title: T1D#12_IGRPp13


title: T1D#11_Flu-MP

status: Public on Aug 15 2016

type: RNA

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

country: USA

institute: Benaroya Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was normalised using quantile normalization, values less than 10 were floored to 10, and the data was transformed to log2 scale within R.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

label_protocol: Biotinylated cRNA targets were prepared from 250 ng of total RNA, using the Illumina TotalPrep RNA Amplification kit (Ambion).

growth_protocol: PBMCs were cultured in RPMI 1640 medium with 10X AB serum, 50uM 2-beta-mercaptoethanol, 25 ml of HEPES, 1 % sodium pyruvate, and 1 % non-essential amino acid.

extract_protocol: RNA was extracted with Qiagen Rneasy mini kit, followed by DNase I treatment and clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyzer.

treatment_protocol: 1x10^6 PBMCs were stimulated with peptides derived from type 1 diabetogenic protein (GAD65, IGRP, PPI, ZnT8) and influenza virus M, and cultured for 24 hours in RPMI 1640 medium with 10X AB serum, 50uM 2-beta-mercaptoethanol, 25 ml of HEPES, 1 % sodium pyruvate, and 1 % non-essential amino acid.

tag: stimulation

value: Flu-MP

tag: time point


title: T1D#1_IGRPC4


title: HC#9_None


title: T1D#12_PPIC3


title: T1D#11_ZnT8p17


title: T1D#10_ZnT8p18


title: T1D#10_GAD65C1


title: HC#9_ZnT8C5


title: T1D#10_None


title: T1D#10_IGRPC4


title: T1D#11_IGRPC4


title: HC#8_ZnT8C5


title: T1D#1_GAD65C1


title: T1D#1_None


title: HC#9_IGRPC4


title: HC#8_None


title: HC#8_PPIC3


title: HC#7_ZnT8C5


title: HC#8_IGRPC4


title: HC#8_Flu-MP


title: HC#5_ZnT8p16


title: HC#7_IGRPC4


title: HC#8_IGRPp13


title: HC#5_ZnT8C5


title: HC#7_GAD65C1


title: HC#7_IGRPp13


title: HC#6_ZnT8p17


title: HC#7_PPIC3


title: HC#7_None


title: HC#6_None


title: HC#8_GAD65C1


title: HC#5_PPIC3


title: HC#5_IGRPp13


title: HC#6_IGRPC4


title: HC#5_IGRPC4


title: HC#7_Flu-MP


title: HC#4_None


title: HC#4_ZnT8p18


title: HC#5_IGRPp12


title: HC#4_IGRPp11


title: HC#4_ZnT8C5


title: HC#4_PPIC3


title: HC#5_None


title: HC#4_IGRPp13


title: HC#5_GAD65C1


title: HC#4_IGRPC4


title: HC#3_ZnT8C5


title: HC#4_GAD65C1


title: HC#3_IGRPC4


title: HC#3_IGRPp14


title: T1D#10_PPIC3


title: HC#2_PPIC3


title: HC#3_Flu-MP


title: HC#2_ZnT8p15


title: HC#2_IGRPC4


title: HC#3_IGRPp13


title: HC#3_PPIC3


title: HC#2_ZnT8C5


title: HC#15_PPIC3


title: HC#2_Flu-MP


title: HC#14_ZnT8p18


title: HC#12_PPIC3


title: HC#12_GAD65C1


title: HC#14_IGRPp13


title: HC#13_ZnT8C5


title: HC#15_IGRPC4


title: HC#14_None


title: HC#12_None


title: HC#12_ZnT8C5


title: HC#3_GAD65C1


title: HC#2_None


title: HC#12_ZnT8p16


title: HC#13_GAD65C1


title: HC#13_IGRPC4


title: HC#15_None


title: HC#15_Flu-MP


title: HC#12_IGRPC4


title: HC#13_PPIC3


title: HC#12_IGRPp12


title: HC#13_Flu-MP


title: HC#14_IGRPC4


title: HC#3_None


title: HC#12_IGRPp13


title: HC#11_ZnT8p17


title: HC#15_GAD65C1


title: HC#2_GAD65C1


title: HC#14_IGRPp12


title: HC#11_ZnT8p15


title: HC#13_None


title: HC#11_ZnT8C5


title: HC#11_IGRPp13


title: HC#11_None


title: HC#11_PPIC3


title: HC#11_IGRPp12


title: HC#11_IGRPC4


title: HC#11_GAD65C1


title: HC#10_ZnT8C5


title: HC#10_None


title: HC#115_FROZEN_NPp1528_1

growth_protocol: PBMCs were cultured in RPMI 1640 medium with 1X serum replacement, 1 mM sodium pyruvate, and penicillin and streptomycin.

treatment_protocol: 1x10^6 PBMCs were stimulated with peptides derived from influenza virus, and cultured for 24 hours in RPMI 1640 medium with with 1X serum replacement, 1 mM sodium pyruvate, and penicillin and streptomycin.


