title: WT_Supercoil_Ctrl_INPUT

description: Control data from naked genomic DNA used to eliminate the false positive binding of BTMP drug

source_name: INPUT fraction of Biotin tagged psoralean in naked DNA of wt in GLU

extract_protocol: Genomic DNA was isolated from Qiagen Gneomic-tip 100/G (Cat no 13343) & Genomic DNA buffer Set (Cat no 19060). Purified DNA was sheared to an average size of 500 bp by 6X 15-second pulses using a Biorupter sonicator.  bTMP was added to purified DNA and incubated in dark for 90 mins and crosslinked with UV at 365nm (800 mJ/cm2). DNA is precipitated using isopropanol and washed with 70% ethannol. Dried Pellate was dissolved in buffer (50mM tris Ph 8.0, 10mM EDTA, 0.1% SDS) and incuabted with Dynabeads MyOne streptavidin (Invitrogen cat no. 65001) overnight at 4C. The beads were washed 2X with each of the following buffers; wash Buffer I (20mM tris-HCL pH 8, 2mM EDTA, 150mM NaCl, 1% triton X, 0.1% SDS), wash buffer II (20mM tris-HCL pH 8, 2mM EDTA, 500mM NaCl, 1% triton X, 0.1% SDS) wash buffer III (250 mM LiCl, 10 mM Tris pH8.0, 0.5% Na deoxycholate, 0.5% NP40, 1mM EDTA) and 1x TE (20 mM Tris pH8.0, 2 mM EDTA). The bTMP-DNA complexes were eluted from the beads in 250 µl elution buffer (95% Formamide, 10mM EDTA ) at 90C for 20 min and eluted samples were precipitated with ethanol. DNA was isolated from the precipitated material along with sheared chromatin input (1/100 of the material used for ChIP).

value: Glucose


title: PW2-A1

status: Public on Jul 02 2018

type: SRA

city: Chicago

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

country: USA

institute: University of Chicago

library_source: transcriptomic

data_processing:
Kallisto was used for alignment against the human transcriptome
Log2(TPM+1)
Applied threshold of detection, set all Log2(TPM+1) values below threshold to 0.
Applied cell filter, removed all cells with less than 40% of transcripts mapping to the human transcriptome.
Applied gene expression filter, removed all genes expressed in less than 5% of the cells
Performed Quantile normalization with the Preprocesscore package within each experimental plate
Performed Limma batch correction to remove variability associated with experimental plate and donor ID, while protecting BCR isotype and specificity.
Genome_build: HG19
Supplementary_files_format_and_content: normalized abundance measurement

molecule: polyA RNA

organism: Homo sapiens

source_name: peripheral blood plasmablast

extract_protocol:
The Smart-seq2 protocol published in Nature Protocols by Picelli et al., 2014, was used to isolate cellular mRNA and generate single-cell libraries for RNA-sequencing.
The Smart-seq2 protocol published in Nature Protocols by Picelli et al., 2014, was used to isolate cellular mRNA and generate single-cell libraries for RNA-sequencing.

tag: donor id

tag: donor gender

value: male

tag: isotype

value: IgG

tag: specificity

value: vaccine

tag: experimental batch


title: ACT88F-MEI9 RNAi D30 Intestine

city: College Station

first: Jason

last: Karpac

state: Texas

address: Reynolds Medical Building

department: Molecular and Cellular Medicine

institute: Texas A&M University Health Sciences Center

data_processing:
Sample libraries were sequenced using the Illumina HiSeq 2500.
Sequence cluster identification, quality pre-filtering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.58 and RTA 1.18.64 software with default parameter settings.
Between 7 and 12 million (1X50) base pair reads were generated per library and mapped to the Drosophila genome (Release 6).
Expression was recorded as RPKM: reads per kbp per million reads.
Gene Ontology clustering analysis was performed using FlyMine
Genome_build: Drosophila genome (Release 6)
Supplementary_files_format_and_content: Expression was recorded as RPKM: reads per kbp per million reads.

molecule: total RNA

organism: Drosophila melanogaster

source_name: Intestine

growth_protocol: All flies were reared on standard yeast and cornmeal based food at 25°C and 65% humidity on a 12 hr light/dark cycle, The standard yeast and cornmeal based food was made with the following protocol: 14g Agar/165.4g Malt Extract/ 41.4g Dry yeast/ 78.2g Cornmeal/ 4.7ml propionic acid/ 3g Methyl 4-Hydroxybenzoate/ 1.5L water.

extract_protocol:
Intact fly thorax and intestines were dissected in PBS. Total RNA was extracted using Trizol reagent and used as template to generate sample libraries for RNA sequencing
sample libraries for RNA sequencing were generated using the TruSeq Stranded Total RNA Library Prep Kit

tag: age

value: 30 days

tag: tissue

value: Intestine

tag: disease state

value: DNA damage model


title: WT_Supercoil_Ctrl_IP

type: genomic

city: Milano

first: Mohamood Adhil

last: Mohammed Iqbal

state: Lombardia

address: Via Adamello 16

country: Italy

institute: IFOM - The FIRC Institute of Molecular Oncology

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R array for 16 hours at 42 C in a hybridization oven at 60 rpm

scan_protocol: Arrays were scanned on Affymetrix geneChip Scanner 3000 7G

data_processing:
The CEL files are processed using rMAT R package for normalization, MAT score calculation and calling enriched regions or peaks. The following commands and parameters are used; i) (Normalization) SetNorm = NormalizeProbes(Set, method="MAT", robust=T, all=T, standard=TRUE, verbose=FALSE), where 'Set' is the probe map object created using CEL file and probe annotation file (Sc03b_MR_v04.bpmap) ii) (MAT score calculation) RD = computeMATScore(SetNorm, dMax=300, verbose=FALSE, cName = InputColumnName), iii) (Calling Enriched Region) peak = callEnrichedRegions(RD, dMax=300, dMerge=300, nProbesMin=8, method=method, threshold=1.5, verbose=FALSE)
Bed file containing the enriched regions with respective MAT score and BedGraph file containing the score for short interval bases. Both bed and bedGraph files are generated using rMAT R package and these files are UCSC genome compatible with sacCer3 reference.

label: biotin

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: IP fraction of Biotin tagged psoralean in naked DNA of wt in GLU

label_protocol: Both IP and Input samples are amplified by using Whole genome amplificatio ki protocol ( Sigma-Aldrich WGA1-50RXN) pripor to labelling with Biotin-N11-ddATP (1nMole/ul).

growth_protocol: 1X10e7 cells were synchronized at G1 phase using Alpha-factor and cells were harvested for "G1" samples. For "S" phase samples cells were released into fresh medium after washing cells with 2X YP-medium. After 15 mins of the realese from alpha factor arrest cells were harvested for Chip protocols

extract_protocol: Genomic DNA was isolated from Qiagen Gneomic-tip 100/G (Cat no 13343) & Genomic DNA buffer Set (Cat no 19060). Purified DNA was sheared to an average size of 500 bp by 6X 15-second pulses using a Biorupter sonicator.  bTMP was added to purified DNA and incubated in dark for 90 mins and crosslinked with UV at 365nm (800 mJ/cm2). DNA is precipitated using isopropanol and washed with 70% ethannol. Dried Pellate was dissolved in buffer (50mM tris Ph 8.0, 10mM EDTA, 0.1% SDS) and incuabted with Dynabeads MyOne streptavidin (Invitrogen cat no. 65001) overnight at 4C. The beads were washed 2X with each of the following buffers; wash Buffer I (20mM tris-HCL pH 8, 2mM EDTA, 150mM NaCl, 1% triton X, 0.1% SDS), wash buffer II (20mM tris-HCL pH 8, 2mM EDTA, 500mM NaCl, 1% triton X, 0.1% SDS) wash buffer III (250 mM LiCl, 10 mM Tris pH8.0, 0.5% Na deoxycholate, 0.5% NP40, 1mM EDTA) and 1x TE (20 mM Tris pH8.0, 2 mM EDTA). The bTMP-DNA complexes were eluted from the beads in 250 µl elution buffer (95% Formamide, 10mM EDTA ) at 90C for 20 min and eluted samples were cleaned with Qiagen PCR clean up kit. For Input, DNA was isolated with sheared chromatin input (1/100 of the material used for ChIP).

tag: strain background

tag: genotype/variation

value: wild type

tag: treatment

tag: temperature

tag: category

value: BTMP DNA-Supercoil

tag: cellcycle

value: S Phase

tag: antibody

value: Dynabeads My One Streptavidin-(Invitrogen)


title: ACT88F-MEI9 RNAi D10 Intestine

value: 10 days


title: ACT88F-MEI9 RNAi D10 thorax

source_name: Thorax

value: Thorax


title: Lwt2

city: Wuhan

first: Weihui

last: Li

address: 1 str Sizisan

country: China

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mycobacterium_smegmatis_MC2_155_uid57701 whole genome using bowtie2 v2-2.0.5
Fragments per kilobase of exon per million fragments mapped(FPKM). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments 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: Mycobacterium smegmatis str. MC2 155 (https://www.ncbi.nlm.nih.gov/genome/?term=Mycobacterium%20smegmatis%20MC2%20155)
Supplementary_files_format_and_content: gene_expression.xls file includes FPKM values for each Sample

organism: Mycolicibacterium smegmatis

source_name: wild type

extract_protocol:
RNA was harvested using Trizol reagent. RNeasy Mini Kit (Cat#74106, Qiagen) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: ACT88F-W1118 D30 Intestine

value: control


title: ACT88F-MEI9 RNAi D30 thorax


title: PW2-A3


title: LX642

source_name: ltmA knockout

value: Msm ltmA::hyg/pMV261


title: ACT88F-W1118 D30 thorax


title: LX641


title: Lwt3


title: LX643


title: ACT88F-W1118 D10 thorax


title: WT_Supercoil_S_28_INPUT

description: Negative supercoiling mapping across the genome

source_name: INPUT fraction of Biotin tagged psoralean of wt in GLU at 28 degree S Phase

extract_protocol: Cells were collected blocked using Sodium Azide (0.1%). bTMP is added and cells were incubated in dark for 90 mins and crosslinked with UV at 365nm (800 mJ/cm2). The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (50mM Hepes KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate) using Zirconia beads. The crosslinked chromatin was sheared to an average size of 500 bp by 6X 15-second pulses using a Biorupter sonicator. The lysate was then centrifuged to remove cell debris. The chromatin fraction is incuabted with Dynabeads MyOne streptavidin (Invitrogen cat no. 65001) overnight at 4C.  The beads were washed 2X with each of the following buffers; wash Buffer I (20mM tris-HCL pH 8, 2mM EDTA, 150mM NaCl, 1% triton X, 0.1% SDS), wash buffer II (20mM tris-HCL pH 8, 2mM EDTA, 500mM NaCl, 1% triton X, 0.1% SDS) wash buffer III (250 mM LiCl, 10 mM Tris pH8.0, 0.5% Na deoxycholate, 0.5% NP40, 1mM EDTA) and 1x TE (20 mM Tris pH8.0, 2 mM EDTA). The bTMP-DNA complexes were eluted from the beads in 250 µl elution buffer (95% Formamide, 10mM EDTA ) at 90C for 20 min and eluted samples were cleaned with Qiagen PCR clean up kit. For Input, DNA was isolated with sheared chromatin input (1/100 of the material used for ChIP).


title: ACT88F-W1118 D10 Intestine


title: KO-2_FAT Tissue

status: Public on Jul 01 2018

city: Seoul

first: Jae whan

last: Song

address: Yonsei-ro 50

department: Department of Biochemistry

country: South Korea

institute: College of Life Science and Biotechnology

data_processing:
Preprocessed reads were matched to reference genome sequence using HISAT2 program and then aligned reads were generated.
StringTie program was used for transcript assambly.
Expression levels were normalized with length of transcript and depth of coverage.
Expression profile data was exported by normalized FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values.
Differentially expressed transcripts included in two or more groups were selected through statistical verification.
In case that the genomic information was known, functional annotation and gene-set enrichment analysis were performed on the basis of GO and KEGG database.
Using SAMTOOLS & BCFTOOLS, variant calling was performed.
Fusion genes were predicted using defuse program.
Genome_build: UCSC mm10

organism: Mus musculus

source_name: Mice Subcutaenous Fat Tissue

extract_protocol:
Removed mice tissues were lysed with ice cooled trizol reagent and total RNAs were isolated.
RNA libraries were prepared with preprocessCore' R guide kit protocol (Part # 15026495)

treatment_protocol: 6 weeks old male mice fed high fat diet for 19 weeks

tag: strain

value: Subcutenous Fat

value: post natal weeks 24

tag: genotype

value: MKRN1 KO

tag: gender


title: WT-2_Liver Tissue

source_name: Mice Liver Tissue

value: Liver

value: WT

value: male


title: WT-1_FAT Tissue


title: KO-1_FAT Tissue


title: WT-2_FAT Tissue


title: A375_bulk_resistant_rep2

city: Cold Spring Harbor

first: Molly

last: Hammell

state: New York

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

data_processing:
Illumina  read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were quantified using kallisto v0.42.5 (RefSeq release 2016-5-25). Exclusions included a minimum raw count value of 1.0 in at least 95% of all samples. Raw read counts were normalized to RPM value and then were log2-transformed with an offset value of 1.0.
Genome_build: Reads were aligned to the transcriptome (hg19, GRCh37.72)
Supplementary_files_format_and_content: Tab-delimited text file includes estimated raw counts for each sample

source_name: Melanoma cell line

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium with 10% Fetal Bovine serum and 1% Pencillin-Streptavadin. Cells were grown to ~80% confluency in 10cm culture dishes and split every 2-3 days. The  BRAF inhibitor resistant cells, "BR", were continuously grown in standard media as described above, supplemented with 1uM PLX-4720.

