title: Genomic DNA from peripheral blood monoculear cells 198

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200490750121_R04C01_Grn.idat
location 1 (triplicate pair 1): 200490750121_R04C01_Red.idat
location 2 (triplicate pair 2): 200490750121_R04C02_Grn.idat
location 2 (triplicate pair 2): 200490750121_R04C02_Red.idat
location 3 (triplicate pair 3): 200556930054_R04C02_Grn.idat
location 3 (triplicate pair 3): 200556930054_R04C02_Red.idat


title: Control_B

status: Public on Mar 21 2020

type: SRA

city: Bronx

first: Andrew

last: Johnston

state: NY

address: 1301 Morris Park Avenue

department: Genetics

country: USA

institute: Albert Einstein College of Medicine

library_source: genomic

data_processing:
library strategy: HELP-tagging
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (versions ELAND - 1.7.0).  Initial data processing was performed using the default read length of 36 bp.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.  To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Genome_build: mm9
Supplementary_files_format_and_content: The hit count files were generated using in house pipeline (WASP - 3.1.4); The first line starts with "total" and displays total number of raw reads aligned to HpaII loci properly. For instance, "total 5249033" ; From the second line onward, each line represents one HpaII locus, showing the ID, chromosome, offset, HpaII count(F strand), HpaII count(R strand), HpaII count(both strands), respectively and space-delimited. For instance, "21 chr1 11961 9.8 17 26.8"
Supplementary_files_format_and_content: A bedgraph of the HpaII loci angle values was generated for each sample using custom script provided in the publication; Angle values represent degree of unmethylation at each HpaII site

molecule: genomic DNA

organism: Mus musculus

source_name: WW6 cells

growth_protocol: mES cells were grown in a feeder cell-free environment on 0.1% gelatin covered dishes, in Dulbecco’s modified Eagle medium (DMEM, Mediatech) supplemented with 10% Fetal Bovine Serum (STEMCELL Technologies cat. no. 06952), 1X Nonessential amino acids (Gibco, cat.no. 11140-050), 1X Nucleoside mix (Sigma), 55 nM 2-Mercaptoethanol (Gibco) and 3,000 units of Leukemia inhibition factor (EMD Millipore ESG1106) per ml, at 37 °C in 5% CO2

extract_protocol:
mES cells were collected by washing and trypsinizing for three minutes, and FACS sorted by the GFP signal present in the transfected plasmid. Genomic DNA was extracted by resuspending the cells in lysis buffer (10 mM TE, 150 mM EDTA and 1% SDS) supplemented with 10 mg/ml of RNase A and 20 mg/ml of Proteinase K, and incubated at 50 °C overnight.  The lysed cells were phenol-chloroform extracted and the resultant DNA was dialyzed in 0.2X SSC buffer (300 mM NaCl and 3 mM Na3C6H5O7, ph 7.0) for 24 hours.  The DNA sample was concentrated in the dialysis bags using polyethylene glycol, following which the quality and concentration of the DNA were measured by Nanodrop spectrophotometry.
Two custom adapters were created for HELP-tagging, referred to as AE and AS.  As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence.  Adapter AS contains an Illumina sequencing primer sequence.  One micrograms of genomic DNA were digested with HpaII and MspI in separate 50 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation.  The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 1 μg of MspI/HpaII-digested DNA , 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl).  After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB).  The restriction fragments were end-repaired to inhibit dimerization of adapters, and tailed with a single dA, at the 3’ end.  After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl).  After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion).  Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen).  The first strand cDNA produced was used as a template for PCR using the following conditions: 98°C for 2 minutes, then 18 cycles of 98°C for 15 seconds, 60°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension.  The product then underwent gel extraction (Qiagen).

treatment_protocol: Cells were transiently transfected after 24 hours of seeding, using 6 µl of Lipofectamine LTX supplemented with 5 µl of Plus reagent per ml (Invitrogen), in serum-free media (OPTI-MEM, Invitrogen), with siRNA targeting Kdm5b, or GFP as control. After 4 hours of transfection, regular cultured media was added to transfected cells to assure optimal culture conditions.

tag: cell line

tag: cell type

value: embryonic stem cells

tag: strain

tag: treatment

value: transfected cells with mock control construct


title: Genomic DNA from peripheral blood monoculear cells 172

type: genomic

city: Jefferson

first: Stancy

last: Joseph

state: Ar

address: 3900 NCTR Road

department: Biochemical Toxicology

institute: FDA/NCTR

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200490750149_R02C01_Grn.idat
location 1 (triplicate pair 1): 200490750149_R02C01_Red.idat
location 2 (triplicate pair 2): 200490750149_R02C02_Grn.idat
location 2 (triplicate pair 2): 200490750149_R02C02_Red.idat
location 3 (triplicate pair 3): 200556930054_R02C01_Grn.idat
location 3 (triplicate pair 3): 200556930054_R02C01_Red.idat

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Reader

data_processing: BeadStudio Software

label: Cy3 and Cy5

organism: Homo sapiens

source_name: Blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from normal human kidney tissue samples using Qiagen DNeasy Kit according to standard instructions

tag: ethnicity

value: AA

tag: disease state

value: Lupus

tag: sledai score

tag: age


title: Genomic DNA from peripheral blood monoculear cells 189

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200490750149_R06C01_Grn.idat
location 1 (triplicate pair 1): 200490750149_R06C01_Red.idat
location 2 (triplicate pair 2): 200490750149_R06C02_Grn.idat
location 2 (triplicate pair 2): 200490750149_R06C02_Red.idat
location 3 (triplicate pair 3): 200556930054_R06C01_Grn.idat
location 3 (triplicate pair 3): 200556930054_R06C01_Red.idat

value: EA


title: Donor 3_TGFbeta_12h

city: San Francisco

first: Mary Helen

last: Barcellos-Hoff

state: CA

address: 2340 Sutter Street

department: Radiation Oncology

institute: UCSF

library_source: transcriptomic

data_processing:
Base calling: HiSeq Control Software HCS
Sequenced reads were mapped to hg38 using TopHat v2.0.12 (Bowtie v2.2.3.0, Samtools v0.1.18.0) with parameters --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 --no-closure-search --no-microexon-search --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3
Reads were counted using htseq-count script from HTSeq v0.5.4p3 with parameters -s no -a 10
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file containing raw counts of each sample

molecule: total RNA

source_name: CD14+ IMC

extract_protocol:
Total mRNA (Qiagen)
Illumina TruSeq RNA Library Preparation Kit v2, Set A (48 samples, 12 indexes) (RS-122-2001)
Oligo-dT for Poly-A tail selection
HiSeq 2500, v4 chemistry

value: CD14+ human immature myeloid cells

tag: individual

value: Donor 3

value: Treated with TGF-beta

tag: time point

value: 12 hours


title: Donor 3_Untreated_12h

value: Un-treated


title: Kdm5b_KD_ H3K4me3

data_processing:
Poor quality bases and adapter sequences were trimmed from reads using Trim Galore! v. 0.3.3 - default parameters.
The trimmed reads were then aligned using Burrows-Wheeler aligner (BWA) v. 0.7.9a to the mm9 mouse genome. First the aln command was used to create a .bai file. Then the samse command using the .bai and original fastq files as input resulted in a .sam file containing the aligned reads
Output SAM files were converted to .bam files and sorted using Picard tools v. 1.117 using the SortSam command with the following parameters: SO=coordinate TMP_DIR=. CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT
Peaks were called using MACS2 v. 2.1.0.20140616 (callpeak command and -g mm parameter) and the proper .bam files for treatment and control (input). Peaks are in .bed format
Genome_build: mm9
Supplementary_files_format_and_content: bed

extract_protocol:
3 million cells crosslinked in 1% formaldehyde were lysed with Farnham and RIPA cold lysis buffers. Following collection, the crude nuclear preparation was processed in a Bioruptor at the high setting for a total of 30 minutes, in cycles of 30 seconds on/30 seconds off. The chromatin was collected by centrifugation and incubated with 5 µg of H3K4me3 antibody overnight.
The immunoprecipitated samples were end-filled using a combination of  T4 DNA polymerase and T4  polynucleotide kinase , 3’ -terminal-A extended with Klenow 5'-3' exo minus, and ligated to pre-annealed TruSeq indexed Illumina adapters. Libraries were amplified using Illumina primers and gel extracted for size selection and primer-dimer removal.  Before sequencing, libraries were tested using the BioAnalyzer to test quality in terms of size and primer-dimer depletion.

value: mouse embryonic stem cells

value: transfected cells with Kdm5b targeting construct

tag: chip antibody


title: Genomic DNA from peripheral blood monoculear cells 195

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200490750121_R02C01_Grn.idat
location 1 (triplicate pair 1): 200490750121_R02C01_Red.idat
location 2 (triplicate pair 2): 200490750121_R02C02_Grn.idat
location 2 (triplicate pair 2): 200490750121_R02C02_Red.idat
location 3 (triplicate pair 3): 200556930054_R02C02_Grn.idat
location 3 (triplicate pair 3): 200556930054_R02C02_Red.idat


title: Control_A


title: Genomic DNA from peripheral blood monoculear cells 183

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200490750149_R05C01_Grn.idat
location 1 (triplicate pair 1): 200490750149_R05C01_Red.idat
location 2 (triplicate pair 2): 200490750149_R05C02_Grn.idat
location 2 (triplicate pair 2): 200490750149_R05C02_Red.idat
location 3 (triplicate pair 3): 200556930054_R05C01_Grn.idat
location 3 (triplicate pair 3): 200556930054_R05C01_Red.idat


title: Kdm5b_KD_Input


title: Control_Input


title: Donor 3_Untreated_8h

value: 8 hours


title: Donor 3_TGFbeta_8h


title: Donor 3_TGFbeta_4h

value: 4 hours


title: Kdm5b_KD B

description: DNase-treated, rRNA-depleted mRNA

data_processing:
sequencing reads were aligned by the WASP pipeline version 3.1.3 (rev. 6589), using gsnap (2012-07-20)
FASTQ files incorperate Phred quality scores. NOTE: In the raw sequence data fastq file reads failing Illumina's purity filter are removed automatically
Cuffflinks was performed for each sample to calculate FPKM values, specifying the strand of the reads (fr-fisrtstrand), performing an initial estimation of the number of reads mapping in multiple locations in the genome (-u), and normalizing by the upper quartile of the number of fragments mapping to individual loci (-N). To calculate differences in expression between samples, the cufflinks results were merged by cuffmerge using a mm9 GTF file obtained from the UCSC Genome Browser as a reference genome, and then used by cuffdiff to calculate differentially expressed genes
Genome_build: mm9
Supplementary_files_format_and_content: Xlsx file containing all RefSeq genes, analyzed by Cufflinks (Cuffdiff) in order to calculate FKPM values.