title: HC#115_FROZEN_NPp1528_2


title: HC#10_IGRPC4


title: HC#115_FROZEN_None_3


title: HC#10_GAD65C1


title: HC#1_ZnT8C5


title: HC#1_GAD65C1


title: HC#10_ZnT8p17


title: HC#1_IGRPC4


title: HC#1_None


title: HC#115_FROZEN_None_2


title: HC#115_FROZEN_MPp54p8_3


title: HC#115_FROZEN_MPp54p8_1


title: HC#115_FROZEN_MPp54p8_2


title: HC#115_FROZEN_None_1


title: HC#115_FRESH_MPp54p8_3


title: HC#115_FRESH_NPp1528_1


title: HC#115_FRESH_None_2


title: HC#115_FRESH_NPp1528_3


title: HC#115_FRESH_NPp1528_2


title: HC#115_FRESH_MPp54p8_2


title: HC#115_FRESH_MPp54p8_1


title: HC#114_YOUNG_NPp68


title: HC#115_FRESH_None_3


title: HC#114_YOUNG_None


title: HC#114_YOUNG_H3p13


title: HC#114_YOUNG_NPp125


title: HC#113_YOUNG_H3p13


title: HC#114_YOUNG_BHp46


title: HC#114_YOUNG_H1p21


title: HC#113_YOUNG_BHp46


title: HC#115_FRESH_None_1


title: HC#113_YOUNG_H1p21


title: HC#115_FROZEN_NPp1528_3


title: HC#112_YOUNG_None


title: HC#113_YOUNG_NPp125


title: HC#112_YOUNG_NPp68


title: HC#112_YOUNG_H1p34


title: HC#112_YOUNG_MPp54p8


title: HC#112_YOUNG_H3p306p3


title: HC#113_YOUNG_None


title: HC#113_YOUNG_NPp68


title: HC#112_YOUNG_BHp46


title: HC#111_OLD_BHp46


title: HC#111_OLD_NPp68


title: HC#111_OLD_None


title: HC#110_YOUNG_None


title: HC#110_YOUNG_H1p33


title: HC#110_YOUNG_MPp6


title: HC#109_OLD_MPp54p8


title: HC#108_YOUNG_BHp28


title: HC#107_OLD_None


title: HC#110_YOUNG_BHp28


title: HC#109_OLD_H1p34


title: HC#10_PPIC3


title: HC#108_YOUNG_None


title: HC#109_OLD_None


title: HC#108_YOUNG_MPp6


title: HC#107_OLD_BHp46


title: HC#109_OLD_H3p306p3


title: HC#108_YOUNG_H1p33


title: HC#106_YOUNG_H3p13


title: HC#105_YOUNG_H3p306p3


title: HC#105_YOUNG_None


title: HC#106_YOUNG_H1p21


title: HC#106_YOUNG_None


title: HC#105_YOUNG_MPp54p8


title: HC#107_OLD_NPp68


title: HC#104_OLD_MPp6

description: Sample name


title: Allergy#9_Feld4p30

treatment_protocol: 1x10^6 PBMCs were stimulated with antigenic peptides derived from silver birch wood and cat, and cultured for 24 hours in RPMI 1640 medium with 10X AB serum, 50uM 2-beta-mercaptoethanol, 25 ml of HEPES, 1 % sodium pyruvate, and 1 % non-essential amino acid.


title: HC#11_IGRPp14


title: HC#104_OLD_H1p33


title: Allergy#9_None


title: HC#104_OLD_None


title: Allergy#35_None


title: HC#102_GAD65p73

treatment_protocol: 1x10^6 PBMCs were stimulated with peptides derived from west nile virus (E, NS2a) and type 1 diabetogenic antigens (GAD65, ZnT8), and cultured for 24 hours in RPMI 1640 medium with 10X AB serum, 50uM 2-beta-mercaptoethanol, 25 ml of HEPES, 1 % sodium pyruvate, and 1 % non-essential amino acid.


title: HC#102_None


title: HC#105_YOUNG_H1p34


title: IRF3-Input-B

status: Public on Jan 18 2016

type: SRA

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

library_source: genomic

data_processing:
ChIP-seq libraries were sequenced on an Illumina HiSeq 2000.
ChIP-seq fastq files were mapped using Bowtie2. Only the uniquely mapped reads were kept for further analysis.
Uniquely aligned reads were peak-called using the Homer suite with a FDR threshold of 0.01.
Called peaks were annotated to the nearest Refseq ID, mm9 build
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files for each sample represent the read coverage at each genomic position

molecule: genomic DNA

organism: Mus musculus

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow precursors were grown in M-CSF conditioned media containing FBS for 6 days prior to stimulation.

extract_protocol:
Purified nuclei from BMDMs were lysed and chromatin was sheared using a Bioruptor prior to immunoprecipitation with anti-RelA, anti-SRF, or anti-IRF3 antibodies
RelA libraries were constructed using Illumina's TruSeq ChIP Sample Prep Kit. SRF and IRF3 libraries were constructed using Kapa's LTP Library Preparation kit, both according to manufactuer's instruction.

treatment_protocol: Lipid A stimulation for 0, 15, 30, 60, or 120 minutes

tag: cell type

value: bone marrow-derived macrophages

tag: strain

tag: genotype

value: wildtype

tag: stimulus

value: lipid A

tag: time

value: INPUT


title: IRF3-Input-A


title: IRF3-60min-A


title: IRF3-120min-A


title: IRF3-0min-B


title: IRF3-30min-B


title: IRF3-30min-A


title: IRF3-15min-B


title: HC#104_OLD_BHp28


title: HC#101_WNVNS2ap2


title: IRF3-120min-B


title: IRF3-60min-B


title: HC#102_ZnT8p65


title: HC#101_WNVEp7


title: HC#103_ZnT8p93


title: HC#103_ZnT8p33


title: IRF3-15min-A


title: HC#101_H1p45

treatment_protocol: 1x10^6 PBMCs were stimulated with peptides derived from influenzavirus H1 and H5, human cytomegalovirus, and candida albian, and cultured for 24 hours in RPMI 1640 medium with 10X AB serum, 50uM 2-beta-mercaptoethanol, 25 ml of HEPES, 1 % sodium pyruvate, and 1 % non-essential amino acid.


