title: EXP_RKO_4_BULK_16


title: MaMel_input

status: Public on May 21 2018

type: SRA

city: Worcester

first: Matthew

last: Hemming

state: MA

address: 364 Plantation Street

country: USA

institute: UMass Medical School

library_source: genomic

data_processing:
All Chip-Seq data were aligned to the human reference genome assembly hg19, GRCh37 (ncbi.nlm.nih.gov/assembly/2758/) using Bowtie2 (version 2.2.1), and gene annotations by gencode annotation release 19 (gencodegenes.org/releases/19.html)
Normalized read density was calculated using Bamliquidator (version 1.0) read density calculator. Aligned reads were extended by 200 bp and the density of reads per base pair was calculated. In each region, the density of reads was normalized to the total number of million mapped reads, generating read density in units of reads per million mapped reads per bp (rpm/bp).
Peak finding was performed using Model-based Analysis for ChIP-Seq (MACS, version 1.4.2). As control, matched input chromatin was used to generate background signal for peak determination.
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format

molecule: genomic DNA

organism: Homo sapiens

source_name: KIT mutant melanoma cell line

growth_protocol: Dulbecco’s modified Eagle’s medium containing 10% FBS, 2 mM L- glutamine, 100 mg/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries for single-end 75 bp sequencing on an Illumina NextSeq 500 were prepared with a ThruPLEX DNA-seq Kit (Rubicon) for ChIP-seq or Nextera DNA Preparation Kit (Illumina) for ATAC-seq.

tag: cell line

value: MaMel

tag: tissue

value: Gastrointestinal stromal tumor (GIST) cell line

tag: chip antibody


title: EXP_RKO_2_BULK_12

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

library_source: transcriptomic

data_processing:
Aligned with Tophat
Htseq-count
DESEQ
Genome_build: hg19

molecule: total RNA

source_name: RKO

growth_protocol: Cell lines were grown in non-adherent spheroid culture in the presence of bFGF and EGF.

extract_protocol:
RNAeasy Micro (Qiagen)
Truseq (Illumina)

value: RKO

tag: control treatment

tag: dormant (lrc) or cycling (bulk)

value: BULK

tag: cell type

value: colorectal cancer cell line


title: GIST-1_KIT e11_input

source_name: GIST tumor

value: Gastrointestinal stromal tumor (GIST)


title: hMSC_input

source_name: Human mesenchymal stem cells (ATCC SCRC-4000)

growth_protocol: MSC Basal Media, MSC Growth Kit, G418 0.2 mg/mL, 100 mg/ml penicillin, and 100 mg/ml streptomycin

value: ATCC SCRC-4000

value: Human mesenchymal stem cells


title: EXP_RKO_3_BULK_14


title: MaMel_H3K27Ac

value: H3K27ac, Abcam ab4729


title: hMSC_H3K27Ac


title: EXP_HT55_4_LRC_39

value: LRC


title: EWS502_H3K27Ac

source_name: Ewing sarcoma cell line


title: EXP_HT55_4_BULK_40


title: EXP_RKO_1_BULK_10


title: EWS502_input


title: GIST-430B_input

source_name: KIT-independent GIST cell line


title: EXP_RKO_1_LRC_9


title: EXP_HT55_3_LRC_37


title: GIST-430B_H3K27Ac


title: GIST-226_input


title: EXP_HT55_2_LRC_35


title: EXP_HT55_3_BULK_38


title: EXP_RKO_2_LRC_11


title: GIST-226_H3K27Ac


title: GIST-48B_input


title: EXP_HT55_2_BULK_36


title: GIST-48B_H3K27Ac


title: EXP_HT55_1_BULK_34


title: GIST-430/654_H3K27Ac

source_name: KIT-dependent GIST cell line


title: EXP_HCT15_3_LRC_5


title: GIST-430/654_input


title: GIST-430_input


title: GIST-T1/816_H3K27Ac


title: EXP_HCT15_4_LRC_7


title: EXP_HCT15_2_BULK_4


title: GIST-430_H3K27Ac


title: EXP_HCT15_1_LRC_1


title: EXP_HCT15_2_LRC_3


title: GIST-882_input

growth_protocol: RPMI containing 10% FBS, 2 mM L- glutamine, 100 mg/ml penicillin, and 100 mg/ml streptomycin


title: EXP_HCT15_3_BULK_6


title: GIST-882_H3K27Ac


title: EXP_HCT15_1_BULK_2


title: GIST-48_input


title: EXP_HT55_1_LRC_33


title: EXP_DLD1_4_LRC_31


title: GIST-48_H3K27Ac


title: EXP_HCT15_4_BULK_8


title: GIST882

description: RNA-seq in a human GIST cell line.

data_processing:
RNA-seq data were aligned using HISAT with expression quantification using Cufflinks to generate gene expression values in FPKM units.
Genome_build: hg19
Supplementary_files_format_and_content: Processed RNA-seq data files with FPKM values are in text format

molecule: polyA RNA

extract_protocol:
Total RNA was isolated using an RNeasy Plus Kit (Qiagen).
Libraries for Illumina NextSeq 500 sequencing were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) and equimolar multiplexed libraries were sequenced with single-end 75 bp reads.

value: KIT-dependent GIST cell line GIST882

tag: treatment


title: GIST-T1/816_input


title: EXP_DLD1_4_BULK_32


title: GIST-T1_input


title: EXP_DLD1_3_LRC_29


title: GIST-T1 ATAC

description: ATAC-seq from human cell line

data_processing:
ATAC-seq data were aligned to the human reference genome assembly hg19, GRCh37 (ncbi.nlm.nih.gov/assembly/2758/) using Bowtie2 (version 2.2.1), and gene annotations by gencode annotation release 19 (gencodegenes.org/releases/19.html)
Normalized read density was calculated using Bamliquidator (version 1.0) read density calculator. Aligned reads were extended by 200 bp and the density of reads per base pair was calculated. In each region, the density of reads was normalized to the total number of million mapped reads, generating read density in units of reads per million mapped reads per bp (rpm/bp).
Peak finding was performed using Model-based Analysis for ChIP-Seq (MACS, version 1.4.2).
Genome_build: hg19
Supplementary_files_format_and_content: Processed ATAC-seq data files are in wiggle format

extract_protocol:
Nuclei were incubated with Nextera transposase (Illumina) and DNA prepared per manufacturers recommendations.
Libraries for paired-end 75 bp sequencing on an Illumina NextSeq 500 were prepared with a Nextera DNA Preparation Kit (Illumina) for ATAC-seq.


title: GIST-48B ATAC

description: ATAC-seq from human cell line

source_name: KIT-Independent GIST cell line


title: EXP_DLD1_3_BULK_30


title: EXP_DLD1_2_LRC_27


title: EXP_DLD1_2_BULK_28


title: GIST-T1_H3K27Ac


title: EXP_DLD1_1_BULK_26


title: CON_ULD5_4_56

value: DMSO d5


title: CON_ULD1_4_52

value: DMSO d1


title: CON_ULD5_3_55


title: EXP_DLD1_1_LRC_25


title: CON_ULD5_2_54


title: CON_ULD5_1_53


title: CON_ULD1_3_51


title: CON_ULD1_2_50


title: CON_ULD1_1_49


title: GIST-2_KIT e11_input


title: CON_CFSED5_4_64

value: CFSE d5


title: CON_CFSED5_3_63


title: PB CD34+ cells from PMF patient PV_27 [CN]

type: genomic

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: GEP data: GSM1294488 in GSE53482

hyb_protocol: Fragmented DNA was hybridized for 16h at 50C on Affymetrix Cytoscan HD Arrays in the Hybridization Oven 645. Cytoscan HD Arrays were washed and stained using the Affymetrix GeneChip Stain Reagents (from the Affymetrix Cytoscan HD Assay kit), according to the standard protocol supplied by Affymetrix).

scan_protocol: Affymetrix Cytoscan HD arrays were scanned using the Affymetrix GCS3000 7G Scanner.

data_processing:
.CEL files were generated from the scanned array image files by the Affymetrix GeneChip Command Console Software and were imported into the Affymetrix Chromosome Analysis Suite v1.2.2 Software.  Copy number data files (.CYCHP files) were generated using the ChAS Analysis Files for the CytoScan HD Array version NA32.1 as a reference.
the .CYCHP files contain the whole genome copy number data for the 31 PMF samples and are accessible using Affymetrix Chromosome Analysis Suite v1.2.2 Software.

label: biotin

source_name: PMF Peripheral Blood Granulocytes

label_protocol: Genomic DNA (250ng) was digested, amplified, purified, fragmented and labeled following Affymetrix’s protocols (Affymetrix Cytoscan Assay kit).

growth_protocol: Granulocytes were purified from 30–50 ml of PB collected from PMF patients. Granulocytes were isolated from the pellet of the Ficoll–Paque gradient after Ammionium Clohride lysis of red blood cells, by means of immunomagnetic CD16+ selection (Miltenyi Biotec; Bergisch Gladbach, Germany).

extract_protocol: Genomic DNA was extracted from granulocytes by means of DNeasy Blood & Tissue Kit (Qiagen) following the manufacturer’s recommendations.

tag: supplier

value: Barosi

value: Myeloproliferative Disease (MPD)

tag: disease

value: Primary myelofibrosis (PMF)

value: neg

value: Peripheral Blood (PB)


title: PB CD34+ cells from PMF patient 5807 [CN]

description: GEP data: GSM1294477 in GSE53482

value: Vannucchi


title: PB CD34+ cells from PMF patient PV_41 [CN]

description: GEP data: GSM1294491 in GSE53482


title: PB CD34+ cells from PMF patient 5760 [CN]

description: GEP data: GSM1024649 in GSE41812

value: pos


title: PB CD34+ cells from PMF patient 5724 [CN]

description: GEP data: GSM1294473 in GSE53482


title: PB CD34+ cells from PMF patient PV_13 [CN]

description: GEP data: GSM1294485 in GSE53482


title: PB CD34+ cells from PMF patient PV_46 [CN]

description: GEP data: GSM1294492 in GSE53482


title: PB CD34+ cells from PMF patient 5017 [CN]

description: GEP data: GSM1024664 in GSE41812


title: PB CD34+ cells from PMF patient 5578 [CN]

description: GEP data: GSM1024654 in GSE41812


title: PB CD34+ cells from PMF patient 5566 [CN]

description: GEP data: GSM1024644 in GSE41812


title: PB CD34+ cells from PMF patient PV_47 [CN]

description: GEP data: GSM1294493 in GSE53482


title: PB CD34+ cells from PMF patient 5767 [CN]

description: GEP data: GSM1294475 in GSE53482


title: CON_CFSED5_2_62

value: colorectal cancer cell line


title: CON_CFSED1_3_59

value: CFSE d1


title: CON_CFSED5_1_61


title: PB CD34+ cells from PMF patient PV_40 [CN]

description: GEP data: GSM1294490 in GSE53482


title: PB CD34+ cells from PMF patient 5782 [CN]

description: GEP data: GSM1024651 in GSE41812


title: NHDF-EV

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description:
micro RNA expression of NHDF-derived EV
NHDF

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: normal human dermal fibroblast of adult-derived extracellular vesicles_LONZA

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: The number of 2.5-3.0×10e5 of BM-MSC was seeded in 10 cm dish and incubated until being confluent. In some experiments, NHDF were used instead of BM-MSC. EV were extracted from these cells.

extract_protocol: RNA samples were extracted from exosomes using miRNesy mini kit (Qiagen).

treatment_protocol: No extrinsic stimuli were applied.

value: NHDF

tag: sample type

value: EV


title: PB CD34+ cells from PMF patient 5757 [CN]

description: GEP data: GSM1024655 in GSE41812


title: PB CD34+ cells from PMF patient 5835 [CN]

description: GEP data: GSM1294478 in GSE53482


title: CON_CFSED1_2_58


title: PB CD34+ cells from PMF patient 5715 [CN]

description: GEP data: GSM1294472 in GSE53482


title: PB CD34+ cells from PMF patient 5005 [CN]

description: GEP data: GSM1024657 in GSE41812


title: PB CD34+ cells from PMF patient 5719 [CN]

description: GEP data: GSM1024646 in GSE41812


title: PB CD34+ cells from PMF patient 5776 [CN]

description: GEP data: GSM1024658 in GSE41812


title: PB CD34+ cells from PMF patient 5786 [CN]

description: GEP data: GSM1294476 in GSE53482


title: PB CD34+ cells from PMF patient 5793 [CN]

description: GEP data: GSM1024663 in GSE41812


title: PB CD34+ cells from PMF patient PV_29 [CN]

description: GEP data: GSM1294489 in GSE53482


title: PB CD34+ cells from PMF patient 5396 [CN]

description: GEP data: GSM1024652 in GSE41812


title: PB CD34+ cells from PMF patient 5733 [CN]

description: GEP data: GSM1294474 in GSE53482


title: PB CD34+ cells from PMF patient 5848 [CN]

description: GEP data: GSM1294479 in GSE53482


title: PB CD34+ cells from PMF patient 5024 [CN]

description: GEP data: GSM1024666 in GSE41812


title: PB CD34+ cells from PMF patient 4831 [CN]

description: GEP data: GSM1024634 in GSE41812


title: CON_CFSED1_4_60


title: tubule DR pool 6

status: Public on May 20 2018

city: Novato

first: Pankaj

last: Kapahi

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description:
translating mRNA
tubule DR-6

hyb_protocol: Sample Hybridization was done according to the manufacturers’ protocol for the 12-plex Gene Expression array platform. NimbleGen’s Sample Tracking Controls (05223512001), Hybridization Kit reagents (05583683001) and Wash Buffers (05584507001) were used. Each 12-plex array was sealed with a H12 mixer, provided with the Gene Expression array. 4μg of each Cy3 labeled sample was loaded onto an array on the 12-plex chip, using a Gilson M100 pipette. Hybridization was done overnight on a NimbleGen Hybridization System 4 unit, at 42°C for 16hrs.

