count --method=directional --per-gene --per-cell --gene-tag=XT.
The duplicates in unique molecular identifiers were discarded.
Using the resulting counts, differentially expressed genes (those with adjusted p-values < 0.1) were extracted by the R library DESeq2 (version 1.22.2).
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-separated text file include UMI count for each sample.

source_name: MuSCs in overloaded plantaris muscle

extract_protocol:
The cells were sorted to each 100 cells into tube contained lysis buffer using Cell sorter.
Libraries were constructed following the protocol as shown previously (Hashimshony et al., 2016).

value: Muscle stem cells

tag: genotype/variation


title: BL_6hr_rep2

description:
BL6-2
Gene expression after 6hr in Botrytis cinerea-infected leaf tissues.
Replicate 2
This Sample represents one channel of a dual-channel array.
The other channel of the array is not included in this study.
Raw data file: MZ13360_4.txt

source_name: Leaves, drl1 mutant, B. cinerea infection, 6hr

value: Columbia

value: drl1 mutant

value: Leaves


title: PU1_Stag2WT_AAN5_BM

city: New York

value: bone marrow

tag: chip antibody


title: BL_6hr_rep3

description:
BL6-3
Gene expression after 6hr in Botrytis cinerea-infected leaf tissues.
Replicate 3
This Sample represents one channel of a dual-channel array.
Raw data file: MZ13361_2.txt

value: Botrytis cinerea strain B05 infection


title: Purβ

value: pur-beta overexpression


title: BW_48hr_rep1

description:
BW48-1
Gene expression after 48hr in Botrytis cinerea-infected leaf tissues.
Replicate 1
This Sample represents one channel of a dual-channel array.
Raw data file: MZ13361_3.txt

value: Wild-type


title: LF_TB4

city: atlanta

first: Jeffery

last: Streelman

address: 950 atlantic drive

institute: georgia institute of technology

data_processing:
Raw sequence reads from RT and TB samples were quality controlled using the NGS QC Toolkit (Patel and Jain 2012). Raw reads with an average PHRED quality score below 20 were filtered out. The remaining reads were further trimmed of low-quality bases at the 3’ end.
Quality controlled reads for each sample were aligned to the Metriaclima zebra genome v1.1 (Brawand et al. 2014) using TopHat v2.0.9 (Kim et al. 2013).
The resulting TopHat2 output bam files were sorted and converted to sam files using samtools v0.19 (Li et al. 2009). Sorted sam files were used as input for the HTSeq-count v0.6.1 program to obtain fragment counts for each locus (Anders et al. 2014).
Fragment counts were scale-normalized across all samples using the calcNormFactors function in the edgeR package v3.6.8 (Robinson et al. 2010). Multidimensional scaling (MDS) plots were also produced via the edgeR package v.3.6.8 to determine the relative consistency among the replicates and samples. Scale-normalized fragment counts were converted into log2 counts per million reads mapped (cpm) with precision weights using voom and fit to a linear model using the limma package v3.20.9 (Smyth 2005; Law et al. 2014). Pairwise contrasts were constructed between RT and TB samples.
Genome_build: MZ_UMD1
Supplementary_files_format_and_content: raw read counts

organism: Labeotropheus fuelleborni

source_name: L. Fuelleborni_Taste Bud

extract_protocol:
Animals were sacrificed and immediately dissected for RNA extraction. A ribbon approximately 1mm x 10mm of epithelium was removed labial to the outer row of teeth from the dentary of experimental animals using a #12 scalpel blade. The extra-osseous soft tissue was removed from the entire jaw to reduce the risk of TB containing epithelium carryover. The bone was then shaved down using a scalpel to expose the bony crypts and intraosseous RT were extracted with fine forceps.
Extracted tissue was quickly placed in RNAlater RNA Stabilization Reagent (Qiagen). Tissues were frozen in liquid nitrogen, homogenized using a mortar and pestle and placed in trizol. Following standard chloroform extraction RNeasy mini columns (Qiagen) were utilized to purify RNA for storage at -80ᴼC. Total RNA was quantified using Qubit (Molecular probes) and quality analyzed using the Agilent 2100 Bioanalyzer System for RNA library preparation. RNA input was normalized to 1µg and libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina- Kit A). Libraries were again quantified, quality assessed, and normalized for sequencing on the HiSeq 2500 Illumina Sequencing System.