title: HC#101_None


title: HC#101_None (#2)


title: HC#102_ZnT8p68


title: HC#101_CMVp86


title: HC#101_Candidap38


title: HC#103_None


title: 120m_rep4

data_processing:
ATAC-seq libraries were sequenced on an Illumina HiSeq 2000.
Adapter sequences were removed with cutadapt -a CTGTCTCTTATA -m 23
All fastq files were mapped using bowtie2 and reads were removed if they were non-unique, in duplicate, aligned to unmapped to mitochondrial genome, or aligned to un-mapped contiguous sequences. Only the remaining reads following these filters were used for subsequent analysis
bedGraph files were geenrated from sorted bam files using makeTagDirectories and makeUCSCfile with -fsize 10e8 -res 1
Reads were imported to SeqMonk. ATAC-accessibility at promoters was calculated by totaling all reads within -500/+150bp from TSS. The raw reads were converted to Reads Per Million by dividing the reads by the the total number of reads per sample. The average RPM from all 4 replicates was used to quantify the fold increase in accessibility over gene promoters
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files for each sample represent the read coverage at each genomic position

growth_protocol: Bone marrow precursors were grown in M-CSF media containing FBS for 6 days prior to stimulation.

extract_protocol:
25,000 BMDM on Day 6 of differentiation were centrifuged and washed once with PBS prior to addition of 50uL cold hypotonic lysis buffer containing 0.1% Igepal to yield nuclei. The lysis reaction was centifuged and the supernatant was discarded. Isolated nuclei were incubated with 1.25uL Tn5 (Nextera) in a 25uL reaction volume and placed in a 37C waterbath for 30 minutes.
All ATAC datasets were generated using Tn5 from Nextera with previously published protocols with minor adjustments (Buenrostro et al, Curr.Protoc. Mol. Biol. 2015). Transposed DNA was cleaned up with a Qiagen MinElute PCR Purification Kit and amplified with a non-saturating PCR to enrich for Transposed DNA. The reaction was size selected on a gel for fragments 200-1000bp and further purified with AMPureXP beads. Libraries were quantified with qPCR and Qubit.

treatment_protocol: Lipid A stimulation for 0 or 120 minutes

value: 120 minutes


title: IRF3-0min-A


title: 120m_rep3


title: 120m_rep2


title: 0m_rep2

value: Unstimulated

value: 0 minutes


title: 0m_rep3


title: 120m_rep1


title: 0m_rep4


title: 5MIN-60 Rep 2

description: chromatin-associated RNA

library_source: transcriptomic

data_processing:
RNA-seq fastq files were aligned to the mouse genome using Tophat v1.3.3 with the following options: -p 4 -a 8 -m 0 -i 70 -I 500000 -g 1 --library-type fr-firststrand --no-novel-indels --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2 --s. Only uniquely mapped reads were kept for downstream analysis.
All aligned reads were imported to SeqMonk. Chromatin-associated RNA expression was calculated by totaling all uniquely aligned reads within the gene body. The raw reads were converted to RPKM by dividing the reads by the total gene length and the total number of uniquely mapped reads. mRNA expression was calculated by totaling all uniquely aligned exonic reads. The raw reads were converted to RPKM by dividing the reads by the cDNA length and the total number of uniquely mapped reads.
Bedgraph files were generated from aligned BAM files using the Bedtools suite: genomeCoverageBed -bg -split, using the mouse mm9 reference genome.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files for each sample represent the read coverage at each genomic position.

growth_protocol: Bone marrow or fetal liver precursors were grown in M-CSF conditioned media containing FBS for 6 days prior to stimulation.

extract_protocol:
Chromatin-associated RNA was biochemically purified as previously described (Bhatt et al, Cell 2012). Chromatin was resuspended in TriReagent and RNA purified using Rneasy columns (Qiagen). rRNA was depleted using the Ribominus Kit (Life Technologies). mRNA was isolated using TriReagent and RNA was purified using RNeasy columns (Qiagen).
All chromatin and mRNA libraries were generated using the Illumina Truseq v.2 kit with a few modifications: strand specific libraries were generated using the dUTP method. Briefly, the second strand cDNA was synthesized in the presence of dUTP. Prior to library amplification, the second strand was degraded with dUTPase.

tag: time (minutes)


