title: Shoot apices, gTFL1_GFP B Rep2 ChIP-Seq

description:
gTFL1_GFP_merged.bigwig
gTFL1_GFP_qval10_peaks.narrowPeak


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C9_AD006_indexed

status: Public on Sep 01 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: MOp

tag: Sex

value: male

tag: age

tag: strain


title: Shoot apices, fd_gTFL1_GFP Rep2 ChIP-Seq

city: Philadelphia

first: Doris

last: Wagner

state: PA

address: 103G Carolyn Lynch Laboratory

department: Department of Biology

institute: University of Pennsylvania

description:
fd_gTFL1_GFP_merged.bigwig
fd_gTFL1_GFP_qval10_peaks.narrowPeak

data_processing:
Base-calling was performed automatically in Illumina BaseSpace
Trimmed sequencing reads were aligned to the Arabidopsis thaliana genome using Bowtie2 v2.3.1 with the `--no-unal` parameter and further processed as per ENCODE guidelines (Landt et al 2012)
For narrowPeak files, significant peaks were identified using MACS2 2.1.1 callpeak on ChIP samples relative to relevant control ChIPs performed in non epitope containing plants using 224 bp read extension and summit q-value ≤ 10^-10.
For bigwig files, reads were extended to 224 bp using bedtools v.2.26.0, normalized to 10 million reads mapped per million reads sequenced (10RPM) and coverage was averaged using bedtools.
Genome_build: TAIR10
Supplementary_files_format_and_content:
bigwig normalized to 10RPKM for single replicates
bigwig normalized to 10RPKM for the mean of three replicates for each sample
bigwig normalized to 10RPKM for the mean of three replicates for each sample after subtracting the relevant background sample
bed file (narrowPeak format) containing peaks called by MACS v2.1.0.20151222 filtered by Q-value < 1e-10

organism: Arabidopsis thaliana

source_name: 42-day old short-day-grown shoot apices

growth_protocol: Plants were grown in short days (8hr light, 16 hr dark ) for 42 days with a light intensity of 120 μMol/m2s

extract_protocol:
ChIP assay was performed according to Yamaguchi et al., 2014. N. Yamaguchi et al., PROTOCOLS: Chromatin Immunoprecipitation from Arabidopsis Tissues. Arabidopsis Book 12, e0170 (2014).
DNA libraries were generated using the ThruPLEX DNA-seq kit (RUBICON GENOMICS, cat. R400406) and quantified by the NEBNext Library Quant Kit (cat. E7630L). Equal amounts of DNA were pooled from each library with different dual indexing primers and sequenced on a Next seq

treatment_protocol: No Treatment

tag: ecotype

tag: transgenics

tag: genotype

tag: tissue

value: shoot apices

tag: chip antibody

value: anti-GFP Thermo Fisher, A-11122


title: Shoot apices, fd_gTFL1_GFP Rep1 ChIP-Seq


title: N449 CAV test

type: RNA

city: Vancouver

first: Bruce

middle: Maxwell

last: McManus

state: BC

address: 1081 Burrard Street

department: UBC James Hogg Research Centre

country: Canada

institute: PROOF Centre of Excellence

description: CAV, test

hyb_protocol: Following fragmentation, the cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 array. Equilibrate probe array to room temperature immediately before use.  Then, heat the hybridization cocktail to 99°C for 5 minutes in heatblock.  Next, wet the array by filling it through one of the septa with appropriate volume of 1X MES Hybridization Buffer using a micropipettor and appropriate tips. Last, incubate the probe array for 10 minutes at 45°C in the hybridization oven with rotation.

scan_protocol: The Probe Array is scanned using the Affymetrix System.  The scanner is controlled by the GeneChip software.  The probe array is scanned after the wash protocols are complete

data_processing: RMA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood, week 104 post-transplant

label_protocol: Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA.

extract_protocol: Isolation begins with a centrifugation step to pellet nucleic acids in the PAXgene Blood RNA Tube. The pellet is washed, resuspended, and incubated in optimized buffers containing Proteinase K to digest proteins. A second centrifugation step is carried out to remove residual cell debris, and the supernatant is transferred to a fresh microcentrifuge tube. Ethanol is added to adjust binding conditions, and the lysate is applied to a PAXgene RNA spin column. During a brief centrifugation, RNA is selectively bound to the silica-gel membrane of the spin column as contaminants pass through. Remaining contaminants are removed in three wash steps, and pure RNA is then eluted in Buffer BR5. Generally, DNase digestion is not required for RNA purified with the PAXgene Blood RNA Kit, since PAXgene silica-gel–membrane technology efficiently removes most of the DNA without DNase treatment. However, further DNA removal is recommended for RNA applications that are sensitive to DNA contamination. In these cases, residual DNA can be removed either by using the RNase-Free DNase Set for on-column DNase digestion, or by treating the eluted RNA with DNase.

tag: gender

value: F

tag: age at transplant

tag: race

value: Caucasian

tag: original disease

value: Other

value: whole blood


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C9_AD008_indexed


title: Shoot apices, gTFL1_GFP B Rep1 ChIP-Seq

value: WT


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D10_AD004_indexed


title: Shoot apices, gTFL1_GFP A Rep2 ChIP-Seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C9_AD004_indexed


title: Shoot apices, gTFL1_GFP A Rep1 ChIP-Seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C8_AD012_indexed


title: Shoot apices, gFD_GUS Rep1 ChIP-Seq

description:
gFD_GUS_merged.bigwig
gFD_GUS_qval10_peaks.narrowPeak

value: anti-GUS Abcam, ab50148


title: Shoot apices, gFD_GUS Rep2 ChIP-Seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C9_AD007_indexed


title: ikb-1(cer9)_L1_r2

city: Barcelona

first: Yolanda

last: Guillén

address: Dr. Aiguader 88 Planta 2 IMIM

country: Spain

institute: IMIM

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC software was used to summarize the quality of the sequenced reads. Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to WBCel235 whole genome using bowtie2 with default parameters
htseq software was used to estimate the raw gene counts
DESeq2 R package was run to infer differentially expressed genes accross samples
Genome_build: WBCel235
Supplementary_files_format_and_content: txt files are generated from htseq and DESeq2 results using R

organism: Caenorhabditis elegans

source_name: Synchronized animal population

growth_protocol: Synchronized animals were collected in M9 buffer after growing for 36 hours (L4 stage) or 5 hours-fed and 3 hours starved (L1 stage) at 25ºC. Suspended worms were washed 5 times in M9 buffer to remove all traces of bacteria.

extract_protocol:
Total RNA was isolated using TRI Reagent (MRC, Inc.) and PureLink® RNA Mini Kit (Ambion) according to manufacturer’s instructions.
Samples were digested with 0.1% collagenase and single-cell suspension was stained as described. Different subpopulations were directly sorted in a total volume of 10  ml of reaction buffer and processed for obtaining cDNA following manufacture’s protocol. cDNA amplification was performed by Long Distance PCR (LD-PCR) and the PCR-amplified cDNA purified by immobilization on AMPure XP beads (Agencourt AMPure XP kit). Samples were analyzed with Agilent High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626). Covaris shearing was used for Illumina Low input sample preparation and Double last bead purification was performed to remove fragments below 200 bp. Next, samples were used to generate an Illumina sequencing library by NEBNext Ultra protocol following kit instructions. After PCR amplification of the library, the quality was checked on a Bioanalyzer and total cDNA was sequenced using an Illumina HiSeq 2000 sequencer.

tag: developmental stage

value: L1 stage

value: Whole animal


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C8_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_D10_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C8_AD010_indexed


title: ikb-1(cer9)_L1_r1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C8_AD004_indexed


title: nfki-1(cer2)_L1_r2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C6_AD001_indexed


title: WT_L1_r2

value: Wildtype


title: nfki-1(cer2)_L1_r1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C8_AD007_indexed


title: nfki-1(cer1)_ikb-1(nr2027)_L4_r2

value: L4 stage

value: nfki-1(cer1)X; ikb-1(nr2027)I


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C8_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C7_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C7_AD004_indexed


title: ikb-1(nr2027)_L4_r2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C7_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C7_AD010_indexed


title: nfki-1(cer1)_ikb-1(nr2027)_L4_r1


title: nfki-1(cer1)_L4_r2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C7_AD006_indexed


title: N451 non-CAV test

description: non-CAV, test

source_name: whole blood, week 130 post-transplant

value: M

value: Non-ischemic cardiomyopathy


title: nfki-1(cer1)_L4_r1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C7_AD001_indexed

value: MOp


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C6_AD004_indexed

value: male


title: WT_L4_r1


title: ikb-1_L1_r2

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC software was used to summarize the quality of the sequenced reads
Reads were aligned to the WBCel235 genome assembly using Bowtie2 (see materials and methods main paper)
htseq software was used to estimate the raw gene counts
peaks were called using MACS2 with the following setting: ChIP threshold FDR (0.1)
Genome_build: WBCel235
Supplementary_files_format_and_content: bed and bigWig files are generated from MACS2 peak calling output using bamtools

growth_protocol: Synchronized animals were collected in M9 buffer after growing for 36 hours (L4 stage) or 5 hours-fed and 3 hours starved (L1 stage) at 25ºC. Suspended worms were washed 5 times in M9 buffer to remove all traces of bacteria, resuspended in FA buffer with protease inhibitors cocktail (Roche) and frozen as drops in liquid nitrogen.

