title: Ifnar1_KO_LPS_4h_S53


title: Ifnar1_KO_LPS_4h_S52

status: Public on Jun 11 2014

type: SRA

city: New York City

first: Rahul

last: Satija

state: NY

address: 101 Avenue of the Americas

country: USA

institute: New York Genome Center

library_source: transcriptomic

data_processing:
We created a Bowtie index based on the UCSC knownGene (8) transcriptome, and aligned paired-end reads directly to this index using Bowtie v 0.12.7 with command line options -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 -a -m 200.
Next, we ran RSEM v1.11 with default parameters on these alignments to estimate expression levels. RSEM’s gene level expression estimates (tau) were multiplied by 1,000,000 to obtain transcript per million (TPM) estimates for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: matrix of gene expression estimates across all samples

molecule: polyA RNA

organism: Mus musculus

source_name: BMDC (Ifnar1-/-, 4h LPS stimulation)

growth_protocol: Cells were cultured and stimulated as previously described (Amit et. al 2009)

extract_protocol: cDNA from each sample was prepared using the SMARTer cDNA synthesis (Clontech). RNA libraries were prepared for sequencing using Nextera XT (Illumina).

tag: strain

tag: cell type

value: BMDC

tag: stimulation

value: Ifnar1-/-, 4h LPS stimulation


title: Ifnar1_KO_LPS_4h_S50


title: Ifnar1_KO_LPS_4h_S45


title: Ifnar1_KO_LPS_4h_S44


title: Ifnar1_KO_LPS_4h_S41


title: Stat1_KO_LPS_4h_S50

source_name: BMDC (Stat1-/-, 4h LPS stimulation)

value: Stat1-/-, 4h LPS stimulation


title: Ifnar1_KO_LPS_4h_S43


title: Ifnar1_KO_LPS_4h_S42


title: Ifnar1_KO_LPS_4h_S36


title: Ifnar1_KO_LPS_4h_S39


title: Ifnar1_KO_LPS_4h_S40


title: Ifnar1_KO_LPS_4h_S38


title: Ifnar1_KO_LPS_4h_S37


title: Ifnar1_KO_LPS_4h_S34


title: Ifnar1_KO_LPS_4h_S33


title: Ifnar1_KO_LPS_4h_S27


title: Ifnar1_KO_LPS_4h_S29


title: Ifnar1_KO_LPS_4h_S32


title: Ifnar1_KO_LPS_4h_S31


title: Ifnar1_KO_LPS_4h_S49


title: Ifnar1_KO_LPS_4h_S47


title: Ifnar1_KO_LPS_4h_S48


title: Ifnar1_KO_LPS_4h_S30


title: Ifnar1_KO_LPS_4h_S21


title: Ifnar1_KO_LPS_4h_S46


title: Ifnar1_KO_LPS_4h_S22


title: Ifnar1_KO_LPS_4h_S19


title: Ifnar1_KO_LPS_4h_S25


title: Ifnar1_KO_LPS_4h_S17


title: Ifnar1_KO_LPS_4h_S20


title: Ifnar1_KO_LPS_4h_S16


title: Ifnar1_KO_LPS_4h_S18


title: Ifnar1_KO_LPS_4h_S23


title: Ifnar1_KO_LPS_4h_S11


title: Ifnar1_KO_LPS_4h_S14


title: Ifnar1_KO_LPS_4h_S13


title: Ifnar1_KO_LPS_4h_S12


title: Ifnar1_KO_LPS_4h_S35


title: Ifnar1_KO_LPS_4h_S26


title: Ifnar1_KO_LPS_4h_S9


title: Ifnar1_KO_LPS_4h_S7


title: Ifnar1_KO_LPS_4h_S6


title: Ifnar1_KO_LPS_4h_S28


title: Ifnar1_KO_LPS_4h_S24


title: Ifnar1_KO_LPS_4h_S5


title: Ifnar1_KO_LPS_4h_S8


title: Ifnar1_KO_LPS_4h_S4


title: IFNB_2h_S95

source_name: BMDC (2h IFN-B Stimulation)

value: 2h IFN-B Stimulation


title: IFNB_2h_S94


title: Ifnar1_KO_LPS_4h_S2


title: Ifnar1_KO_LPS_4h_S3


title: IFNB_2h_S96


title: Ifnar1_KO_LPS_4h_S1


title: IFNB_2h_S93


title: IFNB_2h_S92


title: Ifnar1_KO_LPS_4h_S10


title: Ifnar1_KO_LPS_4h_S15


title: IFNB_2h_S87


title: IFNB_2h_S86


title: IFNB_2h_S88


title: IFNB_2h_S85


title: IFNB_2h_S91


title: IFNB_2h_S84


title: IFNB_2h_S83


title: IFNB_2h_S80


title: IFNB_2h_S79


title: IFNB_2h_S82


title: IFNB_2h_S76


title: IFNB_2h_S74


title: IFNB_2h_S73


title: IFNB_2h_S75


title: IFNB_2h_S68


title: IFNB_2h_S67


title: IFNB_2h_S90


title: IFNB_2h_S71


title: IFNB_2h_S65


title: IFNB_2h_S69


title: IFNB_2h_S70


title: IFNB_2h_S66


title: IFNB_2h_S61


title: IFNB_2h_S63


title: IFNB_2h_S59


title: IFNB_2h_S56


title: IFNB_2h_S64


title: IFNB_2h_S57


title: IFNB_2h_S78


title: IFNB_2h_S53


title: IFNB_2h_S89


title: IFNB_2h_S60


title: IFNB_2h_S52


title: IFNB_2h_S77


title: IFNB_2h_S51


title: IFNB_2h_S54


title: IFNB_2h_S55


title: IFNB_2h_S62


title: IFNB_2h_S72


title: IFNB_2h_S49


title: IFNB_2h_S48


title: IFNB_2h_S47


title: IFNB_2h_S41


title: IFNB_2h_S46


title: IFNB_2h_S58


title: IFNB_2h_S45


title: IFNB_2h_S40


title: IFNB_2h_S37


title: IFNB_2h_S42


title: IFNB_2h_S44


title: IFNB_2h_S39


title: IFNB_2h_S38


title: IFNB_2h_S34


title: IFNB_2h_S32


title: IFNB_2h_S35


title: IFNB_2h_S30


title: IFNB_2h_S36


title: IFNB_2h_S26


title: IFNB_2h_S50


title: IFNB_2h_S25


title: IFNB_2h_S33


title: IFNB_2h_S29


title: IFNB_2h_S31


title: IFNB_2h_S27


title: IFNB_2h_S28


title: IFNB_2h_S24


title: IFNB_2h_S23


title: IFNB_2h_S20


title: IFNB_2h_S19


title: IFNB_2h_S21


title: IFNB_2h_S22


title: IFNB_2h_S18


title: IFNB_2h_S17


title: IFNB_2h_S14


title: IFNB_2h_S16


title: IFNB_2h_S12


title: IFNB_2h_S15


title: IFNB_2h_S10


title: IFNB_2h_S13


title: IFNB_2h_S9


title: IFNB_2h_S6


title: IFNB_2h_S11


title: IFNB_2h_S7


title: IFNB_2h_S43


title: IFNB_2h_S4


title: IFNB_2h_S5


title: IFNB_2h_S1


title: On_Chip_Stimulation_LPS_4h_S93

source_name: BMDC (On Chip 4h LPS Stimulation)

value: On Chip 4h LPS Stimulation


title: On_Chip_Stimulation_LPS_4h_S96


title: On_Chip_Stimulation_LPS_4h_S94


title: On_Chip_Stimulation_LPS_4h_S95


title: On_Chip_Stimulation_LPS_4h_S91


title: On_Chip_Stimulation_LPS_4h_S92


title: On_Chip_Stimulation_LPS_4h_S90


title: On_Chip_Stimulation_LPS_4h_S89


title: On_Chip_Stimulation_LPS_4h_S88


title: On_Chip_Stimulation_LPS_4h_S85


title: On_Chip_Stimulation_LPS_4h_S86


title: On_Chip_Stimulation_LPS_4h_S87


title: On_Chip_Stimulation_LPS_4h_S82


title: On_Chip_Stimulation_LPS_4h_S84


title: On_Chip_Stimulation_LPS_4h_S83


title: IFNB_2h_S8


title: On_Chip_Stimulation_LPS_4h_S78


title: On_Chip_Stimulation_LPS_4h_S77


title: On_Chip_Stimulation_LPS_4h_S80


title: On_Chip_Stimulation_LPS_4h_S79


title: On_Chip_Stimulation_LPS_4h_S76


title: On_Chip_Stimulation_LPS_4h_S75


title: On_Chip_Stimulation_LPS_4h_S66


title: On_Chip_Stimulation_LPS_4h_S74


title: On_Chip_Stimulation_LPS_4h_S64


title: On_Chip_Stimulation_LPS_4h_S73


title: IFNB_2h_S2


title: On_Chip_Stimulation_LPS_4h_S72


title: On_Chip_Stimulation_LPS_4h_S70


title: On_Chip_Stimulation_LPS_4h_S69


title: On_Chip_Stimulation_LPS_4h_S65


title: On_Chip_Stimulation_LPS_4h_S63


title: On_Chip_Stimulation_LPS_4h_S67


title: On_Chip_Stimulation_LPS_4h_S56


title: On_Chip_Stimulation_LPS_4h_S68


title: On_Chip_Stimulation_LPS_4h_S55


title: On_Chip_Stimulation_LPS_4h_S59


title: On_Chip_Stimulation_LPS_4h_S61


title: On_Chip_Stimulation_LPS_4h_S71


title: On_Chip_Stimulation_LPS_4h_S58


title: On_Chip_Stimulation_LPS_4h_S57


title: On_Chip_Stimulation_LPS_4h_S60


title: On_Chip_Stimulation_LPS_4h_S51


title: On_Chip_Stimulation_LPS_4h_S52


title: On_Chip_Stimulation_LPS_4h_S49


title: On_Chip_Stimulation_LPS_4h_S53


title: On_Chip_Stimulation_LPS_4h_S47


title: On_Chip_Stimulation_LPS_4h_S50


title: On_Chip_Stimulation_LPS_4h_S48


title: On_Chip_Stimulation_LPS_4h_S45


title: On_Chip_Stimulation_LPS_4h_S44


title: On_Chip_Stimulation_LPS_4h_S42


title: On_Chip_Stimulation_LPS_4h_S41


title: On_Chip_Stimulation_LPS_4h_S43


title: On_Chip_Stimulation_LPS_4h_S40


title: On_Chip_Stimulation_LPS_4h_S39


title: On_Chip_Stimulation_LPS_4h_S36


title: On_Chip_Stimulation_LPS_4h_S34


title: On_Chip_Stimulation_LPS_4h_S38


title: On_Chip_Stimulation_LPS_4h_S33


title: On_Chip_Stimulation_LPS_4h_S32


title: On_Chip_Stimulation_LPS_4h_S28


title: On_Chip_Stimulation_LPS_4h_S26


title: On_Chip_Stimulation_LPS_4h_S27


title: On_Chip_Stimulation_LPS_4h_S29


title: On_Chip_Stimulation_LPS_4h_S30


title: On_Chip_Stimulation_LPS_4h_S24


title: On_Chip_Stimulation_LPS_4h_S54


title: On_Chip_Stimulation_LPS_4h_S23


title: On_Chip_Stimulation_LPS_4h_S22


title: On_Chip_Stimulation_LPS_4h_S20


title: On_Chip_Stimulation_LPS_4h_S21


title: On_Chip_Stimulation_LPS_4h_S17


title: On_Chip_Stimulation_LPS_4h_S19


title: On_Chip_Stimulation_LPS_4h_S16


title: On_Chip_Stimulation_LPS_4h_S18


title: On_Chip_Stimulation_LPS_4h_S37


title: On_Chip_Stimulation_LPS_4h_S15


title: On_Chip_Stimulation_LPS_4h_S13


title: On_Chip_Stimulation_LPS_4h_S8


title: On_Chip_Stimulation_LPS_4h_S10


title: On_Chip_Stimulation_LPS_4h_S35


title: On_Chip_Stimulation_LPS_4h_S6


title: On_Chip_Stimulation_LPS_4h_S9


title: On_Chip_Stimulation_LPS_4h_S5


title: On_Chip_Stimulation_LPS_4h_S4


title: On_Chip_Stimulation_LPS_4h_S3


title: On_Chip_Stimulation_LPS_4h_S1


title: On_Chip_Stimulation_LPS_4h_S25


title: Flag_RBM47_HITS_CLIP_1

city: New York

first: Christina

middle: Beate

last: Marney

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

description:
Protocol: HITS-CLIP
non-clonal brain metastatic MDA-MB_231 breast cancer cell line derivative expression Flag-tagged wild-type RBM47

data_processing:
filtering (min:0-6:20,mean:5-29:20)
collapsing of exact sequences
stripping of degenerate linker and barcode (14nt, RBM47_1 N(6)-ACGATGTC, RBM47_2 N(6)-AGTTTCGC)
removal of 3' polyA (trim A(20) )
alignment with novoalign (unambigous mapping)
collapsing of PCR duplicates
Genome_build: hg18
Supplementary_files_format_and_content: txt file of RBM47 reproducible, robust binding sites