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and rRNA depleted with Ribozero (Epicentre)
cDNA synthesis was performed by using oligo-dT as well as random hexamers. Actinomycin D was added to the reaction to prevent any possible amplification from contaminating genomic DNA. During second strand synthesis, a dU/VTP mix was used to create directional libraries. Before library preparation, cDNA samples were Covaris-fragmented to 300 bp fragments. The samples were then end-filled, 3’ terminal A-extended and ligated to pre-annealed TruSeq indexed Illumina adapters.  Uracil-DNA-glycosylase (UDG) treatment preceded the PCR reaction to cleave the uridine-containing strand and therefore identify the orientation of each transcript


title: Genomic DNA from peripheral blood monoculear cells 178

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200490750149_R03C01_Grn.idat
location 1 (triplicate pair 1): 200490750149_R03C01_Red.idat
location 2 (triplicate pair 2): 200490750149_R03C02_Grn.idat
location 2 (triplicate pair 2): 200490750149_R03C02_Red.idat
location 3 (triplicate pair 3): 200556930054_R03C01_Grn.idat
location 3 (triplicate pair 3): 200556930054_R03C01_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 248

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200556930010_R06C01_Grn.idat
location 1 (triplicate pair 1): 200556930010_R06C01_Red.idat
location 2 (triplicate pair 2): 200556930010_R06C02_Grn.idat
location 2 (triplicate pair 2): 200556930010_R06C02_Red.idat
location 3 (triplicate pair 3): 200556930090_R06C02_Grn.idat
location 3 (triplicate pair 3): 200556930090_R06C02_Red.idat


title: Donor 3_Untreated_4h


title: Control_H3K4me3


title: Kdm5b_KD A

description: DNase-treated, rRNA-depleted mRNA


title: Donor 2_TGFbeta_36h

value: Donor 2

value: 36 hours


title: Control B

description: DNase-treated, rRNA-depleted mRNA


title: Genomic DNA from peripheral blood monoculear cells 171

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200490750149_R01C01_Grn.idat
location 1 (triplicate pair 1): 200490750149_R01C01_Red.idat
location 2 (triplicate pair 2): 200490750149_R01C02_Grn.idat
location 2 (triplicate pair 2): 200490750149_R01C02_Red.idat
location 3 (triplicate pair 3): 200556930054_R01C01_Grn.idat
location 3 (triplicate pair 3): 200556930054_R01C01_Red.idat


title: Donor 2_Untreated_36h


title: Genomic DNA from peripheral blood monoculear cells 150

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250001_R05C02_Grn.idat
location 1 (triplicate pair 1): 200491250001_R05C02_Red.idat
location 2 (triplicate pair 2): 200491250023_R02C02_Grn.idat
location 2 (triplicate pair 2): 200491250023_R02C02_Red.idat
location 3 (triplicate pair 3): 200491250023_R05C02_Grn.idat
location 3 (triplicate pair 3): 200491250023_R05C02_Red.idat

value: Non-lupus


title: Control A

description: DNase-treated, rRNA-depleted mRNA


title: Genomic DNA from peripheral blood monoculear cells 162

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250001_R06C02_Grn.idat
location 1 (triplicate pair 1): 200491250001_R06C02_Red.idat
location 2 (triplicate pair 2): 200491250023_R03C02_Grn.idat
location 2 (triplicate pair 2): 200491250023_R03C02_Red.idat
location 3 (triplicate pair 3): 200491250023_R06C02_Grn.idat
location 3 (triplicate pair 3): 200491250023_R06C02_Red.idat


title: Donor 2_TGFbeta_12h


title: Genomic DNA from peripheral blood monoculear cells 148

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419076_R04C01_Grn.idat
location 1 (triplicate pair 1): 3998419076_R04C01_Red.idat
location 2 (triplicate pair 2): 3998419078_R04C01_Grn.idat
location 2 (triplicate pair 2): 3998419078_R04C01_Red.idat
location 3 (triplicate pair 3): 3998419078_R04C02_Grn.idat
location 3 (triplicate pair 3): 3998419078_R04C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 154

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419076_R06C01_Grn.idat
location 1 (triplicate pair 1): 3998419076_R06C01_Red.idat
location 2 (triplicate pair 2): 3998419078_R06C01_Grn.idat
location 2 (triplicate pair 2): 3998419078_R06C01_Red.idat
location 3 (triplicate pair 3): 3998419078_R06C02_Grn.idat
location 3 (triplicate pair 3): 3998419078_R06C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 133

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419077_R06C01_Grn.idat
location 1 (triplicate pair 1): 3998419077_R06C01_Red.idat
location 2 (triplicate pair 2): 3998419096_R06C01_Grn.idat
location 2 (triplicate pair 2): 3998419096_R06C01_Red.idat
location 3 (triplicate pair 3): 3998419096_R06C02_Grn.idat
location 3 (triplicate pair 3): 3998419096_R06C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 151

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419076_R05C01_Grn.idat
location 1 (triplicate pair 1): 3998419076_R05C01_Red.idat
location 2 (triplicate pair 2): 3998419078_R05C01_Grn.idat
location 2 (triplicate pair 2): 3998419078_R05C01_Red.idat
location 3 (triplicate pair 3): 3998419078_R05C02_Grn.idat
location 3 (triplicate pair 3): 3998419078_R05C02_Red.idat


title: Donor 2_Untreated_12h


title: Genomic DNA from peripheral blood monoculear cells 135

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419076_R01C01_Grn.idat
location 1 (triplicate pair 1): 3998419076_R01C01_Red.idat
location 2 (triplicate pair 2): 3998419078_R01C01_Grn.idat
location 2 (triplicate pair 2): 3998419078_R01C01_Red.idat
location 3 (triplicate pair 3): 3998419078_R01C02_Grn.idat
location 3 (triplicate pair 3): 3998419078_R01C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 137

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419076_R02C01_Grn.idat
location 1 (triplicate pair 1): 3998419076_R02C01_Red.idat
location 2 (triplicate pair 2): 3998419078_R02C01_Grn.idat
location 2 (triplicate pair 2): 3998419078_R02C01_Red.idat
location 3 (triplicate pair 3): 3998419078_R02C02_Grn.idat
location 3 (triplicate pair 3): 3998419078_R02C02_Red.idat


title: Donor 2_TGFbeta_8h


title: Ba/F3 cells, NCOR1-LYN(+), rep3

type: RNA

city: Kyoto

first: Toshihiro

last: Tomii

address: 465 Kajii-cho, Kamigyo-ku

department: Pediatrics

country: Japan

institute: Kyoto Prefectural Univercity of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˚C on GeneChip Mouse Genome 430 2.0 Array.Arrays were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

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

data_processing: The data were calculated and normalized by R ver 3.6.1 using the MAS 5.0 algorithm.

label: biotin

source_name: Ba/F3, DOX(+)

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3' IVT PLUS Reagent Kit（Affymetrix) from total RNA according to the manufacturer's instructions. Biotinylated cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Extraction of total RNA was performed according to the protocol of the RNeasy Mini Kit (QIAGEN).

tag: genotype

value: expressing NCOR1-LYN


title: Genomic DNA from peripheral blood monoculear cells 165

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419048_R01C01_Grn.idat
location 1 (triplicate pair 1): 3998419048_R01C01_Red.idat
location 2 (triplicate pair 2): 3998419048_R01C02_Grn.idat
location 2 (triplicate pair 2): 3998419048_R01C02_Red.idat
location 3 (triplicate pair 3): 3998419076_R01C02_Grn.idat
location 3 (triplicate pair 3): 3998419076_R01C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 146

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419076_R03C01_Grn.idat
location 1 (triplicate pair 1): 3998419076_R03C01_Red.idat
location 2 (triplicate pair 2): 3998419078_R03C01_Grn.idat
location 2 (triplicate pair 2): 3998419078_R03C01_Red.idat
location 3 (triplicate pair 3): 3998419078_R03C02_Grn.idat
location 3 (triplicate pair 3): 3998419078_R03C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 113

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419077_R02C01_Grn.idat
location 1 (triplicate pair 1): 3998419077_R02C01_Red.idat
location 2 (triplicate pair 2): 3998419096_R02C01_Grn.idat
location 2 (triplicate pair 2): 3998419096_R02C01_Red.idat
location 3 (triplicate pair 3): 3998419096_R02C02_Grn.idat
location 3 (triplicate pair 3): 3998419096_R02C02_Red.idat


title: Ba/F3 cells, NCOR1-LYN(+), rep2


title: Genomic DNA from peripheral blood monoculear cells 132

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419077_R05C01_Grn.idat
location 1 (triplicate pair 1): 3998419077_R05C01_Red.idat
location 2 (triplicate pair 2): 3998419096_R05C01_Grn.idat
location 2 (triplicate pair 2): 3998419096_R05C01_Red.idat
location 3 (triplicate pair 3): 3998419096_R05C02_Grn.idat
location 3 (triplicate pair 3): 3998419096_R05C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 116

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250001_R06C01_Grn.idat
location 1 (triplicate pair 1): 200491250001_R06C01_Red.idat
location 2 (triplicate pair 2): 200491250023_R03C01_Grn.idat
location 2 (triplicate pair 2): 200491250023_R03C01_Red.idat
location 3 (triplicate pair 3): 200491250023_R06C01_Grn.idat
location 3 (triplicate pair 3): 200491250023_R06C01_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 117