extract_protocol:
Packed worms were grounded under liquid nitrogen and brought to 10 ml with FA buffer (50 mM HEPES/KOH pH7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Next, 600 μl of 37% formaldehyde were added and allowed to crosslink for 20 mins at room temperature. Glycine (600 μl; 2.5M) was used to quench the reaction, for 2 mins, and nuclei were recovered by centrifugation (4000 rpm, 5 mins in a microfuge), washed 3 times with FA buffer by resuspending in 5 ml and spinning again. Finally, nuclei were resuspended in 1.6 ml of FA buffer, split into two Eppendorf tubes and sonicated for 10 mins in a Bioruptor® Pico (Diagenode) under standard conditions (30s on, 30s off). After sonication, protein extract was quantified and approximately 2 mg of each sample were spun at full speed for 10 minutes at 4oC and the supernatants (SN) were pooled again. SN were pre-cleared with FA-equilibrated SPA/G beads (GE Healthcare) by rotating for 30 minutes at room temperature, recovered by spinning at 1200 rpm for 2 mins and used for immunoprecipitation (IP). An aliquot of 100 μl was kept as input control at this point. The rest of the sample was split into different tubes for IP with the antibodies of choice. After adding the corresponding antibody (3-10 μg), samples were incubated in a rotator overnight at 4oC and the immunocomplexes were recovered with FA buffer pre-equilibrated SPA/G beads (GE Healthcare) by rotating 2h at 4oC. Beads were pelleted (1200rpm; 2 mins) washed twice with FA buffer (5 mins each); once with FA + 0.5 M NaCl (10 mins); once with FA buffer + 1M NaCl (5 mins); once with lithium buffer (10 mins); twice with TE buffer (5 mins each) and the immunoprecipitated material was recovered by incubation in 100 μl elution buffer (Tris-EDTA; 1% SDS plus inhibitors) 1h at RT. DNA was finally purified by reverse crosslinking at 65oC overnight followed by proteinase K (0.5 or 1 mg/ml, respectively) digestions and purifying with MinElute® PCR purification kit (Qiagen).
Samples were digested with 0.1% collagenase and single-cell suspension was stained as described. Different subpopulations were directly sorted in a total volume of 10  ml of reaction buffer and processed for obtaining cDNA following manufacture’s protocol. cDNA amplification was performed by Long Distance PCR (LD-PCR) and the PCR-amplified cDNA purified by immobilization on AMPure XP beads (Agencourt AMPure XP kit). Samples were analyzed with Agilent High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626). Covaris shearing was used for Illumina Low input sample preparation and Double last bead purification was performed to remove fragments below 200 bp. Next, samples were used to generate an Illumina sequencing library by NEBNext Ultra protocol following kit instructions. After PCR amplification of the library, the quality was checked on a Bioanalyzer and total cDNA was sequenced using an Illumina HiSeq 2000 sequencer.

value: Polyclonal anti-mCherry antibody produced in rabbit [Invitrogen, PA5-34974]


title: ikb-1_L1_r3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C6_AD006_indexed


title: nfki-1_L1_r3

value: Monoclonal Anti-FLAG M2 antibody produced in mouse [Sigma, F3165]


title: ikb-1_L1_r1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C9_AD002_indexed


title: nfki-1_L1_r2


title: ikb-1(nr2027)_L4_r1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C6_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C6_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C5_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C6_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C7_AD008_indexed


title: nfki-1_L1_r1


title: Input_L1_r2


title: H3K36me3_ikb-1(nr2027)_L4

value: Polyclonal anti-H3K36me3 antibody produced in mouse [Abcam, ab95412]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C5_AD006_indexed


title: WT_L4_r2


title: H3K36me3_nfki-1(cer1)_L4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C5_AD007_indexed


title: Input_L1_r1


title: Input_L1_r3


title: H3K36me3_nfki-1(cer1)_ikb-1(nr2027)_L4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C7_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C5_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C6_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C5_AD012_indexed


title: H3K36me3_WT_L4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C5_AD008_indexed


title: HPVpos17 input

city: Ann Arbor

first: Siyu

last: Liu

state: MI

address: 100 Washtenaw avenue

department: Bioinformatics

institute: University of Michigan

data_processing:
The sample quality was first assessed with FastQC, then reads were aligned with bowtie2 after adapter and quality trimming with Trim Galore!.
Peaks for each sample compared to input, i.e. the genome-wide regions of hydroxymethylation, were identified using MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeaks files including individual peaks in each sample

source_name: squamous cell carcinoma

extract_protocol:
Using a sterile scalpel, surface scrapings were taken directly from the frozen tissue blocks from the region of tissue identified as having at least 70% tumor cellularity. Tissue scrapings were processed using the Qiagen AllPrep DNA/RNA/Protein Mini Kit (Valencia, CA, USA) as per manufacturer protocol.
A total of 1μg of genomic DNA was used for shearing, blunt-end repair and phosphorylation process, and a single adenine nucleotide was then added to the 3’ end of the resulting fragments for ligation preparation. DNA was cleaned by Qiagen’s MinElute PCR purification columns (Qiagen, Germantown, MD). DNA samples were denatured and resuspended in ice-cold immunoprecipitation buffer after the addition of DNA spike-ins for hMeDIP (Diagenode Denville, NJ). At this stage, 10% volume of the DNA solutions were kept as inputs, and immunoprecipitation overnight at 4°C with rotation was performed on the remaining solution, after adding a 5hmC-specific antibody (Cat # 39791, Active Motif, Carlsbad, CA). The 5hmC-enriched DNA fragments (IP) were released from the antibody and cleaned-up by Proteinase K (ThermoFisher, Carlsbad, CA) and AMPure XP beads (Beckman Coulter, Brea, CA), respectively. In order to evaluate the percent enrichment over input in the IP, qPCR with primers for spike-ins was conducted. For samples with good percent enrichment over input, PCR amplification was performed for library production, followed by cleaning with AMPure XP beads and quantification with the Qubit assay (ThermoFisher, Carlsbad, CA) and TapeStation High Sensitivity D1000 kit (Agilent, Santa Clara, CA).

tag: tumor stage

value: IVa

tag: hpv-status


title: HPVpos18

value: F


title: HPVpos18 input


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C4_AD010_indexed


title: H3K27me3_nfki-1(cer1)_ikb-1(nr2027)_L4

value: Polyclonal anti-H3K27me3 antibody produced in rabbit [Millipore, 07-449]


title: HPVpos17


title: HPVpos16 input


title: HPVpos15 input


title: H3K27me3_ikb-1(nr2027)_L4


title: H3K27me3_nfki-1(cer1)_L4


title: HPVpos15


title: L969 CAV training

description: CAV, training

source_name: whole blood, week 52 post-transplant

value: Caucasian

value: Other

value: whole blood


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C5_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C4_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C4_AD008_indexed


title: HPVpos13


title: HPVpos14


title: H3K27me3_WT_L4

value: Whole animal


title: HPVpos12 input

value: IVB


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C4_AD012_indexed


title: HPVpos14 input


title: HPVpos11 input

value: II


title: Input_nfki-1(cer1)_L4

value: L4 stage


title: Input_ikb-1(nr2027)_L4


title: HPVpos12

value: M


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C4_AD006_indexed


title: Input_WT_L4

value: Wildtype


title: HPVpos10 input

value: III


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C3_AD012_indexed

value: MOp

value: male


title: HPVpos16


title: HPVpos9

value: IVb


title: HPVpos10


title: HPVpos9 input


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C5_AD001_indexed


title: HPVpos13 input


title: tet2 -/- - repl3

city: North York

first: Vinothkumar

last: Rajan

state: ON

address: 2075 Bayview Ave, Room # M7-413

department: Biological Sciences

institute: Sunnybrook Research Institute

data_processing:
adapter trimming using Trimmomatic (v0.36),
Read mapped to danio rerio GRCz10.89 using STAR aligner (v2.5.2b)
Genome_build: danio rerio GRCz10
Supplementary_files_format_and_content: raw counts

organism: Danio rerio

source_name: Kidney Marrow

extract_protocol: Kidney marrow extracted from adult zebrafish, followed by single-cell suspension generation by vigrous pipetting and passing through 70 micron filter

tag: Stage

value: 3-5 months


title: tet2 -/- - repl2


title: HPVpos8 input


title: Input_nfki-1(cer1)_ikb-1(nr2027)_L4

value: nfki-1(cer1)X; ikb-1(nr2027)I


title: HPVpos7

value: IVa


title: HPVpos7 input


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C3_AD006_indexed

tag: brain region


title: HPVpos8


title: tet2 -/- - repl1


title: HPVpos6 input


title: HPVpos6


title: HPVpos11


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C3_AD010_indexed

tag: Sex


title: HPVpos5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C3_AD008_indexed

tag: age


title: tet2 wt/wt - rep2

value: tet2 wt/wt


title: tet2 wt/wt - rep3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C4_AD004_indexed

tag: strain


title: HPVpos5 input


title: tet2 wt/wt - rep1


title: HPVpos4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C3_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C3_AD007_indexed


title: HPVpos4 input


title: HPVpos2 input


title: HPVpos3

value: III or IV


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C2_AD007_indexed


title: HPVpos2


title: HPVpos1 input


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C2_AD008_indexed


title: HPVpos1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C4_AD002_indexed


title: HPVneg18 input

value: Neg


title: HPVneg18


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C3_AD001_indexed


title: HPVneg17 input


title: HPVneg17


title: HPVpos3 input


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C11_AD010_indexed


title: HPVneg16 input

value: F


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C2_AD001_indexed


title: HPVneg16


title: Subcutaneous adipose tissue biopsy, subject P022, post-intervention

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.52.0).

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: The FASTING study was approved by the Medical Ethics Committee of Wageningen University and registered at ClinicalTrials.gov, identifier: NCT03757767. The study was performed at Wageningen University from November 2018 to January 2019. All participants were recruited in Wageningen and surroundings and gave their written informed consent before participation. Apparently healthy men and women, aged 40-70 years at time of recruitment, with a BMI between 22-30 kg/m2 were included in the study. Exclusion criteria were: consuming more than 2 alcohol consumptions/day or more than 14 consumptions/week, tobacco smokers, drugs users, following a diet within one month before the start of the study, allergic to components of the standardized meal, donated or intended to donate blood from 2 months before the study until the end of the study, unstable body weight, diagnosed with a long-term medical condition that can interfere with the study outcome, use of prescribed medication interfering with study outcome, use of supplements or OTC medication known to interfere with glucose or lipid homeostasis in the week before the start of the study and during the study, pregnant or lactating women, or participation in another biomedical study.

extract_protocol: RNA was isolated using Qiagen RNeasy Mini Kit (Qiagen), quantified using NanoDrop, and quality was checked with the Agilent 2100 bioanalyzer (Agilent Technologies). Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.

treatment_protocol: Subcutaneous adipose tissue biopsies were taken by needle biopsy from the periumbilical area under local anesthesia, two hours after consumption of a standard meal (fed state), and twenty-four hours later, thus 26 hours after consumption of the standard meal (fasted state). The biopsies were rinsed to get rid of remaining blood and were snap frozen in liquid nitrogen. All samples were stored in aliquots at -80°C.

