title: water_water_rep2_array11.4

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

description: Raw Data: Cy3: 257111410011_Arabido_SB_scan_2016-04-22_GE2_1105_Oct12_1_4.txt

hyb_protocol: The hybridization performed on a rotative Agilent Hybridization Oven, 17h at 65°C, 10g. Afterwards, the slide were washed, and scanned.

scan_protocol: Scanning was performed on 2µm NimbleGen MS 200 scanner

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

organism: Arabidopsis thaliana

label_protocol: Amplification and labbeling were performed with MessageAmp™ II aRNA Amplification Kit (Ambion) with Cy5/Cy3 labels

growth_protocol: Plant material used was wild-type Arabidopsis thaliana L. Heynh cultivar 6 Columbia (Col-0). All Arabidopsis plants were grown under long day condition (photoperiod of 16h light at 22°C/ 8h light at 22°C, with 60% relative humidity).

extract_protocol: The RNA was extracted using the NucleoSpin RNA plant extraction kit (Machery-Nagel Hoerdt, France) according the manufacturer`s recommendations.

treatment_protocol: Four Arabidopsis plants represent one biological replicate. Plants were treated with  BTH by spraying with final concentrations of 1mM. Plants were treated the first time 7 days after germination and the second time 10 days after germination. RNA was extracted 21 days after germination.

tag: tissus

value: Four whole plants (leaves)

tag: genetic background

value: wild type

tag: age

value: 21 days after germination

tag: growth protocol

value: long day

tag: harvest date

value: january 2016


title: Pitts_1_Ginkgo_2

status: Public on Dec 04 2018

type: RNA

city: Mainz

first: Jens

last: Marquardt

address: Langenbeckstraße 1

department: Department of Medicine I

country: Germany

institute: Johannes Gutenberg University Mainz

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array normalization was performed with Illumina Genome Studio Gene Expression module xxx using quantile normalisation.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Standard Illumina scanning protocol

growth_protocol: Human hepatoma cell lines WRL68, Huh7, immortalized human hepatocyte cell line THLE5B and primary human HCC cells, Pitts1, have been cultured in DMEM, supplemented with 2mM L-glutamine, 1unit/ml penicillin/streptomycin, and 10% FCS at 37°C and 5% CO2.

extract_protocol: Total RNAs was extracted using Qiagen RNEasy mini Kit (Qiagen GmBH, Hilden, Germany) following the manufacturer’s protocol. RNA quantity and purity were estimated using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and integrity was assessed by Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: Cells were treated for 72hours with Ginkgo biloba extract (EGb761) at various concentration in dose-finding experiments (50 to 1000μg/ml) and with the inhibitory concentration 50 for each of the hepatoma cell lines (IC50Huh7=252,7μg/ml; IC50WRL68=156,0μg/ml; IC50Pitts1=191,6μg/ml) and THLE5B were treated with median IC50 (200 μg/ml) of all hepatoma cells for functional analyses.

tag: treatment


title: water_water_rep1_array11.3

country: France

description: Raw Data: Cy5 : 257111410011_Arabido_SB_scan_2016-04-22_GE2_1105_Oct12_1_3.txt

source_name: Arabidopsis thaliana L. Heynh cultivar 6 Columbia (Col-0)

tag: genotype

tag: phenotype


title: bion_flg22_rep2_array11.4

description: Raw Data: Cy5 : 257111410011_Arabido_SB_scan_2016-04-22_GE2_1105_Oct12_1_4.txt

value: Arabidopsis thaliana L. Heynh cultivar 6 Columbia (Col-0)


title: Pitts_1_Ginkgo_3


title: bion_flg22_rep1_array9.3

description: Raw Data: Cy3: 257111410009_Arabido009_scan_2016-01-19_532_635_GE2_1105_Oct12_1_3.txt


title: bion_flg22_rep1_array11.3

description: Raw Data: Cy3: 257111410011_Arabido_SB_scan_2016-04-22_GE2_1105_Oct12_1_3.txt


title: Pitts_1_Ginkgo_1


title: HET.10.3_Glomeruli_S3

type: SRA

city: Parkville

first: Andrew

last: Lonsdale

state: VIC

address: 50 Flemington Rd

country: Australia

institute: Murdoch Children's Research Institute

library_source: transcriptomic

data_processing:
Fastq files were generated using the bcl to fastQ converter 2.17.
Transcript level counts were estimated using Salmon v0.8.2, using the ENSEMBL GRCh38 version of the human transcriptome.
Transcript level counts were converted to gene level counts using the Bioconductor R package tximport v1.3.13.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files with ensemble gene id and the averaged gene length across all 9 samples (salmon-counts-timecourse.txt) and 6 samples (salmon-counts.txt) in the first two columns, followed by 9 columns (salmon-counts-timecourse.txt) and 6 columns (salmon-counts.txt) containing counts for each sample

source_name: Day 17 kidney organoid derived glomeruli, MAFB-BFP heterozygous

extract_protocol:
RNA were extracted using QIAGEN RNeasy micro kit.
TruSeq stranded total RNA with RiboZero rRNA depletion