extract_protocol:
RNA was extracted from flash frozen cell pellets containing ~10e6 cells, using the Trizol Plus RNA Purification Kit which combines standard TRIzol reagent with the Ambion PureLink RNA Mini kit. RNA extracts were then checked to ensure RIN numbers ~9-10.
Stranded RNA-seq libraries were constructed using 500ng of input total RNA per sample and the Illumina TruSeq Stranded Total RNA Sample Prep LS kit, following the Illumina protocol as prescribed, including the use of RiboZero Gold for magnetic bead based rRNA depletion.
RNA-Seq Libraries were sequenced in pools of 3 barcoded samples per lane on an Illumina HiSeq using the PE101 format to a depth of ~50 million fragments per sample.

treatment_protocol: For treated cells, 1uM of drug was added to above mentioned media. Media with drug was prepared fresh every 10 days to ensue that the drug was active

tag: cell line

value: Resistant - Cultured in 1uM PLX-4720


title: A375_bulk_resistant_rep1


title: KO-2_Liver Tissue


title: A375_bulk_parental_rep2

value: Parental - no Treatment


title: 451Lu_bulk_resistant_rep2


title: 451Lu_bulk_resistant_rep1


title: Lwt1


title: A375_bulk_parental_rep1


title: A375 THOC2 2147

type: RNA

city: Nanjing

first: Yan

last: Wang

state: Jiangsu province

address: 12 Jiangwangmiao Street

institute: Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College

description: Gene expression after 48hr in THOC2 rnai cell line

hyb_protocol: Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C(Agilent Technologies)

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version13.1,Agilent Technologies)were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100% of the values in any 1 out of all conditions have flags in Detected were chosen for further data analysis.

source_name: A375 siRNA NC 48h

label_protocol: Total RNA were prepared according to the standard protocol from 500 ng total RNA.

growth_protocol: DMEM + 2mM Glutamine + 15% Foetal Bovine Serum (FBS).

extract_protocol: Total RNA from cells were isolated using mirVana total RNA isolation kit according to the manufacturer’s guidelines.

treatment_protocol: Cells were trypsinized and harvested for RNA isolation.

tag: cell type

value: melanoma cell line


title: KO-1_Liver Tissue


title: Control rep3

city: Godollo

first: Daniel

last: Silhavy

state: US and Canada only

address: Szent-Gyorgyi 4

department: Agricultural Biotechnology Intsitute

country: Hungary

institute: National Agricultural Research and Innovation Cen.

description: N.benthamiana RNA-Seq experiment 1

data_processing:
Read alignment (Hisat2 v2.1.0)
Transciprt assembly (StringTie v1.3.3b)
Differential Gene Expression (DESeq2 v1.18.1)
Genome_build: Solgenomics Niben v1.0.1, TAIR10
Supplementary_files_format_and_content: gtf files were generated using Stringtie v1.3.3b software including the assembled transcript structures and FPKM values.

organism: Nicotiana benthamiana

source_name: N. benthamiana_control-silenced

growth_protocol: Seeds of  Nicotiana benthamiana and Arabidopsis plants were germinated directly on Jiffy pellets (Jiffy-7 44mm; Jiffy International AS, Norway). Then seedlings were transferred to soil. N. benthamiana  plants were grown in a greenhouse. After VIGS-treatment N. benthamiana plants were kept in a growth chamber at 23°C under 14/10 h light/dark conditions. Arabidopsis seedlings were grown at growth chamber at 21°C under 16/8 h light/dark conditions.

extract_protocol:
Total RNA was extracted from 100 mg of leaf tissue (White and Kaper, 1989). Briefly, the homogenized plant materials were resuspended in 600 μL of extraction buffer (0.1 M glycine-NaOH, pH 9.0, 100 mM NaCl, 10 mM EDTA, 2% SDS, and 1% sodium lauroylsarcosine) and mixed with an equal volume of phenol. The aqueous phase was treated with equal volumes of phenol and chloroform, precipitated with ethanol, and resuspended in sterile water.
Libraries were prepared from total RNA samples with Illumina® Ribo-Zero™ rRNA Removal (Plant Leaf) and TruSeq™ v2 RNASeq Library Preparation Kits.

treatment_protocol: Virus-induced gene silencing (VIGS) was used to transiently silence Pelota. N. benthamiana plants were infected with Tobacco Rattle Virus VIGS vector containing a segment from the Pelota or from the PDS gene (called Pelota and control silenced plants, respectively).

value: Control-silenced

value: leaf


title: Pelota rep2

description: N.benthamiana RNA-Seq experiment 1

source_name: N. benthamiana_Pelota

value: Pelota-silenced


title: Pelota rep3

description: N.benthamiana RNA-Seq experiment 1


title: A375 THOC2 NC

description: Gene expression after 48hr in siRNA NC cell line

source_name: A375 THOC2 siRNA 48h


title: Control rep1

description: N.benthamiana RNA-Seq experiment 1


title: WT-1_Liver Tissue


title: 451Lu_bulk_parental_rep1


title: 451Lu_bulk_parental_rep2


title: KD_1: BCL11A knockdown replicate-1

city: Stanford

first: Heshan

last: Peiris

state: California

address: 279 Campus Drive, Beckman Center B300

institute: Stanford University

data_processing:
Reads were then aligned to the human (hg19) using Bowtie version 2.2.7 with splice junctions being defined in GTF file (obtained from UCSC).
Expression at gene level was determined by calculating reads per kilobase per millions aligned reads (FPKM) as well as raw count using RSEM (version 1.2.30).
Differentially expressed genes with fold change were further detected by DEseq2 version 1.10.1 for the two experimental conditions.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files

source_name: Pancreatic beta cells

extract_protocol:
Human beta cells were purified by FACS and RNA was extracted using the RecoverAll nucleic acid extraction (ThermoFisher Scientific #AM1975)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human pseudo islets were infected with lenti-viruses carrying either control vectors (Ctrl) or vectors with a short hairpin targeting BCL11A (KD).

value: Primary human pancreas cells

value: BCL11A knockdown


title: Control rep2

description: N.benthamiana RNA-Seq experiment 1


title: Pelota rep1

description: N.benthamiana RNA-Seq experiment 1


title: KD_3: BCL11A knockdown replicate-3


title: WT_1: Control replicate-1

value: WT Control


title: KD_2: BCL11A knockdown replicate-2


title: WT_2: Control replicate-2


title: Combination-3

city: Columbus

first: Kelly

last: Regan

state: Ohio

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: The Ohio State Univ

data_processing:
Illumina HCS 3.4.0 software was used for basecalling.
Fastq files containing sequenced reads were mapped to the human genome GRCh38p.10 (GENCODE primary assembly GTF v27 and FASTA files) using the STAR program (2.5.3a). Aligned bam files sorted by coordinate were produced.
Read counts were calculated from aligned bam files using the summarizeOverlaps function in the GenomicAlignments R package with the following parameters: mode="Union", singleEnd=FALSE, ignore.strand=TRUE, fragments=TRUE.
Genome_build: GRCh38.p10 (Gencode Release 27)
Supplementary_files_format_and_content: Tab-delimited text files for each sample include raw count values for ENSEMBL ENSG gene IDs.

source_name: A375 melanoma cell line

growth_protocol: A375 melanoma cells were obtained from American Type Cell Culture Collection and maintained in DMEM with 10% FBS, penicillin/streptomycin and plasmocin. Cells were plated in 100mm3 dishes at a seeding density of 2.2 10^6 cells and incubated at 37deg for 24 hr before drug treatment.

extract_protocol:
Cells were harvested with cold PSB and pellets were kept frozen at -80 deg. Total RNA was extracted using the Norgen Biotek total RNA purification plus kit (Cat #48300). RNA purity was assessed using Qubit RNA assay and BioAnalyzer RNA Nanochip tracings.
RNA libraries were prepared for sequencing using the New England Biolabs NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with the protocol for use with NEBNext Poly(A) mRNA magnetic isolation module.  We used 200ng of total RNA for the construction of sequencing libraries.

treatment_protocol: Drug solutions were prepared in cell culture media to reach a final concentraiton of 5uM. Drug treatments were applied in triplicate per condition.

tag: drug exposure

value: Vemurafenib+Tretinoin Combination

tag: treatment dose

value: 5 uM

tag: treatment length

value: 8 hr


title: Vemurafenib-2

value: Vemurafenib


title: Vemurafenib-3


title: WT_3: Control replicate-3

tag: tissue


title: Combination-2


title: Combination-1


title: KD_4: BCL11A knockdown replicate-4


title: WT_4: Control replicate-4


title: Vemurafenib-1


title: Tretinoin-3

value: Tretinoin


title: Tretinoin-1


title: DMSO-3

value: DMSO


title: DMSO-1


title: GCLiPP stimulated Jurkat replicate 3

city: San Francisco

first: Adam

middle: Jacob

last: Litterman

state: CA

address: 513 Parnassus Avenue, UCSF Box 0414, HSE-201

department: Microbiology and Immunology

institute: UCSF

description:
RBP crosslinked RNA
GCLiPP: biotinylated lysate, oligo-dT selection, streptavidin bead capture, Rnase T1 digestion, linker ligation, reverse transcription, cDNA amplification
Processed data files:
Jurkat_GCLiPP_positive_strand_hg38.bw
Jurkat_GCLiPP_negative_strand_hg38.bw
Jurkat_GCLiPP_peaks_hg38.bed
Jurkat_GCLiPP_peaks_CLIPper_hg19.bed

data_processing:
For GCLiPP raw reads were demultiplexed by a custom script and linker trimmed with fastx_trimmer
Linker dimer reads were discarded and one uniquely aligning read with a given di-nucleotide randomer in the 3' RNA linker was kept for further analysis to remove PCR duplicates
GCliPP reads were aligned to hg38 using bowtie2
Peaks were called with in house perl scripts that convolved a normal distribution against observed read distribution at each nucleotide and looked of local maxima of correlation
linker sequence cut with cutadapt GTGTCTTTACACAGCTACGGCGTCG
Genome_build: hg38, hg19
Supplementary_files_format_and_content: bigwig, reads per million at each location in the genome; bed, location of called peaks and voids of GCLiPP read density

source_name: Jurkat

growth_protocol: Jurkat T cells were grown in RPMI supplemented with 10% FCS and 1 X Pen/Strep

extract_protocol:
Cells were lysed by re-suspension in PXL buffer without SDS. Cell debris were pelleted and supernatants were biotinylated with EZ-Link-NHS-SS-Biotin. Poly-A RNA was enriched by pulldown with oligo-dT beads. RNPs were captured with M-280 Streptavidin dynabeads and RNAs were digested with RNAse T1
Linkers were ligated on while RNPs were immobilized on M-280 beads and released by proteinase K digestion, size selected by TBE-Urea PAGE gel, gel extracted, reverse transcribed and used for cDNA amplification

treatment_protocol: Four hours before harvest cells were re-plated in fresh medium (resting) or re-stimulated with PMA/Ionomycin (stimulated). Cells were crosslinked with 8000 mJ high energy (254 nM) UV light

value: Jurkat immortalized T lymphocyte cell line

tag: culture conditions

value: RPMI

tag: restimulation

value: PMA/Ionomycin


title: GCLiPP stimulated Jurkat replicate 1


title: GCLiPP resting Jurkat replicate 2


title: GCLiPP resting Jurkat replicate 3


title: GCLiPP resting Jurkat replicate 1


title: RNA_TAM_NoBCAA_04hr.3

city: Boston

first: Paulo

middle: A.