tag: sex (female=1, male=0)

tag: subjectid

tag: age (yrs)

tag: moment of sampling (pre/post intervention)

value: Post intervention

tag: time of sampling

value: Evening, 26 hours after standardized meal (24 hours after pre-intervention measurement)

tag: nutritional status

value: Fasted

value: Subcutaneous adipose tissue biopsy


title: HPVneg15

tag: gender


title: HPVneg15 input


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C2_AD010_indexed


title: Subcutaneous adipose tissue biopsy, subject P019, post-intervention

tag: tissue


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C1_AD007_indexed


title: HPVneg14

value: II


title: Subcutaneous adipose tissue biopsy, subject P015, post-intervention


title: Subcutaneous adipose tissue biopsy, subject P019, pre-intervention

value: Pre intervention

value: Evening, two hours after standardized meal

value: Fed


title: HPVneg13 input


title: Subcutaneous adipose tissue biopsy, subject P022, pre-intervention


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C2_AD012_indexed

value: MOp

value: male


title: HPVneg12 input


title: Subcutaneous adipose tissue biopsy, subject P015, pre-intervention


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C2_AD002_indexed


title: HPVneg12


title: WT_L1_r1

value: L1 stage

tag: genotype

value: Wildtype

value: Whole animal


title: HPVneg11 input

value: IVa

value: M


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C11_AD008_indexed


title: HPVneg11

value: Neg


title: HPVneg10 input

value: F


title: HPVneg14 input


title: Subcutaneous adipose tissue biopsy, subject P013, post-intervention

value: Post intervention


title: HPVneg9 input

value: III


title: HPVneg10


title: HPVneg9


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C1_AD012_indexed


title: HPVneg13


title: Subcutaneous adipose tissue biopsy, subject P014, pre-intervention


title: Subcutaneous adipose tissue biopsy, subject P013, pre-intervention


title: Subcutaneous adipose tissue biopsy, subject P014, post-intervention

value: Evening, 26 hours after standardized meal (24 hours after pre-intervention measurement)

value: Fasted


title: Subcutaneous adipose tissue biopsy, subject P012, pre-intervention

value: Subcutaneous adipose tissue biopsy


title: HPVneg8

value: II


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C11_AD007_indexed


title: Subcutaneous adipose tissue biopsy, subject P012, post-intervention


title: HPVneg7 input


title: HPVneg7


title: HPVneg6 input

value: IVb


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C1_AD006_indexed


title: HPVneg6


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C1_AD001_indexed


title: HPVneg5 input


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C10_AD006_indexed


title: HPVneg4 input


title: HPVneg5


title: Subcutaneous adipose tissue biopsy, subject P08, pre-intervention

value: Pre intervention

value: Evening, two hours after standardized meal

value: Fed


title: HPVneg4


title: HPVneg8 input


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C11_AD006_indexed

value: MOp

value: male


title: HPVneg3 input


title: HPVneg3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C11_AD004_indexed


title: Subcutaneous adipose tissue biopsy, subject P05, post-intervention


title: HPVneg2 input


title: Subcutaneous adipose tissue biopsy, subject P07, post-intervention


title: Subcutaneous adipose tissue biopsy, subject P08, post-intervention


title: HPVneg2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C11_AD012_indexed


title: HPVneg1


title: Subcutaneous adipose tissue biopsy, subject P05, pre-intervention


title: HPVneg1 input


title: Subcutaneous adipose tissue biopsy, subject P04, post-intervention


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C1_AD004_indexed


title: B2-AS

city: Los Angeles

first: Vassilios

last: Papadopoulos

address: 1985 Zonal Avenue

department: Department of Pharmacology and Pharmaceutical Sciences, School of

institute: University of Southern California

data_processing:
A Roche 454 sequencer at the McGill University and Genome Quebec Innovation Centre for B2-AS spesific RNAs or Illumina Casava1.7 software used for basecalling of total RNA samples.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
For the RNA-seq data, the *.BAM files were used as input for further quantification analysis using SeqMonk software packages (http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/; Babraham Bioinformatics, Cambridge, UK). The number of reads falling in the exons were counted and normalized by the size of database.
The Base Pair quantitation was used to count the actual number of bases. This gives a more fine grained view of the data.
The Mapping of B2-AS from 454 sequencer was crossinlgy compared with the featured genetic elements of SINE B2.
Genome_build: mm9
Supplementary_files_format_and_content: base pair quantitation counts in text format

source_name: testes

growth_protocol: MA-10 mouse Leydig tumor cells, a gift from Dr. M. Ascoli (University of Iowa), were maintained in Dulbecco modified Eagle medium/Ham F-12 medium supplemented with 5% heat-inactivated fetal bovine serum and 2.5%  horse serum at 37°C and 5% CO2.

extract_protocol:
MA-10 cell lysates were collected and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard 454 sequencer or Illumina protocols

tag: cell line

value: MA-10 cells

value: testes

tag: cell type

value: Leydig cell tumor

value: WT


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C10_AD008_indexed


title: Subcutaneous adipose tissue biopsy, subject P07, pre-intervention


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C10_AD004_indexed


title: DU145_Sen_71

first: Evan

middle: T

last: Keller

address: 2800 Plymouth Rd

data_processing:
Samples were sequenced on Illumina HiSeq 2500 for DU145 cell line and Illumina HiSeq 4000 with single end option for PC3 cell line.
Samples were aligned to Human genome hg38 using bowtie alignment tool.
Poor quality cells were removed as determined using the Fluidigm Singular package.
Genome_build: Human genome hg38
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts

growth_protocol: Cells were cultered in RPMI 1640 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Cells were trypsinized in 0.05% Trypsin EDTA for 5-10 mins at 37°C and washed with media.  The cell suspension was loaded into the Fluidigm C1TM machine and processed into single cell cDNA libraries according to the manufacturer protocol.
Full length mtotal RNA-seq libraries were generated from single cells captured using the Fluidigm C1TM Single Cell mtotal RNA Seq IFC, 10-17 um and Fluidigm C1TM Single-Cell Reagent Kit for mtotal RNA Seq.  Full length cDNA was converted into sequence ready libraries using SMART-seq v4 Ultra Low Input total RNA kit for Fluidigm C1TM System and SeqAmpTM DNA Polymerase.  Library preparation was completed using Nextera XT DNA library prep kit.

treatment_protocol: Docetaxel resistance was maintained with the addition of 10 nM docetaxel in DMSO in growth media while sensitive cells were maintained with the addition of a final concentration of 0.1% DMSO.

tag: docetaxel

value: Sensitive

tag: disease state

value: Prostate cancer


title: DU145_Sen_68


title: DU145_Sen_67


title: DU145_Sen_66


title: DU145_Sen_70


title: DU145_Sen_65


title: Subcutaneous adipose tissue biopsy, subject P01, post-intervention

value: Post intervention


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C10_AD010_indexed

tag: brain region


title: DU145_Sen_64


title: DU145_Sen_63


title: Subcutaneous adipose tissue biopsy, subject P04, pre-intervention


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B9_AD010_indexed

tag: Sex


title: Subcutaneous adipose tissue biopsy, subject P01, pre-intervention


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C10_AD012_indexed

tag: age


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C10_AD007_indexed

tag: strain


title: DU145_Sen_60


title: DU145_Sen_62


title: DU145_Sen_61


title: DU145_Sen_69


title: DU145_Sen_72


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B9_AD007_indexed


title: DU145_Sen_57


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B9_AD006_indexed


title: DU145_Sen_58


title: DU145_Sen_56


title: DU145_Sen_55


title: DU145_Sen_54


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B8_AD008_indexed


title: DU145_Sen_53


title: DU145_Sen_52


title: DU145_Sen_59


title: DU145_Sen_51


title: DU145_Sen_50


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B9_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B9_AD002_indexed


title: DU145_Sen_47


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B8_AD007_indexed


title: DU145_Sen_46


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B8_AD001_indexed


title: DU145_Sen_45


title: DU145_Sen_44


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B8_AD010_indexed


title: DU145_Sen_49


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B9_AD004_indexed


title: DU145_Sen_43


title: DU145_Sen_42


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_C10_AD002_indexed


title: DU145_Sen_41


title: DU145_Sen_39


title: DU145_Sen_48


title: DU145_Sen_37


title: DU145_Sen_40


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B8_AD004_indexed


title: DU145_Sen_36


title: DU145_Sen_38


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B9_AD001_indexed


title: DU145_Sen_35


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B7_AD008_indexed


title: DU145_Sen_34


title: RNA-seq of Sus scrofa: skeletal muscle at D180, replicate1

city: Shenzhen

first: Zhonglin

last: Tang

state: GuangDong

address: No.7, Pengfei road, Dapeng District

department: Agricultural Genome Institute at Shenzhen

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
Illumina Covaris S220 software used for basecalling.
After removing reads containing adapters, reads containing poly-N, and low-quality reads from the raw data using the Trimmomatic software, the RNA-seq reads were aligned to the porcine reference genome using Hisat2 (v2.0.4)  with parameter of --rna-strandness RF, other parameters were set as default.
The expression level of each gene was quantified by calculating fragments per kilobase of exon per million fragments (FPKM) values using StringTie (v1.3.1) in a reference-based approach.
Genome_build: Suscrofa 11.1
Supplementary_files_format_and_content: Landrance_muscle_FPKM.xlsx

organism: Sus scrofa

source_name: skeletal muscle

extract_protocol:
Total RNA was isolated using TRIzol™ reagent (Invitrogen, CA, USA), followed by rRNA depletion and DNaseI treatment (Qiagen, Hilden, Germany).
For each RNA sample, a paired-end strand-specific library was constructed with an insert size of ~350 bp according to the Illumina Ribo-Zero protocol.   The RNA-seq libraries were sequenced on the Illumina HiSeq X Ten platform (Illumina, CA, USA) and 150-bp paired-end reads were generated (Novogene, Beijing, China).