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419077_R03C01_Grn.idat
location 1 (triplicate pair 1): 3998419077_R03C01_Red.idat
location 2 (triplicate pair 2): 3998419096_R03C01_Grn.idat
location 2 (triplicate pair 2): 3998419096_R03C01_Red.idat
location 3 (triplicate pair 3): 3998419096_R03C02_Grn.idat
location 3 (triplicate pair 3): 3998419096_R03C02_Red.idat


title: Ba/F3 cells, NCOR1-LYN(+), rep1


title: Ba/F3 cells, NCOR1-LYN(-), rep3

source_name: Ba/F3, DOX(-)

value: control


title: Donor 2_TGFbeta_4h


title: Genomic DNA from peripheral blood monoculear cells 140

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250001_R04C02_Grn.idat
location 1 (triplicate pair 1): 200491250001_R04C02_Red.idat
location 2 (triplicate pair 2): 200491250023_R01C02_Grn.idat
location 2 (triplicate pair 2): 200491250023_R01C02_Red.idat
location 3 (triplicate pair 3): 200491250023_R04C02_Grn.idat
location 3 (triplicate pair 3): 200491250023_R04C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 102

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250001_R01C02_Grn.idat
location 1 (triplicate pair 1): 200491250001_R01C02_Red.idat
location 2 (triplicate pair 2): 200491250018_R01C02_Grn.idat
location 2 (triplicate pair 2): 200491250018_R01C02_Red.idat
location 3 (triplicate pair 3): 200491250018_R04C02_Grn.idat
location 3 (triplicate pair 3): 200491250018_R04C02_Red.idat

value: AA


title: Donor 2_Untreated_4h


title: Genomic DNA from peripheral blood monoculear cells 115

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250001_R05C01_Grn.idat
location 1 (triplicate pair 1): 200491250001_R05C01_Red.idat
location 2 (triplicate pair 2): 200491250023_R02C01_Grn.idat
location 2 (triplicate pair 2): 200491250023_R02C01_Red.idat
location 3 (triplicate pair 3): 200491250023_R05C01_Grn.idat
location 3 (triplicate pair 3): 200491250023_R05C01_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 87

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250001_R01C01_Grn.idat
location 1 (triplicate pair 1): 200491250001_R01C01_Red.idat
location 2 (triplicate pair 2): 200491250018_R01C01_Grn.idat
location 2 (triplicate pair 2): 200491250018_R01C01_Red.idat
location 3 (triplicate pair 3): 200491250018_R04C01_Grn.idat
location 3 (triplicate pair 3): 200491250018_R04C01_Red.idat

value: Lupus


title: Ba/F3 cells, NCOR1-LYN(-), rep2


title: Donor 1_TGFbeta_36h

value: Donor 1


title: Genomic DNA from peripheral blood monoculear cells 99

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419077_R04C02_Grn.idat
location 1 (triplicate pair 1): 3998419077_R04C02_Red.idat
location 2 (triplicate pair 2): 3998419094_R04C01_Grn.idat
location 2 (triplicate pair 2): 3998419094_R04C01_Red.idat
location 3 (triplicate pair 3): 3998419094_R04C02_Grn.idat
location 3 (triplicate pair 3): 3998419094_R04C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 107

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419077_R06C02_Grn.idat
location 1 (triplicate pair 1): 3998419077_R06C02_Red.idat
location 2 (triplicate pair 2): 3998419094_R06C01_Grn.idat
location 2 (triplicate pair 2): 3998419094_R06C01_Red.idat
location 3 (triplicate pair 3): 3998419094_R06C02_Grn.idat
location 3 (triplicate pair 3): 3998419094_R06C02_Red.idat

value: EA


title: Genomic DNA from peripheral blood monoculear cells 108

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250001_R03C02_Grn.idat
location 1 (triplicate pair 1): 200491250001_R03C02_Red.idat
location 2 (triplicate pair 2): 200491250018_R03C02_Grn.idat
location 2 (triplicate pair 2): 200491250018_R03C02_Red.idat
location 3 (triplicate pair 3): 200491250018_R06C02_Grn.idat
location 3 (triplicate pair 3): 200491250018_R06C02_Red.idat


title: Donor 1_Untreated_36h

value: CD14+ human immature myeloid cells


title: Genomic DNA from peripheral blood monoculear cells 81

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419077_R03C02_Grn.idat
location 1 (triplicate pair 1): 3998419077_R03C02_Red.idat
location 2 (triplicate pair 2): 3998419094_R03C01_Grn.idat
location 2 (triplicate pair 2): 3998419094_R03C01_Red.idat
location 3 (triplicate pair 3): 3998419094_R03C02_Grn.idat
location 3 (triplicate pair 3): 3998419094_R03C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 128

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419077_R04C01_Grn.idat
location 1 (triplicate pair 1): 3998419077_R04C01_Red.idat
location 2 (triplicate pair 2): 3998419096_R04C01_Grn.idat
location 2 (triplicate pair 2): 3998419096_R04C01_Red.idat
location 3 (triplicate pair 3): 3998419096_R04C02_Grn.idat
location 3 (triplicate pair 3): 3998419096_R04C02_Red.idat


title: WT4

city: yokohama

first: Ryota

last: Inoue

address: Fukuura 3-9, Kanazawa-ku

department: Endcriology and Metabolism

institute: Yokohama City University

hyb_protocol: Cy3-labelled cRNA was fragmented by using Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Gene Expression Microarrays (G4858A) in a rotating Agilent hybridization oven. After hybridization, microarrays were washed with GE Wash Buffer 1 (Agilent) and GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters.
The microarray intensities ([WT](raw) and [Tg](raw)) were processed by the percentile shift method (75th percentile) using the GeneSpring GX12.5 (Agilent Technologies) to normalize the range of expression intensities

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

extract_protocol: total RNA was prepared using the Rneasy total RNA extraction kit (QIAGEN) following the manufacturer's recommendations.

treatment_protocol: Isolated islets from βUCP2Tg mice or WT mice were incubated  in RPMI 1640 supplemented with 200 mg/dL glucose, 10% FBS, 1% penicilin/streptmycin.The cultures were incubated for 8 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: gender

value: male

tag: tissue

value: islets


title: Donor 1_TGFbeta_12h

value: Treated with TGF-beta

value: 12 hours


title: Donor 2_Untreated_8h

value: Un-treated


title: Genomic DNA from peripheral blood monoculear cells 109

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250001_R04C01_Grn.idat
location 1 (triplicate pair 1): 200491250001_R04C01_Red.idat
location 2 (triplicate pair 2): 200491250023_R01C01_Grn.idat
location 2 (triplicate pair 2): 200491250023_R01C01_Red.idat
location 3 (triplicate pair 3): 200491250023_R04C01_Grn.idat
location 3 (triplicate pair 3): 200491250023_R04C01_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 96

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250001_R03C01_Grn.idat
location 1 (triplicate pair 1): 200491250001_R03C01_Red.idat
location 2 (triplicate pair 2): 200491250018_R03C01_Grn.idat
location 2 (triplicate pair 2): 200491250018_R03C01_Red.idat
location 3 (triplicate pair 3): 200491250018_R06C01_Grn.idat
location 3 (triplicate pair 3): 200491250018_R06C01_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 72

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419077_R01C02_Grn.idat
location 1 (triplicate pair 1): 3998419077_R01C02_Red.idat
location 2 (triplicate pair 2): 3998419094_R01C01_Grn.idat
location 2 (triplicate pair 2): 3998419094_R01C01_Red.idat
location 3 (triplicate pair 3): 3998419094_R01C02_Grn.idat
location 3 (triplicate pair 3): 3998419094_R01C02_Red.idat


title: Donor 1_Untreated_12h


title: WT3


title: Genomic DNA from peripheral blood monoculear cells 105

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250001_R02C02_Grn.idat
location 1 (triplicate pair 1): 200491250001_R02C02_Red.idat
location 2 (triplicate pair 2): 200491250018_R02C02_Grn.idat
location 2 (triplicate pair 2): 200491250018_R02C02_Red.idat
location 3 (triplicate pair 3): 200491250018_R05C02_Grn.idat
location 3 (triplicate pair 3): 200491250018_R05C02_Red.idat


title: Donor 1_TGFbeta_8h

value: 8 hours


title: Ba/F3 cells, NCOR1-LYN(-), rep1


title: Genomic DNA from peripheral blood monoculear cells 80

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250013_R06C02_Grn.idat
location 1 (triplicate pair 1): 200491250013_R06C02_Red.idat
location 2 (triplicate pair 2): 200491250032_R03C02_Grn.idat
location 2 (triplicate pair 2): 200491250032_R03C02_Red.idat
location 3 (triplicate pair 3): 200491250032_R06C02_Grn.idat
location 3 (triplicate pair 3): 200491250032_R06C02_Red.idat


title: Donor 1_Untreated_8h


title: Genomic DNA from peripheral blood monoculear cells 76

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419077_R02C02_Grn.idat
location 1 (triplicate pair 1): 3998419077_R02C02_Red.idat
location 2 (triplicate pair 2): 3998419094_R02C01_Grn.idat
location 2 (triplicate pair 2): 3998419094_R02C01_Red.idat
location 3 (triplicate pair 3): 3998419094_R02C02_Grn.idat
location 3 (triplicate pair 3): 3998419094_R02C02_Red.idat


title: Donor 1_TGFbeta_4h

value: 4 hours


title: Genomic DNA from peripheral blood monoculear cells 66

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250013_R05C02_Grn.idat
location 1 (triplicate pair 1): 200491250013_R05C02_Red.idat
location 2 (triplicate pair 2): 200491250032_R02C02_Grn.idat
location 2 (triplicate pair 2): 200491250032_R02C02_Red.idat
location 3 (triplicate pair 3): 200491250032_R05C02_Grn.idat
location 3 (triplicate pair 3): 200491250032_R05C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 62