scan_protocol: After the 12-plex chip was washed and dried, the chip was scanned on a GenePix 4200A scanner at 300PMT, 100POW. Arrays were then quantitated using NimbleGen’s NimbleScan2 software.

data_processing: Arrays were normalized using ArrayStar.

organism: Drosophila melanogaster

source_name: pools of 100 individual female 13 day old flies on DR food for 10 days

label_protocol: 150ng of total RNA was amplified for each experimental sample using Sigma’s TransPlex Complete Whole Transcriptome Amplification Kit (WTA2). Only 1/5th of the amplified sample library was used for the secondary amplification reaction. Amplified dscDNA samples were then purified using Qiagen’s QIAquick PCR Purification Kit (28104) and processed on the QIAcube according to the manufacturers’ standard protocol, “QIAquick PCR Purification-Standard.” Sample quality and concentration were assessed using a Nanodrop and Agilent’s Bioanalyzer (DNA 7500 Kit (5067-1506)). Amplification was randomized across experimental groups. 1μg of dscDNA was labeled with Cy3 for each experimental sample, using the NimbleGen (Roche) One-Color DNA Labeling Kit (05223555001) according to the manufacturers’ protocol. Cy3 labeling was randomized across experimental groups.

growth_protocol: The adult flies were developed on standard stock food (Caltech food recipe).

extract_protocol: RNA immunoprecipitation was performed on ice or at 4°C. FLAG antibody conjugated beads were equilibrated three times for 10 minutes with 2ml of equilibration buffer. The beads were then equilibrated once with 2ml of equilibration buffer with 2mg/ml yeast tRNA, 2mg/ml BSA and 100U RNasin Plus for 10 minutes. Approximately 100 female flies (200 female flies for neuron samples) were homogenized with 2ml of homogenization buffer, incubated on ice for 10 minutes, and spun down at 14,000g for 10 minutes. Supernatant was then added to the equilibrated beads and incubated for 3 hours with rotation. After incubation, the mixture was spun down and the supernatant was discarded (or saved for further analysis). Beads were then washed four times with 2ml of ice cold wash buffer for 10 minutes each. Bound ribosome and mRNA were eluted with either the elution buffer for 30 minutes or with ice cold Trizol-LS (Invitrogen # 10296-028) for 10 minutes. The eluted ribosome and mRNA were collected for RNA extraction. The RNA  quality and concentration were assessed using a Nanodrop and Agilent’s Bioanalyzer (RNA 6000 Nano Kit (5067-15811)). RNA immunoprecipitation and extraction were randomized across experimental groups.

treatment_protocol: The adult flies developed on standard stock food were transferred to either AL (5% yeast extract (YE)) or DR (0.5% YE) food within 2-3 days of eclosion. Flies were treated with AL or DR diet for 10 days.

tag: strain

value: +/+; +/+; C42-GAL4/UAS-RpL13A-His6FLAG

tag: protocol

value: DR food

value: tubule


title: tubule DR pool 4

description:
translating mRNA
tubule DR-4


title: tubule AL pool 3

description:
translating mRNA
tubule AL-3

source_name: pools of 100 individual female 13 day old flies on AL food for 10 days

value: AL food


title: tubule DR pool 5

description:
translating mRNA
tubule DR-5


title: tubule AL pool 2

description:
translating mRNA
tubule AL-2


title: tubule AL pool 4

description:
translating mRNA
tubule AL-4


title: tubule DR pool 3

description:
translating mRNA
tubule DR-3


title: tubule AL pool 1

description:
translating mRNA
tubule AL-1


title: tubule DR pool 2

description:
translating mRNA
tubule DR-2


title: BM-MSC-EV

description:
micro RNA expression of BM-MSC-derived EV
3543 (BMMSC)

source_name: human bone marrow mesenchymal stromal/stem cell-derived extracellular vesicles_3543

value: BM-MSC


title: neuron AL pool 3

description:
translating mRNA
neuron AL-3

source_name: pools of 200 individual female 13 day old flies on AL food for 10 days

value: neuron


title: tubule AL pool 5

description:
translating mRNA
tubule AL-5


title: PB CD34+ cells from PMF patient 5196 [CN]

description: GEP data: GSM1024641 in GSE41812


title: neuron AL pool 1

description:
translating mRNA
neuron AL-1


title: neuron DR pool 4

description:
translating mRNA
neuron DR-4

source_name: pools of 200 individual female 13 day old flies on DR food for 10 days


title: neuron DR pool 5

description:
translating mRNA
neuron DR-5


title: muscle DR pool 3

description:
translating mRNA
muscle DR-3

value: +/+; +/+; MHC-GAL4/UAS-RpL13A-His6FLAG

value: muscle


title: neuron DR pool 1

description:
translating mRNA
neuron DR-1


title: neuron DR pool 2

description:
translating mRNA
neuron DR-2


title: muscle DR pool 2

description:
translating mRNA
muscle DR-2


title: neuron AL pool 2

description:
translating mRNA
neuron AL-2


title: neuron DR pool 3

description:
translating mRNA
neuron DR-3


title: muscle DR pool 6

description:
translating mRNA
muscle DR-6


title: neuron AL pool 5

description:
translating mRNA
neuron AL-5


title: muscle DR pool 5

description:
translating mRNA
muscle DR-5


title: neuron AL pool 4

description:
translating mRNA
neuron AL-4


title: muscle AL pool 5

description:
translating mRNA
muscle AL-5


title: muscle DR pool 1

description:
translating mRNA
muscle DR-1


title: PB CD34+ cells from PMF patient 5008 [CN]

description: GEP data: GSM1024647 in GSE41812

value: Myeloproliferative Disease (MPD)

value: Primary myelofibrosis (PMF)


title: muscle AL pool 2

description:
translating mRNA
muscle AL-2


title: heart DR pool 6

description:
translating mRNA
heart DR-6

value: heart


title: muscle AL pool 3

description:
translating mRNA
muscle AL-3


title: muscle AL pool 4

description:
translating mRNA
muscle AL-4


title: heart DR pool 4

description:
translating mRNA
heart DR-4


title: muscle AL pool 1

description:
translating mRNA
muscle AL-1


title: muscle AL pool 6

description:
translating mRNA
muscle AL-6


title: GoldCLIP_YFP_UVC_replicate2

city: Beijing

first: Ming

last: Wang

state: Beijing

address: #15 Datun Road, Chaoyang, Beijing 100101, China

department: Key Laboratory of RNA Biology

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

description:
GoldCLIP
GoldCLIP_YFP_UVC.norm.plus.bw
GoldCLIP_YFP_UVC.norm.minus.bw

data_processing:
Sequenced reads were trimmed for adaptor sequence and masked for low-quality sequence. If multiple reads have exactly the same insert sequence and random barcode, only one is kept, after that, the random barcode and experimental barcode (positions 1-9) were removed.
The processed reads were first mapped to the spike-in genome (dm3, download from UCSC) using Bowtie v1.1.2 with parameters -f -p 8 -v 2 -k 1--best --sam --un, unmapped reads in previous step were mapped to a library of mature rRNAs, tRNAs and the mitochondrial genome by allowing multiple hits (rRNAs: RefSeq id, NR_023363.1, NR_003285.2, NR_003287.2, and NR_003286.2; tRNAs: downloaded from Genomic tRNA Database (http://gtrnadb.ucsc.edu) and only those from Homo_sapiens were retained, and CCA was appended to the 3′ end of the sequences). Mapping was performed using Bowtie v1.1.2 with parameters -f -p 8 -v 2 -k 1--best --sam --un. The remaining unmapped reads were aligned to the human genome (hg19) using Bowtie with parameters  -f -p 8 -v 2 -m 1 --best --strata --sam.
Peak identification was performed on uniquely mapped reads by CLIPper4 (available at https://github.com/YeoLab/clipper/releases/tag/1.0) was done with options -s hg19 -o --bonferroni --superlocal --threshold-method binomial --save-pickle.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files containing RT stops of GoldCLIP datasets mapped to the hg19 build of the human genome. Add data are normalized to a library depth of 10,000,000 reads. Bed files containing peaks of GoldCLIP datasets identified by CLIPper.

source_name: Human Embryonic Kidney 293 cells

growth_protocol: Transgenetic 293 cells were routinely generated by re-plating with DMEM media supplimently with 10% FBS (typically 2–3 × 10^6 cells into a T75 flask). Puromycin was added to a final concentration of 0.5 μg/ml.

extract_protocol:
Lysates were lysed in PBS supplemented with 1% Triton, clarified from debri, and HaloTag-protein-RNA complexes were isolated using Magne Halo Beads (Promega).
Libraries were prepared according to the iCLIP library construction protocol (Konig, Zarnack et al. 2011). Briefly, RNA in the Halo-RBP-RNA complex was released and reverse transcribed. Then cDNAs were gel purified and cyclized. The cyclized cDNAs were annealed to a complementary oligo which allows BamHI digestion to linearize the cDNAs The linearized cDNAs were then amplified by PCR to add Illumina adaptors. The final libraries were purified and sequenced on either Illumina X10 or HiSeq 2500 platform.

tag: genotype

value: Halo-YFP transgenetic


title: heart DR pool 5

description:
translating mRNA
heart DR-5


title: CON_CFSED1_1_57


title: heart AL pool 5

description:
translating mRNA
heart AL-5


title: GoldCLIP_YFP_UVC_replicate1


title: heart AL pool 2

description:
translating mRNA
heart AL-2


title: heart DR pool 2

description:
translating mRNA
heart DR-2


title: gut DR pool 6

description:
translating mRNA
gut DR-6

value: gut


title: heart AL pool 4

description:
translating mRNA
heart AL-4


title: heart DR pool 1

description:
translating mRNA
heart DR-1


title: GoldCLIP_PTB_UVA_replicate1

description:
GoldCLIP
GoldCLIP_PTB_UVA.norm.plus.bw
GoldCLIP_PTB_UVA.norm.minus.bw

value: Halo-PTB transgenetic


title: gut DR pool 3

description:
translating mRNA
gut DR-3


title: heart DR pool 3

description:
translating mRNA
heart DR-3


title: heart AL pool 1

description:
translating mRNA
heart AL-1


title: gut DR pool 4

description:
translating mRNA
gut DR-4


title: gut DR pool 2

description:
translating mRNA
gut DR-2


title: GoldCLIP_PTB_UVA_replicate2


title: tubule AL pool 6

description:
translating mRNA
tubule AL-6


title: heart AL pool 3

description:
translating mRNA
heart AL-3


title: gut DR pool 1

description:
translating mRNA
gut DR-1


title: tubule DR pool 1

description:
translating mRNA
tubule DR-1


title: gut DR pool 5

description:
translating mRNA
gut DR-5


title: neuron DR pool 6

description:
translating mRNA
neuron DR-6


title: WT_prog_3.5_HB_rep3

city: Stockholm

first: Johan

last: Ericson

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Instituet

description:
P1201_503
WT_Prog_3.5_Control-P1201_503

data_processing:
Clustered using cBot and sequenced on HiSeq2500 (HiSeq Control Software 2.2.38/RTA 1.18.61) with a 1x51 setup in RapidHighOutput mode. Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite
Reads were mapped with Tophat/2.0.4 to the Mouse genome assembly, build GRCm38 using default parameters settings.
Gene counts were generated using htseq/0.6.1 on bam files with duplicates included.
FPKMs for genes and transcripts were generated using cufflinks/2.1.1 on bamfiles with duplicates included.
Voom normalized logCPM values were obtained using voom function from R limma package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM, Counts and Voom normalized values for each sample

organism: Mus musculus

source_name: Prominin-1 sorted neural progenitors (3 days)

growth_protocol: Cells were grown in monolayer conditions.