last: Gameiro

state: MA

address: 240 Longwood Ave., Building C2, Room 325

institute: Harvard Medical School

data_processing:
We trimmed the adapters sequences from the raw sequencing reads and then aligned the trimmed reads to human rRNA sequences and removed reads mapping to rRNAs (5S, 5.8S, 18S, and 28S). We aligned remaining reads to the union of human reference transcript sequences: defined RefSeq; GENCODE lncRNAs; human body Mpap lncRNAs. The unmapped reads were then aligned to human reference genome sequence (hg19) using Tophat (Trapnell et al., 2009). We counted number of reads in canonical ORFs of protein coding genes, excluding 15aa downstream start codon and 5aa upstream stop codon.
Genome_build: hg19
Supplementary_files_format_and_content: .txt, containing reads per kilobase of transcript per million mapped reads (RPKM) in each sample, log2 ribosome occupancy (RO) fold change, translation efficiencies (TE) and TE differences (TE Diff).

source_name: Breast epithelial cell

growth_protocol: MCF10A-ER-Src cells were grown at 37C with 5% CO2 in phenol red-free DMEM-F12 medium containing 5% charcoal-stripped horse serum, penicillin/streptomycin (1X), EGF (200ng/ml), hydrocortisone (0.5 µg/ml final), cholera toxin (100 ng/ml) and insulin (10 µg/ml) as described previously (Iliopoulos et al. Cell, 2009). MCF10A-ER-Src cells were treated with 1 µM 4-hydroxy-tamoxifen (transformed cells) or with ethanol as vehicle-control (non-transformed cells) for 24 hours, and subjected to nutrient deprivation as indicated.

extract_protocol:
For ribosome profiling, cells were washed with ice-cold PBS containing 100µg/ml cycloheximide, and flash-frozen with detergent lysis containing Turbo DNase I and 100µg/ml cycloheximide. DNase I-treated lysates were subjected to RNase I digestion, and ribosome-protected fragments purified as previously described (Ingolia et al. Nature Protocols 2012). For RNA sequencing, total RNA was extracted with the Qiazol reagent and on-column isolated with the miRNeasy kit (Qiagen), enriched for poly(A) RNA using Oligo d(T)25 magnetic bead purification (NEB, cat. No. S1419S), and chemically fragmented with ZnCl2.
Both ribosome-protected RNA fragments and fragmented poly(A) RNA were PAGE purified on a 15% TBE-Urea gel, 3’end ligated to a pre-adenylated universal miRNA linker (5′-rAppCTGTAGGCACCATCAAT–NH2-3′, NEB, cat. no. S1315S), converted into cDNA using Superscript III reverse transcriptase, circularized, depleted for ribosomal RNA using biotinylated probes, and PCR amplified using Illumina indexed primers as previously described (Ingolia et al. Nature Protocols 2012).

tag: passages

value: ER-Src expressing

value: Tamoxifen


title: RNA_TAM_NoCys_04hr.3

tag: treatment


title: RNA_TAM_NoG_04hr.3


title: RNA_EtOH_Ctrl_04hr.3

value: Ethanol


title: RNA_TAM_NoQ_04hr.2


title: RNA_TAM_NoBCAA_04hr.2


title: RNA_TAM_NoG_04hr.2


title: RNA_EtOH_NoCys_04hr.3


title: RNA_TAM_Ctrl_04hr.3


title: RNA_TAM_Ctrl_04hr.2


title: Tretinoin-2


title: DMSO-2


title: RNA_EtOH_NoCys_04hr.2


title: RNA_TAM_Torin_4hr.1


title: GCLiPP stimulated Jurkat replicate 2


title: RNA_EtOH_NoG_04hr.2


title: RNA_EtOH_Ctrl_04hr.2


title: RNA_EtOH_NoBCAA_04hr.3


title: RNA_TAM_NoCys_04hr.2


title: RNA_EtOH_NoQ_04hr.2


title: RNA_EtOH_NoG_04hr.3


title: RNA_TAM_NoQ_4hr.1


title: RNA_EtOH_Ctrl_04hr.1


title: RNA_EtOH_NoQ_4hr.1


title: RNA_TAM_Ctrl_04hr.1


title: EtOH_NoBCAA_04hr.3

description: Ribosome protected RNA fragments

data_processing:
Library strategy: Ribo-seq
We trimmed the adapters sequences from the raw sequencing reads and then aligned the trimmed reads to human rRNA sequences and removed reads mapping to rRNAs (5S, 5.8S, 18S, and 28S). We aligned remaining reads to the union of human reference transcript sequences: defined RefSeq; GENCODE lncRNAs; human body Mpap lncRNAs. The unmapped reads were then aligned to human reference genome sequence (hg19) using Tophat (Trapnell et al., 2009). We counted number of reads in canonical ORFs of protein coding genes, excluding 15aa downstream start codon and 5aa upstream stop codon.
Genome_build: hg19
Supplementary_files_format_and_content: .txt, containing reads per kilobase of transcript per million mapped reads (RPKM) in each sample, log2 ribosome occupancy (RO) fold change, translation efficiencies (TE) and TE differences (TE Diff).


title: RNA_TAM_NoQ_30min.1


title: TAM_Ctrl_04hr.3

description: Ribosome protected RNA fragments


title: TAM_NoBCAA_04hr.3

description: Ribosome protected RNA fragments


title: TAM_NoCys_04hr.3

description: Ribosome protected RNA fragments


title: RNA_EtOH_NoQ_30min.1


title: RNA_EtOH_NoBCAA_04hr.2


title: TAM_NoG_04hr.3

description: Ribosome protected RNA fragments


title: EtOH_Ctrl_04hr.3

description: Ribosome protected RNA fragments


title: EtOH_NoG_04hr.3

description: Ribosome protected RNA fragments


title: EtOH_NoCys_04hr.3

description: Ribosome protected RNA fragments


title: EtOH_NoCys_04hr.2

description: Ribosome protected RNA fragments


title: TAM_NoQ_04hr.2

description: Ribosome protected RNA fragments


title: EtOH_NoBCAA_04hr.2

description: Ribosome protected RNA fragments


title: TAM_NoG_04hr.2

description: Ribosome protected RNA fragments


title: TAM_Ctrl_04hr.2

description: Ribosome protected RNA fragments


title: EtOH_NoG_04hr.2

description: Ribosome protected RNA fragments


title: EtOH_NoQ_04hr.2

description: Ribosome protected RNA fragments


title: TAM_NoCys_04hr.2

description: Ribosome protected RNA fragments


title: EtOH_Ctrl_04hr.2

description: Ribosome protected RNA fragments


title: TAM_NoQ_04hr.1

description: Ribosome protected RNA fragments


title: TAM_Ctrl_04hr.1

description: Ribosome protected RNA fragments


title: EtOH_NoQ_04hr.1

description: Ribosome protected RNA fragments


title: EtOH_Ctrl_04hr.1

description: Ribosome protected RNA fragments


title: TAM_Torin_04hr.1

description: Ribosome protected RNA fragments


title: EtOH_NoCys_04hr.1

description: Ribosome protected RNA fragments


title: TAM_Ctrl_30min.2

description: Ribosome protected RNA fragments


title: TAM_NoBCAA_04hr.2

description: Ribosome protected RNA fragments


title: TAM_NoQ_30min.2

description: Ribosome protected RNA fragments


title: TAM_NoQ_30min.1

description: Ribosome protected RNA fragments


title: EtOH_NoQ_30min.2

description: Ribosome protected RNA fragments


title: EtOH_Ctrl_30min.2

description: Ribosome protected RNA fragments


title: TAM_Ctrl_30min.1

description: Ribosome protected RNA fragments


title: EtOH_NoQ_30min.1

description: Ribosome protected RNA fragments


title: EtOH_Ctrl_30min.1

description: Ribosome protected RNA fragments


title: RAGKO_Spleen INFECTED at 8th P.chabaudi_rep 3

city: Worcester

first: Ricardo

middle: Tostes

last: Gazzinelli

state: Massachusetts

address: 364 Plantation Street

department: Medicine

institute: University of Massachusetts Medical School

description: Gene expression data from splenocytes obtained from infected mice at 8th of P.chabaudi infection

hyb_protocol: Chips were hybridized at 45-C for 16 h and washed with fluidics protocol EukGE-WS2v5 according to Affymetrix’s recommendation

scan_protocol: The arrays were scanned at an emission wavelength of 570 nm at 2.5-mm resolution in the GCS3000 laser scanner (Affymetrix). The intensity of the hybridization for each probe pair was computed by GCOS 1.1 software

data_processing: The expression value (average difference) for each gene was determined by calculating the average of differences in intensity (perfect match intensity – mismatch intensity) between its probe pairs. The expression analysis file created from each sample (chip) was imported into GeneSpring 7.2 (Agilent Technologies, Inc., Palo Alto, CA) for further data characterization. A new experiment was generated after importing data from the same organ in which data were normalized by the array to the 50th percentile of all measurements on that array. Lists of genes that were either induced or suppressed more that two fold between samples from non-infected vs. 6 days infected mice of same genotype were created by filtration-on-fold function within the presented list. The differential expression was evaluated in grouped samples from each mouse genotype (Wt or Knockout mice) and time point (non-infected vs 6 days post infection) using ANOVA. Values correspond to fold increase or suppression (threshold of two fold) of genes between infected Vs non-infected groups of same genotype

source_name: spleen from RAG mice at 8th of P.chabaudi infection

label_protocol: standard Affymetrix protocol

extract_protocol: Spleen from C57BL/6 or knockout mice non-infected or after 6 days post infection with 10E5 P. chabaudi infected red blood cells were harvested and immediately transferred into tubes containing TRIzol® reagent (Invitrogen, Carlsbad CA) and freeze in liquid nitrogen. Sample homogeinization and total RNA isolation were subsequently processed according to the manufacturer’s protocol (Invitrogen). RNA pellets were resuspended in nuclease-free water (Invitrogen) and quantified by ultraviolet spectroscopy for purity and concentration (NanoDrop, Wilmington, DE). Integrity of RNA samples was evaluated by electrophoresis in 1% agarose gel and were assessed further for RNA integrity on the Agilent Bioanalyzer (Santa Clara, CA). Equivalent aliquots of 2.5 µg of total RNA from 12 independent samples (3 non-infected C57BL/6, or MyD88-/- and 3 P. chabaudi infected C57BL/6, or MyD88-/- mice) were assessed using the Affymetrix MOE 430 2.0 GeneChip array GeneChips.

treatment_protocol: Spleen from C57BL/6 or MyD88 knockout mice non-infected or after 6 days post infection with 10E5 P. chabaudi infected red blood

value: Spleen

tag: Sex

value: Female

tag: strain/genotype

value: RAG

tag: age

value: 8 weeks


title: RAGKO_Spleen INFECTED at 8th P.chabaudi_rep 2


title: RAGKO_Spleen INFECTED at 8th P.chabaudi_rep 1


title: RAGKO_Spleen_control NON-INFECTED_rep 2

description: Gene expression data from splenocytes obtained from non-infected mice

source_name: spleen RAG non-infected mice


title: cortex (dMut) on E19, biological rep3

city: Coralville

first: Botond

last: Banfi

state: Iowa

address: 2501 Crosspark Road

department: Anatomy and Cell Biology

institute: University of Iowa

description: brain cortex total RNA from one (dMut) mouse

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Affymetrix Model 7G upgraded scanner

data_processing:
Raw microarray CEL files were imported into Partek Genomics Suite 6.6. Signal intensities for the probe-sets were quantile normalized and median polished using Robust Multichip Average background correction. The signal intensities of exon probe-sets were used to calculate the overall expression level of each gene represented in MJAY. Normalized intensity of each exon probe-set was calculated by adjusting the exon probe-set signals of gt/gt samples with the gene expression difference (between gt/gt and WT) that was measured for the exon-containing gene. The normalized probe-set signals of gt/gt samples were compared with the probe-set signals of WT samples using two-tailed Student t-test. Probe-sets with significantly different signals (P <0.01) were queried against the Affymetrix annotation map file (which contains alternative/constitutive annotations for each measured splicing event), and probe-sets that measure constitutive events or are not annotated to RefSeq transcripts were filtered out. The remaining probe-sets were queried against the “SIB Alt-Splicing track” in the UCSC Genome Browser to identify and remove probe-sets that 1) show more than 50% identity with more than one transcript, 2) measure alternative promoter activity, or 3) measure splicing only in the non-coding regions of mRNAs. The sequences of the remaining probe-sets were queried against the mouse genome to identify those that measure the same splicing events. We required that probe-sets targeting competing isoforms have opposite trends in probe-set signal differences.
MJAY_r2.pgf
MJAY_r2.full.mps

source_name: Srrm3-Srrm4 double mutant (dMut), cortex

label_protocol: Sense-strand cDNA targets were generated using the NuGEN WT-Ovation Exon Module and biotinylated using the NuGEN FL-Ovation cDNA Biotin Module.