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419054_R05C01_Grn.idat
location 1 (triplicate pair 1): 3998419054_R05C01_Red.idat
location 2 (triplicate pair 2): 3998419054_R05C02_Grn.idat
location 2 (triplicate pair 2): 3998419054_R05C02_Red.idat
location 3 (triplicate pair 3): 3998419064_R05C02_Grn.idat
location 3 (triplicate pair 3): 3998419064_R05C02_Red.idat


title: Donor 1_Untreated_4h


title: WT1


title: βUCP2Tg4


title: Genomic DNA from peripheral blood monoculear cells 95

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250001_R02C01_Grn.idat
location 1 (triplicate pair 1): 200491250001_R02C01_Red.idat
location 2 (triplicate pair 2): 200491250018_R02C01_Grn.idat
location 2 (triplicate pair 2): 200491250018_R02C01_Red.idat
location 3 (triplicate pair 3): 200491250018_R05C01_Grn.idat
location 3 (triplicate pair 3): 200491250018_R05C01_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 61

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250013_R05C01_Grn.idat
location 1 (triplicate pair 1): 200491250013_R05C01_Red.idat
location 2 (triplicate pair 2): 200491250032_R02C01_Grn.idat
location 2 (triplicate pair 2): 200491250032_R02C01_Red.idat
location 3 (triplicate pair 3): 200491250032_R05C01_Grn.idat
location 3 (triplicate pair 3): 200491250032_R05C01_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 63

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250013_R06C01_Grn.idat
location 1 (triplicate pair 1): 200491250013_R06C01_Red.idat
location 2 (triplicate pair 2): 200491250032_R03C01_Grn.idat
location 2 (triplicate pair 2): 200491250032_R03C01_Red.idat
location 3 (triplicate pair 3): 200491250032_R06C01_Grn.idat
location 3 (triplicate pair 3): 200491250032_R06C01_Red.idat


title: WT2


title: Genomic DNA from peripheral blood monoculear cells 59

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419054_R04C01_Grn.idat
location 1 (triplicate pair 1): 3998419054_R04C01_Red.idat
location 2 (triplicate pair 2): 3998419054_R04C02_Grn.idat
location 2 (triplicate pair 2): 3998419054_R04C02_Red.idat
location 3 (triplicate pair 3): 3998419064_R04C02_Grn.idat
location 3 (triplicate pair 3): 3998419064_R04C02_Red.idat


title: ST258-KPC3CA_3

city: A Coruña

first: Maria

last: Tomas-Carmona

address: As Xubias, 84

department: Microbiology Department

country: Spain

institute: Instituto de Investigación Biomédica de A Coruña (INIBIC) / Complexo Hospitalario Universitario de A Coruña (CHUAC)

data_processing:
Sequencing was carried out by emulsion PCR with Ion Spheres Particules (IPs). The enrichment of the library carrying IPs and the subsequent loading of the chip was developed in the Ion Chef automated system using the Ion PI Hi-Q Chef Kit (Reference A27198, Thermo Fisher Scientific) and an Ion PI chips v3 (reference A26771, Thermo Fisher Scientific). Chip analysis was carried out on the Ion Proton sequencer (reference 4476610, Thermo Fisher Scientific).
The generated data was analyzed using the specific software of the Torrent Suite 5.6.2 platform (Thermo Fisher Scientific).
The resulting readings (approx. 60 million) were exported in a FASTQ file using the FileExporter 4.6.0.0 (Thermo Fisher Scientific) plugin.
The alignment of the sequences against their respective controls was performed with the STAR software.
Subsequently, the aligned readings were counted using the htseq-count software (HTSeq 0.6.1.p2).The data was normalized using DESeq2.
Genome_build: PRJNA609262

organism: Klebsiella pneumoniae

growth_protocol: The strain were growth in Luria-Bertani medium until exponential growth phase culture (optical density of 0.5 at 600 nm).

extract_protocol:
After RNA extraction, rRNA and tRNA were removed using the Ribo-Zero rRNA removal kits (Bacteria) (reference MRZMB126, Illumina). The rRNA depletion was checked using Agilent RNA ScreenTape Assay (TapeStation 4200 Agilent) and the RNA was quantified by QubitTM RNA HS Assay Kit (reference Q32852, Thermo Fisher Scientific).
The transcriptome libraries were performed using the Ion Total kit RNAseq Kit V2 (reference 4475936, Thermo Fisher Scientific) in combination with the bar codes Ion Xpress TM RNA-Seq Barcode 01-16 Kit (reference 4475485, Thermo Fisher Scientific).

treatment_protocol: Four replicates of each strains (ST258-KPC3 and ST846-OXA48) were exposed to 1/4 of minimum inhibitory concentration (MIC) to chlorhexidine.

value: Adapted chlorhexidine (CA)

tag: run


title: βUCP2Tg1


title: Genomic DNA from peripheral blood monoculear cells 53

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419045_R05C01_Grn.idat
location 1 (triplicate pair 1): 3998419045_R05C01_Red.idat
location 2 (triplicate pair 2): 3998419045_R05C02_Grn.idat
location 2 (triplicate pair 2): 3998419045_R05C02_Red.idat
location 3 (triplicate pair 3): 3998419064_R05C01_Grn.idat
location 3 (triplicate pair 3): 3998419064_R05C01_Red.idat


title: MspI_reference_E10

source_name: E14 cells

value: embryonic stem cells

value: In vitro differentiated for 10days


title: ST258-KPC3CA_2


title: βUCP2Tg3


title: Genomic DNA from peripheral blood monoculear cells 58

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419054_R03C01_Grn.idat
location 1 (triplicate pair 1): 3998419054_R03C01_Red.idat
location 2 (triplicate pair 2): 3998419054_R03C02_Grn.idat
location 2 (triplicate pair 2): 3998419054_R03C02_Red.idat
location 3 (triplicate pair 3): 3998419064_R03C02_Grn.idat
location 3 (triplicate pair 3): 3998419064_R03C02_Red.idat

value: Non-lupus


title: Genomic DNA from peripheral blood monoculear cells 39

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419047_R06C02_Grn.idat
location 1 (triplicate pair 1): 3998419047_R06C02_Red.idat
location 2 (triplicate pair 2): 3998419064_R04C01_Grn.idat
location 2 (triplicate pair 2): 3998419064_R04C01_Red.idat
location 3 (triplicate pair 3): 3998419089_R06C02_Grn.idat
location 3 (triplicate pair 3): 3998419089_R06C02_Red.idat


title: Tsc2flox/flox + Rapamycin_03

city: Shinjuku-ku, Tokyo

first: Hiroyuki

last: Unoki-Kubota

address: 1-21-1 Toyama

department: Department of Diabetic Complications, Diabetes Research Center, Research Institute

institute: National Center for Global Health and Medicine

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

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 μm, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software version 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by 75 percentile shift normalization method.

source_name: Primary podocytes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Glomeruli of Tsc2Δpodocyte and control mice were isolated by magnetic bead-isolation. Isolated glomeruli were cultured on type I collagen-coated multiwell plate dishes (AGC Techno Glass Co. Ltd., Shizuoka, Japan) in RPMI 1640 (Wako Pure Chemical Industries, Ltd.) containing 10 % fetal bovine serum (GE healthcare, Chicago, IL) supplemented with 100 U/ml penicillin, and 100 μg/ml streptomycin (Thermo Fisher Scientific) at 37°C humidified incubator with 5% CO2.

extract_protocol: Total RNA was isolated using RNeasy Mini kit (Qiagen, Hilden, Germany), and was quantified using a NanoDrop-1000 spectrophotometer. RNA quality and integrity were assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Kidney

value: podocytes

value: Male

value: 5 week-old (1 week after rapamycin treatment)


title: βUCP2Tg2


title: ST258-KPC3CA_1


title: MspI_reference_E0

value: Stem condition


title: Genomic DNA from peripheral blood monoculear cells 48

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419045_R03C01_Grn.idat
location 1 (triplicate pair 1): 3998419045_R03C01_Red.idat
location 2 (triplicate pair 2): 3998419045_R03C02_Grn.idat
location 2 (triplicate pair 2): 3998419045_R03C02_Red.idat
location 3 (triplicate pair 3): 3998419047_R05C01_Grn.idat
location 3 (triplicate pair 3): 3998419047_R05C01_Red.idat

value: EA

value: Lupus


title: Genomic DNA from peripheral blood monoculear cells 30

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419047_R04C02_Grn.idat
location 1 (triplicate pair 1): 3998419047_R04C02_Red.idat
location 2 (triplicate pair 2): 3998419064_R02C01_Grn.idat
location 2 (triplicate pair 2): 3998419064_R02C01_Red.idat
location 3 (triplicate pair 3): 3998419089_R04C02_Grn.idat
location 3 (triplicate pair 3): 3998419089_R04C02_Red.idat

value: AA


title: Genomic DNA from peripheral blood monoculear cells 65

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250013_R04C01_Grn.idat
location 1 (triplicate pair 1): 200491250013_R04C01_Red.idat
location 2 (triplicate pair 2): 200491250032_R01C01_Grn.idat
location 2 (triplicate pair 2): 200491250032_R01C01_Red.idat
location 3 (triplicate pair 3): 200491250032_R04C01_Grn.idat
location 3 (triplicate pair 3): 200491250032_R04C01_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 52

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250013_R04C02_Grn.idat
location 1 (triplicate pair 1): 200491250013_R04C02_Red.idat
location 2 (triplicate pair 2): 200491250032_R01C02_Grn.idat
location 2 (triplicate pair 2): 200491250032_R01C02_Red.idat
location 3 (triplicate pair 3): 200491250032_R04C02_Grn.idat
location 3 (triplicate pair 3): 200491250032_R04C02_Red.idat


title: UM-UC-3_NONO-si2

city: Guangzhou

first: Ruihui

last: Xie

state: Guangdong

address: 107 Yan Jiang West Road

country: China

institute: Sun Yat-sen Memorial Hospital, SYSU

description:
siRNA targeting NONO was transfected in the cell.
GCAUCCCUUACAGUUCGAATT

data_processing:
Base-calling: bcl2fastq2 v2.19.1
Data filtering : in house
Read alignment: hisat2 v2.1.0
Transcript assemble: htseq-count v0.6.1
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *xlsx: Excel files include normalized values for each Sample.

source_name: bladder cancer cell line UM-UC-3

growth_protocol: UM-UC-3 was cultured in DMEM (Gibco) supplemented with 10% FBS (Shanghai ExCell Biology, China) and 1% penicillin/streptomycin (Gibco). Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufacturer's instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: siRNA transfections were done with 75 nM siRNA and Lipofectamine RNAimax (Life Technologies) following manufacturer's instructions.