title: 5MIN-60

description: chromatin-associated RNA


title: 5MIN-45 Rep 2

description: chromatin-associated RNA


title: 5MIN-55

description: chromatin-associated RNA


title: 5MIN-50 Rep 2

description: chromatin-associated RNA


title: 5MIN-45

description: chromatin-associated RNA


title: 5MIN-40 Rep 2

description: chromatin-associated RNA


title: 5MIN-50

description: chromatin-associated RNA


title: Allergy#35_Alng1p10


title: 5MIN-30 Rep 2

description: chromatin-associated RNA


title: 5MIN-35 Rep 2

description: chromatin-associated RNA


title: 5MIN-30

description: chromatin-associated RNA


title: HC#101_H5p36


title: 0m_rep1


title: 5MIN-25 Rep 2

description: chromatin-associated RNA


title: 5MIN-25

description: chromatin-associated RNA


title: 5MIN-15 Rep 2

description: chromatin-associated RNA


title: 5MIN-20 Rep 2

description: chromatin-associated RNA


title: 5MIN-20

description: chromatin-associated RNA


title: 5MIN-5 Rep 2

description: chromatin-associated RNA


title: 5MIN-15

description: chromatin-associated RNA


title: 5MIN-10 Rep 2

description: chromatin-associated RNA


title: 5MIN-10

description: chromatin-associated RNA


title: 5MIN-5

description: chromatin-associated RNA


title: MAPK-120 Rep 2

description: chromatin-associated RNA

value: lipid A + MAPK inhibitors


title: MAPK-120

description: chromatin-associated RNA


title: MAPK-30 Rep 2

description: chromatin-associated RNA


title: MAPK-60

description: chromatin-associated RNA


title: 5MIN-35

description: chromatin-associated RNA


title: 5MIN-0

description: chromatin-associated RNA


title: MAPK-15 Rep 2

description: chromatin-associated RNA


title: MAPK-60 Rep 2

description: chromatin-associated RNA


title: MAPK-0

description: chromatin-associated RNA


title: MAPK-0 Rep 2

description: chromatin-associated RNA


title: MAPK-30

description: chromatin-associated RNA


title: MAPK-15

description: chromatin-associated RNA


title: CON-120 Rep 2

description: chromatin-associated RNA


title: CON-120

description: chromatin-associated RNA


title: CON-60 Rep 2

description: chromatin-associated RNA


title: CON-60

description: chromatin-associated RNA


title: CON-30 Rep 2

description: chromatin-associated RNA


title: CON-30

description: chromatin-associated RNA


title: CON-15 Rep 2

description: chromatin-associated RNA


title: CON-0 Rep 2

description: chromatin-associated RNA


title: CON-15

description: chromatin-associated RNA


title: 5MIN-0 Rep 2

description: chromatin-associated RNA


title: CON-0

description: chromatin-associated RNA


title: RELA-120 Rep 2

description: mRNA

source_name: fetal liver macrophages

value: fetal liver macrophages

value: Rela-/-


title: RELA-120.

description: mRNA


title: RELA-60.

description: mRNA


title: RELA-0.

description: mRNA


title: RELA-30.

description: mRNA


title: HC#106_YOUNG_NPp125


title: WT-RELA-120

description: mRNA


title: WT-RELA-120 Rep 2

description: mRNA


title: RELA-30 Rep 2

description: mRNA


title: RELA-0 Rep 2

description: mRNA


title: WT-RELA-60 Rep 2

description: mRNA


title: WT-RELA-30

description: mRNA


title: PAM3-120 Rep 2

description: chromatin-associated RNA


title: WT-RELA-0 Rep 2

description: mRNA


title: PAM3-120

description: chromatin-associated RNA


title: PAM3-60 Rep 2

description: chromatin-associated RNA


title: PAM3-60

description: chromatin-associated RNA


title: PAM3-30 Rep 2

description: chromatin-associated RNA


title: PAM3-15 Rep 2

description: chromatin-associated RNA


title: PAM3-30

description: chromatin-associated RNA


title: PAM3-15

description: chromatin-associated RNA


title: PAM3-0

description: chromatin-associated RNA


title: RELA-60 Rep 2

description: mRNA


title: WT-RELA-60

description: mRNA


title: IFNAR-60 Rep 2

description: chromatin-associated RNA

value: Ifnar-/-


title: IFNAR-0 Rep 2

description: chromatin-associated RNA


title: IFNAR-30

description: chromatin-associated RNA


title: IFNAR-30 Rep 2

description: chromatin-associated RNA


title: WT-RELA-30 Rep 2

description: mRNA


title: IRF3-120 Rep 2

description: chromatin-associated RNA


title: IRF3-60 Rep 2

description: chromatin-associated RNA


title: WT-RELA-0

description: mRNA


title: IFNAR-0

description: chromatin-associated RNA


title: IRF3-60

description: chromatin-associated RNA


title: IRF3-30

description: chromatin-associated RNA


title: IRF3-120

description: chromatin-associated RNA


title: IRF3-15 Rep 2

description: chromatin-associated RNA


title: IRF3-0 Rep 2

description: chromatin-associated RNA


title: IRF3-30 Rep 2

description: chromatin-associated RNA


title: PAM3-0 Rep 2

description: chromatin-associated RNA


title: IRF3-0

description: chromatin-associated RNA


title: TRIF-60 Rep 2

description: chromatin-associated RNA

value: Trif-/-


title: IFNAR-120 Rep 2

description: chromatin-associated RNA


title: TRIF-120

description: chromatin-associated RNA


title: TRIF-120 Rep 2

description: chromatin-associated RNA


title: TRIF-60

description: chromatin-associated RNA


title: TRIF-30 Rep 2

description: chromatin-associated RNA


title: TRIF-30

description: chromatin-associated RNA


title: IFNAR-120

description: chromatin-associated RNA


title: IFNAR-60

description: chromatin-associated RNA


title: TRIF-15

description: chromatin-associated RNA


title: TRIF-0 Rep 2

description: chromatin-associated RNA


title: TRIF-15 Rep 2

description: chromatin-associated RNA


title: MYD88-60 Rep 2

description: chromatin-associated RNA


title: MYD88-30 Rep 2

description: chromatin-associated RNA


title: MYD88-120 Rep 2

description: chromatin-associated RNA


title: MYD88-120

description: chromatin-associated RNA


title: MYD88-60

description: chromatin-associated RNA


title: MYD88-30

description: chromatin-associated RNA


title: IRF3-15

description: chromatin-associated RNA


title: MYD88-0 Rep 2

description: chromatin-associated RNA


title: 5MIN-55 Rep 2

description: chromatin-associated RNA


title: MYD88-15 Rep 2

description: chromatin-associated RNA


title: WTCHX120 Rep 2

description: chromatin-associated RNA

value: lipid A + CHX


title: WTCHX120

description: chromatin-associated RNA


title: WTCHX60 Rep 2

description: chromatin-associated RNA


title: MYD88-15

description: chromatin-associated RNA


title: WTCHX60

description: chromatin-associated RNA


title: WTCHX30

description: chromatin-associated RNA


title: WT120

description: chromatin-associated RNA


title: WTCHX0

description: chromatin-associated RNA


title: WT120 Rep 2

description: chromatin-associated RNA


title: WTCHX0 Rep 2

description: chromatin-associated RNA


title: WT60

description: chromatin-associated RNA


title: TRIF-0

description: chromatin-associated RNA


title: WT60 Rep 2

description: chromatin-associated RNA


title: WT30

description: chromatin-associated RNA


title: WT30 Rep 2

description: chromatin-associated RNA


title: WT15

description: chromatin-associated RNA


title: MYD88-0

description: chromatin-associated RNA


title: WT15 Rep 2

description: chromatin-associated RNA


title: WT0

description: chromatin-associated RNA


title: WT0 Rep 2

description: chromatin-associated RNA


title: WTCHX30 Rep 2

description: chromatin-associated RNA


title: SRF-INPUT

extract_protocol:
Purified nuclei from BMDMs were lysed and chromatin was sheared using a Bioruptor prior to immunoprecipitation with anti-RelA or anti-SRF antibodies
RelA libraries were constructed using Illumina's TruSeq ChIP Sample Prep Kit and SRF libraries were constructed using Kapa's LTP Library Preparation kit, both according to manufactuer's instruction.