growth_protocol: Brain cortexes were dissected from E19 mice.

extract_protocol: RNA from the brain cortex of E19 mice was isolated using Trizol Reagent (Life Technologies), treated with DNase I, and further purified using the RNeasy Mini Kit (Qiagen). RNA samples for microarray analysis were processed using the NuGEN WT-Ovation Pico RNA Amplification System, NuGEN WT-Ovation Exon Module, and NuGEN FL-Ovation cDNA Biotin Module.

value: brain cortex

value: homozygous for mutations in both Srrm3 and Srrm4 (dMut)


title: Blimp1-negative spleen follicular B cell rep4

city: Philadelphia

first: Joel

last: Wilmore

state: PA

address: 3620 Hamilton Walk

institute: University of Pennsylvania

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix GeneChip Scanner 3000 7G System

data_processing: Analysis was performed using the R statistical environment v3.x and the bioconductor suite of packages including the oligo, pd.mogene.2.0.st and mogene20sttranscriptcluster.db. Data with varience filtered (IQR cutoff 0.5) max-mean selected for multiple probes is on the Series record.

source_name: splenic folicular B cell

label_protocol: Samples were biotinylated using an Affymetrix labeling kit

growth_protocol: Plasma cells isolated directly from bone marrow and lamina propria of B6.BlimpGFP mice by FACS sorting.

extract_protocol: FACS-sorted Blimp1-positive bone marrow plasma cells were collected into Trizol reagent, and RNA was isolated.

treatment_protocol: Mice were naïve.

value: spleen follicular


title: RAGKO_Spleen_control NON-INFECTED_rep 1


title: Blimp1-negative spleen follicular B cell rep3


title: IFNgKO_Spleen INFECTED at 8th P.chabaudi_rep 3

source_name: spleen from IFNgKO mice at 8th of P.chabaudi infection

value: IFNgKO


title: cortex (WT) on E19, biological rep4

description: brain cortex total RNA from one (WT) mouse

source_name: wild-type (WT), cortex

value: wild-type (WT)


title: Blimp1-negative spleen follicular B cell rep2


title: cortex (WT) on E19, biological rep1


title: cerebellum (Srrm3gt/gt) on P16, biological rep2

description: cerebellum total RNA from one (Srrm3gt/gt) mouse

source_name: Srrm3 gene-trapped (Srrm3gt/gt), cerebellum

growth_protocol: Cerebellums were dissected from P16 mice.

extract_protocol: RNA from the entire cerebellum of P16 mice was isolated using Trizol Reagent (Life Technologies), treated with DNase I, and further purified using the RNeasy Mini Kit (Qiagen). RNA samples for microarray analysis were processed using the NuGEN WT-Ovation Pico RNA Amplification System, NuGEN WT-Ovation Exon Module, and NuGEN FL-Ovation cDNA Biotin Module.

value: cerebellum

value: homozygous for Srrm3 gene trap (Srrm3gt/gt)


title: cortex (dMut) on E19, biological rep2


title: IFNgKO_Spleen INFECTED at 8th P.chabaudi_rep 2


title: cortex (dMut) on E19, biological rep4


title: cerebellum (WT) on P16, biological rep2

description: cerebellum total RNA from one (WT) mouse

source_name: wild-type (WT), cerebellum


title: Blimp1-negative spleen follicular B cell rep1


title: IFNgKO_Spleen INFECTED at 8th P.chabaudi_rep 1


title: IFNgKO_Spleen_control NON-INFECTED_rep 3

source_name: spleen IFNgKO non-infected mice


title: cerebellum (WT) on P16, biological rep3


title: cerebellum (Srrm3gt/gt) on P16, biological rep3


title: cortex (WT) on E19, biological rep2


title: cerebellum (Srrm3gt/gt) on P16, biological rep1


title: cerebellum (WT) on P16, biological rep4


title: cortex (dMut) on E19, biological rep1


title: cerebellum (Srrm3gt/gt) on P16, biological rep4


title: cortex (WT) on E19, biological rep3


title: cerebellum (WT) on P16, biological rep1


title: Blimp1-positive bone marrow plasma cell IgG rep5

source_name: bone marrow plasma cell

value: bone marrow

tag: sorted fraction

value: IgG


title: Blimp1-positive bone marrow plasma cell IgM rep6

value: IgM


title: Blimp1-positive lamina propria plasma cell IgA rep4

source_name: lamina propria plasma cell

value: lamina propria

value: IgA


title: Blimp1-positive bone marrow plasma cell IgG rep6


title: IFNgKO_Spleen_control NON-INFECTED_rep 1


title: Blimp1-positive bone marrow plasma cell IgM rep5

value: bone marrow IgM


title: Blimp1-positive bone marrow plasma cell IgA rep5


title: Blimp1-positive bone marrow plasma cell IgM rep4


title: Blimp1-positive bone marrow plasma cell IgA rep4


title: Blimp1-positive bone marrow plasma cell IgG rep4


title: genomic DNA-PM98-revised_processing

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: 1. Probe filtering: Removal of systemically poor-quality array probes (resulting in n=442,348 remaining CpG sites) including: (i) probes targeting the sex chromosomes, n=11,648; (ii) sex chromosome cross-hybridizing probes (Price et al., 2013), n=11,412; (iii) polymorphic probes (Price et al., 2013), n=19,957; (iv) 65 rs probes; (v) probes with detection p-value >0.01 or <3 bead replicates in >20% of samples, n=122;  2. Color correction: Color correction for differences in the dynamic range between red and green stains using lumi (Du et al., 2008);   3. Swan normalization: Normalization to correct for differences in the dynamic range of Type I and Type II probes using SWAN (Maksimovic et al., 2012);    4. ComBat row-correction: Removal of probes with <2 values in a batch level (n=25), followed by batch correction using ComBat (Leek et al.) to correct for the location of samples in different chip rows (442,348 CpGs);   5. ComBat chip-correction: Batch correction using ComBat (Leek et al.) to correct for the distribution of samples across chips.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted by standard salt method and purified using Qiagen DNeasy Kit according to standard instructions

tag: fetal sex

value: MALE

value: placental chorionic villi

tag: gestational age (week, rounded)

tag: processing group


title: Blimp1-positive lamina propria plasma cell IgA rep3


title: Blimp1-positive bone marrow plasma cell IgA rep6

value: bone marrow IgA


title: IFNgKO_Spleen_control NON-INFECTED_rep 2

value: Spleen

value: Female

value: 8 weeks


title: Blimp1-positive bone marrow plasma cell IgG rep3


title: Blimp1-positive bone marrow plasma cell IgM rep3


title: genomic DNA-PM74-initial_processing


title: genomic DNA-PM72r-revised_processing

value: FEMALE


title: genomic DNA-PM92-initial_processing


title: genomic DNA-PM76-initial_processing


title: genomic DNA-PM71-revised_processing


title: genomic DNA-PM72-revised_processing


title: Blimp1-positive bone marrow plasma cell IgA rep3


title: genomic DNA-PM66-revised_processing


title: genomic DNA-PM58-initial_processing


title: genomic DNA-PM46-initial_processing


title: genomic DNA-PM47-revised_processing


title: genomic DNA-PM53-revised_processing


title: genomic DNA-PM54-initial_processing


title: genomic DNA-PM55-initial_processing


title: genomic DNA-PM52-revised_processing


title: genomic DNA-PM44-revised_processing


title: genomic DNA-PM4-revised_processing


title: Input_MLL-AF4_AF4-MLL ChIPSeq Rep2

city: Rehovot

first: Rafael

last: Valdés Mas

address: Herzl St 234

country: Israel

institute: Weizmann Institute

library_source: genomic

data_processing:
Alignment and peak detection were performed using the ENCODE (phase-3) histone ChIP-seq pipeline specifications. Reads were aligned to the human reference genome (assembly hg19) using BWA
Removing all reads with a quality score <30
Peaks were called using MACS251 and whole cell extract samples as background samples
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak file with Histone peaks detected in each replicate and condition

source_name: Input_MLL-AF4_AF4-MLL ChIPSeq

growth_protocol: AS PER Bueno et al Cell Research 2013

extract_protocol:
Formaldehyde crosslinked cell extracts were sonicated to 200-500 bp sized particles at 0.5-min intervals with Bioruptor (Diagenode) and the chromatin fraction was divided in three parts and incubated overnight with  antibody
Libraries were prepared using the kit: NEBNext Ultra DNA Library Prep kit for Illumina (Ref.:#7370) following the commercial protocol. Libraries QC: Bioanalyzer and quantification by qPCR using the kit: KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems)

treatment_protocol: AS PER Bueno et al Cell Research 2013

value: human ESC

tag: genotype/variation

value: MLL-AF4 and AF4-MLL expression

tag: chip antibody


title: genomic DNA-PM9-initial_processing


title: genomic DNA-PM32-revised_processing


title: Input_MLL-AF4_AF4-MLL ChIPSeq Rep1

tag: cell type


title: Input_AF4-MLL ChIPSeq Rep2

source_name: Input_AF4-MLL ChIPSeq

value: AF4-MLL expression


title: Blimp1-positive lamina propria plasma cell IgA rep2


title: RealSeq_brain_high_coverage

city: Santa Cruz

first: Sergio

last: Barberan-Soler

address: 2161 Delaware Avenue

institute: Somagenics Inc

description:
Triplicate libraries with 1 ug of brain RNA (AM7962) prepared with RealSeq-AC (Somagenics #500-00012)
Libraries were amplified with 7 cycles of PCR
[processed data files:]
High_coverage_brain.csv
Each library was made from the same input RNA source. This GSM is associated with 3 SRR that represents each technical replicate.

data_processing:
Basecalling performed by Illumina RTA 1.18.54. Reads demultiplexed by MiSeq instrument. Reads trimmed of adapter with cutadapt with the following specifications: For TruSeq and RealSeq libraries: cutadapt -a TGGAATTCTCGGGTGCCAAGG -m 15; For NEBNext libraries: cutadapt -a AGATCGGAAGAGCACACGTCT -m 15; For NEXTFlex libraries: cutadapt -u 4 -a NNNNTGGAATTCTCGGGTGCCAAGG -m 15; For SMARTer libraries: cutadapt -u 3 -a AAAAAAAAAA -m 15; For QIASeq libraries: cutadapt -a AACTGTAGGCACCATCAAT -m 15  Reads were mapped to a bowtie2 index created from miRXplore sequences (Miltanyi Biotec), to bowtie2 index created from high confidence human miRNAs (miRBase 21), or to bowtie2 index created from the complete set of human miRNAs (miRBase 21); Mapping was performed by using bowtie2 with the following parameters: bowtie2 -L8 --local. Raw counts of reads were obtained from sam files, by using samtools and picard-tools. Raw reads were normalized to ‘Reads per million of miRNA reads’ for each processed data file. The ratio of observed/expected (miRXplore_bias and hc_hsa_miRBase_bias) or kit1/kit2 (hc_miRNAs_brain)  was calculated from the mean of triplicate experiments; the log(2) of this ratio was used for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: All processed data files are tab separated files. ‘miRXplore_bias_ratios’  and hc_hsa_miRBase_bias_ratios’ contain the log2 ratios of observed/expected, calculated from the ‘Reads per million of miRNA reads’; ‘hc_miRNAs_brain’ and ‘High_coverage_brain’ contain the ‘Reads per million of miRNA reads’.

source_name: ThermoFisher (AM7962)

extract_protocol:
RNA samples were obtained from Miltenyi Biotec (miRXplore reference pool #130-093-521) and from ThermoFisher (human brain total RNA AM7962)
Experiments with NEBNext (NEB), TruSeq (Illumina), NEXFlex (Bioo Scientific), QIAseq (Qiagen), SMARTer (Takara Bio), and RealSeq-AC (Somagenics) were performed following the manufacturer's’ recommendations. For all kits, 1 pmol of the miRXplore Universal Reference (Miltenyi Biotec #130-093-521) was used as input to test accuracy in detection. 1 μg of brain total RNA (ThermoFisher #AM7962) was used for all kits with the exception of QIAseq, where 500 ng of total RNA was used as per the manufacturer’s recommendations. Independent libraries were prepared in technical triplicates with the same input for all experiments, with the exception of NEXTFlex brain that was performed in duplicate. The number of PCR cycles for each library was determined as per the manufacturer’s recommendations. To determine concentration and quality of libraries, all libraries were analyzed with an Agilent D1000 ScreenTape on a 2200 TapeStation instrument (Agilent), and then quantified with a Qubit dsDNA BR Assay kit on a Qubit 3.0 instrument.