value: Bladder cancer cell line

tag: sirna

value: NONO


title: Genomic DNA from peripheral blood monoculear cells 57

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419054_R02C01_Grn.idat
location 1 (triplicate pair 1): 3998419054_R02C01_Red.idat
location 2 (triplicate pair 2): 3998419054_R02C02_Grn.idat
location 2 (triplicate pair 2): 3998419054_R02C02_Red.idat
location 3 (triplicate pair 3): 3998419064_R02C02_Grn.idat
location 3 (triplicate pair 3): 3998419064_R02C02_Red.idat


title: ST258-KPC3_4

value: Control


title: Tsc2flox/flox + Rapamycin_02


title: Genomic DNA from peripheral blood monoculear cells 51

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419045_R04C01_Grn.idat
location 1 (triplicate pair 1): 3998419045_R04C01_Red.idat
location 2 (triplicate pair 2): 3998419045_R04C02_Grn.idat
location 2 (triplicate pair 2): 3998419045_R04C02_Red.idat
location 3 (triplicate pair 3): 3998419047_R06C01_Grn.idat
location 3 (triplicate pair 3): 3998419047_R06C01_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 43

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419045_R02C01_Grn.idat
location 1 (triplicate pair 1): 3998419045_R02C01_Red.idat
location 2 (triplicate pair 2): 3998419045_R02C02_Grn.idat
location 2 (triplicate pair 2): 3998419045_R02C02_Red.idat
location 3 (triplicate pair 3): 3998419047_R04C01_Grn.idat
location 3 (triplicate pair 3): 3998419047_R04C01_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 40

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419045_R01C01_Grn.idat
location 1 (triplicate pair 1): 3998419045_R01C01_Red.idat
location 2 (triplicate pair 2): 3998419045_R01C02_Grn.idat
location 2 (triplicate pair 2): 3998419045_R01C02_Red.idat
location 3 (triplicate pair 3): 3998419047_R03C01_Grn.idat
location 3 (triplicate pair 3): 3998419047_R03C01_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 32

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419047_R05C02_Grn.idat
location 1 (triplicate pair 1): 3998419047_R05C02_Red.idat
location 2 (triplicate pair 2): 3998419064_R03C01_Grn.idat
location 2 (triplicate pair 2): 3998419064_R03C01_Red.idat
location 3 (triplicate pair 3): 3998419089_R05C02_Grn.idat
location 3 (triplicate pair 3): 3998419089_R05C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 50

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250013_R03C02_Grn.idat
location 1 (triplicate pair 1): 200491250013_R03C02_Red.idat
location 2 (triplicate pair 2): 200491250029_R03C02_Grn.idat
location 2 (triplicate pair 2): 200491250029_R03C02_Red.idat
location 3 (triplicate pair 3): 200491250029_R06C02_Grn.idat
location 3 (triplicate pair 3): 200491250029_R06C02_Red.idat


title: ST258-KPC3_3


title: UM-UC-3_Control

description:
Control siRNA was transfected in the cell.
UUCUCCGAACGUGUCACGUTT

value: Negative control


title: Tsc2flox/flox + Rapamycin_01


title: Genomic DNA from peripheral blood monoculear cells 24

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419047_R02C01_Grn.idat
location 1 (triplicate pair 1): 3998419047_R02C01_Red.idat
location 2 (triplicate pair 2): 3998419047_R02C02_Grn.idat
location 2 (triplicate pair 2): 3998419047_R02C02_Red.idat
location 3 (triplicate pair 3): 3998419089_R02C02_Grn.idat
location 3 (triplicate pair 3): 3998419089_R02C02_Red.idat


title: ST258-KPC3_2


title: P154_Vehicle

city: Baltimore

first: Matthew

middle: D

last: Smith

state: MD

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University

data_processing:
Reads aligning to human ribosoma RNA transcripts were removed with BBSplit
Remaining reads were pseudoaligned against human transcriptome using Salmon v1.1.0
Quantified transcripts were combined into gene level counts with tximport_1.12.3
Differential expression analysis was performed with DESeq2_1.24.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon quant files containing transcript level counts for each sample

source_name: iPSC

growth_protocol: iPSC derived OPCs were sorted on PDGFRa+ and then replated, allowed to proliferate prior to being treated

extract_protocol:
Media was aspirated, cells were washed, then cells were lysed and RNA purified using QIAGEN RNeasy Protocol with gDNA removal column
libraries were generated with Illumina TruSeq Stranded Total RNA LT Sample Prep

treatment_protocol: Cells were treated overnight with either vehicle or human IFNg (10ng/ml)

tag: participant

value: HC

value: iPSC derived OPCs

value: Vehicle

tag: batch


title: UM-UC-3_NONO-si1

description:
siRNA targeting NONO was transfected in the cell.
GGCGAAGUCUUCAUUCAUATT

tag: cell line

tag: cell type


title: ST258-KPC3_1

tag: strain

tag: treatment


title: P154_IFNg

value: IFNg


title: ST846-OXA48CA_4

value: Adapted chlorhexidine (CA)


title: Genomic DNA from peripheral blood monoculear cells 17

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419003_R05C01_Grn.idat
location 1 (triplicate pair 1): 3998419003_R05C01_Red.idat
location 2 (triplicate pair 2): 3998419003_R05C02_Grn.idat
location 2 (triplicate pair 2): 3998419003_R05C02_Red.idat
location 3 (triplicate pair 3): 3998419089_R05C01_Grn.idat
location 3 (triplicate pair 3): 3998419089_R05C01_Red.idat

tag: ethnicity

tag: disease state


title: Tsc2Δpodocyte + Rapamycin_04

value: Kidney

tag: age


title: Genomic DNA from peripheral blood monoculear cells 20

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419047_R01C01_Grn.idat
location 1 (triplicate pair 1): 3998419047_R01C01_Red.idat
location 2 (triplicate pair 2): 3998419047_R01C02_Grn.idat
location 2 (triplicate pair 2): 3998419047_R01C02_Red.idat
location 3 (triplicate pair 3): 3998419089_R01C02_Grn.idat
location 3 (triplicate pair 3): 3998419089_R01C02_Red.idat

tag: sledai score


title: Genomic DNA from peripheral blood monoculear cells 19

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250013_R01C02_Grn.idat
location 1 (triplicate pair 1): 200491250013_R01C02_Red.idat
location 2 (triplicate pair 2): 200491250029_R01C02_Grn.idat
location 2 (triplicate pair 2): 200491250029_R01C02_Red.idat
location 3 (triplicate pair 3): 200491250029_R04C02_Grn.idat
location 3 (triplicate pair 3): 200491250029_R04C02_Red.idat


title: P152_Vehicle


title: Genomic DNA from peripheral blood monoculear cells 38

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250013_R02C02_Grn.idat
location 1 (triplicate pair 1): 200491250013_R02C02_Red.idat
location 2 (triplicate pair 2): 200491250029_R02C02_Grn.idat
location 2 (triplicate pair 2): 200491250029_R02C02_Red.idat
location 3 (triplicate pair 3): 200491250029_R05C02_Grn.idat
location 3 (triplicate pair 3): 200491250029_R05C02_Red.idat


title: ST846-OXA48CA_2


title: P152_IFNg


title: Tsc2Δpodocyte + Rapamycin_03

value: podocytes


title: ST846-OXA48CA_3


title: KW05_Vehicle

value: MS


title: ST258-KPC3CA_4


title: SSC IP

city: Yangzhou

first: Chen

last: Zhang

address: wenhui road

institute: Yangzhou university

description: genomic DNA

data_processing:
Basecalls performed using CASAVA version 1.8
FastQC software for basic quality statistics on raw reads
Using BWA (Burrows Wheeler Aligner), reads can be aligned to the galgal4 genome (Li, H. and R. Durbin, 2009).
Data were filtered using the skewer 0.1.126
Use MACS2 software (Yong Zhang, Tao Liu et al., 2008) (threshold value is pvalue <= 0.005) to complete peak calling analysis, and count the number, width and distribution of peaks
Peak Annotator test for TSS (transcription start site) of each peak-related gene (SalmonDivon and Dvinge et al., 2010). Count the number of peaks based on the distance between peak and TSS sites, and analyze the distance distribution between peak and gene TSS sites .
Genome_build: galgal4
Supplementary_files_format_and_content: peaks file

organism: Gallus gallus

source_name: Spermatogonial stem cells

growth_protocol: The blastoderm cells of the embryonic region of the X-stage fertilized eggs are used to isolate ESC. The isolated blastoderm cells were cultured in DMEM containing 10% FBS, 1000IU/ml LIF, 10ng/ml bFGF and 5ng/ml SCF at 37°C, and 5% CO2 saturated humidity for 24 hours, and then subjected to differential purification of ESC.  Fertilized eggs incubated for 4.5 days were harvested to obtain genital ridges for isolation of PGC. Chicken embryo gneital warts were digested with 0.25% trypsin and 0.05% EDTA for 5-10 minutes. Cells were filtered and differentially cultured in DMEM medium containing 10% FBS for 40 minutes.  Fertilized eggs hatched to 18.5 days were harvested to obtain testes for the isolation of SSC. The testis tissue was digested with collagenase for 30 minutes, and then with trypsin. Cells were cultured in DMEM containing 10% FBS at 37°C and 5% CO2 saturated humidity.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Testis

value: Spermatogonial stem cells

tag: developmental stage

value: Mouse Anti-Histone H3 (di methyl K4, tri methyl K4) antibody [mAbcam 6000] - ChIP Grade (ab6000)


title: Tsc2flox/flox_03

value: Male

value: 4 week-old


title: KW05_IFNg


title: PGC Input

description: genomic DNA

source_name: Primordial germ cells

value: Gonads

value: Primordial germ cells

value: 72 h (stage 27)

tag: chip antibody


title: ST846-OXA48_4

value: Control


title: Tsc2flox/flox + Rapamycin_04

value: 5 week-old (1 week after rapamycin treatment)