value: Taste Bud


title: Ope1: MuSCs in overloaded plantaris muscle


title: BL_6hr_rep1

description:
BL6-1
Gene expression after 6hr in Botrytis cinerea-infected leaf tissues.
Replicate 1
This Sample represents one channel of a dual-channel array.
The other channel of the array is not included in this study.
Raw data file: MZ13360_2.txt


title: Cont2: MuSCs in sham plantaris muscle

source_name: MuSCs in sham plantaris muscle


title: PU1_Stag2KO_AAM4_BM

value: Stag2 KO


title: R1-EN-FF_Biological_replicate_1

value: Female

value: Postpartum

value: Follicular fluid extracellular vesicles

value: Early negative

value: Week 5-6


title: ASD patients 1 [ASD_010]

data_processing: ChAMP analysis pipeline [ Y.Tian et al.,  Bioinformatics (2017)]

source_name: ASD patient_peripheral blood

extract_protocol: Genomic DNA was extracted from peripheral blood samples using the QIAamp DNA blood midi kit

value: ASD

value: Male

value: whole blood


title: PU1_Stag2WT_AAN5_SP

value: spleen

value: Stag2 WT

value: Santa Cruz sc-352


title: LF_TB1


title: BW_6hr_rep3

description:
BW6-3
Gene expression after 6hr in Botrytis cinerea-infected leaf tissues.
Replicate 3
This Sample represents one channel of a dual-channel array.
Raw data file: MZ13361_1.txt

source_name: Leaves, wild-type, B. cinerea infection, 6hr

value: Columbia

value: Leaves


title: LF_RT4

source_name: L. Fuelleborni_Replacement Tooth

value: Replacement Tooth


title: Cont1: MuSCs in sham plantaris muscle

value: Muscle stem cells


title: BW_6hr_rep2

description:
BW6-2
Gene expression after 6hr in Botrytis cinerea-infected leaf tissues.
Replicate 2
This Sample represents one channel of a dual-channel array.
The other channel of the array is not included in this study.
Raw data file: MZ13360_3.txt

value: Wild-type

value: Botrytis cinerea strain B05 infection


title: BL_0hr_rep3

description:
BL-3
Gene expression after 0hr in Botrytis cinerea-infected leaf tissues.
Replicate 3
This Sample represents one channel of a dual-channel array.
The other channel of the array is not included in this study.
Raw data file: MZ13359_4.txt

source_name: Leaves, drl1 mutant, B. cinerea infection, 0hr

value: drl1 mutant


title: LF_RT3


title: BW_6hr_rep1

description:
BW6-1
Gene expression after 6hr in Botrytis cinerea-infected leaf tissues.
Replicate 1
This Sample represents one channel of a dual-channel array.
The other channel of the array is not included in this study.
Raw data file: MZ13360_1.txt


title: Scramble

value: primary hepatocytes

value: scramble


title: Input_Stag2KO_AAN7

value: bone marrow

value: Stag2 KO


title: LF_RT0


title: PU1_Stag2KO_AAN7_SP


title: LF_TB2

value: Taste Bud


title: Input

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

description: Input_peaks.bed pvalue = p<0.001

data_processing:
Filtering: Unpaired sequencing reads were trimmed and subjected to proprietary quality filtration for the Ion Torrent platform (minimum quality threshold 20). Reads with sequence length ranging from 80 to 300 base were used for further analysis.
Alignment: Reads were mapped using bowtie2 against repeat-masked (hg38.fa.masked) and repeat-unmasked (hg38.fa) human genome. Reads were mapped end-to-end with default option.
RM Filtering: Reads were mapped to repeat-masked genome. All reads with ambiguous nucleotide (N) were removed and subjected to peak-calling to get RM CTCF peaks.
Peak calling: MACS2 (single sample peak calling).
Genome_build: hg38
Supplementary_files_format_and_content: bed files with MACS2 called peaks (*peaks.bed) on sample records or overlapping peaks from different conditions made by bedtools intersect -v found on series record.