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells maintained in DMEM supplemented with 10% FBS, 1% sodium pyruvate, 1% penicillin-streptomycin and 0.4% fungizone, 5% CO2, 37C

extract_protocol:
Cells were UV irradiated and subjected to Flag-RBM47 HITS-CLIP
Partial RNAse digestion, A-tailing and PCR amplificiation. Flag-RBM47 bound fragments were reverse transcribled using an oligodT primer containing 5' degenerate, barcoded linker sequence and 3' adapter sequences. cDNA libraries were then generated as described in PMID: 24613350

treatment_protocol: 1ng/ml doxycycline for three days prior to UV irradiation

tag: cell line

value: MDA-MB-231 derivative

tag: tissue

value: breast cancer cell line

tag: transgene


title: On_Chip_Stimulation_LPS_4h_S2


title: RBM47_3

description: Clonal brain metastatic MDA-MB_231 breast cancer cell line derivative Flag-tagged RBM47

data_processing:
FastQ groomer (Galaxy)
alignment with Tophat (unambigous mapping; mean inner distance: 20; st.dev.: 20)
inference of exon junctions (Bayesian method)
summerize alternative splicing events (as in PMID: 22884328)
calculation of average change in inclusion of cassette exons, fishers exact test to compare total reads mapping to included and excluded alternative isoforms in control and RBM47 expressing cells.
Genome_build: hg 18
Supplementary_files_format_and_content: xlsx file containing Gene ID (Entrez), Gene Symbol, genomic coordiates spanning the alternatively spliced region, Inclusion Rate per sample, average inclusion rate Control, average inculsion rate RBM47 expressing cells, average change in inclusion, total RNAseq reads mapping to isoform 1 and 2 in control and RBM47 respectively, odds ratio and p-value derived from Fisher's exact test.

extract_protocol:
Total RNA was prepared via trizol extraction, RQ1 DNAse treatment, Phenol Chloroform extraction and isopropanol precipitation.
Illumina High-throughput TruSeq RNA sample Preparation v2: polyA selection and size selection: 50 - 200bp

treatment_protocol: 10ng/ml doxycycline for three days prior RNA extraction

tag: vector

value: pRetroX-Tight-Pur Flag WT RBM47


title: Flag_RBM47_HITS_CLIP_2


title: RBM47_1


title: RBM47_2


title: Control_3

description: non-clonal brain metastatic MDA-MB_231 breast cancer cell line derivative empty vector control

value: pRetroX-Tight-Pur


title: 10-09-A104a

city: Salt Lake City

first: Katherine

middle: E

last: Varley

state: UT

address: 2000 Circle of Hope, Room 3719

department: Department of Oncological Sciences

institute: Huntsman Cancer Institute University of Utah

data_processing:
TopHat v1.4.1 was used to align 50 million read pairs in the fastq files using with the options –r100 --mate-std-dev 75. GENCODE V9  was used as the transcriptome-index
Cufflinks 1.3.0 was used to calculate gene expression values (Fragments Per Kilobase of transcript Per Million reads, FPKMs) for each GENCODE V9 transcript using the –u option. It generated a gene.fpkm file listing the gene expression for each gene in each sample.
ChimeraScan 0.4.5a was used to align reads and identify fusion transcripts in each of the sequencing libraries using default parameters. It generated a bedpe file listing the fusions detected in each sample.
The ChimeraScan runconfig.xml file generated from running with default parameters included the following variables:   <num_processors>12</num_processors>    <quals>sanger</quals>    <keep_tmp>True</keep_tmp>    <bowtie_path />    <bowtie_args>--best --strata</bowtie_args>    <discord_bowtie_args>--best</discord_bowtie_args>    <multihits>100</multihits>    <mismatches>2</mismatches>    <discord_mismatches>3</discord_mismatches>    <segment_length>25</segment_length>    <trim5>0</trim5>    <trim3>0</trim3>    <min_fragment_length>0</min_fragment_length>    <max_fragment_length>1000</max_fragment_length>    <library_type>fr-unstranded</library_type>    <isize_mean>200</isize_mean>    <isize_stdev>40</isize_stdev>    <homology_mismatches>2</homology_mismatches>    <anchor_min>4</anchor_min>    <anchor_length>8</anchor_length>    <anchor_mismatches>0</anchor_mismatches>    <filter_unique_frags>2.0</filter_unique_frags>    <filter_isize_prob>0.01</filter_isize_prob>    <filter_isoform_fraction>0.01</filter_isoform_fraction>
Genome_build: hg19

source_name: Uninvolved Breast Tissue Adjacent to TNBC Primary Tumor

growth_protocol: De-identified fresh frozen breast cancer specimens, fresh frozen matched uninvolved breast tissue adjacent to tumors, and fresh frozen breast tissue specimens from reduction mammoplasty procedures were obtained from the University of Alabama at Birmingham’s Comprehensive Cancer Center Tissue Procurement Shared Facility.  The specific aliquots of specimens provided for research were chosen based on their quality control by board certified pathologists. After identification by quality control, the uninvolved breast tissue aliquots were not further macro-dissected.  The breast tumor specimens were macro-dissected by the pathologists at the Tissue Procurement Shared Facility to enrich for tumor cell content and remove adjacent normal tissue.  The 28 breast cancer cell lines were cultured as described previously (Oliver et al. Effect of anti-DR5 and chemotherapy on basal-like breast cancer. Breast Cancer Res Treat. 2012 Jun;133(2):417-26).

extract_protocol:
The frozen breast tissue specimens were weighed, transferred to a 15 mL conical tube containing ceramic beads, and RLT Buffer  (Qiagen) plus 1% BME was added so that the tube contained 35 uL of buffer for each milligram of tissue.  The conical tubes containing tissue, ceramic beads and buffer were then shaken in a MP Biomedicals FastPrep machine until the tissue was visibly homogenized (90 seconds at 6.5 meters per second).  The homogenized tissue was stored at -80°C.  Total RNA was extracted from 5 million cultured cells or 350 uL of tissue homogenate (equivalent to 10 mg of tissue) using the Norgen Animal Tissue  RNA Purification Kit (Norgen Biotek Corporation). Cell lysate was treated with Proteinase K before it was applied to the column and on-column DNAse  treatment was performed according to the manufacturer’s instructions. Total RNA was eluted from the columns and quantified using the Qubit RNA Assay Kit and the Qubit 2.0 fluorometer (Invitrogen).
RNA-seq libraries for each sample were constructed from 250 ng total RNA using the polyA selection and transposase-based non-stranded library construction (Tn-RNA-seq) described previously (Gertz et al. Transposase mediated construction of RNA-seq libraries.2012. Genome Res 22 (1):134-141). RNA-seq libraries were barcoded during PCR using Nextera barcoded primers according to the manufacturer (Epicentre). The RNA-seq libraries were quantified using the Qubit dsDNA HS Assay Kit and the Qubit 2.0  fluorometer (Invitrogen) and three barcoded libraries were pooled in equimolar quantities for sequencing. The pooled libraries were sequenced on an Illumina HiSeq 2000 sequencing machine using paired-end 50 bp reads and a 6 bp index  read, and we obtained at least 50 million read pairs from each library.


title: 02-10-A336b

value: Uninvolved Breast Tissue Adjacent to TNBC Primary Tumor


title: 02-04-A023a


title: 01-09-A216a


title: 01-12-A229c


title: 03-09-A088a


title: Control_1


title: On_Chip_Stimulation_LPS_4h_S11


title: 04-08-A021a


title: 04-06-A165a


title: On_Chip_Stimulation_LPS_4h_S12


title: 03-12-A155a


title: 03-10-A452a


title: 04-08-A102c


title: 03-09-A269c


title: 10-11-A139a


title: 02-06-A265a


title: 09-06-A090a


title: 04-01-A170a


title: 03-12-A387a


title: Control_2


title: 11-08-A057b

source_name: Reduction Mammoplasty - No known cancer

value: Reduction Mammoplasty - No known cancer


title: 11-08-A076b


title: 10-04-A001b


title: 03-12-A223a


title: 02-03-A079c


title: 11-01-A098b


title: 03-06-A284a


title: 09-10-A058a

source_name: Uninvolved Breast Tissue Adjacent to ER+ Primary Tumor


title: 09-03-A119a

value: Uninvolved Breast Tissue Adjacent to ER+ Primary Tumor


title: 09-09-A107b


title: 09-12-A183c


title: 10-01-A052a


title: 04-07-A415c


title: 08-02-A356a


title: 06-02-121a


title: 05-09-A160a


title: 05-07-A187a


title: 05-01-A258a


title: 07-12-A271a


title: 03-03-A118a


title: 04-09-A067a


title: 04-08-A206a


title: 06-01-A010b


title: 04-07-A434a


title: 03-02-A014a


title: 02-06-A429a


title: 02-05-A204a


title: 02-01-A056b


title: 03-01-A342a


title: 01-05-A360a


title: 01-05-A183a


title: 01-07-A283b


title: 09-11-A113b


title: 01-03-A208a


title: 01-02-A057b


title: 06-04-A286b

source_name: Triple Negative Breast Cancer Primary Tumor


title: 10-11-A138B

value: Triple Negative Breast Cancer Primary Tumor


title: 04-07-A389b


title: 02-10-A335a


title: 01-01-A062a


title: 03-12-A154a


title: 01-02-A326a


title: 03-07-A523B


title: 03-09-A087c


title: 03-03-A070a


title: 04-08-A020B


title: 03-12-A222a


title: 00-11-A038a


title: 04-01-A168c


title: 02-06-A263c


title: 04-08-A019a


title: 04-08-A101c


title: 01-08-A054a


title: 03-06-A283b


title: 05-09-A223a


title: 10-06-A120c


title: 04-08-A183c


title: 02-03-A078a


title: 09-06-A139A


title: 03-12-A386a


title: 05-05-A201a


title: 08-10-A297d


title: 04-06-A164a


title: 03-02-A158a


title: 09-06-A089A


title: 01-04-A048C


title: 09-06-A120A


title: 09-12-A158B


title: 09-03-A053A


title: 01-09-A215b


title: 03-11-A307c


title: 05-12-A078b


title: 02-06-A195a


title: 05-04-A096a


title: 06-06-A277a


title: 04-07-A416b


title: 03-10-A451c


title: 09-11-A112a

source_name: ER+ Breast Cancer Primary Tumor

value: ER+ Breast Cancer Primary Tumor


title: 09-05-A135a


title: 09-05-A149a


title: 06-01-A009b


title: 10-01-A051a


title: 02-01-A055b


title: 09-03-A118a


title: 09-01-A214e


title: 08-01-A301a


title: 07-12-A271b


title: 08-08-A142a


title: 10-07-A138


title: 10-10-A177A


title: 07-10-A110a


title: 10-09-A101A


title: 07-11-A250a


title: 05-11-A240b


title: 05-09-A159a


title: 05-07-A186a


title: 03-09-A268c


title: 09-10-A057a


title: 09-09-A106a


title: 03-03-A117b


title: 04-09-A066b


title: 04-07-A432a


title: 08-02-A355a


title: 02-01-A013a


title: 02-06-A431a


title: 04-08-A204c


title: 03-03-A069a


title: 03-02-A013a


title: 08-09-A192a


title: 02-05-A203b


title: 01-02-A325a


title: 02-04-A362a


title: 04-07-A414a


title: 01-02-A056a


title: 00-11-A037b


title: 05-01-A256a


title: SUM-102

source_name: Breast Cancer Cell Line

value: Breast Cancer Cell Line


title: 01-07-A281b


title: 01-05-A359a


title: 2-LMP


title: 01-05-A181a


title: 01-03-A373a


title: HCC-1937


title: 01-03-A207a


title: ZR-75-30


title: 01-01-A061a


title: HCC-1569


title: 03-01-A341c


title: BT-20


title: HCC-1187


title: HCC-70


title: SUM-149


title: MDA-MB-157


title: HCC-1599


title: T-47-D


title: MDA-MB-436


title: MCF-7


title: HCC-1954


title: HCC-1143


title: MDA-MB-134


title: MDA-MB-361


title: MDA-MB-468


title: MDA-MB-231


title: BT-549


title: HCC-38


title: BT-474


title: MDA-MB-453


title: ZR-75-1


title: BJ_p53_IR

city: Copenhagen

first: Kristine

last: Williams

address: Ole Maaløes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

library_source: genomic

data_processing:
No filtering of the raw reads were performed prior to alignment.
Raw sequence reads were mapped to the mouse genome using the the BOWTIE tool (version 0.12.7) with default parameters except:  -S -m 1
SAM format alignment files were converted to BAM format using “samtools view”
Peaks/binding sites were called using the Macs2 program with default parameters (“-g hs”) and the IgG as control
Genome_build: hg18
Supplementary_files_format_and_content: Raw files are given BAM format (includes unaligned reads). BAM format files can be converted to FASTQ format. Peaks are given in BED3 format

molecule: genomic DNA

source_name: BJ_DNA damage_p53

growth_protocol: A telomerase-immortalized version of the human diploid BJ fibroblast cell line were cultured in D-MEM (Gibco) supplemented with 10% FBS (Hyclone), penicillin and streptomycin

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. The JMJD3 antibody was generated in rabbits, using affinity-purified GST-JMJD3 (amino acids 798 1095) as described in (PMID 19451217).
Libraries were prepared according to Illumina's instructions.

treatment_protocol: To generate DNA damage, BJ cells were exposed to 10 Gy of ionizing radiation (IR) delivered by X-ray generators and harvested for ChIP after 6 h

value: BJ

value: Human diploid foreskin fibroblasts (BJ) immortalized with hTERT

tag: exposed to

value: 10 Gy of ionizing radiation (IR)

tag: chip antibody

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: BJ_p53_ND

value: none (untreated control)


title: MUT3-dox-25

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

description: Single-cell derived clone (MUT3) of the MDA231 breast cancer cell line transduced with doxycycline-inducible RBM47-I281fs mutant.

data_processing:
Read alignment: Raw FASTQ reads are aligned to human genome (Build hg19) with STAR2.3.0 using default settings.
Expression levels: Reads mapped to each transcript are counted with HTSeq v0.5.4 using default settings.
SAM and HTSeq
Genome_build: GRCh37
Supplementary_files_format_and_content: Normalized read counts mapped to each gene/transcript.

source_name: breast cancer cell line clone, RBM47-I281fs mutant, 25 ng/ml doxycycline

growth_protocol: Cancer cells grown under standard tissue culture conditions.