tag: cell type

tag: clone

value: human iPSC line CRL 2431

value: MAFB +/-


title: MNase_M_0.5_2

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

institute: Institut Pasteur

description: processed data file: mnase_atac_meta_plot_library.tsv.gz

library_source: genomic

data_processing:
ChIP-seq: Reads aligned with Bowtie2 with options “-k 10”. Reads were filtered for mapping quality 255 and edit distance <= 4. Reads with identical barcode, alignment position & strand  were treated as PCR-duplicates and collapsed. Peaks called with MACS2 with options “callpeak -q 0.2 -g mm”. BigWig files were generated by extending reads to mean fragment length.
Mnase-seq & ATAC-seq:  Paired end reads were trimmed by alignment for reverse complementary regions surrounded by relevant adapters. Reads were aligned using Bowtie2 with options “-k 10 -I 0 -X 1000 --no-discordant --no-mixed”. Pairs were filtered for mapping quality 255 and mean edit-distance <= 4.
RNA-seq: Stranded Reads pairs were aligned to the mm9 genome using RSEM-STAR pipeline with options “--seed 1618 --calc-pme --calc-ci --estimate-rspd --forward-prob 0.0 –paired-end”.
MNase/ATAC-seq Meta Plot Library: Mid-points of MNase-fragments (140-200 bp), cut sites of ATAC-seq fragments (0-100 bp), counted at base pair resolution and normalised per million reads, in +/- 1000bp of TSS, EP300 summits, Esrrb Bookmarked Sites, Esrrb Lost Sites and Oct4/Sox2 sites. Mid-point/cutsite data smoothed by sparse Gaussian process regression using Gpy.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: BigWig files, MNase-seq/ATAC-seq: Library of meta-plots in tab-separated format; RNA-seq: Raw and normalised read-counts tab-separated format.

molecule: genomic DNA

organism: Mus musculus

growth_protocol: ES cells were cultured on 0.1% gelatine in DMEM + GlutaMax-I (Gibco, Cat# 31966-021) 10% FCS, 100 μM 2-mercaptoethanol, 1× MEM non-essential amino acids, and 10 ng×ml−1 recombinant LIF (MILTENYI BIOTEC, Cat# 130-099-895). When required medium was supplemented with 1 µM PD0325901 and 3 µM CHIR99021 (Axon Medchem Bv).