title: SSC Input

description: genomic DNA


title: Tsc2flox/flox_04


title: KW04_Vehicle

value: iPSC derived OPCs


title: ST846-OXA48_3


title: Tsc2flox/flox_02


title: ST846-OXA48CA_1


title: Genomic DNA from peripheral blood monoculear cells 14

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250013_R03C01_Grn.idat
location 1 (triplicate pair 1): 200491250013_R03C01_Red.idat
location 2 (triplicate pair 2): 200491250029_R03C01_Grn.idat
location 2 (triplicate pair 2): 200491250029_R03C01_Red.idat
location 3 (triplicate pair 3): 200491250029_R06C01_Grn.idat
location 3 (triplicate pair 3): 200491250029_R06C01_Red.idat

value: AA

value: Lupus


title: ST846-OXA48_2


title: KW04_IFNg

value: IFNg


title: Genomic DNA from peripheral blood monoculear cells 13

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419003_R03C01_Grn.idat
location 1 (triplicate pair 1): 3998419003_R03C01_Red.idat
location 2 (triplicate pair 2): 3998419003_R03C02_Grn.idat
location 2 (triplicate pair 2): 3998419003_R03C02_Red.idat
location 3 (triplicate pair 3): 3998419089_R03C01_Grn.idat
location 3 (triplicate pair 3): 3998419089_R03C01_Red.idat

value: Non-lupus


title: PGC IP

description: genomic DNA


title: Genomic DNA from peripheral blood monoculear cells 12

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250013_R02C01_Grn.idat
location 1 (triplicate pair 1): 200491250013_R02C01_Red.idat
location 2 (triplicate pair 2): 200491250029_R02C01_Grn.idat
location 2 (triplicate pair 2): 200491250029_R02C01_Red.idat
location 3 (triplicate pair 3): 200491250029_R05C01_Grn.idat
location 3 (triplicate pair 3): 200491250029_R05C01_Red.idat

value: EA


title: ESC Input

description: genomic DNA

source_name: Embryonic stem cells

value: Embryo disk

value: Embryonic stem cells

value: stage X


title: Tsc2Δpodocyte_04

value: Kidney

value: podocytes


title: Genomic DNA from peripheral blood monoculear cells 5

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200491250013_R01C01_Grn.idat
location 1 (triplicate pair 1): 200491250013_R01C01_Red.idat
location 2 (triplicate pair 2): 200491250029_R01C01_Grn.idat
location 2 (triplicate pair 2): 200491250029_R01C01_Red.idat
location 3 (triplicate pair 3): 200491250029_R04C01_Grn.idat
location 3 (triplicate pair 3): 200491250029_R04C01_Red.idat


title: Tsc2Δpodocyte_03

value: Male

value: 4 week-old


title: KW03_IFNg

value: MS


title: Genomic DNA from peripheral blood monoculear cells 18

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419003_R06C01_Grn.idat
location 1 (triplicate pair 1): 3998419003_R06C01_Red.idat
location 2 (triplicate pair 2): 3998419003_R06C02_Grn.idat
location 2 (triplicate pair 2): 3998419003_R06C02_Red.idat
location 3 (triplicate pair 3): 3998419089_R06C01_Grn.idat
location 3 (triplicate pair 3): 3998419089_R06C01_Red.idat


title: Tsc2Δpodocyte_02


title: Genomic DNA from peripheral blood monoculear cells 16

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419003_R04C01_Grn.idat
location 1 (triplicate pair 1): 3998419003_R04C01_Red.idat
location 2 (triplicate pair 2): 3998419003_R04C02_Grn.idat
location 2 (triplicate pair 2): 3998419003_R04C02_Red.idat
location 3 (triplicate pair 3): 3998419089_R04C01_Grn.idat
location 3 (triplicate pair 3): 3998419089_R04C01_Red.idat


title: KW03_Vehicle

value: Vehicle


title: Tsc2Δpodocyte + Rapamycin_02


title: ST846-OXA48_1

value: Control


title: Tsc2flox/flox_01


title: Tsc2Δpodocyte_01


title: U251_RC_rep3

status: Public on Mar 20 2020

city: Bethesda

first: Chunzhang

last: Yang

state: Maryland

address: 37 Convent Dr.

department: NOB

institute: NCI

description:
Sequencing instrument used was unknown.  Illumina HiSeq 2500 was listed as a likely option.
U251_RC_3
X1005.Gilbert.6.star.count.txt

data_processing:
Data was processed using ccbrpipeliner: https://github.com/CCBR/Pipeliner
EdgeR was used to define DEG with thresholds FDR < 0.05 and FC > 1.5
IPA was used for functional analysis
Genome_build: hg19
Supplementary_files_format_and_content: CPM TMM counts

source_name: U251 glioma cell line with R132C mutation

extract_protocol: Total RNA was extracted using a QIAGEN RNeasy mini kit.

value: glioma

tag: genotype

value: IDH1 R132C


title: U251_RC_rep2

description:
Sequencing instrument used was unknown.  Illumina HiSeq 2500 was listed as a likely option.
U251_RC_2
X1005.Gilbert.5.star.count.txt


title: Genomic DNA from peripheral blood monoculear cells 1

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419003_R01C01_Grn.idat
location 1 (triplicate pair 1): 3998419003_R01C01_Red.idat
location 2 (triplicate pair 2): 3998419003_R01C02_Grn.idat
location 2 (triplicate pair 2): 3998419003_R01C02_Red.idat
location 3 (triplicate pair 3): 3998419089_R01C01_Grn.idat
location 3 (triplicate pair 3): 3998419089_R01C01_Red.idat

value: AA


title: U251_RC_rep1

description:
Sequencing instrument used was unknown.  Illumina HiSeq 2500 was listed as a likely option.
U251_RC_1
X1005.Gilbert.4.star.count.txt


title: midgut glucose rep2

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 114 ST and 87 AVE

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

description: Gene expression data from dissected midguts of flies raised on glucose-enriched (100 g/L) holidic food for 10 days.

hyb_protocol: 12 ug of cRNA was used for fragmentation, fragmented cRNA was hybridized on GeneChip®Drosophila Genome 2.0 Array, washed and stained according to the Affymetrix protocol (User Guide GeneChip® 3' IVT PLUS Reagent Kit, 2013-2015, Affymetrix).

scan_protocol: Affymetrix GeneChip 3000 7G Scanner

data_processing: The data were analyzed with Expression Console (Affymetrix) using default analysis settings.

organism: Drosophila melanogaster

source_name: midgut

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix GeneChip 3' IVT plus protocol from 100 ng total RNA (User Guide GeneChip® 3' IVT PLUS Reagent Kit, 2013-2015, Affymetrix).

growth_protocol: Flies were raised on standard cornmeal at 25˚C before eclosion.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. 5 whole flies or 10 dissected midguts were used per sample.

treatment_protocol: Adult female flies were raised on either unmodified or glucose-enriched (100 g/L) holidic food for 10 days at 25˚C.

value: midgut

value: 10 days old


title: U251_RH_rep3

description:
Sequencing instrument used was unknown.  Illumina HiSeq 2500 was listed as a likely option.
U251_RH_3
X1005.Gilbert.9.star.count.txt

source_name: U251 glioma cell line with R132H mutation

value: IDH1 R132H


title: whole fly unmodified rep2

description: Gene expression data from whole flies raised on unmodified holidic food for 10 days.

source_name: whole fly

value: whole fly


title: midgut unmodified rep1

description: Gene expression data from dissected midguts of flies raised on unmodified holidic food for 10 days.


title: U251_RH_rep2

description:
Sequencing instrument used was unknown.  Illumina HiSeq 2500 was listed as a likely option.
U251_RH_2
X1005.Gilbert.8.star.count.txt


title: midgut unmodified rep3


title: whole fly unmodified rep1


title: midgut glucose rep3


title: whole fly glucose rep1

description: Gene expression data from whole flies raised on glucose-enriched (100 g/L) holidic food for 10 days.


title: midgut unmodified rep2


title: U251_RH_rep1

description:
Sequencing instrument used was unknown.  Illumina HiSeq 2500 was listed as a likely option.
U251_RH_1
X1005.Gilbert.7.star.count.txt


title: ESC IP

description: genomic DNA

value: Embryo disk

value: Mouse Anti-Histone H3 (di methyl K4, tri methyl K4) antibody [mAbcam 6000] - ChIP Grade (ab6000)


title: Tsc2Δpodocyte + Rapamycin_01

tag: gender

value: 5 week-old (1 week after rapamycin treatment)


title: U251_WT_rep3

description:
Sequencing instrument used was unknown.  Illumina HiSeq 2500 was listed as a likely option.
U251_WT_3
X1005.Gilbert.3.star.count.txt

source_name: U251 glioma cell line

value: WT


title: midgut glucose rep1

tag: tissue


title: whole fly unmodified rep3


title: U251_WT_rep2

description:
Sequencing instrument used was unknown.  Illumina HiSeq 2500 was listed as a likely option.
U251_WT_2
X1005.Gilbert.2.star.count.txt


title: whole fly glucose rep3


title: whole fly glucose rep2


title: Blast cells, K700E 7

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 10900 Euclid Ave.