value: Landrance


title: DU145_Sen_33


title: RNA-seq of Sus scrofa: skeletal muscle at D180, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B7_AD004_indexed


title: DU145_Sen_32


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B6_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B7_AD010_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at D160, replicate3


title: DU145_Sen_31


title: RNA-seq of Sus scrofa: skeletal muscle at D160, replicate2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B8_AD012_indexed


title: DU145_Sen_29


title: DU145_Sen_30


title: RNA-seq of Sus scrofa: skeletal muscle at D140, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B7_AD001_indexed


title: saliva whole DNA from participant 12

type: genomic

first: Kelly

last: Bakulski

address: 1415 Washington Heights

department: Department of Epidemiology

hyb_protocol: sodium bisulfite conversion and cleaning (EZ-96 DNA Methylation™ Kit, Zymo Research) and hybridization to the Infinium MethylationEPIC BeadArray (Illumina) done according to manufacturer's instructions

scan_protocol: BeadArray fluorescence was measured using the Illumina iScan

data_processing: With the ewastools package in R, SNP probe agreement was examined. An epithelial fraction was dropped because the SNP probes did not agree with those in the other three fractions from that participant. Using the minfi package in R, fractions with a probe fail rate of >3% were dropped, and noob preprocessing was done.

label: cy3, cy5

source_name: child saliva

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from lysed cells using the DNeasy Blood & Tissue Kit (Qiagen) following the manufacturer’s protocol.

tag: participant

tag: cell fraction

value: whole


title: DU145_Sen_28


title: RNA-seq of Sus scrofa: skeletal muscle at D160, replicate1


title: RNA-seq of Sus scrofa: skeletal muscle at D180, replicate2


title: DU145_Sen_27


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B5_AD008_indexed


title: saliva large DNA from participant 1

value: large


title: saliva large DNA from participant 14


title: saliva CD45pos DNA from participant 10


title: saliva CD45pos DNA from participant 1


title: DU145_Sen_26


title: saliva large DNA from participant 20


title: saliva CD45pos DNA from participant 6

value: female


title: saliva oragene DNA from participant 6

value: oragene


title: DU145_Sen_25


title: saliva whole DNA from participant 19


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B4_AD006_indexed


title: saliva whole DNA from participant 4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B7_AD006_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at D120, replicate2


title: RNA-seq of Sus scrofa: skeletal muscle at D140, replicate2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B5_AD006_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at D140, replicate1


title: saliva oragene DNA from participant 21


title: DU145_Sen_22


title: RNA-seq of Sus scrofa: skeletal muscle at D120, replicate3


title: saliva CD45pos DNA from participant 23


title: saliva large DNA from participant 18


title: saliva whole DNA from participant 22


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B5_AD001_indexed


title: saliva large DNA from participant 3


title: saliva large DNA from participant 2


title: saliva whole DNA from participant 14


title: saliva whole DNA from participant 5


title: DU145_Sen_24


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B5_AD007_indexed


title: saliva CD45pos DNA from participant 19


title: RNA-seq of Sus scrofa: skeletal muscle at D120, replicate1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B3_AD012_indexed


title: DU145_Sen_23


title: RNA-seq of Sus scrofa: skeletal muscle at D80, replicate3


title: RNA-seq of Sus scrofa: skeletal muscle at D100, replicate3


title: DU145_Sen_19


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B4_AD002_indexed


title: saliva CD45pos DNA from participant 14


title: RNA-seq of Sus scrofa: skeletal muscle at D80, replicate2


title: RNA-seq of Sus scrofa: skeletal muscle at D100, replicate2


title: RNA-seq of Sus scrofa: skeletal muscle at D100, replicate1


title: DU145_Sen_18


title: DU145_Sen_20


title: DU145_Sen_17


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B4_AD007_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at D80, replicate1


title: saliva whole DNA from participant 10


title: RNA-seq of Sus scrofa: skeletal muscle at D60, replicate3


title: DU145_Sen_16


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B3_AD010_indexed


title: DU145_Sen_15


title: RNA-seq of Sus scrofa: skeletal muscle at D60, replicate2


title: RNA-seq of Sus scrofa: skeletal muscle at D60, replicate1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B4_AD012_indexed


title: saliva CD45pos DNA from participant 21


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B4_AD010_indexed


title: DU145_Sen_14


title: RNA-seq of Sus scrofa: skeletal muscle at D40, replicate3


title: saliva CD45pos DNA from participant 7


title: RNA-seq of Sus scrofa: skeletal muscle at D40, replicate2


title: DU145_Sen_13


title: RNA-seq of Sus scrofa: skeletal muscle at D40, replicate1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B3_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B3_AD004_indexed


title: DU145_Sen_21


title: DU145_Sen_12


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B4_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B3_AD008_indexed


title: saliva large DNA from participant 9


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B5_AD002_indexed


title: DU145_Sen_11


title: RNA-seq of Sus scrofa: skeletal muscle at D30, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B2_AD012_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at D30, replicate2


title: DU145_Sen_9


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B3_AD002_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at D20, replicate3


title: saliva whole DNA from participant 15


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B2_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B5_AD004_indexed


title: DU145_Sen_8


title: RNA-seq of Sus scrofa: skeletal muscle at D20, replicate2


title: saliva whole DNA from participant 9


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B2_AD006_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at D20, replicate1


title: DU145_Sen_5


title: DU145_Sen_10


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B1_AD002_indexed


title: DU145_Sen_6


title: RNA-seq of Sus scrofa: skeletal muscle at D9, replicate3


title: saliva CD45pos DNA from participant 17


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B1_AD006_indexed


title: DU145_Sen_4


title: DU145_Sen_3


title: saliva CD45pos DNA from participant 5


title: RNA-seq of Sus scrofa: skeletal muscle at D9, replicate2


title: RNA-seq of Sus scrofa: skeletal muscle at D9, replicate1


title: DU145_Sen_7


title: RNA-seq of Sus scrofa: skeletal muscle at D30, replicate1


title: DU145_Sen_2


title: saliva large DNA from participant 11


title: saliva large DNA from participant 23


title: saliva oragene DNA from participant 5


title: DU145_Sen_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B2_AD001_indexed


title: Class 2 tracheal HRV+orkambi rep2 [RF191]

city: Crawley, Perth

first: Emma

last: de Jong

state: WA

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

data_processing:
RNA-Seq libraries were sequenced on the Illumina® HiSeq 2500 platform using the RAPID mode
100bp single-end reads, followed by bcl2fastq conversion and de-multiplexing
Read libraries were mapped to the GRCh37 (hg19) Human genome using HISAT2 (v2.0.4)
Gene-level quantitation (counts) of HISAT2 alignments was performed using SummarizeOverlaps
Genome_build: hg19
Supplementary_files_format_and_content: genecounts.csv file contains a matrix of raw gene counts (unfiltered and un-normalised data)

source_name: Class 2 tracheal HRV+orkambi

growth_protocol: Primary airway epithelial cells cultured using conditional re-programming as described in PMID 29269735

extract_protocol:
RNA was extracted using the Ambion Purelink® RNA mini kit (Thermo Scientific) per the manufacturer’s instructions.  KAPA Stranded mRNA-Seq kit (KAPABiosystems (Roche)) was used for mRNA capture, with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard KAPABiosystems protocols

treatment_protocol: Primary epithelial cell cultures were assessed under 4 conditions: no infection (control), infection with RV1b (MOI 12) and RV1b infection (MOI 12) following 100 nM ivacaftor or 3 μM lumacaftor/100 nM ivacaftor. Cell supernatants were removed of cellular debris by centrifugation at 1,000 x g for 2 minutes and  archived at -80°C. Then, 350 μL of cell lysis buffer containing 1% (v/v) β-mercaptoethanol was added to the cell monolayer for 4 minutes before harvesting and archived at -80°C.

tag: mutation class

value: Class 2

tag: age (years)

value: tracheal

tag: treatment

value: airway epithelial cells


title: RNA-seq of Sus scrofa: skeletal muscle at D0, replicate2


title: RNA-seq of Sus scrofa: skeletal muscle at D0, replicate1


title: saliva large DNA from participant 6


title: Class 2 tracheal HRV rep2 [RF190]

source_name: Class 2 tracheal HRV

value: HRV


title: saliva whole DNA from participant 20

value: male


title: RNA-seq of Sus scrofa: skeletal muscle at D0, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B3_AD006_indexed

value: MOp


title: RNA-seq of Sus scrofa: skeletal muscle at E105, replicate3


title: Class 2 tracheal control rep2 [RF188]

source_name: Class 2 tracheal control

value: control


title: saliva CD45pos DNA from participant 18


title: saliva CD45pos DNA from participant 24


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B2_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B1_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B8_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B1_AD004_indexed


title: saliva whole DNA from participant 1


title: Class 2 nasal HRV+orkambi rep2 [RF187]

source_name: Class 2 nasal HRV+orkambi

value: nasal


title: Class 2 nasal HRV rep2 [RF186]

source_name: Class 2 nasal HRV


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B1_AD007_indexed


title: saliva whole DNA from participant 23


title: Class 2 nasal control rep2 [RF184]

source_name: Class 2 nasal control


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B1_AD010_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B2_AD007_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E105, replicate1


title: RNA-seq of Sus scrofa: skeletal muscle at E105, replicate2


title: saliva large DNA from participant 10


title: RNA-seq of Sus scrofa: skeletal muscle at E100, replicate2


title: Class 3 nasal HRV+ivacaftor rep6 [RF183]

source_name: Class 3 nasal HRV+ivacaftor

value: Class 3


title: Class 3 tracheal HRV+ivacaftor rep1 [RF182]

source_name: Class 3 tracheal HRV+ivacaftor


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B1_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B11_AD010_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E100, replicate1


title: saliva CD45pos DNA from participant 4


title: saliva large DNA from participant 15


title: saliva whole DNA from participant 3


title: saliva CD45pos DNA from participant 3


title: saliva large DNA from participant 24


title: saliva whole DNA from participant 2


title: saliva whole DNA from participant 17


title: saliva CD45pos DNA from participant 22


title: saliva large DNA from participant 12


title: RNA-seq of Sus scrofa: skeletal muscle at E95, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B11_AD012_indexed


title: Class 2 tracheal HRV+orkambi rep1 [RF179]


title: saliva whole DNA from participant 24


title: RNA-seq of Sus scrofa: skeletal muscle at E95, replicate2


title: Class 2 tracheal HRV rep1 [RF178]


title: RNA-seq of Sus scrofa: skeletal muscle at E90, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B11_AD002_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E95, replicate1


title: Class 2 tracheal control rep1 [RF176]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B11_AD006_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E100, replicate3


title: LNCap plko

first: Chongwei

last: Xie

address: Futain,Shenzhen

institute: Shenzhen Hospital

description: control LNCaP cell line

hyb_protocol: standard agilent protocol

scan_protocol: standard agilent protocol

data_processing: performed by Shanghai Biotechnology Corporation.