extract_protocol:
ATAC-Seq: 5x104 cells pellets were resuspended in 25 µl TD buffer (Nextera kit; Illumina, Cat# FC-121-1030). After the addition of 2.5 µl of transposase TDE1 and 22.5 µl nuclease free water, reactions were mixed and incubated for 30min at 37oC. Reactions were stopped by adding the appropriate volume of Binding Buffer and the DNA was purified using the Qiagen MinElute PCR Kit according to manufacturer’s protocol. The purified DNA was either stored at -20oC or used directly for library preparation.
ATAC-seq: Reactions were prepared mixing 10 µl transposed DNA, 2.5 µl 25 µM primer Ad1.noMX, 2.5 µl 25 µM primer Ad2 from (Buenrostro et al. 2013), 9 µl Nuclease Free Water, 1 µl of a 1:8 dilution of Quant-iT Picogreen dye (Invitrogen, Cat# P11496) and 25µl of KAPA HiFi HotStart 2× Master Mix (Kapa Bioscience Cat# KK2502). Amplification was carried out under the following conditions: Pre-amplification: 1 cycle: 5’ at 72°C; 30” at 98°C; 5 cycles: 10” at 98°C; 30” at 63°C; 1’ at 72°C; Amplification: 1 cycle: 30” at 98°C; 11/12 cycles: 10” at 98°C; 30” at 63°C; 1’ at 72°C. After amplification libraries were purified with SPRI beads, using a sample to bead ratio of 1: 1.4.
Cell-cycle RNA-seq: ES cells were sorted on the basis of Hoechst and GFP levels in three populations (early G1, late G1 and G2) as previously described (Festuccia et al. 2016). RNA was extracted with TRIzol (ThermoFisher, Cat# 15596026). Samples were DNAse I treated (Qiagen, Cat# 79254), phenol/chloroform extracted and ethanol precipitated.
ChIP-seq and MNase-seq: Precipitated DNA was resuspended in 37.5µl of water and mixed with 2µl of 10mM dNTPs, 5µl of NEB T4 ligase buffer, 2.5µl of NEB T4 polymerase (Cat# M0203L), 0.5µl of NEB Klenow polymerase (Cat# M0210L) and 2.5µl of NEB T4 PNK (Cat# M0201L). Samples were incubated 30min at 20oC. DNA was purified with 90µl of SPRI beads and 50µl isopropanol and eluted in 21µl of water. DNA was mixed with 2.5µl of NEB Buffer #2, 1µl of 5mM dATP, 1.5µl of NEB Klenow 3'-5' exo minus (Cat# M0212L), and incubated at 37oC for 30min. DNA was purified with SPRI beads as before, but using a volume of 45µl of beads and 25µl isopropanol. DNA was elute in 20µl of water and mixed with 2.5µl of NEB T4 ligase buffer, 1.25µl of a 0.2µM solution of annealed adapters (See below), and 2.5µl of NEB concentrated T4 ligase (Cat# M0202M) and incubated overnight at 16oC. DNA was purified with SPRI beads as before, but using a volume of 35µl of beads and no isopropanol, eluting in 20 µl of water. Sample were mixed with 1µl of a 1:10 dilution of Quant-iT Picogreen dye (Invitrogen, Cat# P11496), 25µl of KAPA HiFi HotStart 2× master Mix (Kapa Bioscience Cat# KK2502), 1µl of 10µM PCR 1.0 and 1µl of PCR 2.0 Illumina primers. The amplification mix was distributed in two wells of a LightCycler 384 plate (Roche, Cat# 4729749001) and on a LightCycler 480 II instrument (Roche, Cat# 05015243001) using the following program: 1’ at 98°C; N cycles: 10” at 98°C; 20” at 64°C; 45” at 72°C. The number of cycles N was determined on real time by monitoring the fluorescence such that the amplification was stopped during the exponential phase. Samples were removed from the plate and purified with SPRI beads using 70µl beads, no isopropanol, and eluting in water. Barcoded adaptor: 5’P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-IIIIII-NNNNNNNN-ATCTCGTATGCCGTCTTCTGCTTG. 5’P indicates the presence of a 5’phosphate group. IIIIII represent the six base index nucleotides, and NNNNNNNN a stretch of 8 random nucleotides used for single molecule barcoding. Universal adapter: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T. * indicates the presence of a phosphorothioate bond between the last C and T.
ChIP-seq/Mnase-seq Chromatin preparation: Interphase cells were resuspended in 2 ml of swelling buffer (25 mM Hepes pH 7.95, 10 mM KCl, 10 mM EDTA) and 0.5% IGEPAL. After 30 min on ice, the suspension was passed 40 times in a dounce homogenizer. Both mitotic and interphase cells were resuspended in 300 μl of TSE150 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH8, 150 mM NaCl) buffer, freshly supplemented with 1× PIC. Samples were sonicated in 1.5 ml tubes (Diagenode) using a Bioruptor Pico (Diagenode) for 7 cycles divided into 30 s ON–30 s OFF sub-cycles at maximum power. After centrifugation (30 min, full speed, 4 °C), the supernatant was either used immediately for immunoprecipitation or stored at −80 °C until use.
ChIP-seq: Chromatin was pre-cleared for 3 hours rotating on-wheel at 4 °C in 300 μl of TSE150 containing 50 μl of protein G Sepharose beads 50% slurry, previously blocked with BSA and yeast tRNA. Immunoprecipitations with anti-ESRRB mouse monoclonal (1µg per 2x106cells, 5 μg per 107 cells; Perseus Proteomics, Cat# H6-705-00), anti-NANOG rabbit polyclonal (0.6 μg per 2x106cells, 3 μg per 107 cells; Cosmobio, Cat#  REC-RCAB001P); anti-POU5F1 goat polyclonal (0.6 μg per 2x106cells, 3 μg per 107 cells; Santa Cruz Biotechnology, Cat # sc-5279); anti-SOX2 goat polyclonal (0.6 μg per 2x106cells, 3 μg per 107 cells; Santa Cruz Biotechnology, Cat # sc- 17320), were performed overnight rotating on-wheel at 4 °C in 500 μl of TSE150. Twenty-five microliters of blocked protein G beads 50% slurry was added for 4 h rotating on-wheel at 4 °C. Beads were pelleted and washed for 5 min rotating on-wheel at room temperature with 1 ml of buffer in the following order: 3 × TSE150, 1 × TSE500 (as TSE150 but 500 mM NaCl), 1× washing buffer (10 mM Tris-HCl pH8, 0.25M LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1 mM EDTA), and 2 × TE (10 mM Tris-HCl pH8, 1 mM EDTA). Elution was performed in 100 μl of elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8) for 15 min at 65 °C after vigorous vortexing. Eluates were collected after centrifugation and beads rinsed in 150 μl of TE-SDS1%. After centrifugation, the supernatant was pooled with the corresponding first eluate. For both immunoprecipitated and input chromatin, the crosslinking was reversed overnight at 65 °C, followed by proteinase K treatment, phenol/chloroform extraction and ethanol precipitation.
Chip-seq: Fixation DSG+FA.  ES cells were crosslinked in PBS-DSG 2 mM at pH 7.0 (Sigma, Cat# 80424-5 mg) for 50 min at room temperature with occasional shaking and incubated for 10 min in 2 ml PBS 1% formaldehyde after washing in PBS. Crosslinking was stopped with 0.125 mM glycine for 5 min at room temperature. Fixation FA: ES cells crosslinked in 3 ml of pre-warmed DMEM/FCS/LIF for 10 min at room temperature adding 1% formaldehyde (Thermo, Cat# 28908). Crosslinking was stopped with 0.125 M glycine for 5 min at room temperature.
H3 ChIP-seq:  ChIP was performed as described using 5 µg of anti-Histone H3 rabbit polyclonal (Abcam, Cat# ab1791).
MNase-seq: Cells fixed in formaldehyde as for ChIP were pre-incubated for 10 min at 37°C and ½ U, 16 U or 128 U of MNase (Expressed in KUntiz, 1 Kunitz is equivalent to 10 gel units, NEB Cat# M0247S) added to the reaction. Cells were incubated for further 10 min at 37°C, inverting the tubes occasionally. The reaction was stopped on ice by adding 500ul of 2 × STOP buffer (2% Triton X-100, 0.2% SDS, 300mM NaCl, 10mM EDTA). Tubes were left rotating overnight on a wheel to allow diffusion of the digested fragments. The cell suspension was spun down and the supernatant stored at -80°C. Samples were then incubated over night at 65°C in TE 1% SDS to revert the crosslinking, and treated with Proteinase K. DNA was phenol/chloroform extracted, ethanol precipitated, and RNase treated. 50 µl of DNA was purified with 90µl of SPRI beads and 50 µl isopropanol.
RNA-seq:Ribo-depleted, stranded and paired-end RNA-seq libraries were prepared and sequenced by Novogene Co Ltd.