value: brain


title: Blimp1-positive bone marrow plasma cell IgG rep2

value: bone marrow


title: Blimp1-positive bone marrow plasma cell IgM rep2


title: Blimp1-positive bone marrow plasma cell IgA rep2


title: Blimp1-positive lamina propria plasma cell IgA rep1


title: QIAseq_brain

description:
Triplicate libraries with 500 ng of brain RNA (AM7962) prepared with QIAseq miRNA (Qiagen #331505)
Libraries were amplified with 13 cycles of PCR
[processed data files:]
hc_miRNAs_brain_ratios_v2.csv
Each library was made from the same input RNA source. This GSM is associated with 3 SRR that represents each technical replicate.


title: genomic DNA-PM84-initial_processing


title: Input_AF4-MLL ChIPSeq Rep1


title: genomic DNA-PM35-revised_processing


title: SMARTer_brain

description:
Triplicate libraries with 1 ug of brain RNA (AM7962) prepared with SMARTer smRNA-Seq (Clontech #635029)
Libraries were amplified with 7 cycles of PCR
[processed data files:]
hc_miRNAs_brain_ratios_v2.csv
Each library was made from the same input RNA source. This GSM is associated with 3 SRR that represents each technical replicate.


title: Blimp1-positive bone marrow plasma cell IgM rep1


title: genomic DNA-PM41-initial_processing


title: Input_MLL-AF4 ChIPSeq Rep2

source_name: Input_MLL-AF4 ChIPSeq

value: MLL-AF4 expression


title: Input_MLL-AF4 ChIPSeq Rep1


title: NEXTFlex_brain

description:
Triplicate libraries with 1 ug of brain RNA (AM7962) prepared with NEXTFlex Small RNA (Bioo #5132-05)
Libraries were amplified with 12 cycles of PCR
[processed data files:]
hc_miRNAs_brain_ratios_v2.csv
Each library was made from the same input RNA source. This GSM is associated with 2 SRR that represents each technical replicate.


title: genomic DNA-PM29-revised_processing


title: genomic DNA-PM40-revised_processing


title: Input_EmptyVector ChIPSeq Rep2

source_name: Input_EmptyVector ChIPSeq

value: empty vector


title: genomic DNA-PM269-revised_processing


title: genomic DNA-PM227-initial_processing


title: NEBNext_brain

description:
Triplicate libraries with 1 ug of brain RNA (AM7962) prepared with NEBNext Multiplex Small RNA (NEB #E7300S)
Libraries were amplified with 12 cycles of PCR
[processed data files:]
hc_miRNAs_brain_ratios_v2.csv
Each library was made from the same input RNA source. This GSM is associated with 3 SRR that represents each technical replicate.


title: TruSeq_brain

description:
Triplicate libraries with 1 ug of brain RNA (AM7962) prepared with TruSeq Small RNA (Illumina #RS-200-0012)
Libraries were amplified with 11 cycles of PCR
[processed data files:]
hc_miRNAs_brain_ratios_v2.csv
Each library was made from the same input RNA source. This GSM is associated with 3 SRR that represents each technical replicate.


title: genomic DNA-PM233-initial_processing


title: genomic DNA-PM264-initial_processing


title: genomic DNA-PM243-initial_processing


title: RealSeq_brain

description:
Triplicate libraries with 1 ug of brain RNA (AM7962) prepared with RealSeq-AC (Somagenics #500-00012)
Libraries were amplified with 7 cycles of PCR
[processed data files:]
hc_miRNAs_brain_ratios_v2.csv
Each library was made from the same input RNA source. This GSM is associated with 3 SRR that represents each technical replicate.


title: Blimp1-positive bone marrow plasma cell IgG rep1

value: IgG


title: CHD7f/f;Vav1-cre bone marrow CD48-CD150+LSK, biological rep4

city: New York

first: Hsuan-Ting

last: Huang

state: NY

address: 550 First Ave, Smilow 1307

institute: NYU School of Medicine

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 2.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: GeneChips were scanned using  a GeneChip 3000 7G scanner to collect fluorescence signal.

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes.  Default values provided by Affymetrix were applied to all analysis parameters. Intensity CEL files were normalized with the Robust Multichip Average (RMA) algorithm.

source_name: CHD7f/f; Vav1-cre bone marrow LT-HSCs

label_protocol: Biotinylated cRNA were prepared according to the the NuGEN Ovation Pico WTA system v2 user guide and the Affymetrix GeneChip Expression Analysis Technical Manual.  Briefly, 50ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated an RNA priming region.  Second-strand cDNA synthesis was followed by ribo-SPIA linear amplification of each transcript using an isothermal reaction with RNase, RNA primer and DNA polymerase, and the resulting ssDNA was assessed by Bioanalyzer, fragmented and biotinylated by terminal transferase end labeling.

growth_protocol: 12-week old mice bone marrow cells were harvested unmanipulated

extract_protocol: RNA was isolated using Qiagen RNeasy minikit (Qiagen) according to the  manufacturer's instructions.

treatment_protocol: To purify HSCs, total bone marrow (BM) cells were lineage depleted using biotinylated antibodies to CD3, CD5, CD19, B220, Gr1, Mac1 and anti-biotin MACS beads on a MACS column (Miltenyi Biotec). Lineage depleted BM cells then stained with lineage antibodies (B220, Gr1, Mac1, CD3e, Ter119), c-kit, Sca1, CD48 and CD150.  LSKCD48-CD150+ cells were sorted directly to TRIzol®LS solution (Ambion) on a BD FACS Aria.

tag: strain background

value: 12 weeks

value: long-term hematopoietic stem and progenitor cells (LT-HSPCs)

value: LSKCD48-CD150+ cells


title: Blimp1-positive bone marrow plasma cell IgA rep1

value: IgA


title: genomic DNA-PM30-revised_processing

value: placental chorionic villi


title: genomic DNA-PM205-initial_processing

value: MALE


title: genomic DNA-PM249-initial_processing


title: genomic DNA-PM226-revised_processing


title: genomic DNA-PM263-initial_processing


title: H3K79me3 MLL-AF4_AF4-MLL ChIPSeq Rep3

source_name: H3K79me3 MLL-AF4_AF4-MLL ChIPSeq


title: CHD7f/f;Vav1-cre bone marrow CD48-CD150+LSK, biological rep3


title: genomic DNA-PM38-revised_processing


title: SMARTer_miRXplore

description:
synthetic RNA oligonucleotides
Triplicate libraries with 1 pmol of Miltenyi Biotec miRXplore pool (130-093-521) prepared with SMARTer smRNA-Seq (Clontech #635029)
Libraries were amplified with 7 cycles of PCR
[processed data files:]
miRXplore_bias_ratios_v2.csv
hc_hsa_miRBase_bias_ratios_v2.csv
Each library was made from the same input RNA source. This GSM is associated with 3 SRR that represents each technical replicate.

organism: synthetic construct

source_name: Miltenyi Biotec (130-093-521)

value: synthetic construct


title: QIAseq_miRXplore

description:
synthetic RNA oligonucleotides
Triplicate libraries with 1 pmol of Miltenyi Biotec miRXplore pool (130-093-521) prepared with QIAseq miRNA (Qiagen #331505)
Libraries were amplified with 13 cycles of PCR
[processed data files:]
miRXplore_bias_ratios_v2.csv
hc_hsa_miRBase_bias_ratios_v2.csv
Each library was made from the same input RNA source. This GSM is associated with 3 SRR that represents each technical replicate.


title: NEXTFlex_miRXplore

description:
synthetic RNA oligonucleotides
Triplicate libraries with 1 pmol of Miltenyi Biotec miRXplore pool (130-093-521) prepared with NEXTFlex Small RNA (Bioo #5132-05)
Libraries were amplified with 12 cycles of PCR
[processed data files:]
miRXplore_bias_ratios_v2.csv
hc_hsa_miRBase_bias_ratios_v2.csv
Each library was made from the same input RNA source. This GSM is associated with 3 SRR that represents each technical replicate.


title: H3K79me3 MLL-AF4_AF4-MLL ChIPSeq Rep1


title: H3K79me3 AF4-MLL ChIPSeq Rep4

source_name: H3K79me3 AF4-MLL ChIPSeq


title: NEBNext_miRXplore

description:
synthetic RNA oligonucleotides
Triplicate libraries with 1 pmol of Miltenyi Biotec miRXplore pool (130-093-521) prepared with NEBNext Multiplex Small RNA (NEB #E7300S)
Libraries were amplified with 12 cycles of PCR
[processed data files:]
miRXplore_bias_ratios_v2.csv
hc_hsa_miRBase_bias_ratios_v2.csv
Each library was made from the same input RNA source. This GSM is associated with 3 SRR that represents each technical replicate.


title: H3K79me3 MLL-AF4_AF4-MLL ChIPSeq Rep2


title: CHD7f/f;Vav1-cre bone marrow CD48-CD150+LSK, biological rep1


title: CHD7f/f;Vav1-cre bone marrow CD48-CD150+LSK, biological rep2


title: CHD7f/f bone marrow CD48-CD150+LSK, biological rep4

source_name: CHD7f/f bone marrow LT-HSCs


title: genomic DNA-PM181-initial_processing


title: TruSeq_miRXplore

description:
synthetic RNA oligonucleotides
Triplicate libraries with 1 pmol of Miltenyi Biotec miRXplore pool (130-093-521) prepared with TruSeq Small RNA (Illumina #RS-200-0012)
Libraries were amplified with 11 cycles of PCR
[processed data files:]
miRXplore_bias_ratios_v2.csv
hc_hsa_miRBase_bias_ratios_v2.csv
Each library was made from the same input RNA source. This GSM is associated with 3 SRR that represents each technical replicate.


title: genomic DNA-PM167-initial_processing


title: CHD7f/f bone marrow CD48-CD150+LSK, biological rep3


title: RealSeq_mirXplore

description:
synthetic RNA oligonucleotides
Triplicate libraries with 1 pmol of Miltenyi Biotec miRXplore pool (130-093-521) prepared with RealSeq-AC (Somagenics #500-00012)
Libraries were amplified with 5 cycles of PCR
[processed data files:]
miRXplore_bias_ratios_v2.csv
hc_hsa_miRBase_bias_ratios_v2.csv
Each library was made from the same input RNA source. This GSM is associated with 3 SRR that represents each technical replicate.


title: PLAGL2 O/E - 3B

city: Saint Louis

first: Blair

middle: B

last: Madison

state: MO

address: 660 S Euclid Ave

institute: Washington University School of Medicine

description: transfected for constitutive PLAGL2 expression (clone 3) with Piggybac transposon, later passage

data_processing:
FastQ files are aligned to the transcriptome and the whole-genome with STAR
Performed a standard EdgeR and Sailfish analysis of gene-level/exon-level features on the uniquely count of aligned, unambiguous reads per feature as determined by Subread:featureCounts using a negative-binomial test or generalize-linear negative-binomial model, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: excel files include RPKM values for each sample

growth_protocol: Enteroids were grown in serum-free ENR medium.

extract_protocol:
Enteroids were dissociated from matrigel by gentle trituration, pelleted, and then homogenized in Trizol. Samples were then purified further using the Qiagen Rneasy clean-up kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untreated, except PLAGL2 over-expression

value: small intestinal enteroid

tag: strain

tag: passage

tag: plagl2 expression level

value: high


title: H3K79me3 AF4-MLL ChIPSeq Rep2

value: human ESC


title: PLAGL2 O/E - 3A

description: transfected for constitutive PLAGL2 expression (clone 3) with Piggybac transposon, earlier passage


title: H3K79me3 AF4-MLL ChIPSeq Rep1


title: H3K79me3 AF4-MLL ChIPSeq Rep3


title: PLAGL2 O/E - 1B

description: transfected for constitutive PLAGL2 expression (clone 1) with Piggybac transposon, later passage

value: low


title: genomic DNA-PM158-initial_processing

tag: tissue


title: genomic DNA-PM155-initial_processing

value: FEMALE


title: a_arenosa_inoculated_toxicmetalsubstrate_rep2

city: Kraków

first: Piotr

last: Rozpądek

address: Gronostajowa 7a

department: Małopolska Centre of Biotechnology

country: Poland

institute: Jagiellonian University

description: Gene expression

hyb_protocol: Gene Expression Hybridization Kit was used for fragmentation and hybridization and Gene Expression Wash Buffer Kit was used for washing slides after hybridization following the manufacturers instructions.