extract_protocol:
PrepEase® RNA Spin Kit (USB).
After quality control with Agilent BioAnalyzer, total RNA underwent polyA selection and TruSeq library preparation according to instruction provided by Illumina. Samples were barcoded and run on a HiSeq 2000 in a 75bp/75bp paired-end run.

treatment_protocol: Cells treated with increasing concentrations of doxycycline.

tag: doxycycline concentration

value: 25 ng/ml


title: BJ_JMJD3_IR

source_name: BJ_DNA damage_JMJD3

tag: chip antibody ref.


title: MUT3-dox-1

source_name: breast cancer cell line clone, RBM47-I281fs mutant, 1 ng/ml doxycycline

value: 1 ng/ml


title: DY36T2


title: MUT3-dox-5

source_name: breast cancer cell line clone, RBM47-I281fs mutant, 5 ng/ml doxycycline

value: 5 ng/ml


title: WT10-dox-5

description: Single-cell derived clone (WT10) of the MDA231 breast cancer cell line transduced with doxycycline-inducible wildtype RBM47.

source_name: breast cancer cell line clone, WT RBM47, 5 ng/ml doxycycline

value: breast cancer cell line


title: BJ_JMJD3_ND


title: MUT3-dox-2.5

source_name: breast cancer cell line clone, RBM47-I281fs mutant, 2.5 ng/ml doxycycline

value: 2.5 ng/ml


title: MUT3-dox-0

source_name: breast cancer cell line clone, RBM47-I281fs mutant, 0 ng/ml doxycycline

value: 0 ng/ml


title: SUM-159


title: WT6-dox-25

description: Single-cell derived clone (WT6) of the MDA231 breast cancer cell line transduced with doxycycline-inducible wildtype RBM47.

source_name: breast cancer cell line clone, WT RBM47, 25 ng/ml doxycycline


title: N254_4

city: London

first: Gitta

last: Stockinger

address: The Ridgeway

department: Division of Molecular Immunology

country: United Kingdom

institute: National Institute for Medical Research

data_processing:
Illumina Casava1.9 software used for basecalling.
Reads pairs were mapped using bowtie version 0.12.7 with parameters "-v 3 -a --best -y -I 0 -X 10000" to the transcriptome of GRCh37
Reads mapping uniquely to a gene were counted, and normalised by the total reads per library.
Genome_build: GRCh37
Supplementary_files_format_and_content: Files ps_tt_gel_raw.txt (text, tab-delimit, read counts per gene) and ps_tt_gel_norm.txt (text, tab-delimit, normalised read counts per gene).  Boths files are linked as supplementary files on the Series record.

source_name: Healthy_N254, Healthy, Antagonist

growth_protocol: Eight psoriatic patients of European descendent (5 males, 3 females; mean age 52 years, range 30-63 years) not receiving any systemic treatment at the time of visit were recruited at the Psoriasis-Center, University Medical Center Schleswig-Holstein, Kiel (Germany) following an examination by an expert clinician; one 6 mm full-thickness skin biopsy was obtained from the margin of a lesion and one from non lesional skin at least 5 cm apart from any psoriatic lesion at the same anatomical site. Full patient demographics are shown in Supplementary Table 1. Four 5 mm full-thickness skin biopsies were obtained from discarded healthy skin from female donors of European descendent (mean age 51 years, range 36-74 years) undergoing plastic surgery procedures at Guy’s and St. Thomas’ Hospital, London (UK).

extract_protocol:
Total RNA from human skin was obtained using the Mirvana Kit (Life Technologies) according to the manufacturer’s instructions
cDNA libraries were prepared using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's instructions.

treatment_protocol: All lesional and non lesional skin biopsies were quartered and one quarter of each was stored in RNA-later (Life Technologies) at 4oC until further use. The remaining three quarters were cultured with either 0.1% DMSO (vehicle control), the AhR agonist FICZ (250 nM) or the AhR antagonist CH-2233191 (3 μM) in IMDM (Sigma) containing 2% Pen-Strep-Gln solution (Sigma) and 10% knockout Serum replacement factor (Life Technologies) at 37°C in humidified 5% CO2/95% air for 16h. Skin biopsies from healthy donors were processed in the same ways as those of patients.

tag: patient

tag: patient id

tag: gender

value: F

tag: age

tag: tissue/treatment id

value: Healthy

tag: treatment

value: Antagonist


title: WT10-dox-0

source_name: breast cancer cell line clone, WT RBM47, 0 ng/ml doxycycline

tag: cell type


title: WT10-dox-2.5

source_name: breast cancer cell line clone, WT RBM47, 2.5 ng/ml doxycycline

tag: cell line


title: WT10-dox-1

source_name: breast cancer cell line clone, WT RBM47, 1 ng/ml doxycycline


title: WT6-dox-1


title: N254_3

source_name: Healthy_N254, Healthy, Agonist

tag: tissue

value: Agonist


title: WT6-dox-2.5

tag: transgene


title: BJ_IgG_ND

value: Rabbit IgG

value: Sigma-Aldrich


title: WT6-dox-0


title: N253_4

source_name: Healthy_N253, Healthy, Antagonist


title: N253_3

source_name: Healthy_N253, Healthy, Agonist


title: N254_2

source_name: Healthy_N254, Healthy, Culture/DMSO

value: Culture/DMSO


title: N253_1

source_name: Healthy_N253, Healthy, Untreated

value: Untreated


title: N253_2

source_name: Healthy_N253, Healthy, Culture/DMSO


title: N252_4

source_name: Healthy_N252, Healthy, Antagonist


title: N254_1

source_name: Healthy_N254, Healthy, Untreated


title: WT10-dox-25


title: N252_1

source_name: Healthy_N252, Healthy, Untreated


title: N250_3

source_name: Healthy_N250, Healthy, Agonist


title: N250_4

source_name: Healthy_N250, Healthy, Antagonist


title: N252_2

source_name: Healthy_N252, Healthy, Culture/DMSO


title: N250_1

source_name: Healthy_N250, Healthy, Untreated


title: N252_3

source_name: Healthy_N252, Healthy, Agonist


title: N248_3

source_name: Healthy_N248, Healthy, Agonist


title: N248_2

source_name: Healthy_N248, Healthy, Culture/DMSO


title: SK-BR-3

source_name: Breast Cancer Cell Line

value: Breast Cancer Cell Line


title: N248_4

source_name: Healthy_N248, Healthy, Antagonist


title: WT6-dox-5

source_name: breast cancer cell line clone, WT RBM47, 5 ng/ml doxycycline


title: N248_1

source_name: Healthy_N248, Healthy, Untreated


title: K9_4

source_name: Disease_K9, Lesion, Antagonist

value: M

value: Lesion


title: N250_2

source_name: Healthy_N250, Healthy, Culture/DMSO


title: Wild type -nucleosomes 1500U

city: Bethesda

first: David

middle: Johannes

last: Clark

state: MD

address: 6 Center Drive Bldg 6A Rm 2A02

department: DDB

institute: NICHD, NIH

description: Biological replicate 2 (digested with 1500U MNase)

data_processing:
Nucleosome sequences were aligned to the yeast genome (SacCer2) using Bowtie2.
Nucleosome occupancy maps were created using programs described by Cole et al. (2011) Nucleic Acids Res. 39, 9521-9535. The processed data were converted to the bigwig files supplied here.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: All strains were grown to mid-log phase (OD600 about 0.8) at 30 degC in synthetic complete medium, except MCY3860, which was grown in galactose and then switched to glucose, in which it arrested at OD ~ 0.8 (due to depletion of the essential Rsc8/Swh3 protein)

extract_protocol:
Nuclei were digested with micrococcal nuclease. Mono-nucleosomal DNA was gel-purified.
The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.

tag: strain

tag: genotype/variation

value: MATalpha his3-delta-200 lys2-801 leu2-3,112 ura3-52

value: digested with 1500U MNase


title: K9_8

source_name: Disease_K9, Nonlesion, Antagonist

value: Nonlesion


title: Wild type -nucleosomes 900U

description: Biological replicate 2 (digested with 900U MNase)

value: digested with 900U MNase


title: K8_8

source_name: Disease_K8, Nonlesion, Antagonist


title: K9_7

source_name: Disease_K9, Nonlesion, Agonist


title: K8_7

source_name: Disease_K8, Nonlesion, Agonist


title: K9_1

source_name: Disease_K9, Lesion, Untreated


title: K9_5

source_name: Disease_K9, Nonlesion, Untreated


title: K9_2

source_name: Disease_K9, Lesion, Culture/DMSO


title: K8_5

source_name: Disease_K8, Nonlesion, Untreated


title: K8_6

source_name: Disease_K8, Nonlesion, Culture/DMSO


title: K8_4

source_name: Disease_K8, Lesion, Antagonist


title: Wild type -nucleosomes

description: Biological replicate 1


title: K8_2

source_name: Disease_K8, Lesion, Culture/DMSO


title: Rsc8-depleted - nucleosomes

description: Biological replicate 1

value: MATalpha swh3-delta-1::HIS3 his3-delta-200 lys2-801 ura3-52 (pGAL::SWH3-URA3)


title: Rsc8-depleted - nucleosomes  1300U

description: Biological replicate 2 (digested with 1300U MNase)

value: digested with 1300U MNase


title: K8_3

source_name: Disease_K8, Lesion, Agonist


title: Rsc8-depleted - nucleosomes 1100U

description: Biological replicate 2 (digested with 1100U MNase)

value: digested with 1100U MNase


title: K8_1

source_name: Disease_K8, Lesion, Untreated


title: K6_4

source_name: Disease_K6, Lesion, Antagonist

value: F


title: K6_6

source_name: Disease_K6, Nonlesion, Culture/DMSO


title: K6_7

source_name: Disease_K6, Nonlesion, Agonist


title: K6_1

source_name: Disease_K6, Lesion, Untreated


title: K6_5

source_name: Disease_K6, Nonlesion, Untreated


title: K6_3

source_name: Disease_K6, Lesion, Agonist


title: K5_8

source_name: Disease_K5, Nonlesion, Antagonist

value: Antagonist


title: K5_7

source_name: Disease_K5, Nonlesion, Agonist

value: Agonist


title: K9_6

source_name: Disease_K9, Nonlesion, Culture/DMSO


title: K6_2

source_name: Disease_K6, Lesion, Culture/DMSO


title: K5_4

source_name: Disease_K5, Lesion, Antagonist


title: K5_6

source_name: Disease_K5, Nonlesion, Culture/DMSO


title: K5_5

source_name: Disease_K5, Nonlesion, Untreated


title: K5_3

source_name: Disease_K5, Lesion, Agonist


title: K5_2

source_name: Disease_K5, Lesion, Culture/DMSO


title: K5_1

source_name: Disease_K5, Lesion, Untreated


title: K9_3

source_name: Disease_K9, Lesion, Agonist


title: K4_8

source_name: Disease_K4, Nonlesion, Antagonist


title: K4_6

source_name: Disease_K4, Nonlesion, Culture/DMSO


title: K4_4

source_name: Disease_K4, Lesion, Antagonist


title: K4_7

source_name: Disease_K4, Nonlesion, Agonist


title: K6_8

source_name: Disease_K6, Nonlesion, Antagonist


title: K4_5

source_name: Disease_K4, Nonlesion, Untreated


title: K4_2

source_name: Disease_K4, Lesion, Culture/DMSO


title: K4_3

source_name: Disease_K4, Lesion, Agonist


title: K3_8

source_name: Disease_K3, Nonlesion, Antagonist


title: K3_7

source_name: Disease_K3, Nonlesion, Agonist


title: K4_1

source_name: Disease_K4, Lesion, Untreated


title: K3_5

source_name: Disease_K3, Nonlesion, Untreated


title: K3_1

source_name: Disease_K3, Lesion, Untreated


title: K3_6

source_name: Disease_K3, Nonlesion, Culture/DMSO


title: K2_7

source_name: Disease_K2, Nonlesion, Agonist


title: K3_3

source_name: Disease_K3, Lesion, Agonist


title: K2_8

source_name: Disease_K2, Nonlesion, Antagonist


title: K2_5

source_name: Disease_K2, Nonlesion, Untreated


title: K2_4

source_name: Disease_K2, Lesion, Antagonist


title: K3_2

source_name: Disease_K3, Lesion, Culture/DMSO


title: K2_6

source_name: Disease_K2, Nonlesion, Culture/DMSO


title: X. tropicalis brain small RNAs

city: Heidelberg

first: Maria

last: Warnefors

address: Center for Molecular Biology of Heidelberg University (ZMBH)

country: Germany

institute: University of Heidelberg

description: small RNA

data_processing: There are no processed data files associated with this submission. This is because the data were only used to test presence/absence of 15 transcripts that had been identified based on published datasets. We did not run any genome-wide expression analysis or similar.

organism: Xenopus tropicalis

source_name: brain

extract_protocol:
RNA was extracted from 20-30 mg of tissue, using the QIAgen miRNeasy mini kit according to the manufacturer's instructions. The RNA quality was checked using a Fragment Analyzer.
2ug of total RNA were used to prepare small RNA libraries: after a purification of the small RNA on a 15% TBU acrylamide gel, the libraries were generated using the Illumina TruSeq(R) Small RNA Sample Prep Kit and the quality assessed using a Fragment Analyzer.