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Hisat2 (version 2.1.0):  Used to map reads to human genome GRCh38
bedtools:  Used to assemble transcripts
edgeR:  Used to identify differenentially expressed genes
Genome_build: GRCH38/hg38
Supplementary_files_format_and_content: tab-delimited text file includes normalized expression

source_name: Blast cell

extract_protocol:
RNA was extraced from purified blast cells using  RNeasy kits (Qiagen) column cleanup
RNAlibraries were prepared for sequencing using Clontech SMART-Seq v4 Ultra-low input RNA Kit 4.

value: myelodysplastic syndrome (MDS)

value: SF3B1 -K700E mutation

value: untreated

value: bone marrow blast cells


title: Blast cells, K700E 5


title: Blast cells, K700E 6


title: Blast cells, K700E 4


title: U251_WT_rep1

description:
Sequencing instrument used was unknown.  Illumina HiSeq 2500 was listed as a likely option.
U251_WT_1
X1005.Gilbert.1.star.count.txt


title: Genomic DNA from peripheral blood monoculear cells 29

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419047_R03C02_Grn.idat
location 1 (triplicate pair 1): 3998419047_R03C02_Red.idat
location 2 (triplicate pair 2): 3998419064_R01C01_Grn.idat
location 2 (triplicate pair 2): 3998419064_R01C01_Red.idat
location 3 (triplicate pair 3): 3998419089_R03C02_Grn.idat
location 3 (triplicate pair 3): 3998419089_R03C02_Red.idat

source_name: Blood

value: EA

value: Non-lupus


title: Blast cells, WT 3


title: Blast cells, WT 2


title: Blast cells, WT 1


title: 2094G4BFR-M1

city: Monrovia

first: Claude

middle: J

last: Rogers

address: 1225 S. Shamrock Ave.

institute: ChromoLogic

data_processing:
Demultiplexing performed in Basespace using FASTQ Generation v1.0.0
Timming performed in Basespace using FASTQ Toolkit v2.2.0 and the following settings: minimal read length = 18; Adaptor sequence to trim from the 3’-end: AACTGTAGGCACCATCAAT; trim bases at the 5’-end with a quality score less than 30; maximum read length = 40; minimum read score = 20
miRNA alignment performed in Basespace using Small RNA v1.0.1 and “Mus musculus/mm10” as species
Sequence runs with less than 100,000 miRNA reads or less than 25% identified mature miRNA content were rejected
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts for the indicated miRNA (rows) and sample (columns) in csv format

source_name: Plasma

extract_protocol:
Circulating miRNA was isolated from 25 µL of plasma using the miRCIRY RNA Isolation Kit (Biofluids; Exiqon).
Libraries for sequencing were prepared using the QIAseq miRNA Library Kit; (Qiagen) with 5.8 µL of miRNA extracts as input, a 1:5 dilution of the 3’-adaptor, a 1:2.5 dilution of the 5’-adaptor, a 1:5 dilution of the RT primer, and 22 amplification cycles. The concentrations of the prepared libraries were determined via Bioanalyzer analysis (2100 Electrophoresis Bioanalyzer, Agilent). Libraries with an adapter dimer peak (~160 nt) at least five times greater than the library peak (~180 nt) were not sequenced.

value: F

tag: time point

tag: irradiated

value: TRUE


title: 2096G4BFR-PT

value: PT


title: 2094G4BFR-D5


title: 2096G4BFR-D5


title: 2093G4BFR-D5


title: 2095G4BFR-D5


title: 2093G4BFR-PT


title: 2093G4BFR-M1


title: 2096G4BFR-M1


title: 2092G4BFR-PT


title: 2095G4BFR-M1


title: 2092G4BFR-M1


title: 2092G4BFR-D5


title: 2095G4BFR-PT


title: 2091G4BFR-D5


title: 2091G4BFR-M1


title: Normoxia-1

city: Hangzhou

first: Yuan-Qiang

last: Lu

address: 79 Qingchun Road

department: Emergency Medicine

institute: the First Affiliated Hospital, School of Medicine, Zhejiang University

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

scan_protocol: 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. 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: HUVEC were incubated under 95% air/5% CO2.

label_protocol: 0.2 μg total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol: Total RNA was isolated from HUVEC cells in the control group and the hypoxia/re-oxygenated group using TRIzol (Life Technologies) following the manufacturer’s instructions. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: HUVEC (Procell Life Science ＆ Technology Co,. Ltid.) were replaced with fresh medium at 37℃ in a humidified atmosphere of 5% CO2 and 95% air which the O2 concentration was about 20% for 12 hours before exposure to hypoxia. Hypoxia cultures (5% O2) were incubated under 5% O2, 5% CO2 and 90% N2 by 3131 Single Tri-gas 184L incubator (Thermo Fisher scientific, Shanghai, China). Hypoxia/re-oxygenation group HUVEC were incubated under hypoxia for 3 hours followed by 1 hour 95% air/5% CO2. HUVEC cultured only in 95% air/5% CO2 were used as the normoxia control group.

value: Normoxia

value: HUVEC


title: Normoxia-2


title: 2091G4BFR-PT


title: Hypoxia/re-oxygenation-2

source_name: HUVEC were incubated under hypoxia for 3 hours followed by 1 hour 95% air/5% CO2.

value: Hypoxia/re-oxygenation


title: 2090G4BFR-D5


title: Hypoxia/re-oxygenation-3


title: 2094G4BFR-PT


title: 2090G4BFR-PT


title: 2089G4BFR-M1


title: Normoxia-3


title: 2089G4BFR-D5


title: Hypoxia/re-oxygenation-1


title: 2089G4BFR-PT


title: 2088G4BFS-M1

value: FALSE


title: 2088G4BFS-PT


title: 2086G4BFS-D5


title: 2087G4BFS-PT


title: 2088G4BFS-D5


title: 2087G4BFS-D5


title: 2086G4BFS-M1


title: 2086G4BFS-PT


title: 2085G4BFS-M1


title: 2085G4BFS-PT


title: 2083G4AFR-M1


title: 2084G4AFR-D2


title: 2080G4AFR-M1


title: 2083G4AFR-PT


title: 2082G4AFR-D2


title: 2081G4AFR-M1


title: 2082G4AFR-PT


title: 2080G4AFR-D2


title: 2081G4AFR-PT


title: 2082G4AFR-M1


title: 2081G4AFR-D2


title: 2079G4AFR-D2


title: 2079G4AFR-M1


title: 2079G4AFR-PT


title: 2080G4AFR-PT


title: Genomic DNA from peripheral blood monoculear cells 3

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419003_R02C01_Grn.idat
location 1 (triplicate pair 1): 3998419003_R02C01_Red.idat
location 2 (triplicate pair 2): 3998419003_R02C02_Grn.idat
location 2 (triplicate pair 2): 3998419003_R02C02_Red.idat
location 3 (triplicate pair 3): 3998419089_R02C01_Grn.idat
location 3 (triplicate pair 3): 3998419089_R02C01_Red.idat