extract_protocol:
ZymoPureTM kit
Illumina TruSeq; polyA-selection

treatment_protocol: RA and SAG applied 0-3 DDC (days in differentiation conditions)

tag: genotype/variation

value: wild type

tag: cell status

value: d3.5 ESC differentiation


title: WT_prog_3.5_HB_rep1

description:
P1201_501
WT_Prog_3.5_Control-P1201_501

value: Prominin-1 sorted neural progenitors (3 days)


title: WT_d3 rep2

description:
P1827_132
WT_Nondiff_3_Control-P1827_132

source_name: Differentiating mouse embryonic stem cells (3days)

value: d3 ESC differentiation


title: ribosome footprints_ltm_ifn_vir

city: Seattle

first: Rasi

last: Subramaniam

address: 1100 Fairview Ave N

institute: Fred Hutch

description:
Ribo-Seq + LTM sample, treated with IFN-b for 10 hr and infected with influenza virus (reassortant A/PeurtoRico/1934 and A/WSN/1933) for last 5 hrs
ribosome footprints

data_processing:
Library strategy: Ribo-Seq
[Pre-processing and alignment] For Ribo-Seq libraries, we trimmed polyA tails using cutadapt 1.12 with parameters --adapter=AAAAAAAAAA --length=40 --minimum-length=25 to retain trimmed reads that were between 25nt and 40nt in length. For RNA-Seq libraries, we first reverse complemented the read to obtain the sense orientation using fastx reverse complement 0.0.13  with parameters --Q33, and then trimmed reads to 40nt. To remove rRNA, we discarded trimmed reads aligning to four human rRNA sequences (28S:NR 003287.2, 18S:NR 003286.2, 5.8S:NR 003285.2, and 5S:NR 023363.1) from the hg38 genome. The alignment was done using bowtie 1.1.1 with parameters --seedlen=23  --threads=8. We aligned the remaining non-rRNA to human transcripts (Gencode v24 using rsem 1.2.31 with parameters --output-genome-bam --sort-bam-by-coordinate. We also aligned the non-rRNA reads to an influenza genome containing both low and high CTG NP using the above rsem parameters including the extra options --seed-length 21 --bowtie-n 3
[Calculating transcript coverage] The posterior probablilty score from rsem (ZW field in the BAM output) was used to calculate coverage for reads on transcripts. For influenza reads, we consider only reads that map to the positive sense of influenza transcripts. We performed variable trimming based on fragment length, reads  that were between 25 and 32 nucleotides in length were assigned to a P-site at 14 nucleotides from the 5’ end of the read, and reads between 33 and 39 nucleotides were assigned to a P-site at 15 nucleotides from the 5’ end of the read.For human transcripts, a set of nonredundant protein-coding transcripts was compiled by using the Gencode v24 annotations and applying the following criteria: The corresponding CDS must be part of the Consensus CDS (CCDS) project, must be labeled as a principal transcript by APPRIS; For each gene, we selected the lowest numbered CCDS ID, and for each CCDS, we selected the lowest numbered transcript ID.
[Calling translation initiation sites] We used a zero-truncated negative binomial distribution (ZTNB) to statistically model the background distribution of Ribo-Seq and Ribo-Seq + LTM counts in transcripts with more than 50 positions with non-zero counts. We first added the Ribo-Seq and the Ribo-Seq + LTM read counts of the two neighboring positions to each position in the genome (referred to as pooled counts below). Candidate start sites were identified based on the following criteria: For influenza 949 transcripts, the ZTNB-based P-value for the Ribo-Seq + LTM pooled count at that location must be <0.01 and 1000-fold higher than the P-value of the Ribo-Seq pooled counts at the same location, or must have an absolute value less than 10−7. For host transcripts, we required the Ribo-Seq + LTM P-value to be only 100-fold higher than the P-value of the Ribo-Seq pooled counts. Additionally, for host transcripts, we required that the read counts be greater than an absolute threshold across all transcripts. This threshold was estimated by requiring P<0.05 in a ZTNB model fit to the bottom 99% of all non-zero P-site Ribo-Seq + LTM pooled counts across all transcripts. Only the highest pooled counts within each 30nt window was called as a candidate TIS. From the called TIS, we assigned the identity of the start codon by looking at a window -1 to +1 nucleotides from the TIS peak and assigning the start codon based on following hierarchy: ATG, CTG, TTG, GTG, ATA, ATC, ATT, AAG, ACG, AGG, and other. If there are multiple near cognate codons in the window, the codon was assigned based on the order in the above list.
Genome_build: hg 38
Supplementary_files_format_and_content: Processed CSV data file is output from RSEM and includes host genscript gene id, transcript id(s), gene length, posterior probability score (expected count), transcripts per million (TPM), fragments per kilobase mapped (FPKM)
Processed TSV data files contain all host or influenza translation initiation sites called in any sample and information about the translation initiation site including transcript, transcript position, distance from annotated translation initiation site, codon, peptide length, and reading frame. Host file also contains information for the raw Ribo-Seq and Ribo-Seq + LTM counts and statistics from the ZNTB model.

source_name: A549 cells

growth_protocol: Cells were seeded 16 hrs prior to start of assay to be 70 % confluent at treatment, using two 15 cm plates per sample

extract_protocol:
Samples were flash frozen in liquid nitrogen and lysed.
A portion of the lysate was used to generate RNA-Seq libraries using NEBNext 893 Ultra Directional RNA Library Prep Kit  after depleting ribosome RNA using the Ribozero Gold kit. For ribosome profiling, we performed nuclease footprinting treatment by adding RNase I . We collected ribosome protected mRNA fragments using MicroSpin S-400 HR Columns, and purified RNA from the flow through for size selection. We gel-purified ribosome protected fragments with length between 26 and 34 nt using RNA oligo size markers. We used polyA tailing instead of linker ligation, performed reverse transcription, circularization of cDNA, and PCR amplification of cDNA. Libraries were sequenced on Illumina HiSeq 2500 in 50bp single end mode.

treatment_protocol: At the start of treatment, samples treated with IFN-b were given media containing IFN-b at 20 U/ml, treatment with IFN was for 10 hrs total. 5 hrs after IFN-b treatment was started, samples were infected with influenza virus, viral infection proceeded for 5 hrs. For Ribo-Seq + LTM samples, the last 30 min of treatment occured in the presence of 5 μM

value: human lung adenocarcinoma epithelial cells

tag: pathogen

value: influenza virus mixture of low and high CTG NP (reassortant A/PeurtoRico/1934 (PA, PB1, PB2) and A/WSN/1933 (M, NS, HA, NA) and either low or high CTG PR8 NP)

value: IFN-b (20 U/ml)


title: mrna_vir

description: RNA-Seq sample, infected with influenza virus (reassortant A/PeurtoRico/1934 and A/WSN/1933) for 5 hrs

data_processing:
[Pre-processing and alignment] For Ribo-Seq libraries, we trimmed polyA tails using cutadapt 1.12 with parameters --adapter=AAAAAAAAAA --length=40 --minimum-length=25 to retain trimmed reads that were between 25nt and 40nt in length. For RNA-Seq libraries, we first reverse complemented the read to obtain the sense orientation using fastx reverse complement 0.0.13  with parameters --Q33, and then trimmed reads to 40nt. To remove rRNA, we discarded trimmed reads aligning to four human rRNA sequences (28S:NR 003287.2, 18S:NR 003286.2, 5.8S:NR 003285.2, and 5S:NR 023363.1) from the hg38 genome. The alignment was done using bowtie 1.1.1 with parameters --seedlen=23  --threads=8. We aligned the remaining non-rRNA to human transcripts (Gencode v24 using rsem 1.2.31 with parameters --output-genome-bam --sort-bam-by-coordinate. We also aligned the non-rRNA reads to an influenza genome containing both low and high CTG NP using the above rsem parameters including the extra options --seed-length 21 --bowtie-n 3
[Calculating transcript coverage] The posterior probablilty score from rsem (ZW field in the BAM output) was used to calculate coverage for reads on transcripts. For influenza reads, we consider only reads that map to the positive sense of influenza transcripts. We performed variable trimming based on fragment length, reads  that were between 25 and 32 nucleotides in length were assigned to a P-site at 14 nucleotides from the 5’ end of the read, and reads between 33 and 39 nucleotides were assigned to a P-site at 15 nucleotides from the 5’ end of the read.For human transcripts, a set of nonredundant protein-coding transcripts was compiled by using the Gencode v24 annotations and applying the following criteria: The corresponding CDS must be part of the Consensus CDS (CCDS) project, must be labeled as a principal transcript by APPRIS; For each gene, we selected the lowest numbered CCDS ID, and for each CCDS, we selected the lowest numbered transcript ID.
[Calling translation initiation sites] We used a zero-truncated negative binomial distribution (ZTNB) to statistically model the background distribution of Ribo-Seq and Ribo-Seq + LTM counts in transcripts with more than 50 positions with non-zero counts. We first added the Ribo-Seq and the Ribo-Seq + LTM read counts of the two neighboring positions to each position in the genome (referred to as pooled counts below). Candidate start sites were identified based on the following criteria: For influenza 949 transcripts, the ZTNB-based P-value for the Ribo-Seq + LTM pooled count at that location must be <0.01 and 1000-fold higher than the P-value of the Ribo-Seq pooled counts at the same location, or must have an absolute value less than 10−7. For host transcripts, we required the Ribo-Seq + LTM P-value to be only 100-fold higher than the P-value of the Ribo-Seq pooled counts. Additionally, for host transcripts, we required that the read counts be greater than an absolute threshold across all transcripts. This threshold was estimated by requiring P<0.05 in a ZTNB model fit to the bottom 99% of all non-zero P-site Ribo-Seq + LTM pooled counts across all transcripts. Only the highest pooled counts within each 30nt window was called as a candidate TIS. From the called TIS, we assigned the identity of the start codon by looking at a window -1 to +1 nucleotides from the TIS peak and assigning the start codon based on following hierarchy: ATG, CTG, TTG, GTG, ATA, ATC, ATT, AAG, ACG, AGG, and other. If there are multiple near cognate codons in the window, the codon was assigned based on the order in the above list.
Genome_build: hg 38
Supplementary_files_format_and_content: Processed CSV data file is output from RSEM and includes host genscript gene id, transcript id(s), gene length, posterior probability score (expected count), transcripts per million (TPM), fragments per kilobase mapped (FPKM)
Processed TSV data files contain all host or influenza translation initiation sites called in any sample and information about the translation initiation site including transcript, transcript position, distance from annotated translation initiation site, codon, peptide length, and reading frame. Host file also contains information for the raw Ribo-Seq and Ribo-Seq + LTM counts and statistics from the ZNTB model.


title: ribosome footprints_ltm_vir

description:
Ribo-Seq + LTM sample, infected with influenza virus (reassortant A/PeurtoRico/1934 and A/WSN/1933) for 5 hrs
ribosome footprints


title: mrna_ifn

description: RNA-Seq sample, treated with IFN-b for 10 hrs


title: mrna_untr

description: RNA-Seq sample, untreated


title: gut AL pool 6

description:
translating mRNA
gut AL-6

value: AL food


title: gut AL pool 5

description:
translating mRNA
gut AL-5


title: gut AL pool 4

description:
translating mRNA
gut AL-4


title: gut AL pool 3

description:
translating mRNA
gut AL-3


title: germ line DR pool 2

description:
translating mRNA
germ line DR-2

value: +/+; NGT-GAL4/+; UAS-RpL13A-His6FLAG/+

value: DR food

value: germ line


title: ribosome footprints_ltm_ifn

description:
Ribo-Seq + LTM sample, treated with IFN-b for 10 hrs
ribosome footprints


title: germ line DR pool 6

description:
translating mRNA
germ line DR-6


title: ribosome footprints_ltm_untr

description:
Ribo-Seq + LTM sample, untreated
ribosome footprints


title: germ line DR pool 3

description:
translating mRNA
germ line DR-3


title: WT_d3 rep1

description:
P1827_131
WT_Nondiff_3_Control-P1827_131

value: Differentiating mouse embryonic stem cells (3days)


title: gut AL pool 1

description:
translating mRNA
gut AL-1


title: germ line DR pool 4

description:
translating mRNA
germ line DR-4


title: mrna_ifn_vir

description: RNA-Seq sample, treated with IFN-b for 10 hr and infected with influenza virus (reassortant A/PeurtoRico/1934 and A/WSN/1933) for last 5 hrs


title: germ line DR pool 5

description:
translating mRNA
germ line DR-5


title: gut AL pool 2

description:
translating mRNA
gut AL-2


title: germ line AL pool 5

description:
translating mRNA
germ line AL-5


title: WT_d1 rep2

description:
P1827_128
WT_Nondiff_1_Control-P1827_128

source_name: Differentiating mouse embryonic stem cells (1day)