source_name: LNCaP cell line

label_protocol: RNA extraction, construction of libraries, and microarray using human gene expression 4x44K microarray (Agilent Technologies, Santa Clara, CA, USA) were performed by Shanghai Biotechnology Corporation (Shanghai, China).

growth_protocol: LNCaP cells were cultured in 1640 medium (Gibco) containing 10% fetal bovine serum (Gibco), 1×penicillin/streptomycin in a 5% CO2 incubator at 37°C.

extract_protocol: LNCaP samples were prepared in TRIzol solution.

treatment_protocol: Lentivirus based shRNA(targetted or non-targetted) were used to tranduct LNCaP cell. shRNA was constructed into pLKO.1-puro plasmid(sigma). Knocking down of Gabarapl1 was confirmed by real-time PCR with at least 75% reduction.

value: LNCaP cell line

value: prostate tumor

tag: genotype/variation


title: saliva large DNA from participant 4


title: RNA-seq of Sus scrofa: skeletal muscle at E90, replicate2


title: LNCap gab_2

description: Gabarapl1 knockdown LNCaP cell line

value: Gabarapl1 knockdown


title: Class 3 tracheal HRV+ivacaftor rep2 [RF180]


title: RNA-seq of Sus scrofa: skeletal muscle at E90, replicate1

value: Landrance


title: Class 2 nasal HRV+orkambi rep1 [RF175]


title: Class 2 nasal HRV rep1 [RF174]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B10_AD001_indexed


title: Jurkat_cells_123IUdR_6h_after _withdrawl_2600Decays_rep2

city: Juelich

first: Marcus

last: Unverricht-Yeboah

address: Wilhelm-Johnen-Strasse

department: Department of Safety and Radiation Protection

country: Germany

institute: Forschungszentrum Juelich

description:
62571_1_2
Gene_expression_6h_after _2600_I-123-decays/cell(20h_exposure)_replicate2

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl following the manufacturers instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F, Agilent) for 17 hours at 65°C in a rotating  hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer 1 (Agilent) and 1 minute with 37°C  Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides as recommended by Agilent.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent, Protocol GE1-v5_95_Feb07) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3- CTP  labeled cRNA was prepared from 0.4 ug RNA using the Quick-Amp Labeling Kit, One-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (RNeasy Mini Kit QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: To maximize the incorporation of 123IUdR into the DNA, the Jurkat cells were synchronized by aphidicolin. To reduce the potential cytotoxic effects of aphidicolin, the cells were allowed to progress through the S-phase and to complete the G2/M-phase. At the second entry into the S-phase, Jurkat cells were incubated with 123IUdR for the following 20 h. To maximize the uptake of 123IUdR into the DNA fluorodeoxyuridine and deoxycytidine  was added to the cell culture medium. Non-irradiated controls were run in parallel to the experimental cell cultures following identical protocols except that the radioactive 123IUdR was replaced by non-radioactive IUdR.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  All extracted RNA samples were found to be of good quality.

treatment_protocol: Gene expression was analyzed after adding 123IUdR for 20 h to cell cultures and an additional 6 h after withdrawal of 123IUdR as well as 6 h and 24 h after α- and γ-irradiation using the determined equi-effect doses/activities. For each radiation quality, non-irradiated controls were run in parallel to the experimental cell cultures following identical protocols. Three biological replicates were prepared for each dose and each point in time.

value: T-Lymphoma cell line

tag: gender

value: isolated from a 14years old boy


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A9_AD010_indexed


title: Jurkat_cells_123IUdR_6h_after _withdrawl_2600Decays_rep1

description:
62570_1_2
Gene_expression_6h_after _2600_I-123-decays/cell(20h_exposure)_replicate1

tag: tissue


title: saliva CD45pos DNA from participant 9


title: Class 2 nasal control rep1 [RF172]


title: RNA-seq of Sus scrofa: skeletal muscle at E85, replicate2


title: Class 3 nasal HRV+ivacaftor rep2 [RF171]

value: female


title: RNA-seq of Sus scrofa: skeletal muscle at E85, replicate3


title: saliva oragene DNA from participant 23

value: oragene


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B10_AD004_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E85, replicate1


title: Jurkat_cells_123IUdR_6h_after _withdrawl_50Decays_rep3

description:
62568_1_1
Gene_expression_6h_after _50_I-123-decays/cell(20h_exposure)_replicate3


title: Class 3 nasal HRV+ivacaftor rep4 [RF170]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B11_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A9_AD012_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E80, replicate3


title: Jurkat_cells_123IUdR_6h_after _withdrawl_50Decays_rep2

description:
62571_1_3
Gene_expression_6h_after _50_I-123-decays/cell(20h_exposure)_replicate2


title: Jurkat_cells_123IUdR_6h_after _withdrawl_50Decays_rep1

description:
62570_1_3
Gene_expression_6h_after _50_I-123-decays/cell(20h_exposure)_replicate1


title: Jurkat_cells_123IUdR_6h_after _withdrawl_2600Decays_rep3

description:
62569_1_1
Gene_expression_6h_after _2600_I-123-decays/cell(20h_exposure)_replicate3


title: Class 3 nasal HRV+ivacaftor rep3 [RF168]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A9_AD006_indexed


title: saliva CD45pos DNA from participant 20


title: Class 3 tracheal HRV+ivacaftor rep3 [RF167]


title: Jurkat_cells_123IUdR_6h_after _withdrawl_0Decays_rep3

description:
62567_1_1
Gene_expression_6h_after _0_I-123-decays/cell(20h_exposure)_replicate3


title: saliva CD45pos DNA from participant 15


title: RNA-seq of Sus scrofa: skeletal muscle at E80, replicate1


title: Class 3 tracheal HRV+ivacaftor rep4 [RF166]


title: RNA-seq of Sus scrofa: skeletal muscle at E75, replicate3


title: Class 3 nasal HRV+ivacaftor rep5 [RF164]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A9_AD004_indexed


title: Jurkat_cells_123IUdR_6h_after _withdrawl_0Decays_rep2

description:
62571_1_4
Gene_expression_6h_after _0_I-123-decays/cell(20h_exposure)_replicate2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A9_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B11_AD004_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E75, replicate2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B11_AD008_indexed


title: Class 3 nasal HRV rep6 [RF163]

source_name: Class 3 nasal HRV


title: RNA-seq of Sus scrofa: skeletal muscle at E80, replicate2


title: Jurkat_cells_123IUdR_6h_after _withdrawl_0Decays_rep1

description:
62570_1_4
Gene_expression_6h_after _0_I-123-decays/cell(20h_exposure)_replicate1


title: RNA-seq of Sus scrofa: skeletal muscle at E75, replicate1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B10_AD012_indexed


title: Jurkat_cells_Alpha_24h_1Gy_rep3

description:
67107_1_2
Gene_expression_24h_after_1Gy_Alpha-irradiation


title: Class 3 tracheal HRV rep1 [RF162]

source_name: Class 3 tracheal HRV


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A8_AD006_indexed


title: Jurkat_cells_Alpha_24h_1Gy_rep2

description:
67106_1_4
Gene_expression_24h_after_1Gy_Alpha-irradiation


title: RNA-seq of Sus scrofa: skeletal muscle at E70, replicate3


title: Class 3 tracheal HRV rep2 [RF160]


title: saliva whole DNA from participant 18

value: whole


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B10_AD002_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E70, replicate2


title: saliva CD45pos DNA from participant 12


title: saliva large DNA from participant 5

value: large


title: Jurkat_cells_Alpha_24h_1Gy_rep1

description:
67106_1_2
Gene_expression_24h_after_1Gy_Alpha-irradiation


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A8_AD012_indexed


title: Class 2 tracheal HRV+orkambi rep3 [RF150]

value: Class 2

value: tracheal

value: airway epithelial cells


title: RNA-seq of Sus scrofa: skeletal muscle at E70, replicate1


title: Class 2 tracheal HRV rep3 [RF149]

value: male

value: HRV


title: RNA-seq of Sus scrofa: skeletal muscle at E65, replicate3


title: Jurkat_cells_Alpha_24h_0Gy_rep2

description:
67106_1_3
Gene_expression_24h_after_0Gy_Alpha-irradiation


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A8_AD010_indexed

value: MOp


title: Jurkat_cells_Alpha_24h_0Gy_rep3

description:
67107_1_1
Gene_expression_24h_after_0Gy_Alpha-irradiation


title: Class 2 tracheal control rep3 [RF147]

value: control


title: RNA-seq of Sus scrofa: skeletal muscle at E65, replicate2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B10_AD010_indexed


title: Class 2 nasal HRV+orkambi rep3 [RF146]

value: nasal


title: saliva large DNA from participant 7


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_B10_AD008_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E65, replicate1


title: saliva large DNA from participant 22


title: Class 2 nasal HRV rep3 [RF145]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A7_AD012_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E60, replicate3


title: Class 2 nasal control rep3 [RF143]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A8_AD007_indexed


title: Class 3 nasal HRV rep2 [RF142]

value: Class 3


title: RNA-seq of Sus scrofa: skeletal muscle at E60, replicate1


title: Class 3 nasal HRV rep4 [RF141]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A7_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A7_AD010_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E55, replicate3


title: Class 3 nasal HRV rep3 [RF139]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A7_AD007_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E55, replicate2


title: Class 2 nasal HRV+orkambi rep5 [RF138]


title: RNA-seq of Sus scrofa: skeletal muscle at E60, replicate2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A7_AD002_indexed


title: Jurkat_cells_Alpha_6h_1Gy_rep1

description:
67103_1_2
Gene_expression_6h_after_1Gy_Alpha-irradiation


title: RNA-seq of Sus scrofa: skeletal muscle at E55, replicate1


title: Class 2 nasal HRV rep5 [RF137]


title: Jurkat_cells_Alpha_6h_1Gy_rep2

description:
67104_1_2
Gene_expression_6h_after_1Gy_Alpha-irradiation


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A7_AD001_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E50, replicate3


title: Jurkat_cells_Alpha_6h_0Gy_rep3

description:
67105_1_1
Gene_expression_6h_after_0Gy_Alpha-irradiation


title: Class 2 nasal control rep5 [RF135]