tag: Sex

value: Male

tag: individual

tag: tissue type

value: brain


title: X. tropicalis heart small RNAs

description: small RNA

source_name: heart

value: heart


title: K2_2

source_name: Disease_K2, Lesion, Culture/DMSO

value: Culture/DMSO


title: K2_3

source_name: Disease_K2, Lesion, Agonist


title: K2_1

source_name: Disease_K2, Lesion, Untreated

value: Untreated


title: K1_8

source_name: Disease_K1, Nonlesion, Antagonist

value: M


title: K1_7

source_name: Disease_K1, Nonlesion, Agonist


title: K1_5

source_name: Disease_K1, Nonlesion, Untreated


title: K1_6

source_name: Disease_K1, Nonlesion, Culture/DMSO


title: K1_4

source_name: Disease_K1, Lesion, Antagonist

value: Lesion


title: K1_3

source_name: Disease_K1, Lesion, Agonist


title: MU_7

city: Nanjing

first: Shi

last: Guixia

state: Jiangsu

address: Weigang num.1

country: China

institute: Nanjing Agricultural University

data_processing:
Dirty raw reads were discarded via the following four steps: 1. reads with adaptors were removed; 2. reads with unknown nucleotides larger than 5% were removed; 3. reads with low quality (more than half of the base quality less than 5) were removed; 4. clean reads were obtain.
Clean reads were mapped to reference genome and genes sequences respectively using SOAP2 (Li, 2009). Mismatches no more than  5 bases were allowed in the alignment.
The calculation of Unigene expression uses RPKM method (Reads Per kb per Million reads) (Mortazavi, Williams et al. 2008)
Genome_build: Glycine max v1.1 genes
Supplementary_files_format_and_content: tab-delimited text files include gene length, coverage and RPKM values for each Sample

organism: Glycine max

source_name: Pods

growth_protocol: All of the plants were cultivated in field under natural conditions.

extract_protocol:
Total RNA was extracted from pods at 7DAF of WT and cco with the Plant RNA Extract Kit (TianGen, Beijing, China) according to the manufacturer’s instructions.
Beads with oligo (dT) were used to isolate poly (A) mRNA after total RNA was collected. Fragmentation buffer was added to digest the mRNA to generate short frag-ments. These short fragments were used as templates, and random hexamer-primers were used to synthesise first-strand cDNA. Second-strand cDNA was synthesised in a reaction containing buffer, dNTPs, RNase H and DNA polymerase I. Short fragments were purified using the QIAquick PCR extraction kit (QIAGEN) and eluted in EB buffer for end preparation and poly (A) addition. Subsequently, the short fragments were ligated with sequencing adaptors. For PCR amplification, we selected suitable fragments to use as templates based on the results of agarose gel electrophoresis. The libraries were sequenced using the Illumina HiSeq™ 2000 system.

tag: cultivar

value: Nannong 94-16

value: curled-cotyledon mutant

value: Pods

tag: developmental stage

value: 7 days after fertilisation


title: K1_1

source_name: Disease_K1, Lesion, Untreated

tag: patient


title: HIV_24hr_rep3

status: Public on Jun 10 2014

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description:
24_9
HIV-1 infection
Total RNA-seq

data_processing:
mRNA-seq data was processed previously and is part of a different study. It was referenced in this study. The mRNA-seq data can be found in GEO GSE38006. This data set refers to the Whole Transcriptome data from similar samples.
Reads were aligned to the human reference genome (hg19, build GRCh37) using the gapped aligner software TopHat and Ht-seq, HIV-1 genome (GenBank accession no. K02013), and Human Non-coding ENCODE project (Gencode v17).
We trimmed from 90nt to 75nt. We then mapped the 75-nt reads to human ribosomal sequences using the short-read aligner software Bowtie to remove potential rRNA sequences. We also removed sequences that mapped to the HIV-1 genome. To quantify transcript expressions, we mapped all reads that remained unmapped to the human reference genome (hg19, build GRCh37, downloaded from UCSC genome browser, http://genome.ucsc.edu) using the gapped aligner software TopHat. RefSeq transcript annotations were supplied to facilitate the mapping of reads spanning known splicing junctions. Based on these human genome mapping results, we then estimated the expression abundances at both transcript and locus levels for RefSeq-annotated genes using the transcript assembly software Cufflinks. Read sequences that mapped to more than one genomic location were excluded from expression quantification. For visualization, BAM files were generated using TopHat and samtools and displayed using the UCSC genome browser.
Genome_build: GRCh37 (human), GenBank K02013 (HIV-1), Gencode v17 (human non-coding ENCODE project).
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values for each Sample using Htseq.

organism:
Homo sapiens
Human immunodeficiency virus 1

source_name: Total RNA from HIV-infected SUPT1 at 24 hours post-infection

extract_protocol:
Approximately 20 μg of total RNA from each sample was submitted to the Beijing Genomics Institute (BGI) for sequencing. In brief, ribosomal RNAs (rRNAs) were depleted using the RiboMinus™ Human/Mouse Transcriptome Isolation Kit (Invitrogen, CA).
rRNA-depleted RNAs were fragmented, and cDNA synthesis was primed using random hexamers. Short fragments were purified for an average insert size of 200 nt, and then ligated with proprietary adapters. The 2x90 nt paired-end sequencing was done using an Illumina HiSeq™ 2000.

tag: human cell line

tag: human cell type

value: CD4+ T cell line

tag: infection

tag: time

value: 12 hours post-infection


title: HIV_24hr_rep2

description:
24_8
HIV-1 infection
Total RNA-seq

value: 24 hours post-infection


title: WT-Bud2

city: Chongqing

first: Guojian

last: HU

address: No. 174 Shazhengjie, Shapingba

department: School of Life Sciences

institute: Chongqing University

data_processing:
3' adaptor sequence removal: since Tags are only 21nt long while the sequencing reads are 49nt long, raw sequences are with 3' adaptor sequences
Empty reads removal (reads with only 3' adaptor sequences but no Tags)
Low quality Tags removal (Tags with unknown sequences 'N')
Removal of Tags which are too long or too short, leaving Tags of 21nt long
Removal of Tags with a copy number of 1 (probably be sequencing error)
Generate Clean Tags
Genome_build: Tomato WGS Scaffolds (SL2.40)
Supplementary_files_format_and_content: tab-spaced text files include Tag sequences, Copynumber and the number of transcripts per million clean tags (TPM)

organism: Solanum lycopersicum

growth_protocol: Wild-type (WT) tomato (cv. Micro-TOM) and transgenic plants were grown in greenhouse conditions with temperature ranging from 18 ℃ to 25 ℃

extract_protocol:
Total RNA was isolated from 1-2 mm floral buds at stage 6-8 of three individual 35S::REVRis (T2 generation of Line 1) plants and corresponding WT controls by TRIZOL method. RNA quantity and quality were assayed using the Agilent 2100 Bioanalyzer (Agilent Technologies). Three aliquots of RNA from transgenic or WT plants were pooled, respectively, and sent to Illumina Cluster Station and Illumina HiSeq™ 2000 System (BGI Inc.) for RNA library construction and deep sequencing.
Specified Experimental Process: Extract 6 μg total RNA, use Oligo(dT) magnetic beads adsorption to purify mRNA, and then use Oligo(dT) as primer to synthesize the first and second-strand cDNA. The 5' ends of tags can be generated by two types of Endonuclease: NlaIII or DpnII (see table 1 for recognition sites). Usually, the bead-bound cDNA is subsequently digested with restriction enzyme NlaIII, which recognizes and cuts off the CATG sites. The fragments apart from the 3' cDNA fragments connected to Oligo(dT) beads are washed away and the Illumina adaptor 1 is ligated to the sticky 5' end of the digested bead-bound cDNA fragments. The junction of Illumina adaptor 1 and CATG site is the recognition site of MmeI, which is a type of Endonuclease with separated recognition sites and digestion sites. It cuts at 17bp downstream of the CATG site, producing tags with adaptor 1. After removing 3' fragments with magnetic beads precipitation, Illumina adaptor 2 is ligated to the 3' ends of tags, acquiring tags with different adaptors of both ends to form a tag library. After 15 cycles of linear PCR amplification, 105bp fragments are purified by 6% TBE PAGE Gel electrophoresis. After denaturation, the single-chain molecules are fixed onto the Illumina Sequencing Chip (flowcell). Each molecule grows into a single-molecule cluster sequencing template through Situ amplification. Then add in four types of nucleotides which are labeled by four colors, and perform sequencing with the method of sequencing by synthesis (SBS). Each tunnel will generate millions of raw reads with sequencing length of 49bp.

value: 1-2mm buds

value: MicroTom

value: stage 6-8

tag: genotype

value: WT


title: HIV_24hr_rep1

description:
24_7
HIV-1 infection
Total RNA-seq


title: HIV_12hr_rep2

description:
12_8
HIV-1 infection
Total RNA-seq

source_name: Total RNA from HIV-infected SUPT1 at 12 hours post-infection


title: HIV_12hr_rep1

description:
12_7
HIV-1 infection
Total RNA-seq


title: 3-AT treatment, 60 min

city: Berkeley

first: Liana

middle: F

last: Lareau

state: CA

address: Barker Hall 424

department: California Institute for Quantitative Biosciences

institute: University of California, Berkeley

data_processing:
library strategy: Ribo-Seq (ribosome profiling)
Cloning linker sequences were trimmed from Illumina reads. Trimmed sequences were aligned to S. cerevisiae ribosomal and noncoding RNA sequences using bowtie v. 0.12.7 or v. 1.0.0 to remove rRNA reads. The non-rRNA reads were aligned to the S. cerevisiae genome as a first pass to remove any reads that mapped to multiple locations. Reads that passed this filter were then aligned to the S. cerevisiae transcriptome with bowtie, allowing two mismatches and only reporting alignments of reads that mapped uniquely in the transcriptome (bowtie -v 2 -m 1 -a --norc --best –strata). A list of read counts and read lengths per nucleotide position in the transcriptome, based on the 5’ end of the mapped read, was generated.
The counts of small and large footprints from ribosomes with each codon positioned in the inferred A site were generated from the list of reads at each nucleotide position. The large footprints were defined as 28 nt reads with the 5’ end 15 nt upstream of the codon at position i, and 29 nt reads with the 5’ end 16 nt upstream of i. Small footprints included 20 nt and 21 nt reads with the 5’ end 15 nt upstream of i and 21 nt and 22 nt reads with the 5’ end 16 nt upstream of i. For each gene, the analysis included codons 51 through the second codon before the stop codon, to avoid the region at the beginning of genes from which ribosomes have been depleted by runoff elongation during harvest. Genes with fewer than 10 footprints in total were excluded, as were any non-unique 20mer regions within genes.
Genome_build: sacCer2
Supplementary_files_format_and_content: A percodon.txt file for each sample provides the count of small and large ribosome footprints at each codon, starting at the 51st codon of each gene. Files include gene symbol, codon position, codon sequence, and count of small and large ribosome footprints with that position in the inferred A site. Genes with fewer than 10 footprints are excluded.

source_name: 3-AT treatment, 60 min

growth_protocol: Yeast were innoculated from an overnight culture into 500mL of SC-His media then grown at 30C from a starting OD of 0.2 to a final OD of ~0.6.

extract_protocol:
Cells were harvested by filtration then frozen in liquid N2 and pulverized using a Retsch mixer mill. Lysis buffer was added to cell powder and lysates were clarified by centrifugation. RNAse I was added to cell lysate. After RNAse digestion, lysate was sedimented in a linear 10%-50% sucrose gradient at 35000rpm for 3 hours. Gradients were fractionated and the monosome peak fraction was collected. RNA was purified using a miRNeasy Mini kit from Qiagen.
RNA was size selected using 18 and 34 nt size markers then treated to remove the 3’ phosphate and ligated to the Universal miRNA cloning linker from New England Biolabs. Ligated fragments were reverse transcribed using a primer complementary to the cloning linker which introduced sequencing adapters. RNA template was removed and cDNA was circularized using CircLigase ssDNA ligase from Epicentre. Ribosomal RNAs were removed by hybridization to subtraction oligos. Libraries were amplified with PCR. Libraries were then sequenced on an Illumina Genome Analyzer 2 or an Illumina HiSeq 2000.

treatment_protocol: 3-amino-1,2,4-triazole was added to mid-log cells to reach a final concentration of 100mM, then cells were grown with shaking for 60 min prior to harvest.

tag: treatment


title: RM-Bud2


title: HIV_12hr_rep3

description:
12_9
HIV-1 infection
Total RNA-seq


title: Anisomycin replicate 2

source_name: Anisomycin

growth_protocol: Yeast were innoculated from an overnight culture into 500mL of YEPD media then grown at 30C from a starting OD of 0.2 to a final OD of ~0.6.

treatment_protocol: Anisomycin was added to mid-log cells at 100 µg/mL and cells were allowed to grow for an additional 30 minutes prior to harvest. Anisomycin was also present at 100 µg/mL in the lysis buffer.

value: anisomycin


title: 3-AT treatment, 10 min

source_name: 3-AT treatment, 10 min

treatment_protocol: 3-amino-1,2,4-triazole was added to mid-log cells to reach a final concentration of 100mM, then cells were grown with shaking for 10 min prior to harvest.


title: Cycloheximide replicate 2

source_name: Cycloheximide

treatment_protocol: Cycloheximide was added to cells prior to harvest at 100 µg/mL and was also present at 100 µg/mL in the lysis buffer.