value: d1 ESC differentiation


title: WT_d2 rep2

description:
P1827_130
WT_Nondiff_2_Control-P1827_130

source_name: Differentiating mouse embryonic stem cells (2days)

value: d2 ESC differentiation


title: ribosome footprints_cyclo_ifn_vir

description:
Ribo-Seq sample, treated with IFN-b for 10 hr and infected with influenza virus (reassortant A/PeurtoRico/1934 and A/WSN/1933) for last 5 hrs
ribosome footprints


title: WT_d1 rep1

description:
P1827_127
WT_Nondiff_1_Control-P1827_127

value: Differentiating mouse embryonic stem cells (1day)


title: ribosome footprints_cyclo_vir

description:
Ribo-Seq sample, infected with influenza virus (reassortant A/PeurtoRico/1934 and A/WSN/1933) for 5 hrs
ribosome footprints


title: ribosome footprints_cyclo_ifn

description:
Ribo-Seq sample, treated with IFN-b for 10 hrs
ribosome footprints


title: germ line AL pool 4

description:
translating mRNA
germ line AL-4


title: germ line DR pool 1

description:
translating mRNA
germ line DR-1


title: WT_d2 rep1

description:
P1827_129
WT_Nondiff_2_Control-P1827_129

value: Differentiating mouse embryonic stem cells (2days)


title: germ line AL pool 3

description:
translating mRNA
germ line AL-3


title: PB CD34+ cells from PMF patient 4771 [CN]

description: GEP data: GSM1024660 in GSE41812

value: Vannucchi

value: Myeloproliferative Disease (MPD)

value: Primary myelofibrosis (PMF)

value: pos

value: Peripheral Blood (PB)


title: germ line AL pool 2

description:
translating mRNA
germ line AL-2


title: germ line AL pool 6

description:
translating mRNA
germ line AL-6


title: fat body DR pool 6

description:
translating mRNA
fat body DR-6

value: fat body


title: fat body DR pool 4

description:
translating mRNA
fat body DR-4


title: GoldCLIP_PTB_UVC_replicate2

description:
GoldCLIP
GoldCLIP_PTB_UVC.norm.plus.bw
GoldCLIP_PTB_UVC.norm.minus.bw

value: Halo-PTB transgenetic


title: GoldCLIP_PTB_UVC_replicate1


title: fat body DR pool 5

description:
translating mRNA
fat body DR-5


title: germ line AL pool 1

description:
translating mRNA
germ line AL-1


title: WT_ESCs rep1

description:
P1827_125
WT_Nondiff_ESCs_Control-P1827_125

source_name: Mouse embryonic stem cells E14

value: wild type

value: d0 ESC differentiation

value: Mouse embryonic stem cells E14


title: fat body DR pool 3

description:
translating mRNA
fat body DR-3

value: DR food


title: GoldCLIP_PTB_NoUV_replicate2

description:
GoldCLIP
GoldCLIP_PTB_NoUV.norm.plus.bw
GoldCLIP_PTB_NoUV.norm.minus.bw


title: GoldCLIP_PTB_NoUV_replicate1


title: muscle DR pool 4

description:
translating mRNA
muscle DR-4

value: +/+; +/+; MHC-GAL4/UAS-RpL13A-His6FLAG

value: muscle


title: WT_ESCs rep2

description:
P1827_126
WT_Nondiff_ESCs_Control-P1827_126


title: ribosome footprints_cyclo_untr

description:
Ribo-Seq sample, untreated
ribosome footprints

value: human lung adenocarcinoma epithelial cells


title: Tuft_Thy_4

status: Public on May 19 2018

city: San Francisco

first: Joshua

last: Pollack

address: 2 Tower Pl.  Ste 800

institute: Pionyr Immunotherapeutics

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed of any presence of the Illumina adapter, then mapped to GRCm38.78 whole genome using STAR: Dobin A, Gingeras TR et al. "STAR: Ultrafast Universal RNA-seq Aligner." Bioinformatics. 2013 Jan 1;29(1):15-21.
Unique alignments were aggregated across all isoforms on a per-gene basis, using only reads mapping to exons, using rna-STAR.
Normalization and differential expression estimation was performed using DESeq2: Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550.
Genome_build: GRCm38.78 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text files include raw per-gene values for each sample

source_name: thymus epithelium

extract_protocol:
For thymic epithelium, thymi were isolated, cleaned of fat and transferred to DMEM + 2% FBS on ice. Thymi were minced with a razor blade and tissue pieces were moved with a glass Pasteur pipette to 15 ml tubes and vortexed briefly in 10 ml of media. Fragments were allowed to settle before removing the media and replacing it with 4 ml of digestion media containing 2% FBS, 100 μg mL-1 DNase I (Roche), and 100 μg mL-1 Liberase TM (Sigma-Aldrich) in DMEM. Tubes were moved to a 37° C water bath and fragments were triturated through a glass Pasteur pipette at 0 min and 6 min to mechanically aid digestion. At 12 min, tubes were spun briefly to pellet undigested fragments and the supernatant was moved to 20 ml of 0.5% BSA (Sigma-Aldrich), 2 mM EDTA (TekNova), in PBS (MACS buffer) on ice to stop the enzymatic digestion. This was repeated twice for a total of three 12 min digestion cycles, or until there were no remaining tissue fragments. The single cell suspension was then pelleted and washed once in MACS Buffer. Density-gradient centrifugation using a three-layer Percoll gradient (GE Healthcare) with specific gravities of 1.115, 1.065, and 1.0 was used to enrich for stromal cells. Cells isolated from the Percoll- light fraction, between the 1.065 and 1.0 layers, were then washed and resuspended for staining.
Cells were sorted directly into lysis buffer from the Dynabead mRNA Direct Purification Kit (ThermoFisher) and poly A RNA was isolated according to the manufacturer’s protocol.
[amplification protocol] Amplified cDNA was prepared using the NuGen Ovation RNA-Seq system V2 kit, according to the manufacturer’s protocol
Sequencing libraries were generated using the Nextera XT library preparation kit with multiplexing primers, according to manufacturer’s protocol (Illumina)

tag: age

value: 12 weeks

tag: Sex

value: M

tag: mouse status

value: naïve

tag: number of mice

value: thymus

value: tuft cells

tag: sorting gate

tag: cells sorted


title: Tuft_Thy_1

tag: tissue

tag: cell type


title: Tuft_Thy_3


title: Tuft_SI_4

source_name: small intestine epithelium

extract_protocol:
For single cell epithelial preparations from small intestines, tissues were flushed with PBS, opened, and rinsed with PBS to remove intestinal contents. Intestinal tissue was cut into 2-5 cm pieces and incubated rocking at 37° C in 15 mL HBSS (Ca+2/Mg+2-free) supplemented with 5mM dithiothreitol (DTT, Sigma-Aldrich), 5% fetal calf serum (FCS, VWR), and 10mM HEPES (Gibco). Tissues were vortexed vigorously and supernatant was discarded. Tissues were then incubated rocking at 37° C in 15 mL HBSS (Ca+2/Mg+2-free) supplemented with 5mM EDTA (Invitrogen), 5% FCS, and 10mM HEPES. Tissues were vortexed thoroughly and released epithelial cells were passed through a 70 μm filter. Tissues were then incubated in fresh EDTA/HBSS solution for 15 minutes, vortexed, and filtered. Supernatants were pooled and washed once before staining for flow cytometry.
Cells were sorted directly into lysis buffer from the Dynabead mRNA Direct Purification Kit (ThermoFisher) and poly A RNA was isolated according to the manufacturer’s protocol.
[amplification protocol] Amplified cDNA was prepared using the NuGen Ovation RNA-Seq system V2 kit, according to the manufacturer’s protocol
Sequencing libraries were generated using the Nextera XT library preparation kit with multiplexing primers, according to manufacturer’s protocol (Illumina)

value: small intestine


title: Tuft_SI_3


title: BJAB-KSHV rep1

city: Philadelphia

first: Rajnish

middle: Kumar

last: Singh

state: Pennsylvania

address: 202B Johnson Pavilion 3610 Hamilton walk

department: Otorhinolaryngology

institute: University of Pennsylvania

data_processing:
CLC bio (Qiagen) was used for read alignment
The reads for sequencing data were aligned with HHV8 or human genome
Differential gene expression were calculated CLC bio software
Genome_build: hg19, NC_009333.1

source_name: BJAB-KSHV

growth_protocol: Cells were grown in RPMI medium supplemented with 7% bovine growth serum at 37°C/5%CO2

extract_protocol:
RNA from cells growing in culture was isolated using trizole reagent by standard phenol chloroform extraction
Library for RNA sequencing was preapred using Illumina RNA sequencing sample prep kit

treatment_protocol: 100µM Cobalt chloride for 48 hours

tag: cell line

value: BJAB-KSHV

value: B-cell line


title: BJAB-CoCl2 rep1

value: BJAB

tag: treated with

value: 100µM Cobalt chloride for 48 hrs


title: BJAB-KSHV-CoCl2 rep1


title: Epi_SI_2

value: total epithelium


title: BJAB CoCl2 rep2

source_name: BJAB CoCl2


title: Epi_SI_3


title: BJAB-KSHV rep2


title: BJAB-KSHV-CoCl2 rep2


title: Tuft_SI_2


title: Tuft_Thy_2


title: Epi_SI_1


title: fat body AL pool 4

description:
translating mRNA
fat body AL-4

value: AL food

value: fat body


title: fat body AL pool 3

description:
translating mRNA
fat body AL-3


title: 72hr_MuSCs_RNA-seq 2

city: Lexington

first: Darrell

middle: Orlyn

last: Ricke

address: 244 Wood Street

department: Group 48 Bioengineering Systems & Technology

institute: MIT Lincoln Laboratory

data_processing:
R/Bioconductor DESeq 2 was used to calculate differential expression (DE) of transcripts
Genome_build: mouse genome (mm9)
Supplementary_files_format_and_content: Excel, gene TPM

extract_protocol:
Frozen tissue thawed, homogenized, cells lysed
10 ng of isolated total RNA from satellite cells was used to produce cDNA libraries using the SmartSeq4 protocol (Clonetech)

treatment_protocol: Freeze injury was induced by applying a 6 mm diameter steel probe (cooled to the temperature of dry ice, −70C) to the belly of the TA muscle (directly below incision site) for 10 seconds

tag: timepoint (after injury healing)

value: 72 hours

value: tibialis anterior muscle

value: muscle satellite cells (MuSCs)

tag: timepoint


title: fat body DR pool 2

description:
translating mRNA
fat body DR-2

tag: strain

tag: protocol

value: DR food


title: RFPp_low_4

source_name: thymus

value: 5-6 weeks

value: mixed

value: tamoxifen treated (2mg)

value: epithelial cells


title: RFPp_low_3

value: thymus


title: BJAB rep1

source_name: BJAB


title: fat body AL pool 1

description:
translating mRNA
fat body AL-1

source_name: pools of 100 individual female 13 day old flies on AL food for 10 days


title: fat body AL pool 6

description:
translating mRNA
fat body AL-6


title: BJAB rep2


title: 48hr_MuSCs_RNA-seq 2

value: 48 hours


title: 72hr_MuSCs_RNA-seq 1


title: RFPp_low_2


title: RFPp_low_1


title: 48hr_MuSCs_RNA-seq 1


title: fat body DR pool 1

description:
translating mRNA
fat body DR-1

source_name: pools of 100 individual female 13 day old flies on DR food for 10 days


title: RFPp_hi_4


title: 3hr_MuSCs_RNA-seq 2

value: 3 hours


title: fat body AL pool 5

description:
translating mRNA
fat body AL-5


title: 3hr_MuSCs_RNA-seq 1


title: 24hr_MuSCs_RNA-seq 2

value: 24 hours


title: RFPp_hi_1


title: RFPp_hi_2


title: 168hr_MuSCs_RNA-seq 2

value: 168 hours


title: RFPn_low_3


title: 168hr_MuSCs_RNA-seq 1


title: RFPn_low_2


title: RFPn_hi_4


title: RFPn_hi_3


title: RFPn_hi_1


title: RFPn_low_1


title: WT_prog_3.5_HB_rep2

description:
P1201_502
WT_Prog_3.5_Control-P1201_502

tag: genotype/variation

value: wild type

value: d3.5 ESC differentiation

value: Prominin-1 sorted neural progenitors (3 days)


title: RFPp_hi_3


title: 24hr_MuSCs_RNA-seq 1


title: fat body AL pool 2

description:
translating mRNA
fat body AL-2

value: AL food

value: fat body


title: RFPn_low_4


title: RFPn_hi_2


title: 10 days after day length switch - replicate 3

city: Manchester

first: Manoj

last: Kumar

state: Lancashire

address: Oxford Road

department: Faculty of Biology, Medicine and Health

institute: University of Manchester

hyb_protocol: GeneChip Hybridzation Oven 645; Fluidics protocol: EukGE-WS2

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Partek GS 6.6 using RMA algorithm

organism: Arabidopsis thaliana

source_name: 10 days after day length switch

label_protocol: Biotinylated cDNA samples from each of the three replicates for each hypocotyl stage were  synthesised

growth_protocol: Col-0 plants were grown under short day conditions for 6 weeks and switched to long days to induce flowering. Seeds were sterilized in 70% ethanol for 5 minutes, washed in sterile water three times and stratified at 4oC in the dark for 2 days before being germinated on ½ MS media with 1% agar. After 1 week, the seedlings were transferred to individual pots containing Levington F2 compost mixed with vermiculite and perlite (10:1:1). Plants were grown in controlled environment chambers at 22oC under either short (8hr light) or long days (16hr light).