tag: antibody

value: none, input


title: SRF-0

value: SRF


title: RelA-INPUT-Rep2


title: RELA-120

value: RelA


title: SRF-120


title: SRF-15


title: SRF-60


title: RELA-30-Rep2


title: RelA-INPUT


title: RELA-120-Rep2


title: RELA-15-Rep2


title: RELA-60-Rep2


title: RELA-30


title: RELA-0-Rep2


title: RELA-15


title: RELA-0


title: SRF-30


title: RELA-60


title: TRIB1_rep3

status: Public on Apr 13 2015

city: Ottawa

first: Ruth

last: McPherson

state: Ontario

address: 40 Ruskin

country: Canada

institute: UOHI

description: Gene expression data from primary hepatocytes from donor 3 treated  with a TRIB1 specific antisense nucleotide

hyb_protocol: Hybridization performed according to Affymetrix WT Plus reagent kit guidelines

scan_protocol: Scanning was performed on a GenChip Scanner 3000

data_processing: The data were analyzed using Affymetrix Expression Console using default settings

label: Biotin

source_name: TRIB1 knock-down

label_protocol: Labeling performed according to Affymetrix WT Plus reagent kit guidelines

growth_protocol: Upon receival, media was changed to low glucose DMEM containing 10% serum, Penicillin/Streptomycin and antimycotics (GA-1000)  for overnight acclimatization.  Oligonucleotide treatments  were initiated the following day for 48 h.

extract_protocol: Ambion WT kit

treatment_protocol: treatment with 2'-O-(2-methoxy)ethyl  phosphorothioate backbone oligonucleotides and RNAimax for 48 h

value: Primary Hepatocytes plated on collagen


title: TRIB1_rep2

description: Gene expression data from primary hepatocytes from donor 2 treated  with a TRIB1 specific antisense nucleotide


title: NT_rep2

description: Gene expression data from primary hepatocytes from donor 2 treated  with a non-target antisense nucleotide

source_name: Control Knock-down


title: NT_rep1

description: Gene expression data from primary hepatocytes from donor 1 treated  with a non-target antisense nucleotide


title: NT_rep3

description: Gene expression data from primary hepatocytes from donor 3 treated  with a non-target antisense nucleotide


title: lib355

status: Public on Jan 06 2015

data_processing:
fastq files were created from .bcl files via Illumina's CASAVA 1.8.2
reads were aligned to Hg19 via Omicsoft sequence aligner (OSA) version 2.0.1
gene counts were generated by HTSeq version 0.5.4p3
TMMs were generated with Bioconductor package EdgeR
Genome_build: Hg19
Supplementary_files_format_and_content: tab delimited file contains TMM normalized counts

source_name: Whole Blood

extract_protocol: Fresh blood samples were collected from healthy subjects and subjects diagnosed type 1 diabetes, amyotrophic lateral sclerosis, and sepsis, as well as multiple sclerosis patients before and 24 hours after the first treatment with IFN-beta. At the time of blood draw, an aliquot of whole blood was collected into a Tempus tube (Invitrogen), while the remainder of the primary fresh blood sample was processed to highly pure populations of neutrophils, monocytes, B cells, CD4 T cells, CD8 T cells, and natural killer cells. RNA was extracted from each of these cell subsets, as well as the whole blood samples, and processed into RNA sequencing (RNAseq) libraries (Illumina TruSeq). Sequencing libraries were analyzed on an Illumina HiScan, with a target read depth of ~20M reads. Reads were demultiplexed, mapped to human gene models (ENSEMBL), and tabulated using HTSeq. Read count data were normalized by the TMM procedure (edgeR package).

tag: age

tag: cellcount

tag: celltype

value: Whole Blood

tag: collectiondate

value: September 12 2012

tag: diseasestatus

value: ALS

tag: donorid

tag: gender:

tag: index

tag: race

tag: samplename

tag: smoker

tag: time since last flare (months)

tag: time since steroid dose

tag: time since symptom onset (yrs)

tag: years since diagnosis


title: Ctrl4 FLU_8h

status: Public on Apr 07 2015

description: SAMPLE 11

data_processing: The data were normalised using quantile normalisation with in R. PALO (p<0.05 present in at least one) were used to filter the data.

growth_protocol: PBMCs were cultured in RPMI 16-40 medium with 10% fetal bovine serum.

treatment_protocol: 0.5x10^6 PBMCs were washed twice with PBS and infected with influenza A/California/4/2009 virus at MOI=2 in RPMI containing 0.3% bovine serum albumin and 1ug/mL TPCK-treated trypsin.