title: Jurkat_cells_Alpha_6h_0Gy_rep1

description:
67103_1_1
Gene_expression_6h_after_0Gy_Alpha-irradiation


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A6_AD012_indexed


title: Jurkat_cells_Alpha_24h_0Gy_rep1

description:
67106_1_1
Gene_expression_24h_after_0Gy_Alpha-irradiation


title: Jurkat_cells_Gamma_24h_10Gy_rep3

description:
69960_1_2
Gene_expression_24h_after_10Gy_Gamma-irradiation


title: saliva CD45pos DNA from participant 11


title: Jurkat_cells_Gamma_24h_10Gy_rep2

description:
69880_1_4
Gene_expression_24h_after_10Gy_Gamma-irradiation


title: Jurkat_cells_Alpha_6h_0Gy_rep2

description:
67104_1_1
Gene_expression_6h_after_0Gy_Alpha-irradiation


title: RNA-seq of Sus scrofa: skeletal muscle at E50, replicate2


title: Class 2 tracheal HRV+orkambi rep5 [RF134]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A6_AD010_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E50, replicate1


title: Jurkat_cells_Gamma_24h_0Gy_rep3

description:
69960_1_1
Gene_expression_24h_after_0Gy_Gamma-irradiation


title: Class 2 tracheal HRV rep5 [RF133]


title: RNA-seq of Sus scrofa: skeletal muscle at E45, replicate3


title: Jurkat_cells_Gamma_24h_10Gy_rep1

description:
69880_1_2
Gene_expression_24h_after_10Gy_Gamma-irradiation


title: saliva whole DNA from participant 6


title: Jurkat_cells_Gamma_24h_0Gy_rep2

description:
69880_1_3
Gene_expression_24h_after_0Gy_Gamma-irradiation


title: RNA-seq of Sus scrofa: skeletal muscle at E45, replicate2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A7_AD006_indexed


title: Class 2 tracheal control rep5 [RF131]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A8_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A8_AD004_indexed


title: Class 3 tracheal HRV rep3 [RF130]


title: Class 3 nasal HRV rep5 [RF127]


title: Class 3 tracheal HRV rep4 [RF129]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A6_AD001_indexed


title: Jurkat_cells_Gamma_24h_0Gy_rep1

description:
69880_1_1
Gene_expression_24h_after_0Gy_Gamma-irradiation


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A6_AD006_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E40, replicate3


title: RNA-seq of Sus scrofa: skeletal muscle at E40, replicate2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A5_AD010_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E40, replicate1


title: Jurkat_cells_Alpha_6h_1Gy_rep3

description:
67105_1_2
Gene_expression_6h_after_1Gy_Alpha-irradiation


title: Class 3 tracheal control rep1 [RF125]

source_name: Class 3 tracheal control


title: RNA-seq of Sus scrofa: skeletal muscle at E33, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A5_AD008_indexed


title: Class 3 tracheal control rep2 [RF123]


title: RNA-seq of Sus scrofa: skeletal muscle at E33, replicate2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A6_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A6_AD008_indexed


title: RNA-seq of Sus scrofa: skeletal muscle at E33, replicate1


title: RNA-seq of Sus scrofa: skeletal muscle at E45, replicate1


title: Class 2 nasal HRV rep4 [RF121]


title: WGBS of Sus scrofa: skeletal muscle at D180, replicate3

data_processing:
Illumina Covaris S220 software used for basecalling.
After transforming the Sus scrofa reference genome to a bisulfite-converted version (C-to-T and G-to-A conversion) and then indexing it using bowtie2, the bisulfite-treated clean reads were mapped to the reference genome using the Bismark software (v 0.12.5) was used to perform alignments with default parameters
The sequencing depth and coverage of the methylcytosine were summarized after deletion of the duplicated reads. The methylation level of each CpG site was defined as the number of methylated reads (C) divided by the total number of methylated reads (C) and unmethylated reads (T) at the same positions in the reference genome.
Genome_build: Suscrofa 11.1
Supplementary_files_format_and_content: C_level_result.txt.gz

extract_protocol:
Total DNA for WGBS was extracted and fragmented by sonication to 200−300 bp using a Covaris S220 (Covaris, Woburn, MA, USA), followed by end repair and A-ligation. After ligation to cytosine-methylated barcodes, the DNA fragments were treated twice with bisulfite using an EZ DNA Methylation-GoldTM Kit (Zymo Research, Orange, CA, USA).
The libraries were then prepared according to the Illumina standard DNA methylation analysis protocol. The WGBS libraries were sequenced on the Illumina HiSeq X Ten platform (Illumina, CA, USA) and 150-bp paired-end reads were generated.


title: Class 3 nasal control rep6 [RF126]

source_name: Class 3 nasal control


title: Jurkat_cells_Gamma_6h_0Gy_rep2

description:
67104_1_3
Gene_expression_6h_after_0Gy_Gamma-irradiation


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A5_AD006_indexed


title: Jurkat_cells_Gamma_6h_0Gy_rep3

description:
67105_1_3
Gene_expression_6h_after_0Gy_Gamma-irradiation


title: Jurkat_cells_Gamma_6h_10Gy_rep1

description:
67103_1_4
Gene_expression_6h_after_10Gy_Gamma-irradiation


title: Jurkat_cells_Gamma_6h_10Gy_rep3

description:
67105_1_4
Gene_expression_6h_after_10Gy_Gamma-irradiation


title: WGBS of Sus scrofa: skeletal muscle at D180, replicate2


title: Jurkat_cells_Gamma_6h_0Gy_rep1

description:
67103_1_3
Gene_expression_6h_after_0Gy_Gamma-irradiation


title: Class 2 tracheal HRV+orkambi rep4 [RF118]


title: Jurkat_cells_Gamma_6h_10Gy_rep2

description:
67104_1_4
Gene_expression_6h_after_10Gy_Gamma-irradiation


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A5_AD007_indexed


title: Late-passage#2

city: Daejeon

first: Yi-deun

last: Jung

address: 125 Gahac-ro, Yusung-Gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: adipose-derived human mesenchymal stem cell

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Adipose-derived human mesenchymal stem cells were cultured in Dulbecco’s modified Eagle’s medium (Gibco) supplemented with 10% feta bovine serum (Gibco), 100 units/ml penicillin, and 100 ug/ml streptomycin (Gibco) in humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen, 15596-018).

treatment_protocol: Adipose-derived human mesenchymal stem cells were incubated at 37°C in 5% CO2 and grown to 50-60 % confluence, transfected with siRNAs against DGCR8 (siDGCR8) and GFP control (siGFP;ST Pharm) at a concentration of 32 nM using Lipofectamine 2000 (Invitrogen).

tag: pdl


title: Late-passage#3

value: adipose-derived human mesenchymal stem cell


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A5_AD004_indexed

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: Class 2 nasal HRV+orkambi rep4 [RF122]


title: WGBS of Sus scrofa: skeletal muscle at D180, replicate1

source_name: skeletal muscle

value: Landrance


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A4_AD010_indexed


title: Class 2 tracheal HRV rep4 [RF117]


title: WGBS of Sus scrofa: skeletal muscle at D160, replicate3


title: Class 2 tracheal control rep4 [RF115]


title: Early-pasage#2


title: Class 3 nasal control rep2 [RF114]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A6_AD007_indexed


title: Early-pasage#1


title: WGBS of Sus scrofa: skeletal muscle at D160, replicate2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A5_AD012_indexed


title: WGBS of Sus scrofa: skeletal muscle at D160, replicate1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A4_AD008_indexed


title: Class 3 nasal control rep4 [RF113]


title: Class 3 nasal control rep3 [RF111]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A3_AD006_indexed


title: WGBS of Sus scrofa: skeletal muscle at D140, replicate3


title: Class 3 tracheal control rep3 [RF107]


title: WGBS of Sus scrofa: skeletal muscle at D140, replicate2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A4_AD006_indexed


title: WGBS of Sus scrofa: skeletal muscle at D140, replicate1


title: Class 3 tracheal control rep4 [RF106]


title: WGBS of Sus scrofa: skeletal muscle at D120, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A4_AD002_indexed


title: Class 3 nasal control rep5 [RF104]


title: Early-pasage#3


title: BXPC3 siRNA_Control

city: Heidelberg

first: Martin

last: Berger

address: INF 581

institute: DKFZ

description: BXPC3 siRNAControl.mean

hyb_protocol: Hybridization was performed in GEX-HCB buffer at 58 °C with a concentration of 100 ng cRNA/ μl, uncapped in a wet chamber for 20 h. Spike in controls for low, medium and highly present RNAs were added, as well as mismatch control and biotinylation control oligonucleotides.

scan_protocol: Microarray scanning was performed on a Beadstation array scanner, with the setting adjusted to a scaling factor of 1 and PMT settings at 430.

data_processing:
Data analysis was performed by normalization of the signals using the quantile normalization algorithm without background subtraction, and differentially regulated genes were defined by calculating the standard deviation differences of a given probe by student t-test.
Gene expression was considered significantly changed for a fold change of at least ± 1.5, a p value of 0.005

source_name: control siRNA

label_protocol: Biotin labeled cRNA samples for hybridization on Illumina Human Sentrix – 12 Beadchip arrays (Illumina, San Diego, CA) were processed according to ILLUMNA’s recommended sample labeling procedure founded on the modified Eberwine protocol.

growth_protocol: Two human pancreatic adenocarcinoma cell lines (BXPC3 and Miapaca) were cultured in RPMI-1640 (Invitrogen, Germany) and DMEM medium, respectively (Sigma Aldrich, Germany). The media were supplemented with 10 % fetal bovine serum and L-glutamine (2 mM), penicillin (100 IU/ml) and streptomycin (100μg/ml) (Invitrogen, Karlsruhe, Germany). The cells were trypsinized with 0.25 % Trypsin/EDTA solution and maintained under standard incubation conditions (5 % CO2, 37 °C) in a humidified atmosphere.

extract_protocol: After 72h of exposure, the treated cells were harvested and washed; total RNA was extracted from cell pellets with the RNeasy Mini kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol.