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10 % FBS at 37C and 5%CO2.

extract_protocol:
Lysates were clarified from sonicated nuclear lysates and protein-DNA complexes were isolated using specific antibodies.
The Ion Xpress(TM) Plus Fragment Library Kit (Cat. no. 4471269) was used for library preparation. All the steps were performed as per manufacturer’s instructions for sequencing on Ion Torrent S5 platform without any barcoding.

treatment_protocol: HEK293T cells were transduced with following shRNA lentiviruses: non-targeting (CT), CGGBP1-silencing (KD) and CGGBP1-overexpressing (OE). For stable transduction, control and CGGBP1 shmiR transduced cells were selected with 10 ug/ml puromycin.

tag: antibody

value: none (input)

tag: cell line


title: Hep3B-input

city: Shanghai

first: Jing

last: Yang

address: 25/Ln 2000 Xietu Road

institute: Shanghai Cancer Institute, Renji Hospital

description: R19023218-Hep3B-input5-2-3-JZ2018904260321

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the h19 genome assembly using Bowtie  2.0 The original data was compared to the reference genome using Bowtie 2.0 software.
Data were filtered using the picard version 2.19.0 software
peaks were called using MACS version 2.1.2 with the following setting: band width(300), model fold[5, 50], pvalue cutoff(5.00e-02).
Genome_build: hg19
Supplementary_files_format_and_content: xls files were generated using MACS version 2.1.2.

growth_protocol: Hep3B cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco, New York, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, New York, USA), 100 U/mL penicillin and 100 μg/mL streptomycin (Sigma-Aldrich, St. Louis, USA) at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
TCF12 antibody (CST11825, Danvers, MA, USA) and protein A magnetic beads were incubated with the lysate overnight at 4 °C and then reverse crosslinked.
Libraries were prepared according to KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series- KK8504

value: Hepatocellular carcinoma cells

tag: chip-antibody


title: Hep3B-TCF12

value: CST11825, Danvers, MA, USA


title: H3K27me3_CT_ChIP-seq

description: H3K27me3_CT_peaks.bed pvalue = p<0.001

value: SC-130356 (Santa Cruz Biotechnology)

tag: cggbp1 status

value: endogenous


title: MZ_TB3

organism: Maylandia zebra

source_name: M. zebra_Taste Bud


title: Input_Stag2WT_AAN5

value: Stag2 WT


title: 212_Wang_HiC_BWX4921_xyl90m

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into restriction fragments (2398 HindIII fragments). Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genome of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Header: 10kb bins of B. subtilis genome; Column: 10kb bins of B. subtilis genome; matrix value: normalized Hi-C interaction scores
Supplementary_files_format_and_content: Files ending with .csv: comma-separated values files of ChIP-seq results.

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

growth_protocol: Bacillus subtilis strains were derived from the prototrophic strain PY79 (Youngman et al 1983, PMID: 6300908). Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus) at specified temperature.

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908; Wang et al 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-SMC, anti-ScpA, anti-ScpB, anti-ParB or anti-GFP antibodies according to previous publication (Graham et al 2014, PMID: 24829297).
Standard library construction protocol was used for Illumina Nextseq 500 sequencing platform (Hi-C) or Illumina Miseq (ChIP-seq). Illumina Truseq indexes were used.