value: cycloheximide


title: case_8

first: Shurjo

middle: Kumar

last: Sen

address: 10 Center Drive, Room 7N317

institute: NHGRI

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were aligned using TopHat v1.0.14 with the parameters  -m 2 -p 4 -g 10
The TopHat output SAM files were converted to BAM files using samtools view -T
The BAM files were converted to BED format using the bamToBed script from the BEDTools suite using the -split option
The BED files were converted to WIG format using a custom script
Genome_build: hg18
Supplementary_files_format_and_content: UCSC WIG format files containing RNA-Seq expression

source_name: coronary artery calcification case

extract_protocol:
2.5 ml of peripheral blood was drawn into PAXgene RNA tubes and RNA extraction was done using the PAXgene Blood RNA Kit IVD (Qiagen). RNA-Seq libraries were constructed from 1 µg of RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: male

tag: ancestry

value: Caucasian

tag: age (yrs)

tag: sample group

value: coronary artery calcification case

value: peripheral blood


title: case_7

tag: tissue


title: CK_7

value: Nannong 94-16

tag: genotype/variation

value: wild type


title: Untreated replicate 3

source_name: Untreated

treatment_protocol: untreated

tag: strain

value: untreated


title: case_6


title: case_5


title: case_2


title: case_3


title: case_1


title: case_4


title: K1_2

source_name: Disease_K1, Lesion, Culture/DMSO

tag: patient id

value: M

tag: age

tag: tissue/treatment id

value: Lesion

value: Culture/DMSO


title: control_8

source_name: control

value: control


title: control_5


title: control_6


title: K3_4

source_name: Disease_K3, Lesion, Antagonist

tag: patient

value: F

value: Antagonist


title: control_4


title: control_3


title: control_2


title: Ebf1

city: Boston

first: Evan

last: Rosen

state: MA

address: 3 Blackfan Cir

department: Endocrinology

institute: Beth Israel Deconess Medical Center

data_processing:
ChIP-seq reads were aligned to mouse genome (mm9) using MAQ
Duplicated reads were removed using Samtools.
Reads were sorted by Samtools
peaks were called using in-home made algorihtm.
peaks of same epitopes from different treatments were merged.

source_name: mouse adipocyte

growth_protocol: Mature 3T3-L1 adipocytes were cross-linked with 1% formaldehyde 10 days after induction with MDI。

extract_protocol:
anti-Ebf1 antibody (Abnova H00001879-M01) was used to pick up Ebf1- bound regions.
DNA fragments were repaired to blunt ends by T4 DNA polymerase and phosphorylated with T4 Polynucleotide kinase using the END-IT kit (Epicentre). Then, a single ?A? base was added to 3? ends with Klenow (3??5? exo?, 0.3 U/µl). Double-stranded Solexa adaptors (75 bp with a ?T? overhang) were ligated to the fragments with DNA ligase (0.05 U/µl). Ligation products between 275 and 700 base pairs were gel purified on 2% agarose to remove unligated adaptors, and subjected to 18 PCR cycles. Completed libraries were quantified with PicoGreen (As decribed in PMID:  17603471).

tag: cell type

tag: epitope

tag: antibody


title: control_1


title: WSB_11060

city: Bar Harbor

first: Steven

middle: C

last: Munger

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
Basecalls were performed with CASAVA version 1.8.0
Fragmented fastq files from CASAVA were concatenated together, and then reads that did not pass quality filtering were removed with fastq_illumina_filter (http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/)
Read Alignment - Individualized transcriptomes (isoform sequences) derived from the genome fasta file and corresponding gene annotation gtf files were used to construct Bowtie-compatible indexes with the rsem-prepare-reference command in RSEM software (Li and Dewey, 2010; RSEM version 1.2.1). For inbred genomes (CAST, NCBIM37), each Ensembl transcript identifier corresponds to a single sequence. The Bowtie aligner (version 0.12.8) was used to align reads to transcript sequences. Alignments with up to three mismatches (-v 3) across the 100bp read were considered valid, but only the best “strata” of alignments were reported. For a given read, the best stratum is the alignment(s) with the least mismatches.
Transcript Abundance Quantitation - Estimates of isoform and gene-level abundance were obtained with RSEM (Li and Dewey 2010). Bowtie alignment files in .bam format were input into the rsem-calculate-expression command. Based on the library fragment size distributions observed on the Agilent Bioanalyzer, fragment length mean was specified as 280bp with a standard deviation of 50bp (RSEM parameters --fragment-length-mean 280 –fragment-length-sd 50). For reads with multiple valid isoform alignments, RSEM implements an expectation-maximization (EM) algorithm that assigns all or a proportion of each multimapping read to one or more isoforms based on the number of uniquely-aligning reads to those transcripts. RSEM estimates isoform expression (counts), and gene-level counts are calculated as the sum of the corresponding isoforms.
Normalization - For each sample, RSEM count estimates were normalized to the upper quartile value (after trimming zeros).
Genome_build: Mouse NCBIM37/mm9. Individualized diploid DO genomes were based on NCBIM37 coordinates.
Supplementary_files_format_and_content: All processed data files are tab-deliminited txt files. Each file contains a data matrix with rows representing Ensembl gene id's and columns representing samples. Only genes with non-zero values in ≥85% of samples were included in the final analysis.

source_name: Liver

growth_protocol:
Male and female Diversity Outbred mice (J:DO Stock# 009376) were obtained from The Jackson Laboratory (Bar Harbor, ME). Animals were received at 3 weeks of age, housed at The Jackson Laboratory, and given free access to either standard rodent chow containing 6% fat by weight (LabDiet 5K52, LabDiet, Scott Distributing, Hudson, NH) or high-fat chow containing 22% fat by weight (TD.08811, Harlan Laboratories, Madison, WI) from wean age throughout the study. Animals were phenotyped for multiple metabolic and hematological parameters as described in Svenson et al. (2012), and then sacrificed at 26 weeks of age. Liver samples were collected from each animal and stored in RNAlater® solution (Life Technologies) at -80°C.
Male mice from each of the eight DO founder strains (n= 16 for each strain, n= 128 total) were obtained from The Jackson Laboratory. Mice were received at ~3 weeks of age, housed at the University of Wisconsin Madison, and beginning at 4 weeks of age given free access to either a control diet containing 17% kcal fat (TD.8010) or a high-fat, high-sucrose diet containing 45% kcal from fat and 34% (by weight) sucrose (TD.08811). Both diets were from standard rodent chow containing 6% fat by weight (LabDiet 5K52, LabDiet, Scott Distributing, Hudson, NH) or high-fat chow containing 22% fat by weight (TD.08811, Harlan Laboratories, Madison, WI) from wean age throughout the study. With the exception of NZO mice, animals were sacrificed at 26 weeks of age, and liver samples were collected, snap frozen, and shipped on dry ice to The Jackson Laboratory for RNA-seq analysis. Due to a high level of lethality of NZO mice that were maintained on the high-fat/high-sucrose diet, all NZO mice were sacrificed at 20 weeks of age.

extract_protocol:
Livers were dissected and stored in RNAlater at -80C (DO samples), or snap frozen and stored on dry ice (founder strain samples). Total RNA was isolated using the Trizol Plus RNA extraction kit (Life Technologies) with on-column DNase digestion.
Following the Illumina TruSeq standard protocol, indexed mRNA-seq libraries were generated from 1μg total RNA followed by QC and quantitation on the Agilent Bioanalyzer and the Kapa Biosystems qPCR library quantitation method.

tag: sample id

value: WSB/EiJ

tag: age (weeks)

tag: genotyped sex

value: Male

tag: diet

value: Standard Chow

tag: block

tag: flowcell

tag: lane

tag: barcode

value: ATCACG

value: liver


title: WSB_11319

value: TGACCA

tag: tissue


title: WSB_11468

tag: strain

value: CGATGT


title: control_7

tag: gender

value: male

tag: ancestry

value: Caucasian

tag: age (yrs)