value: AA

value: Lupus


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value: M


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title: 1029G1AFR-M1


title: 1029G1AFR-PT


title: 1031G1AFR-M1


title: 1028G1AFS-M5


title: 1028G1AFS-M4


title: 1031G1AFR-PT


title: 1028G1AFS-M3


title: 1028G1AFS-M1


title: 1028G1AFS-M2


title: 1028G1AFS-PT


title: 1028G1AFS-D2


title: 1027G1AFS-M4


title: 1027G1AFS-M5


title: 1027G1AFS-M3


title: 1027G1AFS-M1


title: 1027G1AFS-M2


title: 1027G1AFS-PT


title: 1027G1AFS-D2


title: 1026G1AFS-M4


title: 1026G1AFS-M6


title: 1026G1AFS-M5


title: 1026G1AFS-M2


title: 1026G1AFS-D2


title: 1028G1AFS-M6


title: 1025G1AFS-M5


title: 1026G1AFS-PT


title: 1025G1AFS-M3


title: 1027G1AFS-M6


title: 1025G1AFS-M2


title: 1025G1AFS-M4


title: 1025G1AFS-D2


title: 1025G1AFS-M1


title: 1025G1AFS-PT


title: 1024G1BMR-M6


title: 1024G1BMR-M3


title: 1024G1BMR-M4


title: 1024G1BMR-M5


title: 1024G1BMR-M2


title: 1024G1BMR-PT


title: 1024G1BMR-M1


title: 1024G1BMR-D5


title: 1026G1AFS-M3


title: 1023G1BMR-M2


title: 1026G1AFS-M1


title: 1023G1BMR-M5


title: 1025G1AFS-M6


title: 1023G1BMR-D5


title: 1023G1BMR-M3


title: 1023G1BMR-PT


title: 1022G1BMR-M6


title: 1022G1BMR-M4


title: 1022G1BMR-M5


title: 1022G1BMR-M3


title: 1022G1BMR-M2


title: 1021G1BMR-M4


title: 1022G1BMR-PT


title: 1021G1BMR-M3


title: 1023G1BMR-M4


title: 1022G1BMR-M1


title: 1022G1BMR-D5


title: 1021G1BMR-PT


title: 1021G1BMR-D5


title: 1021G1BMR-M2


title: 1020G1BMR-PT


title: 1019G1BMR-M5


title: 1020G1BMR-M1


title: 1020G1BMR-M2


title: 1020G1BMR-M4


title: 1019G1BMR-M1


title: 1019G1BMR-M4


title: 1020G1BMR-D5


title: 1019G1BMR-M2


title: 1019G1BMR-M3


title: 1019G1BMR-D5


title: 1019G1BMR-PT


title: 1018G1BMR-M1


title: 1018G1BMR-M2


title: 1018G1BMR-M4


title: 1021G1BMR-M1


title: 1018G1BMR-D5


title: 1017G1BMR-M4


title: 1017G1BMR-M5


title: 1018G1BMR-PT


title: 1020G1BMR-M3


title: 1017G1BMR-M2


title: 1017G1BMR-PT


title: 1017G1BMR-D5


title: 1016G1BMS-M6


title: 1016G1BMS-D5


title: 1016G1BMS-M5


title: 1016G1BMS-M2


title: 1016G1BMS-PT


title: 1016G1BMS-M3


title: 1016G1BMS-M1


title: 1015G1BMS-M5


title: 1015G1BMS-M6


title: 1018G1BMR-M3


title: 1015G1BMS-M4


title: 1015G1BMS-M3


title: 1015G1BMS-M2


title: 1015G1BMS-D5


title: 1015G1BMS-M1


title: 1015G1BMS-PT


title: 1017G1BMR-M3


title: 1017G1BMR-M1


title: 1014G1BMS-M6


title: 1014G1BMS-M4


title: 1014G1BMS-M5


title: 1014G1BMS-M3


title: 1016G1BMS-M4


title: 1014G1BMS-M2


title: 1014G1BMS-M1


title: 1013G1BMS-M6


title: 1023G1BMR-M1


title: 1013G1BMS-M5


title: 1014G1BMS-PT


title: 1013G1BMS-M3


title: 1013G1BMS-M4


title: 1013G1BMS-M2


title: 1013G1BMS-D5


title: 1013G1BMS-M1


title: 1013G1BMS-PT


title: 1012G1AMR-M4


title: 1012G1AMR-M5


title: 1012G1AMR-M3


title: 1012G1AMR-M2


title: 1012G1AMR-M1


title: 1012G1AMR-D2


title: 1011G1AMR-M4


title: 1011G1AMR-M5


title: 1012G1AMR-PT


title: 1011G1AMR-M3


title: 1011G1AMR-M1


title: 1011G1AMR-D2


title: 1011G1AMR-PT


title: 1014G1BMS-D5


title: 1030G1AFR-M6


title: 1010G1AMR-M5


title: 1010G1AMR-M4


title: 1010G1AMR-M6


title: 1011G1AMR-M2


title: 1010G1AMR-M3


title: 1010G1AMR-M2


title: 1010G1AMR-D2


title: 1009G1AMR-M6


title: 1010G1AMR-PT


title: 1009G1AMR-M5


title: 1009G1AMR-M4


title: 1009G1AMR-M2


title: 1009G1AMR-M3


title: 1009G1AMR-M1


title: 1009G1AMR-D2


title: 1008G1AMR-M4


title: 1008G1AMR-M5


title: 1008G1AMR-M3


title: 1008G1AMR-D2


title: 1008G1AMR-M1


title: 1008G1AMR-PT


title: 1007G1AMR-M5


title: 1008G1AMR-M2


title: 1007G1AMR-M4


title: 1007G1AMR-M3


title: 1007G1AMR-M2


title: 1010G1AMR-M1


title: 1007G1AMR-D2


title: 1007G1AMR-PT


title: 1006G1AMR-M1


title: 1006G1AMR-M2


title: 1007G1AMR-M1


title: 1006G1AMR-PT


title: 1005G1AMR-M5


title: 1005G1AMR-M3


title: 1006G1AMR-D2


title: 1005G1AMR-D2


title: 1005G1AMR-M1


title: 1009G1AMR-PT


title: 1004G1AMS-M6


title: 1005G1AMR-M2


title: 1005G1AMR-M4


title: 1005G1AMR-PT


title: 1004G1AMS-M4


title: 1004G1AMS-M3


title: 1004G1AMS-M2


title: 1004G1AMS-D2


title: 1004G1AMS-PT


title: 1004G1AMS-M1


title: 1003G1AMS-M6


title: 1003G1AMS-M4


title: 1003G1AMS-M3


title: 1003G1AMS-M5


title: 1003G1AMS-M2


title: 1003G1AMS-PT


title: 1003G1AMS-D2


title: 1002G1AMS-M6


title: 1003G1AMS-M1


title: 1002G1AMS-M3


title: 1002G1AMS-M5


title: 1002G1AMS-M1


title: 1002G1AMS-M4


title: 1002G1AMS-M2


title: 1002G1AMS-D2


title: 1002G1AMS-PT


title: 1001G1AMS-M4


title: 1004G1AMS-M5


title: 1001G1AMS-M5


title: 1001G1AMS-M3


title: 1001G1AMS-M2


title: 1001G1AMS-D2


title: 1001G1AMS-PT


title: 2091G4BFR-RBC

source_name: RBC

extract_protocol:
Tissue miRNA was extracted from 20 mg of homogenized tissues in QIAzol (Qiagen) with the miRNEasy Kit (Qiagen).
Libraries for sequencing were prepared using the QIAseq miRNA Library Kit; (Qiagen) with 5.8 µL of miRNA extracts as input, a 1:5 dilution of the 3’-adaptor, a 1:2.5 dilution of the 5’-adaptor, a 1:5 dilution of the RT primer, and 22 amplification cycles. The concentrations of the prepared libraries were determined via Bioanalyzer analysis (2100 Electrophoresis Bioanalyzer, Agilent). Libraries with an adapter dimer peak (~160 nt) at least five times greater than the library peak (~180 nt) were not sequenced.


title: 2082G4AFR-RBC


title: 2092G4BFR-RBC


title: 2085G4BFS-RBC


title: 2089G4BFR-RBC


title: 2081G4AFR-RBC


title: 2077G4AFR-RBC


title: 1001G1AMS-M6


title: 2076G4AFS-RBC


title: 2075G4AFS-RBC


title: 2073G4AFS-RBC


title: 2074G4AFS-RBC


title: 1087G3BFS-RBC


title: 1075G3AFS-RBC


title: 1076G3AFS-RBC


title: 1089G3BFR-RBC


title: 1086G3BFS-RBC


title: 1073G3AFS-RBC


title: 1074G3AFS-RBC


title: 1069G3BMR-RBC


title: 1065G3BMR-RBC


title: 2094G4BFR-RBC


title: 1064G3BMS-RBC


title: 1063G3BMS-RBC


title: 2087G4BFS-RBC


title: 2086G4BFS-RBC


title: 1056G3AMR-RBC


title: 1055G3AMR-RBC


title: 1051G3AMS-RBC


title: 2094G4BFR-WBC

source_name: WBC


title: 2092G4BFR-WBC


title: 1050G3AMS-RBC


title: 1061G3BMS-RBC


title: 2091G4BFR-WBC


title: 1049G3AMS-RBC


title: 2089G4BFR-WBC


title: 2086G4BFS-WBC


title: 1085G3BFS-RBC


title: 2077G4AFR-WBC


title: 2082G4AFR-WBC


title: 2085G4BFS-WBC


title: 2073G4AFS-WBC


title: 1089G3BFR-WBC


title: 1086G3BFS-WBC


title: 1076G3AFS-WBC


title: 2074G4AFS-WBC


title: 1073G3AFS-WBC


title: 1087G3BFS-WBC


title: 1065G3BMR-WBC


title: 1069G3BMR-WBC


title: 1001G1AMS-M1


title: 1052G3AMS-RBC


title: 1063G3BMS-WBC


title: 1064G3BMS-WBC


title: 2088G4BFS-RBC


title: 1062G3BMS-RBC


title: 1062G3BMS-WBC


title: 2076G4AFS-WBC


title: 1056G3AMR-WBC


title: 1061G3BMS-WBC


title: 1052G3AMS-WBC


title: 1055G3AMR-WBC


title: 1049G3AMS-WBC


title: 1087G3BFS-Brain

source_name: Brain


title: 1051G3AMS-WBC


title: 1076G3AFS-Brain


title: 1074G3AFS-Brain


title: 1086G3BFS-Brain


title: 1073G3AFS-Brain


title: 1075G3AFS-Brain


title: 2082G4AFR-Brain


title: 2086G4BFS-Brain


title: 2094G4BFR-Brain


title: 2091G4BFR-Brain


title: 2085G4BFS-Brain


title: 2089G4BFR-Brain


title: 2081G4AFR-Brain


title: 2077G4AFR-Brain


title: 2092G4BFR-Brain


title: 2088G4BFS-Brain


title: 2087G4BFS-Brain


title: 1089G3BFR-Brain


title: 2076G4AFS-Brain


title: 1085G3BFS-Brain


title: 1069G3BMR-Brain


title: 2075G4AFS-Brain


title: 1063G3BMS-Brain


title: 1062G3BMS-Brain


title: 1061G3BMS-Brain


title: 1056G3AMR-Brain


title: 2073G4AFS-Brain


title: 1055G3AMR-Brain


title: 1052G3AMS-Brain


title: 1050G3AMS-Brain


title: 1064G3BMS-Brain


title: 1049G3AMS-Brain


title: 1051G3AMS-Brain


title: 2074G4AFS-Brain


title: 1065G3BMR-Brain


title: 1087G3BFS-Lung

source_name: Lung


title: 1085G3BFS-Lung


title: 1073G3AFS-Lung


title: 1074G3AFS-Lung


title: 1086G3BFS-Lung


title: 2089G4BFR-Lung


title: 1089G3BFR-Lung


title: 2092G4BFR-Lung


title: 2091G4BFR-Lung


title: 2088G4BFS-Lung


title: 2087G4BFS-Lung


title: 2086G4BFS-Lung


title: 2077G4AFR-Lung


title: 2085G4BFS-Lung


title: 786-O-PRDM16_2

city: Birmingham

first: Sunil

last: Sudarshan

state: Alabama

address: 1824 6th Avenue South

department: Urology

institute: UAB

data_processing:
The RNA-sequencing of wild type and PRDM16 over-expressing 786-O cells was done in replicates. Adapter sequences and low quality reads were trimmed from fastq files using trim_galore.
With TopHat v2.1.0, trimmed raw read sequences were mapped to Homo sapiens reference genome (hg38). The aligned reads were assembled into genes and their abundance was estimated as  Fragments per Kilobase of exon per Million fragments mapped (FPKM) using Cufflinks v2.2.1.
Differential expression analysis was carried out using Cuffdiff module of Cufflinks. Genes with absolute fold change of  greater than or equal to 1.5 and P-value <0.05 were considered as differentially expressed genes (DEGs)
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file includes FPKM values for each sample from Cufflinks.

source_name: 786-O cells

growth_protocol: Adherent Cells grown in vitro under standard culture conditions.

extract_protocol:
RNA from culture cells were extracted with Direct-zol RNA miniprep kit (Zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells stably transduced with either control vector or PRDM16.

tag: vector

value: PRDM16 lentivirus


title: 786-O-PRDM16_1


title: 1075G3AFS-Lung


title: 2094G4BFR-Lung


title: 1076G3AFS-Lung


title: 2075G4AFS-Lung


title: 2073G4AFS-Lung


title: 786-O-LV_1

value: Control vector


title: 2076G4AFS-Lung


title: 786-O-LV _2


title: 1065G3BMR-Lung


title: 1064G3BMS-Lung


title: 1069G3BMR-Lung


title: 2074G4AFS-Lung


title: 2082G4AFR-Lung


title: 2081G4AFR-Lung


title: S2698KO

city: Beijing

first: Jiu

middle: zhi

last: Xu

state: Beijing

address: Yuanmingyuan West Road NO.2

department: College of Biological sciences

institute: China Agricultural University

description:
S2698KO:gProcessedSignal(raw)
Gene expression of Islr knockout mouse colon.

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized in an Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing:
Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and GeneSpring software was used to analyze the raw data, which are normalized by percentile normalization.
gProcessedSignal(raw)

source_name: Colon, 3.5% DSS in drinking water for 5 days, recover for 1 day

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: No treatment.

tag: genotype/variation

value: Islr knockout

value: Colon

value: Male