treatment_protocol: Two different siRNAs (Invitrogen, Germany) were designed to check for the effect of Lynx1 modulation. These were siRNALynx1-ORF [sense sequence: UUA CUG ACC UUC AUC CUGG (dT) (dT)/ antisense: CCA GGA UGA AGG UCA GUAA (dT) (dT)] and siRNA Lynx1-3UTR [sense sequence: UUG AAG AGG AGA GCA GACC (dT) (dT)/ antisense: GGU CUG CUC UCC UCU UCAA (dT) (dT)]. The Lynx1 gene was knocked down by a higher siRNA concentration (200nM) in BXPC3 than in Miapaca cells (60 pM). Cells were seeded at pre-optimized cell density in six well plates (10 × 104 / 2000 μl), 24h later siRNA was added in OptiMEM media using 4 μl lipofectamine RNAimax (Invitrogen, Germany) for Miapaca and 14 μl Xtreme gene9 for BXPC3 cells as transfecting agents.

tag: cell line

value: human PDAC cell line

value: control siRNA


title: BXPC3 siRNA_Lynx1-ORF

description: 5 GD2.BXPC3 LYNX1- ORF.mean

source_name: Lynx1-ORF siRNA

tag: cell type

value: Lynx1-ORF siRNA


title: Miapaca siRNA_Lynx1-ORF

description: Miapaca siRNALynx1-ORF.mean

value: Miapaca


title: Miapaca siRNA_Lynx1-3UTR

description: Miapaca siRNALynx1-3UTR.mean

source_name: Lynx1-3UTR siRNA

value: Lynx1-3UTR siRNA


title: Miapaca siRNA_Control

description: Miapaca siRNAControl mean


title: WGBS of Sus scrofa: skeletal muscle at D120, replicate2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A3_AD010_indexed


title: Class 2 nasal control rep4 [RF119]


title: WGBS of Sus scrofa: skeletal muscle at D120, replicate1


title: WGBS of Sus scrofa: skeletal muscle at D100, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A3_AD004_indexed


title: WGBS of Sus scrofa: skeletal muscle at D100, replicate2


title: Bioprinted kidney organoid

city: Parkville

first: Kynan

middle: Thomas

last: Lawlor

state: VIC

address: Murdoch Children's Research Institute, Flemington Road

institute: Murdoch Children's Research Institute

data_processing:
The 10x Genomics Cell Ranger pipeline (v1.3.1) was used to align, filter and de-duplicate reads before counting those overlapping genes to produce count matrices for each sample.
Genome_build: hg38
Supplementary_files_format_and_content: The resulting datasets consist of matrix files (matrix.mtx) containing the UMI count values, barcode files (barcodes.tsv) containing the detected cell barcodes and genes files (genes.tsv) containing the ENSEMBL ids of the detected genes.

source_name: CRL1502.C32 human iPSCs

growth_protocol: Kidney organoids were made according to a published protocol (Takasata et al., Generation of kidney organoids from human pluripotent stem cells, Nature protocols 2016, PMID:27560173) with a modification so that cells were aggregated as a cells paste, loaded into a hamilton syringe and deposited on transwells using a NovoGen MMX extrusion-based 3D cellular bioprinter.

extract_protocol:
CRL1502.C32 kidney organoid were dissociated at D7+18 using cold active protease (Liberase) for 20 minutes at 4c. Cells were centrifuged at 1500 rpm for 3minutes to form a pellet. Single cells were resuspended in fresh DMEM F12 media filtered through 20 µm cell strainers to remove clumps, and stored on ice until analysis.
Chromium Single Cell Library kit V2; Illumina HiSeq HT chemistry- 100bp paired end sequencing

value: ES-derived kidney organoid

tag: day of differentiation


title: BR2_pS187H1.4_E2_FLVP

city: Bethesda

first: Ankita

last: Saha

state: Maryland

address: 41 Medlars Drive

institute: National Cancer Institute

data_processing:
Base calling and demultiplexing into FASTQ files was done using bcl2fastq v1.8.4 software (Illumina, San Diego, CA, USA)
Sequence data were mapped with Bowtie2 to the hg19 genome using default settings
Mapped sequence data were analyzed for peaks using HOMER (Hypergeometric Optimization of Motif EnRichment) v4.10
Samples were converted into tag directories, and QC was performed using read mapping and GC bias statistics
Histone peaks were then called from the Tag Directories with default factor settings, except local filtering was disabled (-L 0), peak size was set at 200bp (-size 200) and minimum distance between peaks was set at 150 (-minDist 150)
BigWiggle pileup files were generated using HOMER’s makeBigWig.pl script with default settings
Genome_build: hg19
Supplementary_files_format_and_content: BigWiggle pileup files were generated using HOMER’s makeBigWig.pl script with default settings and uploaded to a UCSC Genome Browser track hub

source_name: MCF7 Cell line

growth_protocol: MCF7 cells were grown in  Charcoal-dextran treated FBS supplemented, phenol-red free RPMI1640 media for 72 hours prior to any treatment.

extract_protocol: Library contruction was carried out accroding to Manufacturer instructions- KAPA biosystems (KK8230) library construction kit. Size selection for 200-500bp was performed using Ampure XP Beads

treatment_protocol:
10nM Beta estradiol dissolved in ethanol was added to the cell samples (Labeled _E2) and ethanol was added to the cell samples (Labeled_Control) for 30 minutes
Drug treatment (flavopiridol) was carried out for 1 Hr prior to E2 addition in samples labeled (_FLVP)

value: Breast Cancer Cells

tag: chip antibody

value: Affinity purified pS187-H1.4 (Custom)


title: BR2_pS187H1.4_Control


title: BR2_pS187H1.4_E2


title: WGBS of Sus scrofa: skeletal muscle at D100, replicate1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A4_AD001_indexed

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

tag: brain region


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A5_AD001_indexed

tag: Sex


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A3_AD007_indexed

tag: age


title: WGBS of Sus scrofa: skeletal muscle at D80, replicate3

tag: strain


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A5_AD002_indexed


title: BR2_panH1.4ChIP_E2

value: Affinity purified panH1.4 (Custom)


title: BR2_panH1.4ChIP_Control


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A3_AD008_indexed

value: male


title: Human PDAC Suit2-007 cells (in vitro cells)

description:
Chip arary data raw_ in vivo_in vitro
In vitro cells (2016_00926)_200665010008_J.mean

hyb_protocol: Standard Illumina Hybridisation Protocol  (Whole-Genome Gene Expression  Direct Hybridization Assay Guide) 750 ng of cRNA were hybridized for 17 hr at 58°C on Illumina Human HT-12-Microarray.

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol  (Whole-Genome Gene Expression  Direct Hybridization Assay Guide)

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore

label: Chip arary data normalized_ in vivo_in vitro

source_name: Human

label_protocol: The Illumina TotalPrep RNA Amplification Kit (life technologies) is used to generate single-stranded cRNA from input amounts of 200ng total RNA  (20190611_130648.submission2.0) and 500ng total RNA (20191121_105523.submission2.0 ). Label: Biotin, Cy3-Streptavidin

growth_protocol: Suit2-007 cells were cultured using T175 cm2 flasks in complete RPMI media, which contained 10% fetal calf serum and 1% glutamine. The cells were maintained at logarithmic phase under standard cell culture (37°C, 100% humidity, 5% CO2 in air) and harvested upon reaching a confluence of 60-80%.

extract_protocol: Total RNA isolation was isolated from these samples as described in the Qiagen RNA isolation kit.

treatment_protocol: For tumor growth in liver and lung environments of nude rats, 8 animals were injected intraportally with a suspension of human PDAC Suit2-007 (~3x106cells/animal) cells in 300 µL. For tumor growth in the pancreas environment, 4 animals were injected orthotopically with a suspension of human PDAC Suit2-007 (~1.5x106 cells/animal) cells in 150 µL. Tumor growth was monitored weekly after which, the animals were  sacrificed after 4 weeks. For cells growing in cell pellets were harvested with trypsin.

tag: sample type

value: cell culture

value: PDAC adherent tumor cells


title: Human PDAC Suit2-007 cells  liver tissue (liver 3c)

description:
Chip arary data raw_ in vivo_in vitro
Liver 3 (2016_01140)_200665010008_H.mean


title: Human PDAC Suit2-007 cells  liver tissue (liver 3a)

description:
Chip arary data raw_ in vivo_in vitro
Liver 1 (2016_01138)_200665010008_F.mean

value: intrapotal


title: BR2_Input_E2

value: none (input)


title: Human PDAC Suit2-007 cells  lung tissue (lung ersatz)

description:
Chip arary data raw_ in vivo_in vitro
Lung 4 (2016_01144)_200665010008_E.mean


title: Human PDAC Suit2-007 cells  liver tissue (liver 4)

description:
Chip arary data raw_ in vivo_in vitro
Liver 4 (2016_01146)_200665010008_I.mean


title: Human PDAC Suit2-007 cells  lung tissue (lung 2c)

description:
Chip arary data raw_ in vivo_in vitro
Lung 3 (2016_01137)_200665010008_D.mean


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A3_AD001_indexed

value: MOp


title: Human PDAC Suit2-007 cells  liver tissue (liver 3b)

description:
Chip arary data raw_ in vivo_in vitro
Liver 2 (2016_01139)_200665010008_G.mean


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A2_AD012_indexed


title: WGBS of Sus scrofa: skeletal muscle at D60, replicate3


title: WGBS of Sus scrofa: skeletal muscle at D80, replicate1


title: BR1_pS187H1.4_E2_FLVP


title: WGBS of Sus scrofa: skeletal muscle at D60, replicate2


title: BR1_panH1.4ChIP_E2_FLVP


title: BR1_pS187H1.4_E2


title: WGBS of Sus scrofa: skeletal muscle at D80, replicate2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A1_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A4_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A2_AD007_indexed


title: WGBS of Sus scrofa: skeletal muscle at D60, replicate1


title: WGBS of Sus scrofa: skeletal muscle at D40, replicate3


title: BR2_Input_Control


title: BR1_pS187H1.4_Control


title: WGBS of Sus scrofa: skeletal muscle at D40, replicate2


title: BR1_panH1.4ChIP_E2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A2_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A1_AD010_indexed


title: BR1_panH1.4ChIP_Control


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A1_AD012_indexed


title: WGBS of Sus scrofa: skeletal muscle at D30, replicate2


title: BR1_Input_Control


title: Human PDAC Suit2-007 cells  lung tissue (lung 2a)

description:
Chip arary data raw_ in vivo_in vitro
Lung 2 (2016_01135)_200665010008_C.mean


title: WGBS of Sus scrofa: skeletal muscle at D30, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A2_AD004_indexed


title: Human PDAC Suit2-007 cells (Rpx treated) rep2

description:
Rpx treated
PDAC adherent tumor cells
Sample 5

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol  (Whole-Genome Gene Expression  Direct Hybridization Assay Guide)

label: Biotin, Cy3-Streptavidin

label_protocol: The Illumina TotalPrep RNA Amplification Kit (life technologies) is used to generate single-stranded cRNA from input amounts of 200ng total RNA  (20190611_130648.submission2.0) and 500ng total RNA (20191121_105523.submission2.0 ).