treatment_protocol:
ChIP-seq and MNase-seq: E14tg2a cells grown in T150 flasks were treated for 4-5 h with 50 ng×ml−1 nocodazole. Shake-off was performed and the cell suspension was filtered through a 10µm filter (pluriSelect, Cat# 43-50010-03). For interphase samples, untreated cells were trypsinised and collected in parallel.
Cell-cycle RNA-seq: GFP Sox2-AID ES cells were cultured in the presence of 0.5mM of auxin (Sigma, Cat# I5148) for 3 hours. During the last 20 minutes 20μM Hoechst-33342 was added.

tag: cell line

value: embryonic stem cells

tag: mnase concentration

tag: cellcycle

value: M

tag: barcode


title: bion_flg22_rep2_array9.4

description: Raw Data: Cy5 : 257111410009_Arabido009_scan_2016-01-19_532_635_GE2_1105_Oct12_1_4.txt


title: WRL68_1_Ginkgo_1


title: water_flg22_rep1_array9.3

description: Raw Data: Cy5 : 257111410009_Arabido009_scan_2016-01-19_532_635_GE2_1105_Oct12_1_3.txt


title: HET.10.2_Glomeruli_S2

value: Day 17 kidney organoid derived glomeruli, MAFB-BFP heterozygous

value: human iPSC line CRL 2430


title: MNase_M_0.5_1


title: water_flg22_rep2_array9.4

description: Raw Data: Cy3: 257111410009_Arabido009_scan_2016-01-19_532_635_GE2_1105_Oct12_1_4.txt


title: MNase_A_128_3

value: I


title: HET.10.1_Glomeruli_S1

value: human iPSC line CRL 2429


title: MNase_M_0.5_3


title: MNase_A_16_3


title: WRL68 1_untreated_3


title: bion_water_rep2_array9.2

description: Raw Data: Cy5 : 257111410009_Arabido009_scan_2016-01-19_532_635_GE2_1105_Oct12_1_2.txt


title: WRL68 1_untreated_2


title: MNase_A_128_2


title: Pitts_1_untreated_3


title: MNase_A_16_2


title: Pitts_1_untreated_2


title: MNase_A_16_1


title: MNase_A_128_1


title: Pitts_1_untreated_1


title: bion_flg22_rep2_array8.4

description: Raw Data: Cy5 : 257111410008_Arabido008_scan_Area1_532_635_GE2_1105_Oct12_1_4.txt


title: bion_water_rep1_array9.1

description: Raw Data: Cy3: 257111410009_Arabido009_scan_2016-01-19_532_635_GE2_1105_Oct12_1_1.txt


title: water_water_rep2_array9.2

description: Raw Data: Cy3: 257111410009_Arabido009_scan_2016-01-19_532_635_GE2_1105_Oct12_1_2.txt


title: MNase_A_0.5_3


title: bion_water_rep2_array8.4

description: Raw Data: Cy3: 257111410008_Arabido008_scan_Area1_532_635_GE2_1105_Oct12_1_4.txt


title: MNase_A_0.5_2


title: bion_flg22_rep1_array8.3

description: Raw Data: Cy3: 257111410008_Arabido008_scan_Area1_532_635_GE2_1105_Oct12_1_3.txt


title: water_water_rep1_array9.1

description: Raw Data: Cy5 : 257111410009_Arabido009_scan_2016-01-19_532_635_GE2_1105_Oct12_1_1.txt


title: WRL68 1_untreated_1


title: K+5

city: Rio de Janeiro

first: Mariana

middle: S

last: Silveira

state: Rio Janeiro

address: Av. Carlos Chagas Filho, 373. Ilha do Fundão., Centro de Ciências da Saúde, Bloco G, sala G2-004/019

department: Neurobiology

country: Brazil

institute: Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro

description: Gene expression after 39 hour after electroporation with plasmid encoding KLf4

hyb_protocol: Agilent Standard Protocol

scan_protocol: AgilentHD_GX_1Color (Green, 5um, 20bit, noXDR)

data_processing: Statistical analyses of the raw data were performed in the GeneSpring 13.0 program. Quantile normalization. No baseline transformation.