extract_protocol: RNA was extracted using TRIzol reagent (Life Technologies), as per the manufacturer's instructions.

treatment_protocol: Hypocotyl tissue was frozen in liquid nitrogen and ground using a mortar and pestle.

tag: ecotype

tag: time

value: 10 days after day length switch

value: Pool of 8 hypocotyls


title: Grand Isle, LA, Not Oiled Site B, pool13

city: Durham

first: Mariano

last: Alvarez

state: NC

address: 2916 Bivins Road

department: Biology

institute: Duke University

description:
Gene expression after field collection
GIBN11
GIBN7
GIBN9

hyb_protocol: For each array, 1650 ng of Cy 3 labeled aRNA was fragmented and hybridized with rotation at 65°C for 17 hours. Samples were hybridized to custom design 4X44k arrays (Agilent Technologies, Inc).  The arrays were washed according to the manufacturer’s protocol.

scan_protocol: The arrays were washed according to the manufacturer’s protocol and then scanned on an Agilent G2505B scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Sporobolus alterniflorus

source_name: leaf, 3rd expanded

label_protocol: cDNA was synthesized from 200 ng of total RNA using the Quick-Amp labeling Kit (Agilent Technologies, Inc.) according the manufacturer’s protocol. The cDNA was used as a template for in vitro transcription (IVT) in the presence of T7 RNA Polymerase and cyanine labeled CTP’s. The amplified, labeled aRNA was purified using the RNeasy Mini Kit (Qiagen).

extract_protocol: RNA was prepared using the QIAGEN RNeasy Plant minikit (QIAGEN) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-8000 spectrophotometer.

treatment_protocol: Samples were collected from field sites and frozen in liquid nitrogen immediately

value: leaf

tag: rna pool


title: 4 days after day length switch - replicate 1

source_name: 4 days after day length switch

value: 4 days after day length switch


title: Bay Saint Louis, MS, Not Oiled, pool16

description:
Gene expression after field collection
BSLN5
BSLN7
BSLN8


title: 2 days after day length switch - replicate 1

source_name: 2 days after day length switch

value: 2 days after day length switch


title: 2 days after day length switch - replicate 3


title: Grand Isle, LA, Not Oiled Site A, pool11

description:
Gene expression after field collection
GIAN1
GIAN2
GIAN9


title: Grand Isle, LA, Not Oiled Site A, pool10

description:
Gene expression after field collection
GIAN3
GIAN4
GIAN8


title: 1 days after day length switch - replicate 3

source_name: 1 days after day length switch

value: 1 days after day length switch


title: Bay Saint Louis, MS, Not Oiled, pool17

description:
Gene expression after field collection
BSLN2
BSLN3
BSLN4


title: 1 days after day length switch - replicate 1


title: Bay Saint Louis, MS, Oiled, pool9

description:
Gene expression after field collection
BSLO2
BSLO3
BSLO5


title: 10 days after day length switch - replicate 2


title: 0 days after day length switch - replicate 3

source_name: 0 days after day length switch

value: 0 days after day length switch


title: Grand Isle, LA, Not Oiled Site B, pool15

description:
Gene expression after field collection
GIBN1
GIBN12
GIBN6


title: 1 days after day length switch - replicate 2


title: Grand Isle, LA, Not Oiled Site B, pool14

description:
Gene expression after field collection
GIBN2
GIBN3
GIBN4


title: 10 days after day length switch - replicate 1


title: 4 days after day length switch - replicate 3


title: Bay Saint Louis, MS, Oiled, pool7

description:
Gene expression after field collection
BSLO10
BSLO4
BSLO6


title: Grand Isle, LA, Not Oiled Site A, pool12

description:
Gene expression after field collection
GIAN5
GIAN6
GIAN7


title: Grand Isle, LA, Oiled Site B, pool6

description:
Gene expression after field collection
GIBO2
GIBO3
GIBO9


title: 2 days after day length switch - replicate 2


title: Bay Saint Louis, MS, Oiled, pool8

description:
Gene expression after field collection
BSLO1
BSLO8
BSLO9


title: 4 days after day length switch - replicate 2


title: Bay Saint Louis, MS, Not Oiled, pool18

description:
Gene expression after field collection
BSLN1
BSLN6
BSLN9


title: 0 days after day length switch - replicate 2


title: Grand Isle, LA, Oiled Site A, pool3

description:
Gene expression after field collection
GIAO1
GIAO2
GIAO3


title: Grand Isle, LA, Oiled Site A, pool1

description:
Gene expression after field collection
GIAO5
GIAO6
GIAO7


title: Grand Isle, LA, Oiled Site B, pool5

description:
Gene expression after field collection
GIBO1
GIBO4
GIBO7


title: Grand Isle, LA, Oiled Site A, pool2

description:
Gene expression after field collection
GIAO10
GIAO4
GIAO9


title: 0 days after day length switch - replicate 1


title: Blood_GEN41_MVL496-1

status: Public on May 18 2018

city: Quebec

first: Bénédicte L.

last: Tremblay

state: Quebec

address: Pavillon des Services, 2440 Hochelaga Blvd

department: School of Nutrition

country: Canada

institute: Institute of Nutrition and Functional Foods (INAF), Laval University

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: The FlexArray software (version 1.6) and the lumi R package were used to analyze and normalize gene expression levels. More specifically, robust multi-array analysis, variance stabilizing transformation, and quantile normalization were used for background correction, variance stabilization, and normalization, respectively.

source_name: Whole blood

label_protocol: standard Illumina protocol

extract_protocol: Blood samples were collected from an antecubital vein into PAXgeneTM tubes after 12-h overnight fast and 48-h alcohol abstinence. Total RNA was isolated and purified from whole blood using PAXgene Blood RNA Kit (QIAGEN) for all 48 subjects.

tag: family

tag: family member

value: Mother

tag: Sex

value: Female

value: blood


title: Blood_GEN48_MVL503-1

value: Boy

value: Male


title: Blood_GEN38_MVL493-1


title: Blood_GEN49_MVL504-1


title: Blood_GEN45_MVL500-1


title: Grand Isle, LA, Oiled Site B, pool4

description:
Gene expression after field collection
GIBO5
GIBO6
GIBO8


title: Blood_GEN40_MVL495-1


title: Blood_GEN33_MVL489-1


title: Blood_GEN47_MVL502-1


title: Blood_GEN43_MVL498-1


title: Blood_GEN50_MVL505-1

value: Girl


title: Blood_GEN30_MVL486-1


title: Blood_GEN46_MVL501-1

value: Father


title: Blood_GEN44_MVL499-1


title: Blood_GEN39_MVL494-1


title: Blood_GEN36_MVL492-1


title: WT  [Cpn + oxLDL ]

city: Los Angeles

first: Shuang

last: Chen

address: 8700 Beverly blvd

department: Pediatrics

institute: Cedars Sinai Medical Center

description: Gene expression data from wt peritoneal macrophage

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: WT Peritoneal  macrophages

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Resident peritoneal macrophages were collected and the pooled cells were incubated overnight in RPMI 1640 medium (Cellgro) with 10% FBS at 37°C in 5% CO2 and non-adherent cells were rinsed away.

extract_protocol: RNA was puriﬁed using the RNeasy kit (QIAGEN, Valencia, CA), including treatment with DNase.

treatment_protocol: Peritoneal macrophages, pooled from three mice, were stimulated C.pn with  oxLDL for 8h

value: WT

tag: treatment

value: chlamydia pneumoniae infection+ox-Ldl

value: Peritoneal  macrophages


title: Blood_GEN42_MVL497-1


title: WT PBS

value: PBS treament


title: NLRP3 KO [Cpn + oxLDL]

description: Gene expression data from NLRP3 KO peritoneal macrophage

source_name: NLRP3 KO Peritoneal  macrophages

value: NLRP3 KO


title: Blood_GEN27_MVL508-1


title: Blood_GEN28_MVL484-1


title: Blood_GEN32_MVL488-1


title: Blood_GEN24_MVL480-1


title: Blood_GEN25_MVL481-1


title: Blood_GEN26_MVL482-1


title: Blood_GEN29_MVL485-1


title: Blood_GEN34_MVL490-1


title: Blood_GEN31_MVL487-1


title: Blood_GEN23_MVL479-1


title: Blood_GEN22_MVL478-1


title: Blood_GEN20_MVL476-1


title: Blood_GEN06_MVL462-1


title: Blood_GEN02_MVL506-1


title: Blood_GEN21_MVL477-1


title: Blood_GEN08_MVL464-1


title: Blood_GEN19_MVL507-1


title: Blood_GEN16_MVL472-1


title: Blood_GEN14_MVL470-1


title: OX40L-APC_ATACSeq

city: HOUSTON

first: Xiaolong

last: Zhang

state: Texas

address: 6670 Bertner Avenue, R7-211

department: Immunobiology & Transplant Research Center

institute: Houston Methodist Research Institute

data_processing:
ATAC-seq was performed at Active Motif
ATAC-seq peaks were detected with DANPOS2 deregion function and visualized using UCSC genome browser with peak height normalized against the Gapdh locus. Gain and loss regions are defined by height q-value < 0.01 and log2 fold change > 2. Associated genes are selected based on region from upstream 3kb to downstream 10 kb of gene promoter.
Pathway enrichment analysis was performed using DAVID
Genome_build: mm10
Supplementary_files_format_and_content: wig

source_name: Spleen cells

growth_protocol: Naive CD4+ T cells (CD4+CD62L+Foxp3−) were FACS sorted from Foxp3-GFP reporter mice with FACSaria. The sorted naive CD4+ T cells (1 × 105 cells/well) were stimulated with anti-CD3 plus equal numbers of Wt APCs or OX40L-Tg APC in the presence of TGF-β1 (3 ng/ml; R&D system) and IL-2 (10 ng/ml; R&D system) for 48 hours.

extract_protocol:
ATAC-seq was performed at Active Motif (Carlsbad, CA).
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD4+ T cells were harvested after the culture and resuspended in 500 µl of growth media plus 5% DMSO, and then transferred to a 1.7 ml microfuge tube on ice. The cells were frozen at a slow cooling rate.

value: OX40L-Tg APCs


title: WT-APC_ATACSeq

value: Wt APCs


title: Blood_GEN01_MVL458-1


title: Blood_GEN09_MVL465-1


title: Blood_GEN05_MVL461-1


title: Blood_GEN07_MVL463-1


title: Blood_GEN11_MVL467-1


title: Blood_GEN18_MVL474-1


title: Blood_GEN10_MVL466-1


title: Blood_GEN03_MVL460-1


title: Blood_GEN17_MVL473-1


title: Blood_GEN15_MVL471-1


title: RMS095

city: Columbus

first: Genevieve

last: Kendall

state: OH

address: 700 Children's Drive, WA5014

institute: Nationwide Children's Hospital / The Ohio State University

description: rhabdomyosarcoma tumor

hyb_protocol: Hybridization was carried out according to the manufacturer’s suggested protocol.

scan_protocol: Arrays were scanned with the Affymetrix GeneChip Scanner using the default parameters.

data_processing:
The probe-level data were background adjusted, normalized and summarized by a Robust Multi-array Average (RMA) algorithm implemented in the software package affy of the Bioconductor project release 1.58.0, running in the R statistical environment version 3.1.0 using default parameters.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: rhabdomyosarcoma

label_protocol: Total RNA from tumors was reverse-transcribed using a T7-Oligo(dT) Promoter Primer, followed by RNAseH-mediated second-strand cDNA synthesis.  Biotinylated cRNA probe was prepared with MessageAmp II (Ambion).

extract_protocol: Total RNA was extracted from 101 rhabdomyosarcoma patient tumors using Trizol.