scan_protocol: Acquisition and analysis of hybridization intensities were performed using Agilent DNA Microarray Scanner G2505C.

data_processing: Data were extracted and background subtracted using the standard procedures from the Agilent Feature Extraction (FE) Software version 10.7.3.1

organism: Arabidopsis arenosa

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted from frozen in liquid nitrogen, ground leaves (from 3 plants per sample) with the Total RNA Mini Kit (Biorad, US). RNA purity and quantity was determined by Biospec-Nano (SHIMADZU) The integrity of RNA was assessed with the Agilent 2100 Bioanalyzer (USA) and RNA 6000 Nano Kit (Agilent, Germany).

treatment_protocol: Seedlings were inoculated in vitro, in MSR medium and after 10 days transplanted to pot cultures to sterile substrate from mine dump "Bolesław" mixed with sterile sand in a 2:1 v:v ratio. Multipots were placed in 23x45x18 cm plexiglass chambers covered with polyamide gauze. Plants were grown for 28 days in a Panasonic MLR-352H-PE, JPN chamber with a 16h photoperiod, 100-120 μmol·m-2·s-1 PAR,  21/17°C day/night temperature and 50% humidity.

value: root


title: a_arenosa_inoculated_toxicmetalsubstrate_rep1

description: Gene expression


title: CHD7f/f bone marrow CD48-CD150+LSK, biological rep1

value: bone marrow


title: a_arenosa_notinoculated_toxicmetalsubstrate_rep2

description: Gene expression


title: H3K79me3 MLL-AF4 ChIPSeq Rep3

source_name: H3K79me3 MLL-AF4 ChIPSeq

value: MLL-AF4 expression


title: CHD7f/f bone marrow CD48-CD150+LSK, biological rep2


title: PLAGL2 O/E - 1A

description: transfected for constitutive PLAGL2 expression (clone 1) with Piggybac transposon, earlier passage


title: H3K79me3 MLL-AF4 ChIPSeq Rep2


title: a_arenosa_notinoculated_toxicmetalsubstrate_rep1

description: Gene expression


title: Vector (GFP) - B

description: transfected for constitutive GFP expression with Piggybac transposon, later passage

treatment_protocol: Untreated, except GFP over-expression


title: genomic DNA-PM153-initial_processing


title: genomic DNA-PM142-initial_processing


title: genomic DNA-PM139-revised_processing


title: a_arenosa_notinoculated_comercialsoil_rep2

description: Gene expression


title: Vector (GFP) - A

description: transfected for constitutive GFP expression with Piggybac transposon, earlier passage


title: H3K79me3 EmptyVector ChIPSeq Rep3

source_name: H3K79me3 EmptyVector ChIPSeq

value: empty vector


title: H3K79me3 EmptyVector ChIPSeq Rep2


title: a_arenosa_notinoculated_comercialsoil_rep1

description: Gene expression


title: genomic DNA-PM130-revised_processing


title: genomic DNA-PM136-initial_processing


title: iN_BEM-3

city: Seoul

first: Yoonhee

last: Jin

address: Yonsei-ro 50

department: Department of Biotechnology

institute: Yonsei University

data_processing:
To map the reads on a reference genome and calculate expression levels between samples, the reads were aligned with Tophat (v2.0.13; http://ccb.jhu.edu/software/tophat/) against mouse genome (mm10).
Aligned reads were subjected to Cuffdiff (v2.2.0; http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/). For library normalization and dispersion estimation, geometric and pooled methods were applied (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/).
Cuffdiff data were then added to CummeRbund (v2.8.2; http://compbio.mit.edu/cummeRbund/manual_2_0.html) to visualize RNA-sequencing data. Cuffdiff provides various output files, and using one of its outputs, “gene_exp.diff”, DEGs (Differentially Expressed Genes) were identified.
First, using Cuffdiff status code, genes that only have “OK” status were extracted. Status code indicates whether each condition contains enough reads in a locus for a reliable calculation of expression level, and “OK” status means the test is successful to calculate gene expression level. For the second filtering, 2 fold change was calculated and genes belonging to the following range were selected: Up-regulated: log2[case]-log2[control] > log2(2) =1, Down-regulated: log2[case]-log2[control] < log2(1/2) =-1.
Filtering conditions were adjusted p values below 0.05 and false discovery rate (FDR) values below 0.01, and 2-fold or higher were considered as differentially expressed
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include DEG

source_name: Induced neuronal cells

growth_protocol: PMEFs were transfected with 3 transcriptional factors (Brn2, Ascl1, Myt1l) and cultured for 30 days to be converted to induced neuronal (iN) cells.

extract_protocol:
Total RNA was extracted using the RNA prep kit (Takara Bio lnc., Kusatsu, Shiga, Japan). (Illumina Truseq stranded mRNA library prep kit was used with 1 ug of total RNA for the construction of sequencing libraries
The mRNA sequencing libraries were prepared using Illumina Truseq stranded mRNA library prep kit (Illumina, San Diego, CA, USA). The mRNA was then purified and fragmented from total RNA (1 μg) using poly-T oligo-attached magnetic beads with two rounds of purification. Cleaved RNA fragments primed with random hexamers were reverse-transcribed into the first strand cDNA using reverse transcriptase in the presence of random primers. Then, the cDNA fragments had the addition of a single ‘A’ base and subsequent ligation of the adapter. The products were purified and enriched by PCR to create the final strand-specific cDNA library. The quality of the amplified libraries was verified by capillary electrophoresis (Bioanalyzer, Agilent). After performing qPCR using SYBR Green PCR Master Mix system (Applied Biosystems), cDNA libraries were combined such that each indexed sample was present at equimolar concentration in the pool. Cluster generation occurred in the flow cell on the cBot automated cluster generation system (Illumina). Then, the flow cell loaded on HISEQ 2500 sequencing system (Illumina) was sequenced with 2100 bp read length.

value: ICR

value: Induced neuronal cells directly converted from PMEF via brn2, ascl1, myt1l TF delivery and cultured on BEM-coated substrates


title: genomic DNA-PM123-revised_processing


title: H3K79me3 EmptyVector ChIPSeq Rep1


title: H3K79me3 MLL-AF4 ChIPSeq Rep1


title: iN_BEM-1


title: H3K4me3 MLL-AF4_AF4-MLL ChIPSeq Rep4

source_name: H3K4me3 MLL-AF4_AF4-MLL ChIPSeq

value: MLL-AF4 and AF4-MLL expression


title: iN_LM-3

value: Induced neuronal cells directly converted from PMEF via brn2, ascl1, myt1l TF delivery and cultured on laminin-coated substrates


title: H3K79me3 MLL-AF4_AF4-MLL ChIPSeq Rep4


title: H3K4me3 MLL-AF4_AF4-MLL ChIPSeq Rep3


title: iN_BEM-2


title: H3K4me3 MLL-AF4_AF4-MLL ChIPSeq Rep2


title: iN_LM-2


title: H3K4me3 MLL-AF4_AF4-MLL ChIPSeq Rep1


title: iN_LM-1


title: genomic DNA-PM20-initial_processing


title: Input_EmptyVector ChIPSeq Rep1


title: Pneuron-3

source_name: primary cortical neuron

value: primary cortical neuron isolated from ICR embryonic E14.5


title: genomic DNA-PM115-revised_processing

value: placental chorionic villi


title: genomic DNA-PM119-revised_processing

value: MALE


title: genomic DNA-PM120-initial_processing


title: H3K4me3 AF4-MLL ChIPSeq Rep4

source_name: H3K4me3 AF4-MLL ChIPSeq

value: AF4-MLL expression


title: H3K4me3 AF4-MLL ChIPSeq Rep2


title: H3K4me3 AF4-MLL ChIPSeq Rep3


title: Pneuron-1


title: genomic DNA-PM124-initial_processing


title: Pneuron-2


title: 7d_B_12Gy_3

city: Northbrook

first: Michael

last: Falduto

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: Labeled target was applied to Agilent miRNA mouse v19 arrays (Design ID#046065) and hybridized overnight.

scan_protocol: Slides were washed and scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

source_name: Whole Blood 7d exp B 12Gy dose rep 3

label_protocol: Total RNA samples were dephosphorylated, denatured, and end-labeled according to Agilent's protocols.

extract_protocol: RNA was extracted and purified using Ribopure (Ambion) RNA isolation

treatment_protocol: whole body irradiation done with X-rays using the Small Animal Radiation Research Platform (SARRP Xstrahl Ltd.). Mice were placed in plastic containers and exposed to a single surface dose of 0-12 Gy with a dose rate of 1.05 Gy/min. Control mice (0 Gy) were placed in the same plastic container as the irradiated mice and sham irradiated. 3 animals/dose/time-point have been included in the study.

value: Six to eight weeks

tag: gender

value: female

value: whole body


title: PMEF-3

source_name: primary mouse embryonic fibroblast

value: primary mouse embryonic fibroblast isolated from ICR embryo E13.5


title: 7d_B_12Gy_2

source_name: Whole Blood 7d exp B 12Gy dose rep 2


title: 7d_B_12Gy_1

source_name: Whole Blood 7d exp B 12Gy dose rep 1


title: PMEF-2


title: H3K4me3 MLL-AF4 ChIPSeq Rep4

source_name: H3K4me3 MLL-AF4 ChIPSeq

value: human ESC


title: PMEF-1


title: breast cancer with BSC_LR266

city: Lund

first: Martin

last: Sjöström

address: Scheelevägen 2

country: Sweden

institute: Lund University

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing:
The data was norm-exp background corrected and quantile normalized using the neqc function in the limma R package
Norm-exp background corrected with offset of 16, quantile normalized and log2 transformed

source_name: breast cancer operated with breast conserving surgery (BSC)

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevD, (Modification of Amplification kit v 2.2)

extract_protocol: Qiagen AllPrep protocol with Qiacube

tag: er (estrogen receptor status)

value: pos

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: breast cancer with BSC_LR254


title: genomic DNA-PL86-revised_processing

tag: fetal sex


title: H3K4me3 AF4-MLL ChIPSeq Rep1


title: 7d_B_0Gy_3

source_name: Whole Blood 7d exp B 0Gy dose rep 3

tag: age


title: breast cancer with BSC_LR265


title: breast cancer with BSC_LR252

value: neg


title: H3K4me3 MLL-AF4 ChIPSeq Rep3

value: MLL-AF4 expression


title: Skm single muscle fibers 3

city: Minneapolis

first: Mayank

last: Verma

state: MN

address: 2001 6th st se

department: Stem Cell Institute

institute: University of Minnesota

data_processing:
Quality control was performed using FASTQC. Sequences were trimmed using trimmomatic to remove adapter contamination and low quality reads. Trimmed sequences were mapped to mouse mm10 using Hisat2. Transcript assembly was performed using StringTie. Transcript and gene level quantification and analysis was performed using Stringtie and ballgown.
BAM files from Hisat2 were converted to bed graph using bedtools genomecov with -bg, -ibam, and -split. The bed graph files were sorted and the sorted files were converted to bigwig using the bedGraphToBigWig using mm10 for the sequence length.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrix from Stringie in TPM. gene and transcript expression matrix from Ballgown in FPKM. Bigwig files.

source_name: Skm single muscle fibers

extract_protocol:
Approximately 100,000 FACS sorted cells were pelleted at 20,000g for 3 minutes and resuspended in TrizolTM Thermofisher 15596026). Single muscle fibers were isolated from the EDL muscle and allowed to sit for 3 hours to allow for hypercontraction of damaged fibers. 100 pristine fibers were manually selected and pelleted at 20,000g for 3. The pellet was re-suspended in 300ul of TrizolTM. RNA was isolated using the Direct-zolTM RNA microprep (Zymo Research R2062) with on-column DNase digestion.
Total eukaryotic RNA isolates are quantified using a fluorimetric RiboGreen assay.  Total RNA integrity was assessed using capillary electrophoresis (Agilent BioAnalyzer 2100) and RNA Integrity Number (RIN) of 8-10 were used(One sample failed to reach RIN>8). Library preparation was performed on total RNA SMARTer Stranded Total RNA-Seq – Pico Mammalian Kit (Clontech 635007).  10ng of RNA was reverse transcribed into cDNA using random primers. The Template Switching Oligo (TSO) is incorporated during cDNA synthesis and allows for full length cDNA synthesis and strand specificity to be retained. Illumina sequencing adapters and barcodes are then added to the cDNA via limited PCR amplification. Next, mammalian ribosomal cDNA is enzymatically cleaved. Uncleaved fragments were PCR enriched 12-16 cycles. Indexed libraries are then normalized and pooled for sequencing using the Illumina HiSeq2500 with 50bp paired ends run with 20 millions expected reads per sample.