tag: sample group

value: peripheral blood


title: WSB_11538

value: GATCAG


title: WSB_11513

value: GGCTAC


title: WSB_8832

value: High Fat


title: WSB_11289

value: TTAGGC


title: WSB_8772

value: GTCCGC


title: WSB_11405

value: CAGATC


title: WSB_11190

value: GCCAAT


title: WSB_9149

value: WSB/EiJ

value: TAGCTT


title: WSB_11483

value: Male

value: Standard Chow

value: CTTGTA


title: WSB_11553

value: CCGTCC

value: liver


title: WSB_8847


title: WSB_11438

value: ACAGTG


title: PWK_9299

value: PWK/PhJ


title: PWK_10714


title: PWK_10860


title: PWK_10625


title: PWK_10699


title: PWK_10655

value: CGATGT


title: PWK_10875


title: WCE

tag: cell type

value: WCE


title: PWK_10731

value: AGTCAA


title: PWK_10817

value: High Fat

value: TGACCA


title: PWK_10898


title: PWK_9870

value: ATCACG


title: WSB_11304


title: PWK_10913


title: PWK_9885


title: NZO_9447

value: NZO/HILtJ

value: GGCTAC


title: PWK_10640

value: GATCAG


title: NZO_10563


title: NZO_9522


title: NZO_9382

value: ATGTCA


title: NZO_9492

value: Male

value: ACTTGA


title: NZO_9507

value: Standard Chow


title: PWK_9915

value: CAGATC


title: NZO_9462

value: liver


title: NZO_11140


title: NZO_9397

value: GTCCGC


title: NZO_9427


title: NZO_11170


title: NZO_9412


title: PWK_10670

value: PWK/PhJ


title: NZO_9477


title: NZO_11125


title: NOD_8249

value: NOD/ShiLtJ

value: GCCAAT


title: NZO_11155

value: AGTCAA


title: NOD_9000


title: NOD_8234


title: NOD_7211

value: ACAGTG


title: NOD_8955

value: High Fat


title: NOD_8985


title: NOD_8204


title: NOD_8219


title: NOD_7226


title: NOD_10176

value: CTTGTA


title: NOD_10146

value: CGATGT


title: NOD_7196


title: NOD_8264

value: CCGTCC


title: NOD_8727

value: GGCTAC


title: NOD_7181


title: CAST_10273

value: CAST/EiJ


title: NOD_8970

value: Male

value: TGACCA


title: CAST_10258

value: Standard Chow

value: GATCAG


title: CAST_10467

value: liver


title: CAST_10373


title: CAST_11259


title: CAST_10239


title: CAST_11583


title: CAST_11568


title: CAST_11274


title: CAST_10422


title: CAST_10437

value: TTAGGC


title: CAST_10318


title: CAST_10388

value: TAGCTT


title: NZO_9367

value: NZO/HILtJ


title: CAST_10403

value: ACTTGA


title: CAST_10288


title: B6_7305

value: CAGATC


title: B6_8638


title: B6_10224


title: CAST_10303


title: B6_8623


title: B6_7320

value: GTCCGC


title: B6_10209

value: ATGTCA


title: B6_8438


title: B6_8453


title: B6_8608

value: High Fat


title: B6_9937

value: ATCACG


title: B6_9952


title: B6_7275


title: B6_8408

value: ACAGTG


title: B6_7684


title: AJ_7975

value: A/J


title: AJ_7118


title: AJ_7776

value: GGCTAC


title: AJ_7579

value: Male


title: B6_7290


title: AJ_7746


title: AJ_7990


title: AJ_9756

value: CCGTCC


title: AJ_7761

value: Standard Chow


title: AJ_7821

value: CTTGTA


title: AJ_7133

value: liver


title: AJ_7609


title: AJ_7163


title: AJ_7806

value: TGACCA


title: 129S1_7945

value: AGTCAA


title: AJ_7103


title: 129S1_7546


title: B6_7669


title: 129S1_7531


title: 129S1_8378


title: 129S1_7456


title: 129S1_8393

value: GCCAAT


title: 129S1_7639

value: TAGCTT


title: 129S1_7654

value: CGATGT


title: 129S1_7441


title: 129S1_7516


title: M74_2

value: Diversity Outbred heterogeneous stock


title: AJ_9741

value: CAGATC


title: M75_2


title: M73_2


title: M71_2


title: M69_2


title: M72_2


title: M67_2

value: ACTTGA


title: M70_2


title: 129S1_8563

value: TTAGGC


title: AJ_7624

value: High Fat


title: 129S1_7486

value: ATCACG


title: M66_2


title: 129S1_7471

value: ATGTCA


title: 129S1_8144

value: Male


title: M65_2


title: M64_2


title: M62_2


title: 129S1_7960


title: M61_2


title: M63_2


title: M59_2

value: ACAGTG


title: M58_2

value: Standard Chow

value: GGCTAC


title: M60_2

value: liver


title: M57_2


title: 129S1_7501


title: M56_2


title: M55_2


title: M52_2

value: GATCAG


title: M54_2


title: M25_2


title: M68_2


title: M53_2


title: M24_2


title: M21_2


title: M18_2

value: CTTGTA


title: M16_2


title: M20_2

value: TGACCA


title: M15_2


title: M12_2


title: M13_2


title: M08_2


title: M06_2


title: M07_2

value: GCCAAT


title: M11_2


title: M04_2


title: M05_2

value: TAGCTT


title: M02_2

value: Diversity Outbred heterogeneous stock


title: M03_2


title: F72_2

value: Female


title: F75_2


title: F70_2


title: F69_2


title: F68_2


title: M01_2

value: ACTTGA


title: F66_2


title: F67_2


title: F64_2


title: M22_2


title: M19_2


title: M23_2


title: F62_2

value: TTAGGC


title: F61_2


title: F59_2

value: CAGATC


title: F57_2


title: F58_2


title: F60_2


title: F56_2


title: F55_2

value: ATCACG


title: F71_2


title: F51_2

value: CGATGT


title: F52_2


title: F53_2


title: F54_2


title: F23_2

value: High Fat


title: F24_2


title: F21_2


title: F17_2


title: F20_2


title: F65_2


title: F18_2

value: ACAGTG


title: F22_2


title: F19_2


title: F15_2


title: F14_2


title: F11_2


title: F13_2


title: F12_2


title: F06_2


title: F10_2


title: F05_2


title: F08_2


title: F09_2


title: F63_2

value: Standard Chow


title: F03_2


title: F04_2


title: F07_2


title: F01_2

value: GGCTAC


title: F02_2

value: liver


title: F25_2


title: M72_1

value: Male


title: M73_1


title: M75_1


title: M74_1


title: F16_2


title: M70_1a


title: M70_1b


title: M69_1


title: M65_1


title: M68_1


title: M66_1


title: M62_1


title: M61_1


title: M60_1


title: M64_1


title: M59_1


title: M63_1


title: M56_1


title: M52_1

value: GATCAG


title: M14_2


title: M53_1


title: M55_1


title: M57_1


title: M67_1


title: M54_1


title: M58_1


title: M25_1


title: M71_1


title: M22_1

value: CTTGTA


title: M23_1


title: M21_1


title: M20_1

value: TGACCA


title: M18_1


title: M24_1


title: M15_1


title: M14_1

value: GCCAAT


title: M16_1

value: Diversity Outbred heterogeneous stock


title: M13_1


title: M12_1


title: M11_1


title: M19_1


title: M08_1


title: M06_1


title: M07_1


title: M03_1


title: M04_1


title: M02_1


title: M01_1


title: F71_1

value: Female


title: F75_1


title: F72_1


title: F69_1


title: F70_1


title: F67_1


title: F68_1


title: F66_1b


title: F66_1a


title: F64_1


title: F65_1

value: TAGCTT


title: F63_1


title: F60_1


title: F58_1


title: F59_1


title: F62_1

value: TTAGGC


title: F55_1


title: F57_1

value: CAGATC


title: F61_1

value: ATCACG


title: M05_1


title: F53_1


title: F52_1


title: F25_1

value: CGATGT


title: F51_1


title: F24_1

value: High Fat


title: F23_1


title: F21_1


title: F20_1


title: F22_1

value: ACTTGA


title: F19_1


title: F18_1

value: ACAGTG


title: F54_1

value: Standard Chow


title: F17_1

value: liver


title: F14_1


title: F12_1


title: F10_1


title: F03_1


title: F16_1

value: GGCTAC


title: F06_1


title: F11_1


title: F02_1


title: F09_1


title: F01_1


title: F13_1


title: F15_1


title: F04_1


title: F56_1

value: GATCAG


title: F07_1


title: M96_4

value: Male

value: GTGAAA


title: M97_4

value: ATGTCA


title: M98_4

value: Diversity Outbred heterogeneous stock


title: M99_4

value: GTGGCC


title: M95_4

value: GCCAAT


title: M94_4


title: F05_1

value: Female


title: M93_4

value: CCGTCC


title: M90_4

value: CGTACG


title: M89_4


title: M91_4

value: GAGTGG


title: M87_4

value: High Fat

value: TGACCA


title: M88_4


title: M86_4

value: CTTGTA


title: M83_4

value: GTTTCG


title: M84_4

value: ATCACG

value: liver


title: F08_1


title: M78_4


title: M80_4

value: ACTGAT


title: M79_4

value: Male


title: M81_4

value: CGATGT


title: M77_4


title: M174_4

value: Standard Chow

value: CAGATC


title: M76_4

value: Diversity Outbred heterogeneous stock

value: ATGTCA


title: M175_4


title: M173_4

value: TAGCTT


title: M171_4


title: M170_4

value: AGTTCC


title: M168_4

value: CGTACG


title: M167_4


title: M166_4


title: M169_4

value: TTAGGC


title: M164_4


title: M165_4

value: GTGAAA


title: M163_4

value: GTCCGC


title: M162_4

value: ACAGTG


title: M160_4

value: GGCTAC


title: M161_4

value: GATCAG


title: M82_4

value: High Fat

value: TGACCA

value: liver


title: M159_4

value: Male


title: M157_4

value: Standard Chow


title: M158_4

value: ACTGAT


title: M156_4

value: Diversity Outbred heterogeneous stock


title: M151_4


title: M148_4


title: M155_4

value: AGTCAA


title: M154_4


title: M147_4

value: CGATGT


title: M145_4

value: GTTTCG


title: M146_4

value: AGTTCC


title: M149_4


title: M143_4


title: M141_4

value: TTAGGC


title: M172_4


title: M150_4

value: GCCAAT


title: M140_4


title: M139_4


title: M138_4

value: ATCACG


title: M135_4

value: ATTCCT


title: M137_4


title: M133_4


title: M130_4

value: ATGTCA


title: M152_4

value: CGTACG


title: M131_4

value: High Fat


title: M128_4


title: M129_4


title: M125_4

value: GTGAAA


title: M127_4

value: GAGTGG

value: liver


title: M124_4

value: Male

value: Standard Chow


title: M123_4

value: Diversity Outbred heterogeneous stock


title: M126_4


title: M122_4


title: M119_4


title: M120_4


title: M142_4


title: M113_4

value: ACTTGA


title: M112_4


title: M111_4


title: M110_4

value: CTTGTA


title: M118_4

value: GGCTAC


title: M136_4

value: TAGCTT


title: M117_4


title: M114_4


title: M115_4


title: M108_4

value: CCGTCC


title: M106_4


title: M109_4


title: M107_4

value: CGATGT


title: M105_4


title: M103_4


title: M102_4

value: AGTTCC


title: F98_4

value: Female

value: CAGATC


title: F94_4

value: GCCAAT


title: M101_4


title: F99_4

value: High Fat


title: F95_4

value: GTGGCC


title: F96_4

value: ATTCCT


title: F92_4

value: AGTCAA

value: liver


title: M116_4

value: Male

value: Standard Chow


title: M100_4

value: Diversity Outbred heterogeneous stock


title: F91_4


title: F90_4


title: F88_4


title: F87_4


title: F86_4


title: F85_4


title: F84_4

value: GTGAAA


title: F83_4


title: F82_4

value: ACAGTG


title: F89_4


title: M104_4

value: CTTGTA


title: F78_4


title: F80_4

value: ATGTCA


title: F81_4


title: F76_4

value: ATCACG


title: F93_4

value: GGCTAC


title: F175_4

value: Female

value: GTCCGC


title: F173_4

value: GAGTGG


title: F171_4

value: AGTTCC


title: F168_4


title: F166_4

value: TGACCA


title: F169_4


title: F167_4


title: F170_4

value: CAGATC


title: F79_4

value: High Fat

value: GTGGCC


title: F164_4

value: liver


title: F163_4

value: Standard Chow

value: CGATGT


title: F160_4

value: Diversity Outbred heterogeneous stock

value: ACTTGA


title: F162_4

value: GTGAAA


title: F156_4


title: F155_4


title: F77_4

value: ACAGTG


title: F158_4

value: ATGTCA


title: F159_4


title: F154_4


title: F152_4


title: F153_4


title: M134_4

value: Male


title: F150_4

value: Female


title: F149_4

value: GATCAG


title: F148_4


title: F165_4


title: F174_4


title: F161_4


title: F172_4


title: F141_4

value: ACTGAT


title: F145_4

value: TTAGGC


title: F142_4


title: F146_4

value: GAGTGG


title: F147_4


title: F144_4

value: GTTTCG


title: F137_4

value: High Fat

value: CTTGTA


title: F151_4

value: GGCTAC

value: liver


title: F140_4

value: GTGGCC


title: F138_4

value: Diversity Outbred heterogeneous stock

value: TAGCTT


title: F139_4

value: CAGATC


title: F135_4


title: F133_4


title: F136_4


title: F132_4


title: F134_4


title: F157_4

value: Standard Chow

value: AGTCAA


title: F130_4


title: F131_4


title: F126_4


title: F125_4

value: GTCCGC


title: F129_4

value: Female

value: ATCACG


title: F122_4


title: F124_4

value: CGTACG


title: F123_4


title: F121_4


title: F119_4

value: ACTTGA


title: F120_4

value: ACTGAT


title: F117_4

value: TGACCA


title: F116_4


title: F114_4

value: CCGTCC


title: F112_4


title: F115_4

value: GTGAAA


title: F127_4

value: High Fat

value: ACAGTG


title: F108_4

value: CTTGTA

value: liver


title: F109_4

value: Diversity Outbred heterogeneous stock

value: TTAGGC


title: F111_4

value: Standard Chow


title: F113_4

value: TAGCTT


title: F102_4


title: F103_4

value: GTTTCG


title: F107_4

value: Female


title: F104_4

value: AGTCAA


title: F101_4


title: F100_4


title: F106_4

value: ATGTCA


title: F110_4

value: ACTTGA


title: F128_4

value: CGTACG


title: F118_4

value: TGACCA


title: M94_3

value: Male

value: ATCACG


title: M95_3

value: High Fat

value: GCCAAT


title: M96_3

value: GTGAAA


title: M97_3

value: liver


title: M98_3

value: Diversity Outbred heterogeneous stock

value: CAGATC


title: M91_3

value: GAGTGG


title: M90_3


title: M93_3

value: CCGTCC


title: F105_4

value: Standard Chow


title: M89_3

value: ACAGTG


title: M84_3


title: M86_3

value: CTTGTA


title: M99_3

value: GTGGCC


title: M78_3


title: M82_3


title: M80_3

value: ACTGAT


title: M83_3

value: GTTTCG


title: M77_3

value: CGATGT


title: M173_3

value: Male

value: TAGCTT


title: M172_3

value: GATCAG


title: M175_3


title: M81_3

value: High Fat


title: M79_3

value: GCCAAT


title: M76_3

value: ATGTCA

value: liver


title: M171_3

value: Diversity Outbred heterogeneous stock


title: M169_3

value: TTAGGC


title: M168_3

value: CGTACG


title: M166_3

value: Standard Chow


title: M167_3


title: M165_3

value: GTGAAA


title: M164_3


title: M170_3

value: AGTTCC


title: M163_3

value: GTCCGC


title: M87_3

value: TGACCA


title: M88_3


title: M162_3

value: ACAGTG


title: M161_3


title: M160_3

value: GGCTAC


title: M158_3

value: Male

value: ACTGAT


title: M157_3

value: GATCAG


title: M156_3


title: M155_3

value: AGTCAA


title: M154_3


title: M151_3


title: M152_3


title: M142_3

value: High Fat

value: GAGTGG


title: M143_3

value: liver


title: M150_3

value: Diversity Outbred heterogeneous stock

value: GCCAAT


title: M147_3

value: CGATGT


title: M148_3


title: M145_3

value: GTTTCG


title: M149_3


title: M174_3

value: Standard Chow

value: CAGATC


title: M140_3


title: M136_3

value: TAGCTT


title: M138_3

value: ATCACG


title: M135_3

value: ATTCCT


title: M141_3

value: TTAGGC


title: M137_3

value: Male


title: M139_3

value: ACAGTG


title: M159_3


title: M134_3

value: AGTTCC


title: M133_3


title: M129_3


title: M130_3

value: ATGTCA


title: M131_3

value: High Fat


title: M128_3

value: AGTCAA


title: M126_3

value: CGTACG

value: liver


title: M127_3

value: Diversity Outbred heterogeneous stock

value: GAGTGG


title: M146_3


title: M125_3

value: GTGAAA


title: M124_3

value: Standard Chow

value: CGATGT