tag: age

tag: gender

tag: tissue type

value: tumor

tag: rms subtype

value: Alveolar

tag: Stage


title: RMS096

description: rhabdomyosarcoma tumor

value: III


title: RMS101

description: rhabdomyosarcoma tumor

value: I


title: RMS097

description: rhabdomyosarcoma tumor

value: Female

value: IIA


title: Blood_GEN12_MVL468-1

tag: tissue

value: blood


title: RMS098

description: rhabdomyosarcoma tumor

value: Male


title: Blood_GEN13_MVL469-1

value: Mother


title: RMS099

description: rhabdomyosarcoma tumor


title: RMS100

description: rhabdomyosarcoma tumor


title: RMS094

description: rhabdomyosarcoma tumor


title: RMS088

description: rhabdomyosarcoma tumor

value: Embryonal


title: RMS089

description: rhabdomyosarcoma tumor


title: RMS082

description: rhabdomyosarcoma tumor


title: RMS085

description: rhabdomyosarcoma tumor


title: RMS091

description: rhabdomyosarcoma tumor

value: Botryoid


title: RMS081

description: rhabdomyosarcoma tumor


title: RMS087

description: rhabdomyosarcoma tumor


title: RMS084

description: rhabdomyosarcoma tumor


title: RMS083

description: rhabdomyosarcoma tumor


title: RMS080

description: rhabdomyosarcoma tumor


title: RMS092

description: rhabdomyosarcoma tumor


title: RMS077

description: rhabdomyosarcoma tumor


title: RMS076

description: rhabdomyosarcoma tumor


title: RMS086

description: rhabdomyosarcoma tumor


title: RMS079

description: rhabdomyosarcoma tumor


title: RMS074

description: rhabdomyosarcoma tumor


title: RMS075

description: rhabdomyosarcoma tumor


title: RMS078

description: rhabdomyosarcoma tumor


title: RMS090

description: rhabdomyosarcoma tumor


title: RMS093

description: rhabdomyosarcoma tumor


title: C57Bl/6 WT Mouse Lung, Dose 120ppm, 1day, biological replicate 4

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

description: Gene Expression data from mouse whole lungs

hyb_protocol: Affymetrix, GeneChip® High Throughput 3' IVT PLUS Reagent Kit, page40-42 and GeneTitan® Instrument User Guide for Expression Array Plates

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan array scanner to generate CEL files with corresponding intensity values.

data_processing: Affymetrix CEL files were normalized by RMA using Partek Genomic's Suite 6.6 (each strain normalized independently)

source_name: Taconic Biosciences Inc., Germantown, NY

growth_protocol: Adult male mice were acquired from Taconic (Germantown, NY).  Animals were kept in a humidity- and temperature-controlled, HEPA-filtered, mass air-displacement room.  The room was maintained on a 12-hr light-dark cycle (7 AM – 7 PM) at approximately 68-79°F with a relative humidity of approximately 30-70%. All animals were allowed access to Certified PicoLab Rodent 20 diet and reverse osmosis water ad libitum.

extract_protocol: Trizol® (ThermalFisher) organic extraction with Phase Lock Gel™ -Heavy- tubes (5Prime).  Aqueous phase placed in RB(QiaCube sample) tubes and loaded into QiaCube, the RNeasy Mini Protocol used.

treatment_protocol: Animals were placed individually in stainless-steel wire-mesh cages and exposed to styrene or air for a single 6 hour exposure.  On the morning following the last inhalation exposure, mice were euthanized by sodium pentobarbital and exsanguination.  Doses were 0 ppm (air only), 10 ppm, 40 ppm & 120 ppm styrene.

tag: sample type

value: Mus musculus (adult, male, C67Bl/6 WT)

value: Whole Lung

tag: time of exposure

value: 1 day

tag: dose (ppm)


title: C57Bl/6 WT Mouse Lung, Dose 120ppm, 1day, biological replicate 1

label_protocol: Affymetrix, GeneChip® High Throughput 3' IVT PLUS Reagent Kit


title: C57Bl/6 WT Mouse Lung, Dose 120ppm, 1day, biological replicate 5


title: C57Bl/6 WT Mouse Lung, Dose 120ppm, 1day, biological replicate 3


title: C57Bl/6 WT Mouse Lung, Dose 120ppm, 1day, biological replicate 2


title: C57Bl/6 WT Mouse Lung, Dose 40ppm, 1day, biological replicate 3


title: C57Bl/6 WT Mouse Lung, Dose 40ppm, 1day, biological replicate 5


title: C57Bl/6 WT Mouse Lung, Dose 40ppm, 1day, biological replicate 4


title: Blood_GEN35_MVL491-1


title: RMS071

description: rhabdomyosarcoma tumor


title: RMS073

description: rhabdomyosarcoma tumor


title: RMS068

description: rhabdomyosarcoma tumor


title: RMS069

description: rhabdomyosarcoma tumor


title: RMS064

description: rhabdomyosarcoma tumor


title: RMS067

description: rhabdomyosarcoma tumor


title: RMS072

description: rhabdomyosarcoma tumor


title: RMS065

description: rhabdomyosarcoma tumor


title: RMS070

description: rhabdomyosarcoma tumor


title: C57Bl/6 WT Mouse Lung, Dose 40ppm, 1day, biological replicate 1


title: RMS062

description: rhabdomyosarcoma tumor


title: RMS061

description: rhabdomyosarcoma tumor


title: C57Bl/6 WT Mouse Lung, Dose 40ppm, 1day, biological replicate 2


title: RMS060

description: rhabdomyosarcoma tumor


title: RMS059

description: rhabdomyosarcoma tumor


title: RMS066

description: rhabdomyosarcoma tumor


title: C57Bl/6 WT Mouse Lung, Dose 10ppm, 1day, biological replicate 2


title: RMS063

description: rhabdomyosarcoma tumor


title: RMS058

description: rhabdomyosarcoma tumor


title: C57Bl/6 WT Mouse Lung, Dose 10ppm, 1day, biological replicate 1


title: C57Bl/6 WT Mouse Lung, Dose 10ppm, 1day, biological replicate 5


title: RMS054

description: rhabdomyosarcoma tumor


title: RMS055

description: rhabdomyosarcoma tumor


title: C57Bl/6 WT Mouse Lung, Dose 10ppm, 1day, biological replicate 3


title: RMS056

description: rhabdomyosarcoma tumor


title: C57Bl/6 WT Mouse Lung, Dose 0, 1day, biological replicate 5


title: C57Bl/6 WT Mouse Lung, Dose 0, 1day, biological replicate 4


title: RMS057

description: rhabdomyosarcoma tumor


title: C57Bl/6 WT Mouse Lung, Dose 10ppm, 1day, biological replicate 4


title: RMS052

description: rhabdomyosarcoma tumor


title: RMS050

description: rhabdomyosarcoma tumor


title: RMS049

description: rhabdomyosarcoma tumor


title: RMS051

description: rhabdomyosarcoma tumor


title: RMS053

description: rhabdomyosarcoma tumor


title: RMS046

description: rhabdomyosarcoma tumor


title: RMS044

description: rhabdomyosarcoma tumor


title: RMS045

description: rhabdomyosarcoma tumor


title: RMS048

description: rhabdomyosarcoma tumor


title: C57Bl/6 WT Mouse Lung, Dose 0, 1day, biological replicate 2


title: RMS043

description: rhabdomyosarcoma tumor

value: IV


title: RMS041

description: rhabdomyosarcoma tumor


title: C57Bl/6 WT Mouse Lung, Dose 0, 1day, biological replicate 3


title: RMS040

description: rhabdomyosarcoma tumor


title: RMS042

description: rhabdomyosarcoma tumor


title: C57Bl/6 TG Mouse Lung, Dose 120ppm, 1day, biological replicate 5

value: Mus musculus (adult, male, C67Bl/6 TG)


title: C57Bl/6 TG Mouse Lung, Dose 120ppm, 1day, biological replicate 3


title: RMS039

description: rhabdomyosarcoma tumor

value: IIB


title: RMS036

description: rhabdomyosarcoma tumor

value: tumor


title: C57Bl/6 WT Mouse Lung, Dose 0, 1day, biological replicate 1


title: C57Bl/6 TG Mouse Lung, Dose 120ppm, 1day, biological replicate 4


title: RMS038

description: rhabdomyosarcoma tumor

value: Alveolar


title: RMS047

description: rhabdomyosarcoma tumor

value: Spindle cell


title: RMS034

description: rhabdomyosarcoma tumor


title: C57Bl/6 TG Mouse Lung, Dose 120ppm, 1day, biological replicate 2


title: RMS035

description: rhabdomyosarcoma tumor


title: C57Bl/6 TG Mouse Lung, Dose 120ppm, 1day, biological replicate 1


title: RMS033

description: rhabdomyosarcoma tumor


title: RMS032

description: rhabdomyosarcoma tumor


title: C57Bl/6 TG Mouse Lung, Dose 40ppm, 1day, biological replicate 4


title: RMS037

description: rhabdomyosarcoma tumor

value: I


title: C57Bl/6 TG Mouse Lung, Dose 40ppm, 1day, biological replicate 5


title: C57Bl/6 TG Mouse Lung, Dose 40ppm, 1day, biological replicate 2


title: C57Bl/6 TG Mouse Lung, Dose 40ppm, 1day, biological replicate 3


title: RMS030

description: rhabdomyosarcoma tumor


title: RMS027

description: rhabdomyosarcoma tumor


title: RMS028

description: rhabdomyosarcoma tumor


title: RMS026

description: rhabdomyosarcoma tumor

value: III


title: C57Bl/6 TG Mouse Lung, Dose 40ppm, 1day, biological replicate 1


title: RMS022

description: rhabdomyosarcoma tumor

value: Female

value: IIA


title: RMS023

description: rhabdomyosarcoma tumor


title: RMS025

description: rhabdomyosarcoma tumor

value: Male


title: C57Bl/6 TG Mouse Lung, Dose 10ppm, 1day, biological replicate 4


title: RMS021

description: rhabdomyosarcoma tumor


title: RMS029

description: rhabdomyosarcoma tumor


title: RMS019

description: rhabdomyosarcoma tumor


title: C57Bl/6 TG Mouse Lung, Dose 10ppm, 1day, biological replicate 2


title: RMS018

description: rhabdomyosarcoma tumor


title: RMS015

description: rhabdomyosarcoma tumor


title: C57Bl/6 TG Mouse Lung, Dose 10ppm, 1day, biological replicate 3


title: C57Bl/6 TG Mouse Lung, Dose 10ppm, 1day, biological replicate 1


title: RMS017

description: rhabdomyosarcoma tumor


title: C57Bl/6 TG Mouse Lung, Dose 10ppm, 1day, biological replicate 5


title: RMS016

description: rhabdomyosarcoma tumor


title: RMS031

description: rhabdomyosarcoma tumor


title: RMS014

description: rhabdomyosarcoma tumor

value: IIC


title: RMS012

description: rhabdomyosarcoma tumor


title: C57Bl/6 TG Mouse Lung, Dose 0, 1day, biological replicate 4


title: C57Bl/6 TG Mouse Lung, Dose 0, 1day, biological replicate 5


title: RMS013

description: rhabdomyosarcoma tumor


title: RMS020

description: rhabdomyosarcoma tumor

value: Embryonal


title: RMS024

description: rhabdomyosarcoma tumor


title: RMS011

description: rhabdomyosarcoma tumor


title: RMS010

description: rhabdomyosarcoma tumor


title: RMS009

description: rhabdomyosarcoma tumor


title: C57Bl/6 TG Mouse Lung, Dose 0, 1day, biological replicate 3


title: C57Bl/6 TG Mouse Lung, Dose 0, 1day, biological replicate 2


title: RMS007

description: rhabdomyosarcoma tumor


title: RMS008

description: rhabdomyosarcoma tumor


title: RMS004

description: rhabdomyosarcoma tumor


title: RMS003

description: rhabdomyosarcoma tumor


title: C57Bl/6 KO Mouse Lung, Dose 120ppm, 1day, biological replicate 5

value: Mus musculus (adult, male, C67Bl/6 KO)


title: RMS006

description: rhabdomyosarcoma tumor


title: RMS001

description: rhabdomyosarcoma tumor


title: C57Bl/6 TG Mouse Lung, Dose 0, 1day, biological replicate 1


title: Vian-2018-HIC014

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

description:
splenic B cells isolated from 6-8 weeks old C57BL6/J mouse spleen by negative selection
control
Vian-2018-activated_B_cells_30_hours_WT.hic
Vian-2018-activated_B_cells_30_hours_WT_30.hic

data_processing:
The paired end reads were aligned separately using BWA against the mm9 mouse build or the b37 human build
PCR duplicates, low mapping quality and unligated reads were removed using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Contact matrices were constructed at various resolutions and normalized using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
loops were annotated using HiCCUPS (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016), domains were annotated using Arrowhead (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Genome_build: mm9 (mouse), b37 (human)
Supplementary_files_format_and_content: .hic file (contains contact matrices at various resolutions in an easy to visualize and access format) (see Durand, Robinson, et al Cell Systems 2016)