tag: subject status

value: healthy donor

tag: cell type

value: PBMC

tag: infected with

value: influenza virus A/CA/4/2009 for 8hrs


title: IRF7-/- FLU_8h

description: SAMPLE 17

value: patients with deficiencies for IRF7


title: IRF7-/- NS

description: SAMPLE 16

value: none for 16hrs (uninfected control)


title: IRF7-/- FLU_16h

description: SAMPLE 18

value: influenza virus A/CA/4/2009 for 16hrs


title: TRIB1_rep1

description: Gene expression data from primary hepatocytes from donor 1 treated  with a TRIB1 specific antisense nucleotide


title: Ctrl4 FLU_16h

description: SAMPLE 12


title: UNC93B-/- FLU_8h

description: SAMPLE 14

value: patients with deficiencies for UNC93B


title: Ctrl2 FLU_8h

description: SAMPLE 5


title: 5MIN-40

description: chromatin-associated RNA

value: bone marrow-derived macrophages

tag: strain

tag: genotype

value: wildtype

tag: stimulus

value: lipid A

tag: time (minutes)


title: Ctrl3 FLU_8h

description: SAMPLE 8


title: lib352

tag: age

tag: cellcount

tag: celltype

tag: collectiondate

tag: diseasestatus

tag: donorid


title: UNC93B-/- NS

description: SAMPLE 13


title: UNC93B-/- FLU_16h

description: SAMPLE 15


title: Ctrl2 FLU_16h

description: SAMPLE 6


title: Ctrl1 FLU_16h

description: SAMPLE 3


title: Ctrl3 FLU_16h

description: SAMPLE 9


title: lib353

tag: gender:

tag: index

tag: race

tag: samplename

tag: smoker

tag: time since last flare (months)


title: Ctrl1 NS

description: SAMPLE 1

tag: subject status

tag: cell type

tag: infected with


title: lib354

value: NK

tag: time since steroid dose

tag: time since symptom onset (yrs)

tag: years since diagnosis


title: Ctrl1 FLU_8h

description: SAMPLE 2


title: Ctrl3 NS

description: SAMPLE 7


title: lib351

tag: age

tag: cellcount

value: B-cells


title: Ctrl4 NS

description: SAMPLE 10


title: Ctrl2 NS

description: SAMPLE 4


title: lib350

tag: celltype

value: Monocytes

tag: collectiondate


title: lib349

value: Neutrophils

tag: diseasestatus

tag: donorid


title: lib348

value: Whole Blood

value: August 24 2012

value: MS posttreatment

tag: gender

value: F

tag: index

value: White

value: N

value: 1 month, IV


title: lib347

tag: race

tag: samplename


title: lib346

tag: smoker

tag: time since last flare (months)


title: lib344


title: lib343


title: lib342


title: lib341

value: August 23 2012

value: MS pretreatment


title: lib339


title: lib340


title: lib336


title: lib338


title: lib332

value: Type 1 Diabetes


title: lib330


title: lib335


title: lib328

value: M


title: lib329


title: lib334


title: lib331


title: lib325


title: lib326


title: lib327


title: lib324


title: lib345


title: lib323


title: lib322

value: August 22 2012

value: ALS

tag: gender:


title: lib321

value: NK


title: lib320


title: lib333


title: lib318

value: B-cells


title: lib317

value: Monocytes


title: lib316

value: Neutrophils


title: lib337


title: lib319


title: lib313

value: August 21 2012

value: Healthy Control


title: lib314


title: lib312


title: lib309


title: lib307

value: August 16 2012


title: lib310

value: F


title: lib302


title: lib308

value: Whole Blood


title: lib306


title: lib303


title: lib301

value: February 2 2012

value: White


title: lib299


title: lib305


title: lib298


title: lib304


title: lib296


title: lib297


title: lib300


title: lib295


title: lib294

value: January 25 2012


title: lib315


title: lib311


title: lib293


title: lib290


title: lib292


title: lib291


title: lib288


title: lib286

value: MS posttreatment

value: N


title: lib289


title: lib285


title: lib284


title: lib283


title: lib282


title: lib280


title: lib281


title: lib279

value: MS pretreatment


title: lib275


title: lib276


title: lib273


title: lib278


title: lib272

value: Sepsis

value: Asian


title: lib271

value: NK


title: lib277


title: lib274


title: lib267


title: lib270


title: lib266


title: lib269


title: lib265


title: lib264


title: lib259

value: M


title: lib268

value: B-cells


title: lib261

value: Monocytes


title: lib255


title: lib263


title: lib260

value: Neutrophils


title: lib256


title: lib257


title: lib252

value: Type 1 Diabetes


title: lib251


title: lib249


title: lib254


title: lib247


title: lib250


title: lib246


title: lib245


title: lib244


title: lib248


title: lib262


title: lib241

value: Y

value: 3 weeks, oral


title: lib242

value: F


title: lib243


title: lib258


title: lib240


title: lib239


title: lib237


title: lib238


title: lib236


title: lib232


title: lib235


title: lib253


title: lib228

value: Healthy Control

value: Hispanic


title: lib229


title: lib234

value: White


title: lib233


title: lib230


title: lib231


title: lib227


title: lib226


title: lib225

value: Whole Blood


title: lib224


title: lib223

value: MS posttreatment


title: lib222

value: MS pretreatment


title: lib221


title: Bone Marrow Derived Macrophages

status: Public on Sep 19 2014

data_processing:
Sequenced reads were mapped to the mm9 gemone using Tophat v2.0.10 with parameters --no-coverage-search -g 1 -G mm9.refGene.gtf --library-type fr-firststrand -p 8
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated from strand specific bedGraphs using UCSC executeable bedGraphToBigWig

source_name: terminally differentiated primary cells

extract_protocol:
Cellular fractionation was performed on 2.0 x 107 cells. The chromatin pellet was resuspended in 50ul TRIzol and purified using QIAGEN’s RNeasy column. Chromatin RNA was subjected to rRNA removal with the Mouse/Human Ribominus kit (Invitrogen, Catalog No. K1550-02) and resuspended in 14ul RNase-free water. 200ng was used to construct libraries.
Strand specific cDNA libraries were generated using the Illumina TruSeq RNA Sample Prep Kit v2 with the inclusion of “deoxyuridine triphosphate (dUTP)” method