value: EDL muscle

value: single muscle fibers


title: 7d_B_0Gy_2

state: IL

source_name: Whole Blood 7d exp B 0Gy dose rep 2


title: genomic DNA-PL21-revised_processing

tag: gestational age (week, rounded)

tag: processing group


title: breast cancer with BSC_LR267


title: genomic DNA-PL145-revised_processing


title: genomic DNA-PM114-initial_processing


title: breast cancer with BSC_LR253


title: 7d_B_0Gy_1

source_name: Whole Blood 7d exp B 0Gy dose rep 1


title: H3K4me3 MLL-AF4 ChIPSeq Rep1

tag: genotype/variation

tag: chip antibody


title: genomic DNA-PL72-revised_processing

value: FEMALE


title: genomic DNA-PM112-initial_processing


title: Skm single muscle fibers 2

data_processing:
BAM files from Hisat2 were converted to bed graph using bedtools genomecov with -bg, -ibam, and -split. The bed graph files were sorted and the sorted files were converted to bigwig using the bedGraphToBigWig using mm10 for the sequence length.
Quality control was performed using FASTQC. Sequences were trimmed using trimmomatic to remove adapter contamination and low quality reads. Trimmed sequences were mapped to mouse mm10 using Hisat2. Transcript assembly was performed using StringTie. Transcript and gene level quantification and analysis was performed using Stringtie and ballgown.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrix from Stringie in TPM. gene and transcript expression matrix from Ballgown in FPKM. Bigwig files.

tag: cell type


title: genomic DNA-PM104-initial_processing


title: Skm single muscle fibers 1


title: H3K4me3 EmptyVector ChIPSeq Rep3

source_name: H3K4me3 EmptyVector ChIPSeq

value: empty vector


title: Skm satellite cell 3

source_name: Skm satellite cell

value: Hindlimb muscles

value: satellite cell


title: H3K4me3 EmptyVector ChIPSeq Rep4


title: H3K4me3 MLL-AF4 ChIPSeq Rep2


title: breast cancer with BSC_LR250


title: 7d_A_8Gy_3

source_name: Whole Blood 7d exp A 8Gy dose rep 3

tag: strain


title: 7d_A_8Gy_2

source_name: Whole Blood 7d exp A 8Gy dose rep 2


title: genomic DNA-PL135-revised_processing

value: placental chorionic villi


title: genomic DNA-PL142-revised_processing

value: MALE


title: Skm satellite cell 1


title: H3K4me3 EmptyVector ChIPSeq Rep2


title: 7d_A_4Gy_3

source_name: Whole Blood 7d exp A 4Gy dose rep 3


title: breast cancer with BSC_LR249


title: breast cancer with BSC_LR247


title: breast cancer with BSC_LR248


title: Skm endothelial cell 2

data_processing:
Quality control was performed using FASTQC. Sequences were trimmed using trimmomatic to remove adapter contamination and low quality reads. Trimmed sequences were mapped to mouse mm10 using Hisat2. Transcript assembly was performed using StringTie. Transcript and gene level quantification and analysis was performed using Stringtie and ballgown.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrix from Stringie in TPM. gene and transcript expression matrix from Ballgown in FPKM. Bigwig files.

source_name: Skm endothelial cell

value: endothelial cell


title: H3K4me3 EmptyVector ChIPSeq Rep1


title: Skm endothelial cell 1


title: HCT116 mid S phase fraction replicate 2

city: Edinburgh

first: Lora

last: Boteva

state: City of Edinburgh, Midlothian

address: Crewe Road

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

description:
DNA-seq libarary prepared by isolating nascent DNA from HCT116 cells in mid S phase of the cell cycle
HCT116_2_nodup_1kb

data_processing:
Library strategy: Repli-seq
Fastq files were aligned to hg 19 using Bowtie 2
PCR duplicate removal, file sorting and indexing was performed with Samtools 1.2
Bam files were generated and read density in 1000 bp windows across the genome were calculated using the "multicov" option in Bedtools 2.25
Normalised FPKM values were generated for each window in R
single replication timing value was then calculated from the early, mid and late fraction for each window using the following equation:  R=0.165*FPKMlate/(FPKMearly+FPKMmid+FPKMlate)+0.495* FPKMmid/(FPKMearly+FPKM mid+FPKMlate)+ ).825*FPKMearly/(FPKMearly+FPKMmid+FPKMlate)
The R value was used for comparison between samples
Genome_build: Hg19
Supplementary_files_format_and_content: Replication timing values in 1000 bp windows. Values closer to 1 indicate early replication; values closer to 0 indicate late replicaiton.

source_name: HCT116 cells

growth_protocol: HCT116 (ATCC CCL-247) and RPE1 cells (ATCC CRL-4000) were cultured in DMEM-F12 supplemented with, 3 mM glutamine, 15 mM HEPES, 0.34% sodium bicarbonate, 10% FBS, penicillin (100 U ml−1), streptomycin (100 μg ml−1) and phenol red (8.1 mg l−1).

extract_protocol:
DNA was extracted using phenol-chloroform extraction and ethanol precipitation. Nascent DNA was enriched using a streptavidin pull-down.
Libraries were prepared with a NEBNext® Ultra™ DNA Library Prep Kit for Illumina (NEB), according to manufacturer’s instructions and sample uniquely barcoded using NEBNext Multiplex oligo for Illumina (NEB). Samples were quantified using a BioAnalyzer 2100 with a High Sensitivity DNA Kit (Agilent). Libraries were analysed by Edinburgh Genomics at the University of Edinburgh, UK, who performed quality control and sequencing using an Illumina HiSeq2500, 50 base single-end reads. Samples were indexed as follows: RPE1  1 Early: NEB Index 4, RPE1 1 Mid: NEB Index 6, RPE1 1 Late: NEB Index 12, RPE1 2 Early, NEB Index 4, RPE1 2 Mid: NEB Index 6, RPE1 2 Late: NEB Index 12, HCT116 Early NEB index 4, HCT116 Mid NEB index 6, HCT116 Late NEB Index 12

tag: cell line

tag: cell cycle phase

value: mid S


title: HCT116 early S phase fraction

description:
DNA-seq libarary prepared by isolating nascent DNA from HCT116 cells in the early S phase of the cell cycle
HCT116_2_nodup_1kb

value: early S


title: RPE1 late S phase fraction replicate 2

description:
DNA-seq libarary prepared by isolating nascent DNA from RPE1 cells in the late S phase of the cell cycle
RPE1_2_nodup_1kb.bed

source_name: RPE1 cells

value: late S


title: 7d_A_4Gy_1

source_name: Whole Blood 7d exp A 4Gy dose rep 1

value: Six to eight weeks

value: female

tag: tissue

value: whole body


title: breast cancer with BSC_LR251

value: pos


title: RPE1 mid S phase fraction replicate 2

description:
DNA-seq libarary prepared by isolating nascent DNA from RPE1 cells in mid S phase of the cell cycle
RPE1_2_nodup_1kb.bed


title: 7d_A_2Gy_3

source_name: Whole Blood 7d exp A 2Gy dose rep 3

tag: gender


title: Skm endothelial cell 3


title: HCT116 late S phase fraction replicate 2

description:
DNA-seq libarary prepared by isolating nascent DNA from HCT116 cells in the late S phase of the cell cycle
HCT116_2_nodup_1kb


title: 7d_A_4Gy_2

source_name: Whole Blood 7d exp A 4Gy dose rep 2


title: 7d_A_2Gy_1

source_name: Whole Blood 7d exp A 2Gy dose rep 1


title: 7d_A_2Gy_2

source_name: Whole Blood 7d exp A 2Gy dose rep 2


title: RPE1 late S phase fraction replicate 1

description:
DNA-seq libarary prepared by isolating nascent DNA from RPE1 cells in the late S phase of the cell cycle
RPE1_1_nodup_1kb.bed


title: 7d_A_0Gy_3

source_name: Whole Blood 7d exp A 0Gy dose rep 3


title: breast cancer with BSC_LR244

source_name: breast cancer operated with breast conserving surgery (BSC)

tag: er (estrogen receptor status)


title: RPE1 mid S phase fraction replicate 1

description:
DNA-seq libarary prepared by isolating nascent DNA from RPE1 cells in mid S phase of the cell cycle
RPE1_1_nodup_1kb.bed


title: 7d_A_0Gy_1

source_name: Whole Blood 7d exp A 0Gy dose rep 1


title: 48hr_B_15Gy_3

source_name: Whole Blood 48hr exp B 15Gy dose rep 3


title: breast cancer with BSC_LR245

tag: rt (radiotherapy)


title: breast cancer with BSC_LR239

tag: lr (local recurrence)


title: breast cancer with BSC_LR236

tag: ibtr (ipsilateral breast tumor recurrence)


title: RPE1 early S phase fraction replicate 1

description:
DNA-seq libarary prepared by isolating nascent DNA from RPE1 cells in the early S phase of the cell cycle
RPE1_1_nodup_1kb.bed


title: breast cancer with BSC_LR237

tag: follow-up time (years)


title: breast cancer with BSC_LR234

value: neg


title: miR-324-5p

city: Bhopal

first: Himanshu

last: Kumar

state: MADHYA PRADESH

address: Indore bypass road

department: Biological Sciences

country: India

institute: IISER Bhopal

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, quality filtering of reads was done using sliding window approach,then mapped to GRCh38 whole genome using Tophat2
Transcripts were assembled and their abundances in Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks suite
Genome_build: GRCh38, release 89
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: A549 cells

growth_protocol: A549 cells were cultured in DMEM supplemented with 10% FBS and appropriate concentration of antibiotic and antimycotic.

extract_protocol:
Total RNA isolation by TRIzol™ reagent
Libraries for sequencing were prepared according to manufacturer's protocol using TruSeq RNA Library Prep Kit

treatment_protocol: miRNA mimics were transfected with the help of Lipofectamine 2000 reagent.

tag: infection

tag: transfection


title: breast cancer with BSC_LR242


title: breast cancer with BSC_LR241


title: 7d_A_0Gy_2

source_name: Whole Blood 7d exp A 0Gy dose rep 2

tag: age


title: RPE1 early S phase fraction replicate 2

description:
DNA-seq libarary prepared by isolating nascent DNA from RPE1 cells in the early S phase of the cell cycle
RPE1_2_nodup_1kb.bed


title: breast cancer with BSC_LR243


title: Negative control

value: negative control


title: 48hr_B_15Gy_2

source_name: Whole Blood 48hr exp B 15Gy dose rep 2


title: Mock

value: mock


title: breast cancer with BSC_LR233


title: 48hr_B_12Gy_3

source_name: Whole Blood 48hr exp B 12Gy dose rep 3


title: 48hr_B_12Gy_2

source_name: Whole Blood 48hr exp B 12Gy dose rep 2


title: breast cancer with BSC_LR246


title: 000251Y

city: Sendai

first: Hiroki

last: Sekine

address: 4-1 Seiryo-machi, Aobaku

department: Institute of Development, Aging and Cancer (IDAC)

country: Japan

institute: Tohoku University

data_processing:
Illumina bcl2fastq v2.15.0 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 software.
Peaks were called using MACS version 1.4
Genome_build: mm9
Supplementary_files_format_and_content: peak/bed files were generated using MACS.