title: M123_3


title: M122_3


title: M118_3

value: GGCTAC


title: M114_3


title: M120_3


title: M119_3

value: ATCACG


title: M112_3

value: ATTCCT


title: M113_3

value: ACTTGA


title: M115_3

value: Male


title: M116_3


title: M110_3

value: CTTGTA


title: M108_3

value: CCGTCC


title: M111_3

value: GCCAAT


title: M107_3


title: M105_3

value: ATGTCA


title: M106_3


title: M103_3


title: M102_3

value: AGTTCC


title: M104_3


title: F99_3

value: Female

value: High Fat


title: M100_3

value: Diversity Outbred heterogeneous stock

value: liver


title: M101_3


title: F96_3


title: F98_3

value: CAGATC


title: F94_3


title: F95_3

value: GTGGCC


title: F92_3

value: AGTCAA


title: F91_3

value: TAGCTT


title: F90_3


title: F84_3

value: GTGAAA


title: F87_3


title: F88_3


title: F85_3


title: F82_3

value: ACAGTG


title: F89_3


title: F93_3

value: GGCTAC


title: M109_3

value: Male

value: Standard Chow

value: ACTTGA


title: M117_3


title: F80_3


title: F79_3


title: F78_3


title: F76_3

value: ATCACG


title: F175_3

value: GTCCGC


title: F173_3

value: GAGTGG


title: F174_3

value: Female

value: ATGTCA


title: F170_3

value: Diversity Outbred heterogeneous stock


title: F172_3

value: TGACCA

value: liver


title: F171_3

value: AGTTCC


title: F168_3


title: F169_3

value: AGTCAA


title: F167_3


title: F83_3

value: High Fat

value: GTGGCC


title: F166_3


title: F86_3

value: ATTCCT


title: F164_3


title: F163_3

value: CGATGT


title: F162_3

value: GTGAAA


title: F160_3

value: Standard Chow


title: F159_3


title: F165_3


title: F158_3


title: F157_3


title: F156_3

value: GGCTAC


title: F155_3

value: CAGATC


title: F81_3

value: GCCAAT


title: F154_3


title: F152_3


title: F151_3


title: F150_3


title: F149_3

value: GATCAG


title: F148_3

value: Female


title: F146_3

value: GAGTGG


title: F147_3

value: Diversity Outbred heterogeneous stock

value: TTAGGC


title: F77_3

value: ACAGTG

value: liver


title: F145_3


title: F153_3

value: GTCCGC


title: F141_3

value: High Fat

value: ACTGAT


title: F140_3

value: GTGGCC


title: F139_3


title: F142_3

value: Male


title: F161_3


title: F144_3

value: GTTTCG


title: F137_3

value: CTTGTA


title: F135_3


title: F136_3


title: F132_3


title: F134_3


title: F133_3

value: GGCTAC


title: F131_3

value: TAGCTT


title: F130_3


title: F125_3

value: Standard Chow


title: F128_3

value: CGTACG


title: F121_3

value: Female

value: ATCACG


title: F123_3

value: Diversity Outbred heterogeneous stock


title: F127_3


title: F119_3

value: ACTTGA


title: F122_3


title: F118_3

value: TGACCA


title: F117_3

value: liver


title: F116_3


title: F126_3


title: F115_3

value: GTGAAA


title: F113_3


title: F138_3

value: High Fat


title: F120_3

value: ACTGAT


title: F112_3


title: F111_3

value: TTAGGC


title: F110_3


title: F107_3

value: CCGTCC


title: F108_3


title: F109_3


title: F106_3

value: ATGTCA


title: F102_3

value: ACAGTG


title: F105_3


title: F103_3

value: GTTTCG


title: F129_3


title: F124_3


title: F101_3


title: M99_2

value: Male

value: GTGGCC


title: F100_3


title: M97_2


title: M98_2

value: CAGATC


title: F114_3

value: Female

value: Standard Chow


title: M95_2

value: Diversity Outbred heterogeneous stock

value: GCCAAT


title: M93_2


title: M94_2

value: ATCACG


title: M96_2

value: liver


title: M90_2

value: CGTACG


title: M91_2

value: High Fat

value: GAGTGG


title: M86_2

value: CTTGTA


title: M84_2


title: M88_2

value: GATCAG


title: M87_2

value: TGACCA


title: M89_2

value: ACAGTG


title: M82_2


title: M83_2

value: GTTTCG


title: M81_2

value: Male

value: CGATGT


title: M80_2

value: ACTGAT


title: M79_2


title: M78_2


title: M77_2


title: M76_2

value: ATGTCA


title: M175_2

value: Standard Chow

value: CCGTCC


title: F104_3

value: Diversity Outbred heterogeneous stock

value: Female

value: AGTCAA


title: M173_2

value: TAGCTT

value: liver


title: M171_2


title: M170_2

value: AGTTCC


title: M169_2

value: TTAGGC


title: M168_2

value: CGTACG


title: M172_2

value: GATCAG


title: M167_2


title: M166_2


title: M165_2

value: GTGAAA


title: M162_2

value: ACAGTG


title: M160_2

value: Male

value: GGCTAC


title: M161_2


title: M159_2


title: M158_2

value: ACTGAT


title: M164_2

value: GTTTCG


title: M155_2

value: Standard Chow


title: M156_2


title: M157_2


title: M154_2


title: M152_2


title: M174_2

value: CAGATC


title: M148_2

value: Diversity Outbred heterogeneous stock

value: High Fat

value: GTCCGC


title: M149_2


title: M143_2


title: M151_2


title: M142_2

value: GAGTGG


title: M146_2

value: liver


title: M145_2


title: M150_2

value: GCCAAT


title: M139_2


title: M140_2

value: AGTCAA


title: M138_2

value: ATCACG


title: M137_2

value: GATCAG


title: M135_2

value: ATTCCT


title: M129_2

value: CGATGT


title: M131_2

value: Male


title: M127_2


title: M130_2

value: ATGTCA


title: M126_2

value: CGTACG


title: M163_2


title: M125_2

value: GTGAAA


title: M128_2


title: M122_2

value: Standard Chow


title: M124_2


title: M123_2


title: M120_2


title: M118_2

value: GGCTAC


title: M147_2

value: Diversity Outbred heterogeneous stock


title: M116_2

value: ACTTGA


title: M115_2


title: M117_2


title: M141_2

value: High Fat

value: TTAGGC


title: M113_2

value: liver


title: M134_2

value: AGTTCC


title: M111_2

value: GCCAAT


title: M112_2


title: M136_2

value: TAGCTT


title: M133_2


title: M110_2

value: CTTGTA


title: M109_2


title: M107_2


title: M108_2

value: CCGTCC


title: M106_2


title: M101_2


title: M102_2


title: M103_2

value: ATTCCT


title: M104_2

value: Male


title: M100_2

value: Female


title: M119_2

value: ATCACG


title: F99_2


title: F98_2

value: CAGATC


title: F96_2


title: F93_2


title: F94_2


title: F95_2

value: GTGGCC


title: F92_2

value: AGTCAA


title: F90_2

value: Diversity Outbred heterogeneous stock


title: F88_2


title: F89_2


title: F87_2


title: F85_2


title: M114_2

value: Standard Chow

value: GAGTGG


title: F82_2

value: High Fat

value: ACAGTG


title: F83_2

value: liver


title: F81_2

value: GCCAAT


title: F86_2


title: M105_2

value: ATGTCA


title: F78_2


title: F79_2


title: F77_2


title: F76_2


title: F173_2


title: F174_2


title: F175_2

value: GTCCGC


title: F172_2

value: TGACCA


title: F171_2

value: AGTTCC


title: F170_2


title: F169_2


title: F91_2

value: TAGCTT


title: F166_2

value: Female


title: F84_2

value: GTGAAA


title: F164_2

value: ATCACG


title: F162_2


title: F161_2

value: CAGATC


title: F80_2


title: F163_2

value: CGATGT


title: F167_2

value: Diversity Outbred heterogeneous stock


title: F159_2

value: Standard Chow


title: F158_2


title: F154_2


title: F156_2

value: GGCTAC


title: F153_2


title: F160_2

value: ACTTGA


title: F157_2

value: AGTCAA


title: F151_2

value: liver


title: F152_2

value: GTGGCC


title: F150_2

value: High Fat


title: F149_2

value: GATCAG


title: F168_2

value: GTCCGC


title: F145_2

value: TTAGGC


title: F146_2

value: GAGTGG


title: F142_2

value: Male


title: F141_2

value: Female

value: ACTGAT


title: F144_2

value: GTTTCG


title: F140_2


title: F139_2

value: CAGATC


title: F138_2

value: Diversity Outbred heterogeneous stock

value: TAGCTT


title: SARS_MRC5_IFNbeta_48hrs

city: Baltimore

middle: A

last: Rasko

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome reference build GRCh37.74 using bowtie v0.12.9 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh37.74
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: MRC5 Cell Line

growth_protocol: MRC5 cells were grown in MEM with 10% Fetal Bovine Serum

extract_protocol:
RNA was extracted using Trizol from cells infected in culture.
Poly-A RNA was isolated and indexed libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RNA was isolated at 24 and 48 hours post infection at an MOI of 0.1 and 3 with each virus.

tag: cell line


title: F165_2

value: Standard Chow

value: AGTTCC


title: F137_2

value: CTTGTA


title: SARS_MRC5_IFNbeta_24hrs


title: F155_2

value: liver


title: F136_2

value: GTGGCC


title: F134_2

value: High Fat


title: F135_2


title: MERS_MRC5_Gleevec_24hrs


title: MOCK_MRC5_Gleevec_24hrs


title: SARS_MRC5lowMOI_48hr_3


title: MERS_MRC5_Gleevec_48hrs


title: SARS_MRC5HighMOI_24hr_3


title: F148_2

value: TGACCA


title: MOCK_MRC5_IFNbeta_48hrs


title: F131_2


title: F130_2


title: SARS_MRC5lowMOI_48hr_2


title: SARS_MRC5HighMOI_24hr_2


title: F147_2


title: F128_2

value: CGTACG


title: F127_2

value: ACAGTG


title: F129_2

value: ATCACG


title: MERS_MRC5HighMOI_48hr_1


title: F126_2

value: GGCTAC


title: F125_2

value: Female

value: GTCCGC


title: MERS_MRC5lowMOI_48hr_2


title: F124_2


title: F133_2


title: MERS_MRC5HighMOI_24hr_3


title: MERS_MRC5lowMOI_48hr_3


title: MERS_MRC5HighMOI_24hr_2


title: MERS_MRC5lowMOI_24hr_3


title: F122_2


title: F123_2


title: MERS_MRC5lowMOI_24hr_2


title: F120_2

value: ACTGAT


title: F121_2


title: F119_2

value: ACTTGA


title: MERS_MRC5HighMOI_48hr_3


title: F117_2

value: Diversity Outbred heterogeneous stock


title: SARS_MRC5lowMOI_24hr_1


title: MERS_MRC5lowMOI_24hr_1


title: MOCK_MRC5_3


title: F118_2


title: F113_2

value: TAGCTT


title: MOCK_MRC5_1


title: MOCK_MRC5_2


title: F112_2

value: Standard Chow


title: F114_2

value: CCGTCC


title: F116_2

value: CTTGTA


title: F115_2

value: GTGAAA

value: liver


title: F111_2

value: TTAGGC


title: rng mutant

city: Leeds

first: Kenneth

last: McDowall

address: Clarendon way

department: Faculty of biological sciences

institute: University of Leeds

data_processing:
Basecalls were performed using CASAVA.1.8
Sequence reads were trimmed for adaptor reads and mapped to E. coli K12 MG1655 genome using CLC Genomics Workbench 6.0.1
Genome_build: U00096.2
Supplementary_files_format_and_content: Processed files are in tab delimited format. Separate files are provided for the forward and reverse strands. The start and end coordinates should be the same. Each line in the data set represents the position of the first nucleotide at the 5' end of a sequence that could be mapped to the E. coli genome.

organism: Escherichia coli

source_name: E. coli cell cultures

growth_protocol: All cultures grown up to 0.6 OD600 with shaking at 200 rpm. Samples 1,2,5 and 6 were grown at 30°C whereas samples 3 and 4 were grown at 37°C.

extract_protocol:
Total RNA was isolated as desribed in Kime et al., 2008
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cultures for samples 1 and 2 were incubated at 44°C for 45 min after growth.

tag: analysis

value: in vivo

tag: genotype

value: rng mutant

tag: incubation time


title: F110_2

tag: sample id

tag: age (weeks)

tag: genotyped sex


title: F108_2

tag: diet

tag: block

tag: flowcell


title: F109_2

tag: lane

tag: barcode

tag: tissue


title: F106_2

tag: strain

value: ATGTCA


title: F107_2


title: T170V 10 min

value: in vitro

value: 10 min


title: F105_2

value: Female


title: rng wild-type

value: rng wild-type


title: T170V 0 min

value: 0 min


title: F103_2

value: GTTTCG


title: F101_2

value: Diversity Outbred heterogeneous stock


title: F100_2

value: High Fat


title: F102_2

value: Standard Chow

value: ACAGTG


title: F104_2

value: AGTCAA


title: M99_1

value: Male

value: GTGGCC


title: M97_1

value: liver


title: rne wild-type

value: in vivo

value: rne wild-type


title: M98_1

value: CAGATC


title: rne-3071 ts


title: M94_1

value: ATCACG


title: SARS_MRC5_Gleevec_24hrs


title: M95_1

value: GCCAAT


title: M93_1

value: CCGTCC


title: M91_1

value: GAGTGG


title: M90_1

value: CGTACG


title: M89_1


title: M87_1

value: TGACCA


title: MOCK_MRC5_Gleevec_48hrs


title: F132_2

value: Diversity Outbred heterogeneous stock

value: Female

value: ACTGAT


title: M88_1

value: High Fat

value: GATCAG


title: M86_1

value: Male

value: CTTGTA


title: M83_1

value: GTTTCG

value: liver


title: MERS_MRC5HighMOI_24hr_1


title: MERS_MRC5_IFNbeta_48hrs


title: MOCK_MRC5_IFNbeta_24hrs


title: MERS_MRC5_IFNbeta_24hrs


title: M79_1


title: M81_1

value: CGATGT


title: M82_1


title: M84_1


title: SARS_MRC5HighMOI_48hr_2


title: SARS_MRC5HighMOI_48hr_3


title: M96_1

value: GTGAAA


title: M78_1


title: SARS_MRC5lowMOI_24hr_3


title: M174_1

value: Standard Chow

value: CAGATC


title: M77_1


title: M175_1

value: CCGTCC


title: SARS_MRC5HighMOI_24hr_1


title: M171_1


title: MERS_MRC5lowMOI_48hr_1


title: M172_1


title: M170_1

value: AGTTCC


title: M173_1

value: TAGCTT


title: SARS_MRC5lowMOI_24hr_2


title: M169_1

value: TTAGGC


title: MERS_MRC5HighMOI_48hr_2


title: SARS_MRC5_Gleevec_48hrs


title: M80_1

value: Diversity Outbred heterogeneous stock


title: M168_1

value: CGTACG


title: M76_1

value: ATGTCA


title: M164_1


title: M165_1


title: M163_1

value: GTCCGC


title: M160_1

value: GGCTAC


title: 6hr_Media_Unstim_244_1

city: Ridgefield

first: Jonathan

middle: Daryl

last: Hill

state: CT

address: 900 Ridgebury Road

department: Computational Biology

institute: Boehringer Ingelheim Pharmaceuticals Inc

data_processing:
Basecalling performed by Illumina real-time analysis (RTA) software
FASTQ generation by Casava’s configureBclToFastq.pl script,  allowing 1 mismatch for the indices when assigning the reads to the different samples.
Alignment to human genome using STAR version 2.3
FPKM calculations with Cufflinks 2.1
Differential analysis using HTSeq 0.5.4, followed by the R package Limma
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are Cufflinks output with FPKMs provided for each gene.  The files themselves are tab-delimited text.

source_name: Primary human CD14+/CD16+ monocytes

growth_protocol: Human PBMCs isolated with leukapheresis were purchased from AllCells, frozen in 80% FBS, 10% RPMI, 10% DMSO and stored in liquid nitrogen until used.  Primary human CD14+/CD16+ monocytes were isolated by negative selection (StemCell Technologies) and used directly.  Cells were used at a density of 500,000 cells per well in RPMI, 10% FBS, penicillin/streptomycin.

extract_protocol:
At either 6 or 24 hours the cells were lysed directly in the well with RLT buffer (Qiagen) and RNA was isolated with the RNAeasy kit (Qiagen).
TruSeq v3

treatment_protocol: Compounds were dissolved to 10 mM in DMSO and tested at 500 nM in 0.1% DMSO.  Compounds were pre-incubated with cells for 30 minutes prior to the addition of 100 ng/ml IFNγ and 100 pg/mL LPS (Escherichia coli 0111:B4, Sigma).