growth_protocol: Suit2-007 cells were cultured  using (T75 cm2 flasks) in complete RPMI media, which contained 10% fetal calf serum (FCS) and 1% glutamine.

extract_protocol: The isolation of total RNA was performed as detailed in the Fast Gene RNA isolation kit (NIPPON Genetics Co Ltd). The concentrations of total RNA were determined by a Nanodrop spectrophotometer. A chip array was performed by Genomic and Proteomic Core Facility (microarray unit) at the DKFZ

treatment_protocol: Cells were harvested and seeded in 6-well plates (2.5 × 105 cells/well) and kept under standard culture conditions for 24 h after followed by treatment with 0.312 ng/mL of Rpx corresponding to the IC50. The plates were incubated for 48 h under standard culture conditions, after which they were harvested to obtain cell pellets.


title: Human PDAC Suit2-007 cells  lung tissue (lung 1)

description:
Chip arary data raw_ in vivo_in vitro
Lung 1(2016_01277)_200665010008_B.mean


title: WGBS of Sus scrofa: skeletal muscle at D30, replicate1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A1_AD006_indexed


title: Human PDAC Suit2-007 cells (Untreated) rep1

description:
untreated
PDAC adherent tumor cells
Sample 1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A2_AD002_indexed


title: Human PDAC Suit2-007 cells (Untreated) rep2

description:
untreated
PDAC adherent tumor cells
Sample 2


title: WGBS of Sus scrofa: skeletal muscle at D40, replicate1


title: Late-passage#1

value: adipose-derived human mesenchymal stem cell


title: Human PDAC Suit2-007 cells (Rpx treated) rep3

description:
Rpx treated
PDAC adherent tumor cells
Sample 6


title: Human PDAC Suit2-007 cells (Untreated) rep3

description:
untreated
PDAC adherent tumor cells
Sample 3


title: TEX_MTCH2_KD_C2_2

city: Toronto

first: Aaron

last: Schimmer

address: 610 University avenue

institute: University Health Network

data_processing:
Reads adapters were removed using Trim Galore v. 0.4.0 and reads were aligned against hg19 using Tophat v. 2.0.11. Read counts per gene were obtained through htseq-count v.0.6.1p2 in the mode “intersection_nonempty”.
After removing genes whose cpm (counts per million reads) were less than 0.5, edgeR R package v.3.8.6 was used to normalize the data using the TMM (trimmed mean of M values) method and to estimate differential expression by applying a generalized linear model between the control TEX samples and the TEX cells isolated after MTCH2 knockdown.
Raw gene counts are loaded and sample-normalized using DESeq v.1.18.0
False Discovery Rate, calculated by Benjamini-Hochberg method (useful for hits selection)
Two-condition differential expression was done with the edgeR R package, v.3.8.6
Genome_build: hg19 (RefSeq gene models)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: TEX cell line

growth_protocol: TEX leukemic cells were cultured in IMDM with 20% FCS, 100  units/mL streptomycin, 100 µg/mL penicillin, 20 ng/mL stem cell factor (SCF), 2 ng/mL  IL-3, and 2 mM L-glutamine.

extract_protocol:
RNeasy Plus Mini Kit. Quality of total RNA samples were checked on an Agilent Bioanalyzer 2100 RNA Nano chip following Agilent Technologies’ recommendation. Concentration was measured by Qubit RNA HS Assay ona Qubit fluorometer (ThermoFisher)
RNA library preparation was performed following the NEB NEBNext Ultra Directional Library Preparation protocol

treatment_protocol: shRNA knockdown was performed with lentiviral infections. 2 mL of virus was added to 5 mL of media containing 5.0 x 106 cells and protamine sulfate (5 µg/mL) followed by overnight incubation (37C, 5% CO2). The following day, cells were centrifuged and washed, and re-suspended in 25 mL fresh medium with appropriate puromycin concentration (2.0 ug/ml) and subjected to selection for 3 days.

value: Engineered leukemic stem cell line

value: Blood

tag: genetic modification

value: MTCH2 shRNA


title: Human PDAC Suit2-007 cells from pancreas tissue (pancreas 1b)

description:
Chip arary data raw_ in vivo_in vitro
Pancreas (2016_00918)_200665010008_A.mean

value: orthotopic


title: siDGCR8#2

description: SAMPLE 5

tag: transfection

value: siDGCR8 transfected 7 days


title: Human PDAC Suit2-007 cells (Rpx treated) rep1

description:
Rpx treated
PDAC adherent tumor cells
Sample 4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A11_AD012_indexed

institute: HHMI-Salk-Institute

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56


title: TEX_MTCH2_KD_C2_1


title: BR1_Input_E2


title: WGBS of Sus scrofa: skeletal muscle at D20, replicate2

value: Landrance


title: siDGCR8#1

description: SAMPLE 4


title: WGBS of Sus scrofa: skeletal muscle at D20, replicate1


title: TEX_MTCH2_KD_C1_1


title: TEX_MTCH2_KD_C1_2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A11_AD010_indexed


title: siDGCR8#3

description: SAMPLE 6


title: WGBS of Sus scrofa: skeletal muscle at D20, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A2_AD006_indexed


title: siControl#3

description: SAMPLE 3

value: siControl


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A11_AD006_indexed


title: TEX_GFP_Control_1

value: Scrambled shRNA


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A11_AD004_indexed


title: TEX_No_virus_2

value: Wild-type


title: WGBS of Sus scrofa: skeletal muscle at D9, replicate1


title: WGBS of Sus scrofa: skeletal muscle at D9, replicate2


title: WGBS of Sus scrofa: skeletal muscle at D0, replicate3


title: TEX_No_virus_1


title: siControl#1

description: SAMPLE 1


title: WGBS of Sus scrofa: skeletal muscle at D0, replicate2


title: WGBS of Sus scrofa: skeletal muscle at D9, replicate3


title: siControl#2

description: SAMPLE 2


title: Cell_line_SiHa_5hyp

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

data_processing: The data were normalised using quantile normalization in BeadStudio 3.1.3.0

source_name: Cervical cancer cell line, 5% O2, hyp

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: The cells were incubated in Dulbecco's Modified Eagle medium with GlutaMAX supplemented with 10% fetal calf serum (FCS) and 100 U/ml penicillin/streptomycin (Gibco) under a 5% CO2 atmosphere at 37°C, and subcultured twice a week.

extract_protocol: RNA was extracted using miRNeasy MiniKit (Quiagen), according to the manufacturers’ instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were seeded (1.5x10^6 cells for HeLa, 1.7x10^6 cells for SiHa) in 10 cm plastic dishes 24 hours before exposure to hypoxia at 0.2%, 0.5% 1%, 2% and 5% O2 for 24 hours at 37⁰C, all with 5% CO2, by using an Invivo2200 chamber (Ruskinn Technology Ltd) with accurate O2 and CO2 controls. Normoxic controls (95% air , 5% CO2) were included for all hypoxia experiments.

value: SiHa

tag: histology

value: squamous cell carcinoma

value: Exposed to hypoxic condition (5% O2, 5% CO2) for 24 h at 37C


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A11_AD002_indexed

city: La Jolla

value: male


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A11_AD007_indexed


title: RNAseq_N2_15hr

city: Basel

first: Helge

last: Grosshans

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedriche Miescher Institute for Biomedical Research (FMI)

data_processing:
RNA-seq data were mapped to the C. elegans ce10 genome using the qAlign function (splicedAlignment=TRUE) from the QuasR package in R
Gene expression was quantified using qCount function from the QuasR package in R
Counts were scaled by total mapped library size for each sample
A pseudocount of 8 was added and counts were log2-transformed
Genome_build: ce10
Supplementary_files_format_and_content: Tab-separated: First column contains gene names (Wormbase identifiers), second column contains summed width of exons per gene, following columns contain raw counts of reads overlapping each gene for each sample.

source_name: synchronized population

growth_protocol: a population of L1 synchronized by egg prep and M9 incubation was grown on OP50 containing agar plates at room temperature. Worms were collected hourly by washing of worms with M9 and washing 3 times in M9.

extract_protocol:
RNA was extracted using Trizol and conventional Phenol / Chlorophorm extraction.
Illumina TruSeq mRNA-Seq Sample Prep Kit (Stranded - high input), followed by the Hiseq50 Cycle Single-end reads on HiSeq2500 protocol

tag: timepoint

value: L1 arrested C. elegans larvae


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A10_AD012_indexed


title: TEX_GFP_Control_2


title: WGBS of Sus scrofa: skeletal muscle at E105, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A10_AD010_indexed


title: WGBS of Sus scrofa: skeletal muscle at E105, replicate2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A11_AD008_indexed


title: RNAseq_N2_13hr


title: WGBS of Sus scrofa: skeletal muscle at E105, replicate1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A10_AD008_indexed


title: Cell_line_SiHa_5ctrl

source_name: Cervical cancer cell line, 5% O2, ctrl

tag: treatment

value: Exposed to normoxic (control) condition (95% air , 5% CO2) for 24 h at 37C


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A10_AD006_indexed

value: MOp


title: Cell_line_SiHa_2ctrl

source_name: Cervical cancer cell line, 2% O2, ctrl


title: WGBS of Sus scrofa: skeletal muscle at E100, replicate3


title: RNAseq_N2_16hr


title: Cell_line_SiHa_1hyp

source_name: Cervical cancer cell line, 1% O2, hyp

value: Exposed to hypoxic condition (1% O2, 5% CO2) for 24 h at 37C


title: Cell_line_SiHa_1ctrl

source_name: Cervical cancer cell line, 1% O2, ctrl


title: WGBS of Sus scrofa: skeletal muscle at D0, replicate1