organism: Rattus norvegicus

source_name: Klf4-overexpressing retinal cells sorted 39 hours after electroporation

label_protocol: Agilent Standard Protocol

extract_protocol: Retinal explants cultured for 39 hours after in vitro electroporation were dissociated by incubation with 0.05 mg/mL trypsin and 0.1 mg/mL DNAse and by mechanical homogenization at 37°C for 15 minutes. Dissociated cells were filtered using Cell Strainer 70 μm (Falcon). Transfected (GFP positive cells) were separated from non-transfected cells (GFP negative cells) through FACS. The sorted cells were lysed with Trizol (Invitrogen) and RNA was extracted with a Trizol-Rneasy micro kit (Qiagen) hybrid protocol.

treatment_protocol: P0 Lister hooded rat retinas were dissected and transferred to an electroporation chamber filled with DNA solution in Hanks' balanced salt solution. Five 25V square pulses were delivered for 50 ms with 950 ms intervals. Electroporated retinas were cultured at 37°C in erlenmeyers under orbital agitation.

tag: tissue

value: Retina

value: Postnatal Day 0 + 39 hours in vitro


title: K+2

value: 39 hour after electroporation with plasmid encoding KLf4


title: K+3


title: D. santomea_stage5_replicate3

city: Davis

first: Susan

middle: E.

last: Lott

state: CA

address: 2320 Storer Hall

department: Evolution and Ecoloty

country: USA

institute: University of California, Davis

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta dyak-all-chromosome-r1.3.fa
annotation file used: dyak-all-r1.3.gff
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

molecule: polyA RNA

organism: Drosophila santomea

source_name: single embryo

growth_protocol: All species were maintained on molasses food in uncrowded conditions

extract_protocol:
TRIzol reagent extraction of total RNA from single embryos.
Libraries were constructed using Illumina Tru-Seq kits and indices

treatment_protocol: Eggs were collected from vials, and imaged to determine stage

tag: embryonic stage

value: stage 5

tag: replicate number

value: replicate 3

tag: raw data mixed with d. melanogaster?

value: yes


title: water_water_rep2_array8.2

description: Raw Data: Cy3: 257111410008_Arabido008_scan_Area1_532_635_GE2_1105_Oct12_1_2.txt

tag: tissus

value: Four whole plants (leaves)

tag: genetic background

value: wild type

value: 21 days after germination

value: long day


title: bion_water_rep1_array8.3

description: Raw Data: Cy5 : 257111410008_Arabido008_scan_Area1_532_635_GE2_1105_Oct12_1_3.txt

value: Arabidopsis thaliana L. Heynh cultivar 6 Columbia (Col-0)

tag: age

tag: growth protocol

value: january 2016


title: water_flg22_rep2_array8.2

description: Raw Data: Cy5 : 257111410008_Arabido008_scan_Area1_532_635_GE2_1105_Oct12_1_2.txt

tag: treatment

tag: harvest date


title: C+5

description: Gene expression after 39 hour after electroporation with control plasmid

source_name: Control retinal cells sorted 39 hours after electroporation


title: MNase_A_0.5_1

value: embryonic stem cells


title: K+4


title: D. santomea_stage5_replicate2

value: replicate 2


title: tcfgrna18h1

city: New York

first: wei

last: wang

state: NY

address: 100 washington square east

department: Biology

institute: New York University

data_processing:
reads mapping using TopHat 2.0.12
Reads count was performed using "featureCounts" functions in Rsubread1.28.1 with KH gene models (ver.2013, http://ghost.zool.kyoto-u.ac.jp/datas/KH.KHGene.2013.gff3.zip) with default parameters.
Genome_build: Ciona genome (Joined-scaffold (KH), http://ghost.zool.kyotou.ac.jp/datas/JoinedScaffold.zip)
Supplementary_files_format_and_content: gene expression read counts matrices

organism: Ciona robusta

source_name: Trunk ventral cells

extract_protocol:
200 to 800 cells were directly sorted in 100µl lysis buffer included in RNAqueous®-Micro Total RNA Isolation Kit (Ambion). The total RNA extraction was performed following the manufacturer’s instruction.
250-2000 pg of total RNA was loaded as template for cDNA synthesis using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) with template switching technology. RNA-Seq Libraries were prepared and barcoded using Ovation® Ultralow System V2 1–16 (NuGen).
Bulk RNAseq

value: Multipotent cardiopharyngeal progenitor cells


title: tcfgrna18h2


title: water_flg22_rep1_array8.1

description: Raw Data: Cy3: 257111410008_Arabido008_scan_Area1_532_635_GE2_1105_Oct12_1_1.txt

tag: genotype

tag: phenotype


title: water_water_rep1_array8.1

description: Raw Data: Cy5 : 257111410008_Arabido008_scan_Area1_532_635_GE2_1105_Oct12_1_1.txt