value: Primary CD14+/CD16+ monocytes

tag: timepoint

tag: agent

value: Media

tag: treatment

value: unstimulated

tag: donor


title: 6hr_Media_Unstim_244_2

tag: cell type


title: 6hr_EX_Unstim_5


title: 6hr_Media_Unstim_244_5


title: 6hr_Media_Unstim_244_3


title: M158_1

value: Male

value: ACTGAT

value: liver


title: M161_1

value: Standard Chow

value: GATCAG


title: M166_1

value: GTTTCG


title: 6hr_Media_Unstim_244_4


title: M159_1


title: M157_1


title: 6hr_EX_Unstim_4


title: M156_1


title: M155_1

value: AGTCAA


title: M151_1


title: 6hr_EX_Unstim_2


title: M152_1


title: M154_1

value: AGTTCC


title: 6hr_EX_Unstim_3


title: M150_1

value: High Fat

value: GCCAAT


title: M162_1

value: Diversity Outbred heterogeneous stock

value: ACAGTG


title: 6hr_EX_Unstim_1


title: M167_1


title: M148_1

value: GTCCGC


title: M149_1


title: M147_1

value: CGATGT


title: M145_1


title: 6hr_EX_Stim_5

value: Primary CD14+/CD16+ monocytes

value: stimulated with interferon gamma and LPS


title: M143_1


title: M142_1

value: GAGTGG


title: M146_1

value: Male


title: 6hr_EX_Stim_4


title: 6hr_EX_Stim_3


title: M138_1

value: ATCACG


title: M140_1

value: liver


title: M139_1


title: M137_1


title: M141_1

value: TTAGGC


title: 6hr_DMSO_Stim_5

value: DMSO


title: 6hr_EX_Stim_2


title: M135_1

value: ATTCCT


title: M133_1


title: 6hr_DMSO_Stim_4


title: 6hr_DMSO_Stim_3


title: 6hr_DMSO_Stim_2


title: M131_1


title: M134_1


title: 6hr_DMSO_Stim_1


title: M130_1

value: ATGTCA


title: M129_1


title: M127_1


title: M128_1

value: AGTCAA


title: 6hr_EX_Stim_1


title: 24hr_Media_Unstim_4

value: Media

value: unstimulated


title: M125_1

value: Diversity Outbred heterogeneous stock

value: Standard Chow

value: GTGAAA


title: M126_1

value: High Fat

value: CGTACG


title: 24hr_Media_Unstim_5

value: Primary CD14+/CD16+ monocytes


title: M124_1

value: CGATGT


title: M120_1

value: Male

value: GAGTGG


title: M123_1

value: liver


title: M119_1

value: ATCACG


title: M136_1

value: TAGCTT


title: M122_1

value: ATTCCT


title: M115_1

value: ACTTGA


title: 24hr_EX_Unstim_5


title: 24hr_Media_Unstim_3


title: M118_1

value: GGCTAC


title: M116_1


title: M117_1


title: M113_1


title: 24hr_Media_Unstim_2

value: Media


title: 24hr_EX_Unstim_4

value: unstimulated


title: M112_1

value: Diversity Outbred heterogeneous stock


title: M111_1

value: Standard Chow

value: GCCAAT


title: 24hr_EX_Unstim_3


title: 24hr_EX_Unstim_2


title: M110_1

value: CTTGTA


title: M107_1


title: M109_1


title: 24hr_EX_Unstim_1


title: M108_1

value: CCGTCC


title: M104_1


title: M106_1


title: 24hr_EX_Stim_5

value: Primary CD14+/CD16+ monocytes

value: stimulated with interferon gamma and LPS


title: 24hr_Media_Unstim_1


title: M102_1

value: Male

value: AGTTCC


title: 24hr_EX_Stim_4


title: M103_1

value: liver


title: M105_1

value: ATGTCA


title: 24hr_EX_Stim_3


title: M101_1


title: M100_1

value: Female

value: High Fat


title: M114_1

value: GAGTGG


title: 24hr_EX_Stim_2


title: F99_1

value: ACTTGA


title: F96_1

value: ATTCCT


title: F98_1

value: CAGATC


title: 24hr_EX_Stim_1


title: F92_1

value: Diversity Outbred heterogeneous stock

value: AGTCAA


title: 24hr_DMSO_Stim_5

value: DMSO


title: F93_1

value: GGCTAC


title: F94_1

value: GCCAAT


title: 24hr_DMSO_Stim_2

value: Primary CD14+/CD16+ monocytes


title: F89_1

value: GTGGCC


title: 24hr_DMSO_Stim_3

value: stimulated with interferon gamma and LPS


title: F90_1


title: F88_1


title: F87_1

value: CCGTCC


title: 24hr_DMSO_Stim_1


title: UV_24hr_rep3

description:
24_6
UV inactivated: dead virus
Total RNA-seq

source_name: Total RNA from UV-inactivated virions SUPT1 at 24 hours post-infection

tag: human cell line

tag: human cell type

value: CD4+ T cell line

tag: infection

value: UV-inactivated virions

tag: time

value: 24 hours post-infection


title: F83_1

tag: sample id

tag: age (weeks)

tag: genotyped sex

value: Female

value: High Fat

value: liver


title: F84_1

tag: diet

tag: block

tag: flowcell

value: GTGAAA


title: UV_24hr_rep1

description:
24_4
UV inactivated: dead virus
Total RNA-seq


title: F82_1

tag: lane

tag: barcode

value: ACAGTG

tag: tissue


title: F81_1

tag: strain

value: Diversity Outbred heterogeneous stock


title: F85_1


title: UV_12hr_rep3

description:
12_6
UV inactivated: dead virus
Total RNA-seq

source_name: Total RNA from UV-inactivated virions SUPT1 at 12 hours post-infection

value: 12 hours post-infection


title: F79_1


title: UV_12hr_rep2

description:
12_5
UV inactivated: dead virus
Total RNA-seq


title: F78_1

value: AGTCAA


title: F76_1

value: ATCACG


title: F95_1


title: UV_12hr_rep1

description:
12_4
UV inactivated: dead virus
Total RNA-seq


title: F91_1

value: TAGCTT


title: F175_1

value: Standard Chow

value: GTCCGC


title: Mock_24hr_rep3

description:
24_3
No virus
Total RNA-seq

source_name: Total RNA from mock-infected SUPT1 at 24 hours post-infection

value: mock


title: F174_1

value: ATGTCA


title: 24hr_DMSO_Stim_4

value: Primary CD14+/CD16+ monocytes

tag: timepoint

tag: agent

value: DMSO

tag: treatment

value: stimulated with interferon gamma and LPS


title: F171_1

value: Female

value: AGTTCC


title: F172_1

value: TGACCA

value: liver


title: Mock_12hr_rep3

description:
12_3
No virus
Total RNA-seq

source_name: Total RNA from mock-infected SUPT1 at 12 hours post-infection

tag: human cell line

value: CD4+ T cell line

value: 24 hours post-infection


title: F173_1

value: Diversity Outbred heterogeneous stock

value: GAGTGG


title: F170_1

value: CAGATC


title: F169_1

value: AGTCAA


title: Mock_12hr_rep2

description:
12_2
No virus
Total RNA-seq

tag: human cell type

value: 12 hours post-infection


title: F166_1

value: Standard Chow


title: F86_1

value: High Fat

value: ATTCCT


title: F165_1


title: F168_1

value: GTCCGC


title: F80_1

value: ATGTCA


title: F164_1

value: ATCACG


title: F163_1

value: Female

value: CGATGT


title: F77_1

value: ACAGTG


title: F161_1

value: liver


title: F160_1

value: ACTTGA


title: F159_1


title: F158_1


title: F157_1


title: F155_1


title: F154_1

value: TGACCA


title: F153_1

value: Diversity Outbred heterogeneous stock


title: F152_1

value: GTGGCC


title: Mock_24hr_rep1

description:
24_1
No virus
Total RNA-seq

value: CD4+ T cell line

tag: infection

value: mock

value: 24 hours post-infection


title: F151_1

value: Standard Chow

value: GGCTAC


title: F150_1

value: High Fat

value: GTGAAA


title: F146_1

value: GAGTGG


title: F149_1

value: GATCAG


title: F145_1

value: Female

value: TTAGGC


title: F148_1


title: F167_1

value: GTCCGC


title: Mock_12hr_rep1

description:
12_1
No virus
Total RNA-seq

tag: time

value: 12 hours post-infection


title: F144_1

tag: sample id

value: GTTTCG

value: liver


title: F140_1

value: Diversity Outbred heterogeneous stock

tag: age (weeks)


title: F139_1

tag: genotyped sex

value: CAGATC


title: F142_1

value: Male

tag: diet


title: F162_1

tag: block


title: F141_1

tag: flowcell

value: ACTGAT


title: F156_1

tag: lane


title: F137_1

tag: barcode

value: CTTGTA


title: F136_1

value: GTGGCC

tag: tissue


title: F134_1

tag: strain


title: F138_1

value: TAGCTT


title: Marmoset_27_infected_day4_lesion_2_run_4

data_processing:
Reads were aligned to the Marmoset reference genome using the gapped aligner software STAR and Ht-seq (Callithrix_jacchus.C_jacchus3.2.1.74), MERS genome (GenBank accession no. K02013).
Genome_build: Callithrix jacchus-3.2, MERS-virus (GenBank JX869059)
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values for each animal using Htseq and the GTF provided from ENSEMBL (Callithrix_jacchus.C_jacchus3.2.1.74).

organism: Callithrix jacchus

source_name: Lung, animal 27, day 4, lesion 2

extract_protocol:
We started with 250ul Trizol homogenate from lung and used the Qiagen miRNA kit to extract the RNA.
For Total RNA-seq analysis, approximately 2.5 ug micrograms of total RNA from each sample was submitted. In brief, ribosomal RNAs (rRNAs) were depleted using the RiboZero Human/Mouse/Rat Isolation Kit . The 50 nt single-end sequencing was done using an Illumina MiSeq™.
Libraries were TruSeq Stranded Total RNA and clustering was Illumina version 2 MiSeq reagents.

value: lung

tag: animal number

value: Middle East respiratory syndrome coronavirus (MERS-CoV) infection

tag: day of infection

tag: lesion number

tag: technical replicate


title: Marmoset_27_infected_day4_lesion_2_run_2

tag: treatment


title: Marmoset_27_infected_day4_lesion_2_run_1


title: F133_1

value: High Fat

value: GGCTAC


title: Marmoset_27_infected_day4_lesion_2_run_3


title: Marmoset_Control

source_name: Lung, control animal, day 0, lesion 0

value: control


title: F131_1

value: Female


title: F130_1


title: Marmoset_27_infected_day4_lesion_1_run_3

source_name: Lung, animal 27, day 4, lesion 1


title: F147_1

value: TTAGGC


title: Marmoset_24_infected_day6_lesion_2_run_4

source_name: Lung, animal 24, day 6, lesion 2


title: F129_1

value: ATCACG


title: Marmoset_27_infected_day4_lesion_1_run_1


title: Marmoset_27_infected_day4_lesion_1_run_2


title: F128_1

value: CGTACG


title: Marmoset_24_infected_day6_lesion_2_run_3


title: F135_1

value: liver


title: Marmoset_24_infected_day6_lesion_2_run_2


title: Marmoset_24_infected_day6_lesion_2_run_1


title: F126_1

value: Diversity Outbred heterogeneous stock


title: F125_1

value: Standard Chow

value: GTCCGC


title: Marmoset_24_infected_day6_lesion_1_run_3

source_name: Lung, animal 24, day 6, lesion 1


title: F124_1


title: F123_1


title: Marmoset_24_infected_day6_lesion_1_run_4


title: Marmoset_27_infected_day4_lesion_1_run_4


title: F132_1

value: ACTGAT


title: Marmoset_24_infected_day6_lesion_1_run_2


title: F122_1


title: Marmoset_23_infected_day4_lesion_2_run_4

source_name: Lung, animal 23, day 4, lesion 2


title: Marmoset_23_infected_day4_lesion_2_run_3


title: Marmoset_24_infected_day6_lesion_1_run_1


title: F119_1

value: ACTTGA


title: Marmoset_23_infected_day4_lesion_2_run_2


title: F127_1

value: ACAGTG


title: F118_1

value: TGACCA


title: F117_1


title: Marmoset_23_infected_day4_lesion_1_run_3

source_name: Lung, animal 23, day 4, lesion 1

value: lung


title: Marmoset_23_infected_day4_lesion_2_run_1

value: Middle East respiratory syndrome coronavirus (MERS-CoV) infection


title: F114_1

value: CCGTCC


title: F115_1

value: GTGAAA


title: F113_1

value: TAGCTT


title: Marmoset_23_infected_day4_lesion_1_run_2


title: Marmoset_22_infected_day6_lesion_2_run_3

source_name: Lung, animal 22, day 6, lesion 2


title: Marmoset_23_infected_day4_lesion_1_run_1


title: Marmoset_22_infected_day6_lesion_2_run_2


title: Marmoset_22_infected_day6_lesion_2_run_4


title: F112_1

value: Female


title: F111_1

value: TTAGGC


title: Marmoset_22_infected_day6_lesion_2_run_1


title: F108_1

value: CTTGTA


title: F110_1


title: F109_1


title: F107_1


title: F120_1


title: Marmoset_22_infected_day6_lesion_1_run_4

source_name: Lung, animal 22, day 6, lesion 1


title: Marmoset_22_infected_day6_lesion_1_run_3


title: Marmoset_22_infected_day6_lesion_1_run_1


title: F106_1

source_name: Liver

value: ATGTCA


title: F121_1

value: ATCACG

value: liver


title: F105_1

value: Diversity Outbred heterogeneous stock

value: Standard Chow


title: Marmoset_23_infected_day4_lesion_1_run_4