source_name: activated B cell

extract_protocol:
Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeqX Ten, NextSeq 500, or HiSeq 2500 following the manufacturer's protocols

tag: genotype

value: WT

tag: cell type

value: splenic B cells

value: spleen

tag: strain

value: 6-8 weeks old

tag: protocol

value: in situ HiC

tag: activation time


title: Vian-2018-HIC013


title: RMS002

description: rhabdomyosarcoma tumor


title: RMS005

description: rhabdomyosarcoma tumor


title: Vian-2018-HIC011


title: Vian-2018-HIC010


title: Vian-2018-HIC009


title: C57Bl/6 KO Mouse Lung, Dose 120ppm, 1day, biological replicate 4

value: Whole Lung

value: 1 day


title: Vian-2018-HIC012


title: C57Bl/6 KO Mouse Lung, Dose 40ppm, 1day, biological replicate 2


title: C57Bl/6 KO Mouse Lung, Dose 40ppm, 1day, biological replicate 5


title: C57Bl/6 KO Mouse Lung, Dose 40ppm, 1day, biological replicate 4


title: Vian-2018-HIC020

description:
splenic B cells isolated from 6-8 weeks old C57BL6/J mouse spleen by negative selection
HU_treated
Vian-2018-activated_B_cells_30_hours_HU_treated.hic
Vian-2018-activated_B_cells_30_hours_HU_treated_30.hic

value: activated, 30h, HU


title: C57Bl/6 KO Mouse Lung, Dose 10ppm, 1day, biological replicate 4


title: C57Bl/6 KO Mouse Lung, Dose 40ppm, 1day, biological replicate 1


title: C57Bl/6 KO Mouse Lung, Dose 120ppm, 1day, biological replicate 3


title: Vian-2018-HIC019


title: C57Bl/6 KO Mouse Lung, Dose 120ppm, 1day, biological replicate 2


title: C57Bl/6 KO Mouse Lung, Dose 10ppm, 1day, biological replicate 5


title: Vian-2018-HIC017


title: Vian-2018-HIC018


title: Vian-2018-HIC015


title: Vian-2018-HIC016


title: C57Bl/6 KO Mouse Lung, Dose 40ppm, 1day, biological replicate 3


title: C57Bl/6 KO Mouse Lung, Dose 120ppm, 1day, biological replicate 1


title: C57Bl/6 KO Mouse Lung, Dose 10ppm, 1day, biological replicate 2


title: NKT2_SKG_rep1, ATAC-seq

city: Aurora

first: Laurent

last: Gapin

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical campus

description: normCounts.tsv

data_processing:
Raw data from the sequencer was demultiplexed and FASTQ files were generated using bcl2fastq Conversion Software (Illumina).
ATAC-seq reads were aligned to the mm10 genome assembly using bowtie v 1.0
Unmapped reads were trimmed of adapters and to a length of 36nt with trim_galore and remapped and merged with first bam file
Removed reads mapping to chrM and duplicate reads (Picard)
bam files were filtered to extract fragments less than 100 nt, and peak summits were called using MACS2
Peak summits from individual replicates were expanded to region of 500bp and overlapping regions from all samples were merged
Peaks on chrY or overlapping blacklisted regions were excluded
Tn5 insertion sites per peak were computed for all replicates using all reads and normalized with limma/voom
Genome_build: mm10
Supplementary_files_format_and_content: txt containing normalized ATAC-seq density

extract_protocol:
Cells were lysed in 50ul lysis buffer (10 mM TrisHCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Molecular biology-grade IGEPAL CA-630) to extract nuclei. Nuclei were pelleted at 500xg. Nuclei were resuspended in 50 μL 1× TD buffer containing 2.5 μL transposase (Nextera, Illumina). DNA was purified using MinElute PCR Purification columns and kit (Qiagen).
Treatment with Nextera transposase for 40 minutes at 37°C, followed by PCR amplification.

value: SKG

value: Thymus

value: NKT cell

tag: cell population


title: NKT2_SKG_rep3, ATAC-seq

description: normCounts.tsv


title: NKT2_SKG_rep2, ATAC-seq

description: normCounts.tsv


title: NKT2_BALB_rep1, ATAC-seq

description: normCounts.tsv

value: BALB/c


title: NKT2_BALB_rep3, ATAC-seq

description: normCounts.tsv


title: C57Bl/6 KO Mouse Lung, Dose 10ppm, 1day, biological replicate 3


title: NKT2_BALB_rep2, ATAC-seq

description: normCounts.tsv


title: NKT1_SKG_rep1, ATAC-seq

description: normCounts.tsv


title: NKT1_SKG_rep2, ATAC-seq

description: normCounts.tsv


title: C57Bl/6 KO Mouse Lung, Dose 10ppm, 1day, biological replicate 1


title: C57Bl/6 KO Mouse Lung, Dose 0, 1day, biological replicate 4


title: NKT1_BALB_rep2, ATAC-seq

description: normCounts.tsv


title: chr2 rep3

city: college station

first: Xiuren

address: 2123 tamu

department: biochemistry & biophysics

institute: texas a&m university

data_processing:
Adapters were trimmed by FASTX-Toolkit (ver. 0.0.14)
sRNAs with lengths between 19- to 28-nt were selected and mapped using bowtie (version 1.1.2) to the Arabidopsis genomic sequences
sRNAs reads mapped to selected genomic features or miRNAs were count by BED Tools (v2.26) with 1 bp overlapping
Genome_build: Arabidopsis thaliana (TAIR10)
Supplementary_files_format_and_content: Tab-delimited text files include raw reads counts for each Sample.

source_name: three-week-old plant leaves

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) reagent from leaves of three week-old adult plants.
sRNAs of 19-24 nt were gel-purified and ligated to a pair of adapters at the 5’ and 3’ ends by using T4 RNA ligase (NEB). sRNAs with adapters were transcribed into cDNA and amplified by Illumina sequencing-compatible primers.

value: leaves

value: 3 weeks


title: NKT1_BALB_rep1, ATAC-seq

description: normCounts.tsv


title: C57Bl/6 KO Mouse Lung, Dose 0, 1day, biological replicate 5


title: C57Bl/6 KO Mouse Lung, Dose 0, 1day, biological replicate 3


title: CD-1 Mouse Lung, Dose 120ppm, 1day, biological replicate 4

value: Mus musculus (adult, male, CD-1)


title: chr2 rep2


title: wago-9 IP znfx-1(ne4354) 3

city: Worcester

first: Craig

middle: C

last: Mello

address: 368 Plantation Street

department: RNA Therapeutics Institute

institute: UMASS Med School/HHMI

data_processing:
Remove adapters with cutadapt: cutadapt -a AGATCGGAAG file
Alignment of 22Gs (Short RNA fragments that starts with nucleotide guanine and having the length of 22 nt) to the transcriptome is done with bowtie2
Total read count is normalized to 1 million reads.
Genome_build: WS262
Supplementary_files_format_and_content: csv files containing 22G read, parts per million value, SAM flag, gene name, position.

organism: Caenorhabditis elegans

source_name: wago-9 IP znfx-1(ne4354)

growth_protocol: Synchronous population of worms were grown on 150mm NGM plates on OP-50.

extract_protocol:
Worms or immunoprecipitates from worm lysates were treated with trizol. For input libraries, the extracted RNA was subjected to mirVana enrichment for small RNAs, before library construction.
Libraries were constructed by dephosphorylating g and b phosphates of 22G-RNAs using homemade 5' polyphosphatase PIR-1, ligating 3' adaptor linker using T4 RNA ligase 2 (NEB), ligating 5' adaptor linker using T4 RNA ligase 1(NEB), converting RNA to cDNA using Superscript III (Thermo Fischer Scientific), and then amplified by PCR.

tag: genotype/variation

value: whole worm

tag: ip antibody

value: anti-flag mouse monoclonal antibody M2 (Sigma, Cat# F1804)

tag: molecule subtype

value: wago-9 bound small RNA


title: CD-1 Mouse Lung, Dose 120ppm, 1day, biological replicate 5


title: wago-9 IP znfx-1(ne4354) 1


title: wago-9 IP 3

source_name: wago-9 IP

value: wt


title: se-2 rep2

tag: age


title: se-2 rep1


title: C57Bl/6 KO Mouse Lung, Dose 0, 1day, biological replicate 1

value: Mus musculus (adult, male, C67Bl/6 KO)


title: C57Bl/6 KO Mouse Lung, Dose 0, 1day, biological replicate 2


title: CD-1 Mouse Lung, Dose 40ppm, 1day, biological replicate 3


title: CD-1 Mouse Lung, Dose 120ppm, 1day, biological replicate 2


title: wago-9 IP 2


title: CD-1 Mouse Lung, Dose 120ppm, 1day, biological replicate 1


title: CD-1 Mouse Lung, Dose 40ppm, 1day, biological replicate 4


title: WT rep3


title: CD-1 Mouse Lung, Dose 40ppm, 1day, biological replicate 5


title: wago-9 IP znfx-1(ne4354) 2


title: wago-9 IP 1


title: chr2 rep1


title: CD-1 Mouse Lung, Dose 40ppm, 1day, biological replicate 1


title: CD-1 Mouse Lung, Dose 10ppm, 1day, biological replicate 4


title: WT rep2


title: se-2 rep3


title: wago-9 input znfx-1(ne4354) 3

source_name: wago-9 input znfx-1(ne4354)

value: total small RNA


title: CD-1 Mouse Lung, Dose 40ppm, 1day, biological replicate 2


title: CD-1 Mouse Lung, Dose 120ppm, 1day, biological replicate 3


title: WT rep1


title: wago-9 input znfx-1(ne4354) 2


title: CD-1 Mouse Lung, Dose 10ppm, 1day, biological replicate 5


title: CD-1 Mouse Lung, Dose 10ppm, 1day, biological replicate 1


title: CD-1 Mouse Lung, Dose 10ppm, 1day, biological replicate 3


title: CD-1 Mouse Lung, Dose 10ppm, 1day, biological replicate 2


title: Vian-2018-HIC008

description:
splenic B cells isolated from 6-8 weeks old C57BL6/J mouse spleen by negative selection
control
Vian-2018-activated_B_cells_24_hours_WT.hic
Vian-2018-activated_B_cells_24_hours_WT_30.hic

value: WT

value: splenic B cells

value: spleen

value: 6-8 weeks old

value: in situ HiC


title: CD-1 Mouse Lung, Dose 0, 1day, biological replicate 5

value: Whole Lung

value: 1 day


title: Vian-2018-HIC007


title: wago-9 input 2

source_name: wago-9 input


title: wago-9 input 1


title: Vian-2018-HIC004


title: Vian-2018-HIC006


title: Vian-2018-HIC005


title: csr-1 IP znfx-1(ne4354) 3

source_name: csr-1 IP znfx-1(ne4354)

value: csr-1 bound small RNA


title: Vian-2018-HIC003


title: Vian-2018-HIC002


title: csr-1 IP znfx-1(ne4354) 1


title: wago-9 input znfx-1(ne4354) 1


title: wago-9 input 3


title: Vian-2018-HIC001


title: CD-1 Mouse Lung, Dose 0, 1day, biological replicate 4


title: csr-1 IP 3

source_name: csr-1 IP


title: csr-1 IP 2


title: csr-1 IP 1


title: csr-1 IP znfx-1(ne4354) 2


title: csr-1 input znfx-1(ne4354) 3

source_name: csr-1 input znfx-1(ne4354)


title: CD-1 Mouse Lung, Dose 0, 1day, biological replicate 3


title: csr-1 input znfx-1(ne4354) 2


title: CD-1 Mouse Lung, Dose 0, 1day, biological replicate 2


title: csr-1 input znfx-1(ne4354) 1


title: Meng5/WT/TRAV19

city: San Diego

first: Meng

last: Zhao

address: 9420 Athena Cir

institute: La Jolla Institute of Allergy and Immunology

description:
pre-positive selection
PCR amplicon

data_processing:
The paired-end FASTQ files were run through MIXCR v1.8.3 to get clonal sequences which were then primer trimmed using cutadapt version 1.13
Primeer trimmed clonal sequences were then de-duplicated by removing exact matches
IMGT/HighV-QUEST v1.5.6 was used with default options to determine V and J regions and their usage in the clonal sequences
Genome_build: mm10
Supplementary_files_format_and_content: IMGT HighV-Quest result matrix with rows as sequence Id's and columns as "V-DOMAIN Functionality", "V-GENE and allele", "J-GENE and allele".