title: tcfgrna15h2

tag: cell type


title: HET.14.1_Glomeruli_S4

source_name: Day 21 kidney organoid derived glomeruli, MAFB-BFP heterozygous

tag: clone

value: human iPSC line CRL 2432

value: MAFB +/-


title: D. santomea_stage5_replicate1

value: replicate 1


title: tcfgrna15h1


title: D. persimilis_stage5_replicate4

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta dper-all-chromosome-r1.3.fa
annotation file used: dper-all-r1.3.gff
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

organism: Drosophila persimilis

value: replicate 4


title: D. santomea_stage2_replicate2

value: stage 2


title: D. persimilis_stage5_replicate5

value: stage 5

value: replicate 5


title: D. santomea_stage2_replicate3

value: replicate 3

value: yes


title: C+3

value: Retina

value: Postnatal Day 0 + 39 hours in vitro

value: 39 hour after electroporation with control plasmid


title: D. persimilis_stage5_replicate3


title: controlgrna18hpf2


title: D. santomea_stage2_replicate1


title: C+2


title: controlgrna18hpf1


title: controlgrna15hpf2


title: D. persimilis_stage5_replicate2


title: D. persimilis_stage5_replicate1


title: controlgrna15hpf1


title: D. persimilis_stage2_replicate6

value: replicate 6


title: rad53 mutant 0.5 kGy sample_2

city: Jeongeup

first: Kwang-Woo

last: Jung

address: 29 Geumgu-gil

country: South Korea

institute: Korea Atomic Energy Research Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Trimmomatic v0.32 with adapter seq of TruSeq3-PE.fa and MINLEN:36.
Expected count and deg analysis were conducted using RSEM (v1.2.24) with bowtie2 v2.2.3 and EdgeR v3.8.6 respectively.
Genome_build: BROAD institute : Cryptococcus neoformans var. grubii H99
Supplementary_files_format_and_content: Tab-delimited text files include FPKM and expected counts for each Sample

organism: Cryptococcus neoformans

source_name: rad53 mutant 0.5 kGy sample

growth_protocol: Strains were grown in a 40 ml liquid YPD medium for 16 hr at 30℃. Then, overnight culture was inoculated into 100 ml fresh YPD medium and adjusted to OD600=0.2. The cells were further incubated until OD600 reached approximately 0.6. Fifty ml of cells were pelleted for the zero-time sample and the remaining cells were exposed to γ-radiation (0.5 kGy). After γ-radiation exposure, cells were further incubated at 30℃ for 30 mins.

extract_protocol:
1. Freeze cells in Liquid Nitrogen for 30min. 2. Lyophilize samples overnight. 3. Add 3ml of 3mm glass beads and vortex vigorously until fine powder is created. 4. Add 4ml of Easyblue (dissolve powder completely) and let them sit 5 minutes. 5. Add 800 ul of chloroform (invert 10 times). 6. Let them sit 3 minutes and transfer to 14 ml round bottle tubes. 7. Spin at 10,000 rpm for 15 minutes. 8. Transfer supernatant to new round-bottom tubes. 9. Add 2 ml of isopropanol and capping and gently invert. 10. Store for 5-10 minutes at room temperaturea. 11. Spin for 10 minutes at 10,000 rpm. 12. Pour off supernatant. 13. Add 4 ml of 75% EtOH (made with DEPC dH2O) and invert 4-5 times. 14. Spin for 5 minutes at 8,000 rpm. 15. Pour off EtOH (Let tubes air-dry upside down). 16. Resuspend in appropriate volume of DEPC dH2O. 17. Heat at 55℃ for 10 minutes. 18. Transfer RNA to microtube and mesuring the concentration. 19. For purification of the extracted total RNA, we used Rneasy spin column (Qiagen) following the manufacturer’s protocol.
The library was prepared using the Illumina TruSeq stranded mRNA prep kit.

tag: strain background

tag: genotype/variation

value: rad53 mutant

tag: exposesd to

value: γ-radiation (0.5 kGy)


title: C+4

tag: tissue


title: rad53 mutant 0.5 kGy sample_1

treatment_protocol: Fifty ml of cells were pelleted for the zero-time sample and the remaining cells were exposed to γ-radiation (0.5 kGy). After γ-radiation exposure, cells were further incubated at 30℃ for 30 mins.


title: D. persimilis_stage2_replicate5

tag: embryonic stage


title: rad53 mutant 0 kGy sample_2

source_name: rad53 mutant 0 kGy sample


title: D. persimilis_stage2_replicate3

tag: replicate number


title: rad53 mutant 0 kGy sample_1


title: H99 0.5 kGy sample_2

source_name: H99 0.5 kGy sample

value: wild type


title: D. persimilis_stage2_replicate4

tag: raw data mixed with d. melanogaster?


title: D. persimilis_stage2_replicate2

value: replicate 2


title: BF1_Cy5_5.1: bion_flg22_rep1_array5.1

description: Raw Data: Cy5: 258527510005_2018-02-27_kay3 GE2_SingleTiff_1_1.txt

scan_protocol: Scanning was performed on 2µm NimbleGen MS 200 Scanner

organism: Malus domestica

source_name: Apple cv. Golden Delicious double haploid (GDDH13)

label_protocol: Labelling was performed with G4140-90050_GeneExpression_TwoColor_6.9 (Agilent) protocol

growth_protocol: Apple cv. Golden Delicious double haploid (GDDH13 described by (Lespinasse, 1998)) in-vitro grown plantlets were propagated on MS based medium with BA 0.25mg/L and IBA 0.1mg/l under short day conditions (photoperiod of 8h light at 22°C/ 16h dark at 21°C).