treatment_protocol: Cells were growing in CH medium at 37˚C, xylose was added to 0.5% final concentration for 90 min, fixed by 3% formaldehyde for 30min at room temperature

tag: developmental stage

value: CH, 37C, 0.5percent xylose for 90m

value: parS-delta-9 no a.b., -59 parS no a.b., lacA::PxylA sspB loxP-Erm, rpoC-yfp-ssrA kan

tag: restriction enzyme

value: HindIII


title: MZ_TB1

tag: tissue


title: Hep3B-shTCF12-2

data_processing:
Paired-end sequence files (fastq) were mapped to the reference genome（version:2.0.4） using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Differential expression analysis for mRNA was performed using R package edgeR. Differentially expressed RNAs with |log2(FC)| value >1 and q value <0.05, considered as significantly modulated, were retained for further analysis. This choice is motivated by the decision to maximize the sensitivity of this analysis, in order to perform a massive screening and identify candidate genes to be validated with a wider sample population with real-time PCR analysis.
We performed a Gene Ontology (GO) analysis for biological processes, cellular components and molecular function and a KEGG pathway analysis (Kyoto Encyclopedia of Genes and Genomes http://www.genome.ad.jp/kegg) via enrich R package.
Genome_build: HG38

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: species

value: liver

value: TCF12 knockdown


title: Hep3B-NC

description: HeNC

tag: treatment

value: Negative control


title: MZ_TB2


title: H3K9me3_CT_ChIP-seq

description: H3K9me3_CT_peaks.bed pvalue = p<0.001

value: ab6002 (abcam)


title: H3K9me3_KD_ChIP-seq

description: H3K9me3_KD_peaks.bed pvalue = p<0.001

value: knockdown


title: BL_0hr_rep2

description:
BL-2
Gene expression after 0hr in Botrytis cinerea-infected leaf tissues.
Replicate 2
This Sample represents one channel of a dual-channel array.
The other channel of the array is not included in this study.
Raw data file: MZ13359_2.txt

value: Columbia

value: drl1 mutant

value: Leaves

value: Botrytis cinerea strain B05 infection


title: MZ_RT3

source_name: M. zebra_Replacement Tooth

value: Replacement Tooth


title: BW_0hr_rep3

description:
BW-3
Gene expression after 0hr in Botrytis cinerea-infected leaf tissues.
Replicate 3
This Sample represents one channel of a dual-channel array.
The other channel of the array is not included in this study.
Raw data file: MZ13359_3.txt

source_name: Leaves, wild-type, B. cinerea infection, 0hr

value: Wild-type


title: BW_0hr_rep2

description:
BW-2
Gene expression after 0hr in Botrytis cinerea-infected leaf tissues.
Replicate 2
This Sample represents one channel of a dual-channel array.
The other channel of the array is not included in this study.
Raw data file: MZ13359_1.txt


title: BL_0hr_rep1

description:
BL-1
Gene expression after 0hr in Botrytis cinerea-infected leaf tissues.
Replicate 1
This Sample represents one channel of a dual-channel array.
The other channel of the array is not included in this study.
Raw data file: MZ13358_4.txt


title: Gunpowder-treated_rep3

city: Verona

first: Elodie

last: Vandelle

state: Verona

address: Strada Le Grazie, 15

department: Department of Biotechnology

country: Italy

institute: University of Verona

description: Gene expression in Psa cells grown 24 h in KB medium supplemented with Gunpowder green tea (0.4 mg/ml), replicate 3

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >15 pmol Cy3/ug cRNA) were fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing  25x Agilent fragmentation buffer and 10x Agilent blocking agent following manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer were added to the fragmentation mixture and hybridized to Agilent-078853 8x60K custom microarray chip for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarray chips were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37°C with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing using the Agilent DNA Microarray Scanner with one color scan settings for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to XDR Hi100%, XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid:078853_D_F_20151012) to substract the background and obtain spatially-detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Pseudomonas syringae pv. actinidiae

source_name: Psa cell treated with Gunpowder tea (0.4 mg/ml), replicate 3

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 50 ng of RNA using the Low Input Quick Amp WT Labeling kit (Agilent Techonologies, Santa Clara, CA, USA) according to manufacturer's instructions for prokaryotic samples, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked using the NanoDrop 2000 instrument (Thermo Scientific, Wilmington, DE, USA).

growth_protocol: Psa cells were cultured in liquid KB medium for 24 h at 28°C.

extract_protocol: Two ml of each bacterial suspension were centrifuged and total RNA was extracted from cell pellets using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO, USA). Total RNA quantity, integrity and purity were controlled using a Nanodrop 2000 instrument (Thermo Scientific, Wilmington, DE, USA) and a Bioanalyzer Chip RNA 7500 serie II (Agilent).