source_name: Thymus

extract_protocol:
preselection DP cells were sorted from WT and SKG thymi, and RNA from DP cells were extracted
total RNA from DP cells were reverse transcribed to generate cDNA, which was used as template to do the PCR.
PCR was performed for amplification of the Trav9, Trav11 and Trav19 gene segments with specific forward primers for each Va region each with an Illumina adaptor sequence on the 5’ end and and a reverse primer for the α-chain constant region. PCR products were purified and sequenced on a Miseq system with a MiSeq Reagent Kit v2-500 (Illumina).

value: Thymus

value: double positive thymocytes

tag: genotype/model

value: WT - BALB/c

tag: gene segments


title: Meng2/SKG/TRAV9

description:
pre-positive selection
PCR amplicon

value: SKG


title: Meng6/SKG/TRAV19

description:
pre-positive selection
PCR amplicon


title: CD-1 Mouse Lung, Dose 0, 1day, biological replicate 1

value: Mus musculus (adult, male, CD-1)


title: Meng1/WT/TRAV9

description:
pre-positive selection
PCR amplicon


title: Meng4/SKG/TRAV11

description:
pre-positive selection
PCR amplicon


title: csr-1 input 2

source_name: csr-1 input

value: whole worm


title: Mouse Lung, Dose 40ppm, 1day, biological replicate 5

description: Taconic Biosciences Inc., Germantown, NY

data_processing: Affymetrix CEL files were normalized by RMA using Partek Genomic's Suite 6.6

source_name: whole lung

growth_protocol: Adult male CD-1 mice were acquired from Taconic (Germantown, NY).  Animals were kept in a humidity- and temperature-controlled, HEPA-filtered, mass air-displacement room.  The room was maintained on a 12-hr light-dark cycle (7 AM – 7 PM) at approximately 68-79°F with a relative humidity of approximately 30-70%. All animals were allowed access to Certified PicoLab Rodent 20 diet and reverse osmosis water ad libitum.

treatment_protocol: Animals were placed individually in stainless-steel wire-mesh cages and exposed to styrene or air for a single 6 hour exposure.  On the morning following the last inhalation exposure, mice were euthanized by sodium pentobarbital and exsanguination.  Doses were 0 ppm (air only), 1 ppm, 5 ppm, 10 ppm, 20 ppm, 40 ppm and 120 ppm styrene.

value: adult

tag: gender

value: male

value: 5 day

tag: styrene dose (ppm)


title: Mouse Lung, Dose 120ppm, 1day, biological replicate 3

tag: tissue


title: Mouse Lung, Dose 120ppm, 1day, biological replicate 5

tag: time of exposure


title: Mouse Lung, Dose 120ppm, 1day, biological replicate 2


title: Meng3/WT/TRAV11

description:
pre-positive selection
PCR amplicon


title: Mouse Lung, Dose 120ppm, 1day, biological replicate 4


title: Mouse Lung, Dose 120ppm, 1day, biological replicate 1


title: Mouse Lung, Dose 40ppm, 1day, biological replicate 4


title: Mouse Lung, Dose 40ppm, 1day, biological replicate 2


title: csr-1 input 1

value: wt

value: total small RNA


title: Mouse Lung, Dose 40ppm, 1day, biological replicate 3


title: Mouse Lung, Dose 40ppm, 1day, biological replicate 1


title: Mouse Lung, Dose 20ppm, 1day, biological replicate 5


title: Mouse Lung, Dose 20ppm, 1day, biological replicate 3


title: Mouse Lung, Dose 20ppm, 1day, biological replicate 2


title: chr2 DMS (+) Rep2

data_processing:
Adapters were trimmed by Cutadapt, clean reads over 35bp were retained.
Reads were aligned using Burrows-Wheeler Aligner (BWA) allowing 5% mismatches.
The mapping results were sorted by Picard tools (http://broadinstitute.github.io/picard/) with coordination.
The base calls of aligned reads were summarized  using samtools (v1.5) mpileup.
Genome_build: Arabidopsis thaliana pri-miRNA (pri-miRNA.fa)
Supplementary_files_format_and_content: Tab-delimited text files include A/T/C/G base calls for each Sample.

extract_protocol:
A amount of 0.3 g ground powder was dissolved in 5ml lysis buffer (20mM HEPES pH7.5, 20mM KCl, 2.5mM MgCl2, 25% glycerol, 250mM sucrose, 5mM DTT, 20 μl RNase inhibitor [Thermo Fisher] and 1X Proteinase inhibitor cocktail without EDTA [Roche]). The homogenate was filtered through a double layer of Miracloth. The flow-through was centrifuged at 1500 g for 10min at 4°C. After removing supernatant, the pellet was washed twice with 5ml nuclear resuspension buffer (20mM HEPES pH7.5, 2.5mM MgCl2, 25% glycerol, 0.2% Triton X-100, 20μl RNase inhibitor [Thermo Fisher]). Then the total nuclear RNA was extracted using TRI Reagent (Sigma).
5μg DNase-treated nuclear RNA was mixed with gene-specific RT primers. The reverse transcription was proceeded with TGIRT-III (Ingex). Then pri-miRNAs were amplified using KOD hot start DNA polymerase (Millipore) with gene-specific primers. PCR products were mixed equally and fragmented into 50-200bp using NEBNext dsDNA Fragmentase (NEB), illumine adapters were ligated and amplified by Illumina sequencing-compatible primers.

treatment_protocol: Three-week-old plants were collected and completely covered in 20ml 1X dimethyl sulfate (DMS) reaction buffer (40mM HEPES pH 7.5, 100mM KCl and 0.5mM MgCl2) in a 50 ml Corning tube. DMS (Sigma) was added to a final concentration of 1%. Mock treatment was performed by addition of deionized water. Samples were treated in the DMS reaction buffer or mock solution at room temperature under a vacuum condition for 30 min. To quench the reaction, 5 ml β-Mercaptoethanol was added to a final concentration of 20%, and the mixture was incubated for 2 min under vacuum.

value: leaves

value: 3 weeks


title: Col DMS (+) Rep2


title: chr2 DMS (-)


title: Col DMS (+) Rep1


title: Col-0 DMS (-)


title: A1552ΔvpsA::FRTΔhapR::FRT-TnqstR (5631+ara), replicate 3

city: Lausanne

first: Melanie

last: Blokesch

address: Station 19 / EPFL-SV-UPBLO

department: School of Life Sciences

country: Switzerland

institute: Swiss Federal Institute of Technology Lausanne (EPFL)

data_processing:
Sequencing and data processing was done by Microsynth (Balgach, Switzerland) accoridng to their standard prokaryotic differential gene expression analysis.
Reads were mapped onto the reference genome using the Bowtie2 (version 2.2.9)
Reads were counted using software htseq-count (HTSeq version 0.6.1p1)
Genome_build: Reference genome (NC_002505, NC_002506)
Supplementary_files_format_and_content: .txt files for counts

organism: Vibrio cholerae

source_name: bacterial in vitro culture

growth_protocol: V. cholerae strains were grown in 2 x 2.5 ml LB medium with 0.02% arabinose at 30C until an optical sensity at 600 nm (OD600) of 1.5-1.8 was reached. At this time, the bacteria were harvested by centrifugation at 4C.

extract_protocol:
RNA was isolated using standard RNA isolation kits. The RNA was cleaned up after DNAse treatment using a standard clean-up procedures. Ribodepletion was performed using a Ribo-Zero Magnetic kit (Epicentre) for Gram-negative bacteria.
Stranded Illumina TruSeq RNA libraries were prepared.

treatment_protocol: The harvested bacteria were washed in pre-chilled PBS buffer, lysed through resuspension in Tri reagent, and stored at -80C until their processing.

tag: genetic background

tag: transposon

value: A1552-delta-vpsA::FRT-delta-hapR::FRT with TnqstR transposon

tag: inducer


title: A1552ΔvpsA::FRTΔhapR::FRT-TnqstR (5631+ara), replicate 1


title: csr-1 input 3


title: A1552ΔvpsA::FRTΔhapR::FRT-TnqstR (5631+ara), replicate 2


title: A1552ΔvpsA::FRTΔhapR::FRT-TntfoY-strep (3593+ara), replicate 3

value: A1552-delta-vpsA::FRT-delta-hapR::FRT with TntfoY-strep transposon


title: A1552ΔvpsA::FRTΔhapR::FRT-TntfoX-strep (5490+ara), replicate 3

value: A1552-delta-vpsA::FRT-delta-hapR::FRT with TntfoX-strep transposon


title: A1552ΔvpsA::FRTΔhapR::FRT-TntfoY-strep (3593+ara), replicate 2


title: chr2 DMS (+) Rep1


title: A1552ΔvpsA::FRTΔhapR::FRT-TntfoY-strep (3593+ara), replicate 1


title: A1552ΔvpsA::FRTΔhapR::FRT-TntfoX-strep (5490+ara), replicate 2


title: A1552ΔvpsA::FRTΔhapR::FRT-TntfoX-strep (5490+ara), replicate 1


title: A1552ΔvpsA::FRTΔhapR::FRT-Tn (5489+ara), replicate 3

value: A1552-delta-vpsA::FRT-delta-hapR::FRT with empty Tn transposon


title: Mouse Lung, Dose 10ppm, 1day, biological replicate 4

tag: strain

value: Whole Lung


title: Mouse Lung, Dose 20ppm, 1day, biological replicate 1


title: Mouse Lung, Dose 10ppm, 1day, biological replicate 3


title: Mouse Lung, Dose 10ppm, 1day, biological replicate 5


title: Mouse Lung, Dose 5ppm, 1day, biological replicate 3


title: Mouse Lung, Dose 10ppm, 1day, biological replicate 2


title: Mouse Lung, Dose 10ppm, 1day, biological replicate 1


title: A1552ΔvpsA::FRTΔhapR::FRT-Tn (5489+ara), replicate 1


title: Mouse Lung, Dose 5ppm, 1day, biological replicate 5


title: Mouse Lung, Dose 5ppm, 1day, biological replicate 2


title: Mouse Lung, Dose 5ppm, 1day, biological replicate 4


title: A1552-TnqstR (5501+ara), replicate 3

value: A1552 (WT) with TnqstR transposon


title: A1552-TnqstR (5501+ara), replicate 2


title: Vian-2018-HIC243

description:
splenic B cells isolated from 6-8 weeks old C57BL6/J mouse spleen by negative selection
oligomycin treated
Vian-2018-activated_B_cells_24_hours_oligomycin_30.hic

treatment_protocol: activated for 24 hours with LPS (50 μg/mL; Sigma), IL-4 (2.5 ng/mL; Sigma), and anti-CD180 (RP105) antibody (0.5 μg/mL, BD PharMingen); for acute ATP depletion, 20h-activated cells were shifted to glucose deficient media for 2h then, 2-Deoxy-D-glucose (5mM, Sigma) and Oligomycin (126nM, Sigma) were added to the culture for another 1.5-2h before the harvest.

tag: genotype

value: WT

tag: cell type

value: splenic B cells

value: spleen

value: 6-8 weeks old

tag: protocol

value: in situ HiC

value: activated,24h, oligomycin


title: Mouse Lung, Dose 1ppm, 1day, biological replicate 5

value: adult

value: male

value: 5 day


title: Mouse Lung, Dose 20ppm, 1day, biological replicate 4


title: Mouse Lung, Dose 1ppm, 1day, biological replicate 3


title: Mouse Lung, Dose 5ppm, 1day, biological replicate 1


title: Mouse Lung, Dose 1ppm, 1day, biological replicate 1


title: Vian-2018-HIC242

tag: activation time


title: Mouse Lung, Dose 1ppm, 1day, biological replicate 2


title: A1552-TnqstR (5501+ara), replicate 1


title: A1552ΔvpsA::FRTΔhapR::FRT-Tn (5489+ara), replicate 2


title: A1552-TntfoY-strep (2978+ara), replicate 3

value: A1552 (WT) with TntfoY-strep transposon


title: Mouse Lung, Dose 1ppm, 1day, biological replicate 4


title: Vian-2018-HIC240


title: A1552-TntfoY-strep (2978+ara), replicate 1


title: A1552-TntfoY-strep (2978+ara), replicate 2


title: Vian-2018-HIC241


title: Mouse Lung, Dose 0, 1day, biological replicate 4


title: Mouse Lung, Dose 0, 1day, biological replicate 5


title: Mouse Lung, Dose 0, 1day, biological replicate 3


title: Vian-2018-HIC239


title: Mouse Lung, Dose 0, 1day, biological replicate 1


title: A1552-TntfoX-strep (3420+ara), replicate 3

value: A1552 (WT) with TntfoX-strep transposon


title: A1552-TntfoX-strep (3420+ara), replicate 2


title: A1552-TntfoX-strep (3420+ara), replicate 1


title: Vian-2018-HIC236