tag: strain background

tag: cell type

value: Bone Marrow Derived Macrophages

tag: molecule subtype

value: chromatin associated RNA


title: E14.5 Cortial Neurons

value: E14.5 Cortial Neurons


title: CD4+ CD8+ Thymocytes

value: CD4+ CD8+ Thymocytes


title: CCE

source_name: embryonic stem cells

value: Embryonic Stem cells


title: Lm_OlderAdult1_2hr

status: Public on Aug 09 2014

data_processing:
TopHat v1.3.3 was used from within the Galaxy Bioinformatics platform (https://main.g2.bx.psu.edu/), for mapping of mRNA libraries with the following parameters: tophat -p 4 -a 8 -m 0 -i 70 -I 500000 -g 1 --library-type fr-firststrand --no-novel-indels --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2
Genome graph tracks were generated by using the genomecoverageBed utility in the BedTools suite using the following parameters: –bg –split –ibam
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files contain continuous-valued sequencing data which were created for each sample and can be uploaded and viewed with the UCSC Genome Browser

source_name: peripheral blood

extract_protocol:
Human monocyte RNA was purified from monocytes after using TRIzol reagent (Invitrogen) and RNeasy Mini Kit (Qiagen) and eluted into 30 uL RNase-free water.  Libraries were prepared using 120 ng RNA input.
Illumina's TruSeq v2 library kit was used for library construction. All libraries were constructed per manufacturer's guidlines with the exception of generating strand-specific libraries according to the “deoxyuridine triphosphate (dUTP)” method (Levin et al., 2010).  An Illumina HiSeq 2000 (Illumina, San Diego, CA) was used for sequencing, with a single-end-sequencing length of 50 nt.

value: monocyte

tag: agent

value: Listeria monocytogenes


title: Lm_OlderAdult2_6hr


title: Lm_OlderAdult1_0hr


title: Lm_OlderAdult3_6hr


title: Lm_OlderAdult2_2hr


title: Lm_OlderAdult2_0hr


title: Lm_Adult3_2hr


title: Lm_Adult3_0hr


title: Lm_OlderAdult1_6hr


title: Lm_Adult2_6hr


title: Lm_OlderAdult3_0hr


title: Lm_Adult3_6hr


title: Lm_Adult1_0hr


title: Lm_Adult2_0hr


title: Lm_Adult1_2hr


title: Lm_Adult2_2hr


title: Lm_Adult1_6hr


title: Lm_Neonate3_2hr

source_name: umbilical cord blood


title: Lm_Neonate3_6hr


title: Lm_Neonate3_0hr


title: Lm_Neonate2_0hr


title: Lm_Neonate2_2hr


title: Lm_Neonate1_0hr


title: Lm_Neonate1_2hr


title: LPS_OlderAdult3_6hr

value: LPS


title: Lm_OlderAdult3_2hr


title: LPS_OlderAdult3_1hr


title: LPS_OlderAdult3_0hr


title: LPS_OlderAdult2_1hr


title: LPS_OlderAdult2_0hr


title: LPS_OlderAdult1_6hr


title: LPS_Adult3_1hr


title: LPS_Adult3_6hr


title: LPS_Adult3_0hr


title: LPS_Adult2_0hr


title: LPS_OlderAdult1_0hr


title: LPS_OlderAdult1_1hr


title: LPS_Adult1_1hr


title: Lm_Neonate2_6hr


title: LPS_Adult1_0hr


title: LPS_OlderAdult2_6hr


title: LPS_Adult2_1hr


title: Lm_Neonate1_6hr


title: LPS_Adult2_6hr


title: LPS_Neonate3_0hr


title: LPS_Neonate3_6hr


title: LPS_Adult1_6hr


title: LPS_Neonate2_1hr


title: LPS_Neonate3_1hr


title: LPS_Neonate1_0hr


title: LPS_Neonate2_0hr


title: LPS_Neonate2_6hr


title: LPS_Neonate1_1hr


title: LPS_Neonate1_6hr


title: IFNARKO120

status: Public on Jul 01 2012

data_processing:
Base calling was performed using HCS 1.3.8, RTA 1.10.36, Recipe Fragments 1.3.1/HiScanSQ 1.1.1 software bundle.
Reads were aligned to the mouse genome (mm9) using Tophat with the following parameters:-p 8 -a 8 -m 0 -i 70 -I 500000 -g 1 --library-type fr-unstranded- --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2
Per base report of genome coverage (Bedgraph) was obtained using the Bedtools suite.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph file values represent per base coverage of the genome, and was imported to UCSC Genome Browser to provide a visual representation of genome coverage

source_name: Macrophage

growth_protocol: Bone marrow from male mice were plated at a density of 7x10^5 cells/ml into DMEM containing 20% FBS supplemented with sodium pyruvate, L-glutamine and M-CSF. Media was changed on day three of differentiation. Adherent cells were scraped and replated at a density of 7x10^5 cells/mL into 10 cm plates on day five of differentiation. Cells were stimulated on day six.

extract_protocol: Total RNA was purified from Tri-Reagent using Qiagen RNeasy columns according to manufacturer protocol. 25 ug of total RNA from each sample was enriched for polyadenylated transcripts using the Micro-poly(A) purist kit (Ambion). Libraries were constructed from 100 ng of poly(A) RNA and were not strand specific.

treatment_protocol: Lipid A was added at a concentration of 100ng/ml to each 10 cm plate for the times indicated.