treatment_protocol: Leaves of 20 apple plantlets represent one biological replicate. Plantlets were treated by dipping the whole plantlet into filter sterilized flg22 (1µM) and/or BTH(1mM) solution and placed on fresh growth medium after every treatment. The first treatment was applied 14 days after propagation and the second treatment 17 days after propagation. The plants were harvested 31 days after propagation

value: leaves

tag: cultivar

value: Wild-Type

value: 31 days after propagation

value: short day

value: March 2018


title: H99 0 kGy sample_2

source_name: H99 0 kGy sample


title: BF2_Cy5_3.4: bion_flg22_rep2_array3.4

description: Raw Data: Cy5: 258527510003_2018-02-22_kay1 GE2_SingleTiff_1_4.txt

value: Golden Delicious double haploid (GDDH13)


title: D. persimilis_stage2_replicate1

value: stage 2

value: replicate 1


title: WW2_Cy5_5.2: water_water_rep2_array5.2

description: Raw Data: Cy5: 258527510005_2018-02-27_kay3 GE2_SingleTiff_1_2.txt

value: Water-water


title: BF1_Cy3_3.3: bion_flg22_rep1_array3.3

description: Raw Data: Cy3: 258527510003_2018-02-22_kay1 GE2_SingleTiff_1_3.txt


title: BW2_Cy3_3.4: bion_water_rep2_array3.4

description: Raw Data: Cy3: 258527510003_2018-02-22_kay1 GE2_SingleTiff_1_4.txt

value: BTH-water


title: BF2_Cy3_5.2: bion_flg22_rep2_array5.2

description: Raw Data: Cy3: 258527510005_2018-02-27_kay3 GE2_SingleTiff_1_2.txt


title: H99 0 kGy sample_1


title: BW1_Cy5_3.3: bion_water_rep1_array3.3

description: Raw Data: Cy5: 258527510003_2018-02-22_kay1 GE2_SingleTiff_1_3.txt


title: UV- control rep2

status: Public on Dec 03 2018

city: Gothenburg

first: Martin

last: Boström

address: Medicinaregatan 9A

country: Sweden

institute: University of Gothenburg

data_processing:
Library strategy: CPD-seq
Alignment with Bowtie 2 version 2.3.1, standard parameters
For UV+ cellular and UV- control, the bam files of rep01 and rep02 were merged using Picard MergeSamFiles version 2.18.7, standard parameters
Duplicates were marked with Picard MarkDuplicates version 2.18.7, with the parameter VALIDATION_STRINGENCY=LENIENT
Non-duplicate R1 reads belonging to proper pairs were imported into R and further processed with Bioconductor packages. The 2 bases upstream and on the opposite strand of each read on R1 were saved as CPDs.
The DNA sequence of each CPD was obtained with the R Bioconductor package BSgenome's getSeq function and non-dipyrimidine "CPDs" were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: Bed. The files contain the positions of all CPDs detected by sequencing, with optical duplicates and non-dipyrimidine "CPDs" removed. Duplicated positions indicate that more than one CPD was detected at that position. Due to the low coverage, we found it easier to work with files with each line representing a CPD, rather than using scores to indicate the number of CPDs at any given position.

source_name: untreated cells

growth_protocol: Cells were grown in DMEM + 10 % FCS + pen/strep

extract_protocol:
Genomic DNA was extracted with QIAgen DNA blood mini kit
CPDs were mapped with a modified CPD seq method (Mao et al 2016). Purified DNA 12 mg was sonicated to 400 bp and size selected with SPRI select beads (Life Technologies) and the purified product (approx. 4 ug) subjected to NEBNext end repair and NEBNext dA-tailing modules (NEB). ARC141/142 was then ligated to the sheared and repaired ends O/N with NEBNext Quick Ligation module. DNA was purified with CleanPCR beads and treated with Terminal Transferase (TdT, NEB) and dideoxy ATP (Roche) for 2h at 37 degrees. DNA was purified and incubated with 30 units T4 endonuclease V (NEB) at 37 degrees for 2 h, followed by purification and treatment with APE1 (NEB) at 37 degrees for 1.5 hr. DNA was purified and treated with rSAP (NEB) 37 degrees 1 hr followed by deactivation at 65 degrees for 15 minutes. DNA was purified, denatured at 95 degrees for 5 min, cooled on ice and ligated with the biotin-tagged “ARC double” overnight at 16 degrees with NEBNext quick ligation module. DNA fragments with the biotin tag were captured with Streptavidin Dynabeads (Invitrogen) and the DNA strand without the biotin label was released with 0.15 M NaOH.  This single stranded DNA was used as the template to synthesise double stranded products using ARC153. The now double stranded library was purified and amplified with ARC140 and ARC78-82 to add Illumina barcodes and indexes.