growth_protocol: HeLa-S3 cells were cultured in DMEM medium containing 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
The cells were cross-linked with 1.5 mM EGS (Thermo Scientific) for 20 min, followed by treatment with 1% formaldehyde for 10 min; the samples were then lysed and digested with micrococcal nuclease (New England Biolabs) to shear DNA.ChIP was performed with anti-NRF1 antibody (Cell Signaling, D5B10).The antibody incubation were pereformed overnight at 4℃.
The DNA libraries were prepared from 1 ng of ChIP and input samples quantified with Qubit Fluorometer (Life Technologies), using Mondrian SP+ and Ovation SP Ultralow DR Multiplex System (TaKaRa).braries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For analysis of Nrf1-induced state, the cells were treated with 1μM MG132 for 4 hours

value: cervix adenocarcinoma


title: 48hr_B_0Gy_3

source_name: Whole Blood 48hr exp B 0Gy dose rep 3


title: 48hr_B_12Gy_1

source_name: Whole Blood 48hr exp B 12Gy dose rep 1


title: 000247Y


title: 000248Y

value: anti-NRF1 antibody (Cell Signaling, D5B10)


title: breast cancer with BSC_LR232


title: 48hr_B_15Gy_1

source_name: Whole Blood 48hr exp B 15Gy dose rep 1


title: breast cancer with BSC_LR231


title: breast cancer with BSC_LR228


title: breast cancer with BSC_LR230


title: breast cancer with BSC_LR227


title: 000252Y


title: 48hr_A_8Gy_3

source_name: Whole Blood 48hr exp A 8Gy dose rep 3


title: 48hr_B_0Gy_1

source_name: Whole Blood 48hr exp B 0Gy dose rep 1


title: 48hr_B_0Gy_2

source_name: Whole Blood 48hr exp B 0Gy dose rep 2


title: 48hr_A_8Gy_1

source_name: Whole Blood 48hr exp A 8Gy dose rep 1


title: 48hr_A_4Gy_3

source_name: Whole Blood 48hr exp A 4Gy dose rep 3


title: 48hr_A_4Gy_2

source_name: Whole Blood 48hr exp A 4Gy dose rep 2


title: breast cancer with BSC_LR226

source_name: breast cancer operated with breast conserving surgery (BSC)


title: breast cancer with BSC_LR225


title: 48hr_A_4Gy_1

source_name: Whole Blood 48hr exp A 4Gy dose rep 1


title: 48hr_A_2Gy_3

source_name: Whole Blood 48hr exp A 2Gy dose rep 3


title: 48hr_A_2Gy_2

source_name: Whole Blood 48hr exp A 2Gy dose rep 2


title: 48hr_A_2Gy_1

source_name: Whole Blood 48hr exp A 2Gy dose rep 1


title: breast cancer with BSC_LR219


title: 48hr_A_0Gy_3

source_name: Whole Blood 48hr exp A 0Gy dose rep 3


title: breast cancer with BSC_LR216


title: 48hr_A_0Gy_2

source_name: Whole Blood 48hr exp A 0Gy dose rep 2


title: breast cancer with BSC_LR218


title: 48hr_A_0Gy_1

source_name: Whole Blood 48hr exp A 0Gy dose rep 1


title: 24hr_B_15Gy_3

source_name: Whole Blood 24hr exp B 15Gy dose rep 3


title: 48hr_A_8Gy_2

source_name: Whole Blood 48hr exp A 8Gy dose rep 2


title: breast cancer with BSC_LR211


title: breast cancer with BSC_LR210


title: breast cancer with BSC_LR215


title: 24hr_B_15Gy_1

source_name: Whole Blood 24hr exp B 15Gy dose rep 1


title: 24hr_B_12Gy_3

source_name: Whole Blood 24hr exp B 12Gy dose rep 3


title: 24hr_B_15Gy_2

source_name: Whole Blood 24hr exp B 15Gy dose rep 2


title: breast cancer with BSC_LR217


title: breast cancer with BSC_LR206


title: 24hr_B_12Gy_2

source_name: Whole Blood 24hr exp B 12Gy dose rep 2


title: breast cancer with BSC_LR202


title: breast cancer with BSC_LR207


title: 24hr_B_0Gy_3

source_name: Whole Blood 24hr exp B 0Gy dose rep 3


title: 24hr_B_12Gy_1

source_name: Whole Blood 24hr exp B 12Gy dose rep 1


title: 7d_A_8Gy_1

source_name: Whole Blood 7d exp A 8Gy dose rep 1


title: breast cancer with BSC_LR200

source_name: breast cancer operated with breast conserving surgery (BSC)


title: breast cancer with BSC_LR204


title: breast cancer with BSC_LR208


title: breast cancer with BSC_LR199


title: breast cancer with BSC_LR198


title: breast cancer with BSC_LR194


title: breast cancer with BSC_LR195


title: 24hr_A_8Gy_3

source_name: Whole Blood 24hr exp A 8Gy dose rep 3


title: breast cancer with BSC_LR196


title: 24hr_B_0Gy_1

source_name: Whole Blood 24hr exp B 0Gy dose rep 1


title: breast cancer with BSC_LR193


title: 24hr_A_4Gy_2

source_name: Whole Blood 24hr exp A 4Gy dose rep 2


title: 24hr_A_4Gy_3

source_name: Whole Blood 24hr exp A 4Gy dose rep 3


title: 24hr_A_2Gy_3

source_name: Whole Blood 24hr exp A 2Gy dose rep 3


title: 24hr_A_4Gy_1

source_name: Whole Blood 24hr exp A 4Gy dose rep 1


title: 24hr_A_8Gy_2

source_name: Whole Blood 24hr exp A 8Gy dose rep 2


title: 24hr_A_8Gy_1

source_name: Whole Blood 24hr exp A 8Gy dose rep 1


title: 6hr_B_15Gy_2

source_name: Whole Blood 6hr exp B 15Gy dose rep 2


title: 6hr_B_15Gy_3

source_name: Whole Blood 6hr exp B 15Gy dose rep 3


title: 6hr_B_15Gy_1

source_name: Whole Blood 6hr exp B 15Gy dose rep 1


title: breast cancer with BSC_LR192


title: 24hr_A_2Gy_2

source_name: Whole Blood 24hr exp A 2Gy dose rep 2


title: 24hr_A_0Gy_1

source_name: Whole Blood 24hr exp A 0Gy dose rep 1


title: 24hr_A_0Gy_2

source_name: Whole Blood 24hr exp A 0Gy dose rep 2


title: 24hr_A_0Gy_3

source_name: Whole Blood 24hr exp A 0Gy dose rep 3


title: 24hr_A_2Gy_1

source_name: Whole Blood 24hr exp A 2Gy dose rep 1


title: breast cancer with BSC_LR188

source_name: breast cancer operated with breast conserving surgery (BSC)


title: breast cancer with BSC_LR190


title: breast cancer with BSC_LR186


title: breast cancer with BSC_LR201


title: breast cancer with BSC_LR187


title: 6hr_B_12Gy_2

source_name: Whole Blood 6hr exp B 12Gy dose rep 2


title: breast cancer with BSC_LR183


title: breast cancer with BSC_LR173


title: breast cancer with BSC_LR185


title: breast cancer with BSC_LR176


title: breast cancer with BSC_LR175


title: breast cancer with BSC_LR170


title: breast cancer with BSC_LR174


title: breast cancer with BSC_LR180


title: breast cancer with BSC_LR172


title: breast cancer with BSC_LR181


title: 6hr_B_12Gy_3

source_name: Whole Blood 6hr exp B 12Gy dose rep 3


title: 6hr_B_12Gy_1

source_name: Whole Blood 6hr exp B 12Gy dose rep 1


title: 6hr_B_0Gy_3

source_name: Whole Blood 6hr exp B 0Gy dose rep 3


title: HEART WT N5

city: Cincinnati

first: Jing

last: Chen

state: OH

address: 3333 Burnet Ave

institute: CCHMC

data_processing:
Sequence reads were aligned to the genome by using the standard Illumina sequence analysis pipeline, which was analyzed by the Statistical Genomics and Systems Biology Core at the University of Cincinnati.
basecalling by Illumina Casava
alignment by TopHat
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of raw count for each gene in each sample

source_name: HEART

extract_protocol:
RNeasy Micro kit (Qiagen) was used for total RNA extraction. Each sample, together with Buffer RLT, were added to ceramic-beads (1.4-mm) in tubes and homogenized by using the Precellys homogenizer (Cayman Chemical Company; Ann Arbor, MI). RNA extraction was then performed, following manufacturer’s recommendations.
To prepare the RNA library for sequencing, we used TruSeq RNA Library Prep Kit (Illumina; San Diego, CA), according to manufacturer’s instructions. In brief, poly(A+) RNA was purified from total RNA and then fragmented before cDNA synthesis. Double-strand cDNA fragments were then end-repaired and TA-ligated to the sequencing adapter; the specific index was added to the library during the PCR amplification step. After 12 cycles of PCR enrichment, library quality was evaluated by a Bioanalyzer High Sensitivity chip and quantified by Kapa Library Quantification kit (Kapa Biosystem; Wilmington, MA), using the ABI 9700HT real-time PCR system (Thermo Fisher; Waltham, MA). Next, six individually indexed cDNA libraries were pooled in equal amounts for clustering in the cBot system (Illumina). Libraries were clustered onto a flow cell at concentration of 15 pM, using Illumina’s TruSeq SR Cluster Kit v3, and then sequenced for 50 cycles using TruSeq SBS kit on the Illumina HiSeq system. Each sample was expected to generate ~30 million reads.

value: HEART

tag: developmental stage

tag: genotype


title: breast cancer with BSC_LR169


title: 6hr_B_0Gy_2

source_name: Whole Blood 6hr exp B 0Gy dose rep 2


title: 6hr_A_8Gy_3

source_name: Whole Blood 6hr exp A 8Gy dose rep 3


title: pel1 rep3

city: Godollo

first: Daniel

last: Silhavy

address: Szent-Gyorgyi 4

institute: National Agricultural Research and Innovation Cen.

description: Arabidopsis RNA-Seq experiment

data_processing:
Read alignment (Hisat2 v2.1.0)
Transciprt assembly (StringTie v1.3.3b)
Differential Gene Expression (DESeq2 v1.18.1)
Genome_build: Solgenomics Niben v1.0.1, TAIR10
Supplementary_files_format_and_content: gtf files were generated using Stringtie v1.3.3b software including the assembled transcript structures and FPKM values.

organism: Arabidopsis thaliana

source_name: A. thaliana_pel1

extract_protocol:
Total RNA was extracted from 100 mg of leaf tissue (White and Kaper, 1989). Briefly, the homogenized plant materials were resuspended in 600 μL of extraction buffer (0.1 M glycine-NaOH, pH 9.0, 100 mM NaCl, 10 mM EDTA, 2% SDS, and 1% sodium lauroylsarcosine) and mixed with an equal volume of phenol. The aqueous phase was treated with equal volumes of phenol and chloroform, precipitated with ethanol, and resuspended in sterile water.
Libraries were prepared from total RNA samples with Illumina® Ribo-Zero™ rRNA Removal (Plant Leaf) and TruSeq™ v2 RNASeq Library Preparation Kits.

tag: ecotype/stock

tag: genotype/variation

value: pel1 mutant

value: leaf


title: KIDNEY WT N3

source_name: KIDNEY

value: KIDNEY


title: CEREBELLUM WT N4

source_name: CEREBELLUM

value: CEREBELLUM


title: 6hr_A_8Gy_2

source_name: Whole Blood 6hr exp A 8Gy dose rep 2

tag: strain


title: 6hr_A_4Gy_3

source_name: Whole Blood 6hr exp A 4Gy dose rep 3


title: 6hr_A_8Gy_1

source_name: Whole Blood 6hr exp A 8Gy dose rep 1


title: 6hr_A_4Gy_2

source_name: Whole Blood 6hr exp A 4Gy dose rep 2


title: LIVER WT N1

source_name: LIVER

value: LIVER


title: pel1 rep2

description: Arabidopsis RNA-Seq experiment


title: CEREBELLUM WT 9


title: 6hr_A_4Gy_1

source_name: Whole Blood 6hr exp A 4Gy dose rep 1


title: pel1 rep1

description: Arabidopsis RNA-Seq experiment


title: LUNG WT N2

source_name: LUNG

value: LUNG


title: H226 CD26 siRNA/H226 Control

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: H226 Control

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

growth_protocol: H226 and JMN cells were mediated in RPMI 1640 supplemented with 10% heat-inactivated fetal calf serum, penicillin (100U/ml) and streptmycin (100µg/ml) at 37ºC and 5% CO2.

extract_protocol: Total RNAs were isolated by using Rneasy mini kit (Qiagen).

treatment_protocol: H226 and JMN cells were transfected with control siRNA or CD26 siRNA by using Lipofectamine RNAi MAX. At day 2, total RNAs were isolated.

tag: cell line

tag: cell type

value: mesothelioma

source_name: H226 CD26 siRNA


title: JMN CD26 siRNA/JMN Control

source_name: JMN Control

value: JMN

source_name: JMN CD26 siRNA


title: breast cancer with BSC_LR168

source_name: breast cancer operated with breast conserving surgery (BSC)


title: breast cancer with BSC_LR167


title: breast cancer with BSC_LR166


title: breast cancer with BSC_LR164


title: breast cancer with BSC_LR165


title: 6hr_A_2Gy_3

source_name: Whole Blood 6hr exp A 2Gy dose rep 3

value: Six to eight weeks

value: female

tag: tissue


title: hbs1 rep3

state: US and Canada only

description: Arabidopsis RNA-Seq experiment

source_name: A. thaliana_hbs1

value: hbs1 mutant


title: breast cancer with BSC_LR162

value: pos


title: breast cancer with BSC_LR160


title: KIDNEY WT 8


title: LUNG WT 7


title: breast cancer with BSC_LR178