tag: strain

tag: tissue

value: bone marrow

tag: age

value: 6 weeks

tag: genotype

value: IFNAR-/-

tag: stimulation type

value: Lipid A

tag: stimulation time

value: 120 minutes


title: IFNARKO360

value: 360 minutes


title: IFNARKO30

value: 30 minutes


title: WT360

value: wild type


title: WT120


title: IFNARKO60

value: 60 minutes


title: IFNARKO0

value: unstimulated


title: WT30


title: WT0


title: TRIBAL rep3

status: Public on Feb 14 2014

description: TRIBALC

hyb_protocol: According to the protocols of the Centre for Applied Genomics (The Hospital for Sick Children, Toronto, Ontario, Canada)

source_name: TRIBAL, HepG2

growth_protocol: low glucose DMEM, 10% serum, pen/strep

extract_protocol: Roche total RNA isolation kit

treatment_protocol: Pool of HepG2 cells stably infected with lentiviruses expressing TRIBAL1 (lncRNA) or empty vector (PLVX)

tag: cell line

value: HepG2 Hepatoma cells

tag: genotype/variation

value: TRIBAL overexpression


title: Chromatin_120min

status: Public on May 03 2012

data_processing: BAM: Sequence reads were obtained and mapped to the mouse mm9 genome using Tophat. Uniquely mapping reads with two or fewer mismatches were retained.

growth_protocol: Bone marrow from mixed sex mice were plated at a density of 7x10^5 cells/ml into DMEM containing 20% FBS supplemented with sodium pyruvate, L-glutamine and M-CSF. Media was changed on day three of differentiation. Adherent cells were scraped and replated at a density of 1x10^6 cells/mL into 15 cm plates on day five of differentiation. Cells were stimulated on day six.

extract_protocol: Cells were fractionated according to the protocol described in Pandya-Jones and Black, RNA 2009. Briefly, cells were lysed in 0.15% NP40 buffer and spun over a sucrose cushion to obtain nuclei. Nuclei were lysed in buffer containing 1% NP40 and 1M urea. RNA from the cytoplasmic and nucleoplasmic lysates as well as the chromatin pellet was purified using Qiagen RNeasy columns according to manufacturer protocol. 10 ug of RNA from each sample was depleted of ribosomal RNA using the Invitrogen Human/Mouse Ribominus kit. Libraries were constructed from 500 ng of rRNA-depleted RNA using the dUTP method described in Levin et al, Nat Methods 2010 was used to generate strand-specific sequencing libraries.

treatment_protocol: Lipid A was added at a concentration of 100ng/ml to each 25 cm plate for the times indicated.

tag: subcellular fraction

value: Chromatin


title: CONTROL rep1

description: CONTROL A

scan_protocol: According to the protocols of the Centre for Applied Genomics (The Hospital for Sick Children, Toronto, Ontario, Canada)

source_name: CONTROL, HepG2

value: control


title: CONTROL rep2

description: CONTROL B

data_processing: According to the protocols of the Centre for Applied Genomics (The Hospital for Sick Children, Toronto, Ontario, Canada)


title: TRIBAL rep2

description: TRIBALB

label_protocol: According to the protocols of the Centre for Applied Genomics (The Hospital for Sick Children, Toronto, Ontario, Canada)


title: Chromatin_15min

value: 15 minutes


title: Chromatin_60min


title: CONTROL rep3

description: CONTROL C


title: TRIBAL rep1

description: TRIBALA


title: Chromatin_0min

value: 0 minutes


title: Rep3, TRIBAL ASO

description: Biological replicate 3 of 4, TRIBAL-specific oligo

hyb_protocol: Each experimental or control Cy-5 labeled cRNA sample was mixed with equimolar amount of Cy-3 labeled reference cRNA and were hybridized to Agilent SurePrint G3 Hmn GE 8×60K oligonucleotide microarrays (Agilent Technologies Inc., Mississauga, ON, Canada).

scan_protocol: Arrays were scanned on an Agilent G2505B scanner; Data from the scanned images were extracted using Agilent Feature Extraction software version 11

data_processing: A reference randomized block design was used to analyze gene expression microarray data which were normalized using LOcally WEighted Scatterplot Smoothing (LOWESS) regression modeling method

label_protocol: cyanine labelling using 200 ng total RNA (Agilent protocol)

growth_protocol: Cell culture, low glucose DMEM with 10% serum

extract_protocol: Roche High Pure RNA isolation kit

treatment_protocol: RNAimax treatment for with  antisense oligos for 48 h

value: Huh7 hepatoma cells

value: TRIB1 knockdown

source_name: Agilent's universal reference total RNA

tag: reference composition

value: Pooled RNA from 10 tissues


title: Rep4, TRIBAL ASO

description: Biological replicate 4 of 4, TRIBAL-specific oligo


title: Rep1, non-target ASO

description: Biological replicate 1 of 4, non-target oligo


title: Rep2, non-target ASO

description: Biological replicate 2 of 4, non-target oligo


title: Rep4, non-target ASO

description: Biological replicate 4 of 4, non-target oligo


title: Rep3, non-target ASO

description: Biological replicate 3 of 4, non-target oligo


title: Chromatin_30min


title: Rep1, TRIBAL ASO

description: Biological replicate 1 of 4, TRIBAL-specific oligo


title: Nucleoplasmic_30min

value: Nucleoplasmic


title: Rep2, TRIBAL ASO

description: Biological replicate 2 of 4, TRIBAL-specific oligo


title: Nucleoplasmic_60min

value: Lipid A


title: Nucleoplasmic_0min


title: WT60

value: bone marrow

value: 6 weeks


title: Nucleoplasmic_15min


title: Cytoplasmic_60min

value: Cytoplasmic


title: Nucleoplasmic_120min

value: 120 minutes


title: Cytoplasmic_15min


title: Cytoplasmic_0min


title: Cytoplasmic_30min

value: 30 minutes


title: Cytoplasmic_120min