treatment_protocol: Psa cells were cultured in liquid KB (controls) or in KB supplemented with Gunpowder tea at 0.4 mg/ml EGCG (tea treated)

value: 24 h Gunpowder green tea-treatment (0.4 mg/ml)


title: 211_Wang_HiC_BWX4921_xyl60m

treatment_protocol: Cells were growing in CH medium at 37˚C, xylose was added to 0.5% final concentration for 60 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37C, 0.5percent xylose for 60m

tag: genotype


title: BW_0hr_rep1

description:
BW-1
Gene expression after 0hr in Botrytis cinerea-infected leaf tissues.
Replicate 1
This Sample represents one channel of a dual-channel array.
The other channel of the array is not included in this study.
Raw data file: MZ13358_3.txt

tag: ecotype/background


title: H3K4me3_KD_ChIP-seq

description: H3K4me3_KD_peaks.bed pvalue = p<0.001

value: ab8580 (abcam)


title: 210_Wang_HiC_BWX4921_xyl30m

treatment_protocol: Cells were growing in CH medium at 37˚C, xylose was added to 0.5% final concentration for 30 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37C, 0.5percent xylose for 30m


title: Gunpowder-treated_rep1

description: Gene expression in Psa cells grown 24 h in KB medium supplemented with Gunpowder green tea (0.4 mg/ml), replicate 1

source_name: Psa cell treated with Gunpowder tea (0.4 mg/ml), replicate 1


title: Untreated_rep2

description: Gene expression in untreated Psa cells grown 24 h in KB medium, replicate 2

source_name: Psa cell untreated, replicate 2

value: untreated


title: Gunpowder-treated_rep2

description: Gene expression in Psa cells grown 24 h in KB medium supplemented with Gunpowder green tea (0.4 mg/ml), replicate 2

source_name: Psa cell treated with Gunpowder tea (0.4 mg/ml), replicate 2


title: canine mammary tumour tissue [G1]

city: Guangzhou

first: Kun

last: Jia

address: Wushan Street

department: College of Veterinary Medicine

institute: South China Agricultural University

data_processing:
paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
The reads were aligned to the reference genome/transcriptome with bowtie2 software and circRNAs were detected and identified with find_circ software.
Raw junction reads for all samples were normalized by total mapped reads and log2 transformed.
Differentially expressed circRNAs were identified by ttest between two groups, and fold change between two samples.
Genome_build: cm6
Supplementary_files_format_and_content: excel format

organism: Canis lupus familiaris

source_name: mammary

extract_protocol:
Canine mammary tumour tissues and their adjacent normal tissues were immediately flash frozen with liquid nitrogen and the total RNA was extracted from the samples using Trizol reagent (TaKaRa, Japan), following the manufacturer's instructions.
Total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, USA). 10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

value: tumour


title: canine mammary tumour tissue's adjacent normal tissue [G2]

value: adjacent normal tissue


title: H3K27me3_KD_ChIP-seq

description: H3K27me3_KD_peaks.bed pvalue = p<0.001

value: SC-130356 (Santa Cruz Biotechnology)


title: MZ_RT1


title: Untreated_rep3

description: Gene expression in untreated Psa cells grown 24 h in KB medium, replicate 3

source_name: Psa cell untreated, replicate 3


title: H3K4me3_CT_ChIP-seq

description: H3K4me3_CT_peaks.bed pvalue = p<0.001

value: endogenous


title: Untreated_rep1

description: Gene expression in untreated Psa cells grown 24 h in KB medium, replicate 1

source_name: Psa cell untreated, replicate 1


title: canine mammary tumour tissue's adjacent normal tissue [D2]


title: 209_Wang_HiC_BWX4921_xyl00m

treatment_protocol: Cells were growing in CH medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37C, no xylose

value: parS-delta-9 no a.b., -59 parS no a.b., lacA::PxylA sspB loxP-Erm, rpoC-yfp-ssrA kan

value: HindIII