tag: cell line

tag: cancer type

value: malignant melonoma


title: UV+ naked

source_name: naked DNA treated with 1000 J/m2 UVC


title: FSHD1.2

city: Leiden

first: Anita

last: van den Heuvel

state: Zuid-Holland

address: Einthovenweg 20, Postbus 9600, 2300 RC Leiden

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Sequenced data was analyzed using the 10x Genomics software, Cell Ranger analysis pipeline version 1.2.0 (default settings)
Reads were aligned to the Genome Reference Consortium Human Build 38 (GRCh38).
Genome_build: GRCh38
Supplementary_files_format_and_content: Expression matrix providing the number of reads (UMIs) per gene, per cell

source_name: FSHD1 patient-derived primary myocytes

growth_protocol: Human primary myoblast cell lines originated from the University of Rochester biorepository (http://www.urmc.rochester.edu/fields-center/). Myoblasts were cultured in DMEM/F-10 medium (# 41550-021, Life technologies), supplemented with 20% heat-inactivated Fetal Bovine Serum (FBS; #10270, Gibco/Life Technologies), 1% penicillin/streptomycin (#15140122, Gibco/Life Technologies), 10ng/ml rhFGF (#C-60240, Bio-Connect) and 1μM dexamethasone (#D2915, Sigma-Aldrich). For terminal myogenic differentiation, myoblast were cultured for 3 days in DMEM/F-12 (# 41966-029, Life Technologies) supplemented with 15% KnockOut Serum Replacer (KOSR; #10828-028, Life Technologies). Myocyte fusion was inhibited by adding EGTA to the medium to a final concentration of 1.4mM.

extract_protocol:
Differentiated cell cultures were trypsinized and resuspended in 10ml differentiation medium. Samples were centrifuged for 5 min at 1000 rpm (128 rcf) at room temperature. Cell pellets were washed once in 10ml PBS/0.04% (w/v) Bovine Serum Albumin (BSA #A7906, Sigma Aldrich), transferred through a 50um cell strainer (#04-004-2327, Sysmex) and resuspended in PBS/0.04% BSA (w/v) to a final concentration of 2,000 cells/µl. Next, samples were prepped for scRNAseq according to the Chromium™ Single Cell 3’ v1 RNA sequencing specification. For all samples, targeted cell count was 1,000 cells per sample.
The generated cDNA was used for Illumina Next-generation sequencing (NGS) using a NextSeq500-v2 150 cycle kit.

tag: disease state

value: Facioscapulohumeral muscular dystrophy

value: muscle biopsy-derived primary myocytes

tag: Sex

value: Female


title: FSHD2.2

source_name: FSHD2 patient-derived primary myocytes


title: CTRL.2

source_name: Healthy control individual-derived primary myocytes

value: healthy control


title: FSHD1.1

value: Male


title: WW1_Cy3_5.1: water_water_rep1_array5.1

description: Raw Data: Cy3: 258527510005_2018-02-27_kay3 GE2_SingleTiff_1_1.txt

tag: treatment

tag: age

tag: growth protocol

tag: harvest date


title: FSHD2.1

tag: cell type


title: BW1_Cy5_3.1: bion_water_rep1_array3.1

description: Raw Data: Cy5: 258527510003_2018-02-22_kay1 GE2_SingleTiff_1_1.txt

tag: genotype

tag: phenotype


title: CTRL.1


title: BW2_Cy3_3.2: bion_water_rep2_array3.2

description: Raw Data: Cy3: 258527510003_2018-02-22_kay1 GE2_SingleTiff_1_2.txt


title: WW2_Cy5_3.2: water_water_rep2_array3.2

description: Raw Data: Cy5: 258527510003_2018-02-22_kay1 GE2_SingleTiff_1_2.txt


title: WW1_Cy3_3.1: water_water_rep1_array3.1

description: Raw Data: Cy3: 258527510003_2018-02-22_kay1 GE2_SingleTiff_1_1.txt


title: UV+ cellular rep 1

source_name: cells treated with 1000 J/m2 UVC


title: UV- control rep1


title: UV+ cellular rep 2


title: shKlf4_KLF4_2posDox

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped to mm10 using STAR guided by GTF and ChIP-Seq reads were mapped using bowtie2
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
ChIP-Seq peak calling was performed using MACS
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig (coverage for mapped reads)

source_name: mouse prostate stem cell line

growth_protocol: Cells were cultured in medium (a mixture of basal and luminal epithelial growth media (Salm et al., 2000a) with conditioned medium from a prostatic smooth muscle cell line (Salm et al., 2000b) (40:40:20, vol/vol/vol) (Salm et al., 2005)).

extract_protocol:
Total RNA was extracted using an RNeasy mini kit (Qiagen, CA).
RNA-Seq: The Akt transformed prostate stem cell line was infected with shKlf4 (shKlf4) or non-silencing control (shCon) lentivirus. After 48 hr cells were selected by puromycin for 2 days and passaged for 10 days to allow cells to undergo EMT. The infected shCon and shKlf4 cells were collected for RNA extraction. Another cohort of shKlf4 cells was infected with BFP tagged Doxycycline inducible human KLF4 (shKlf4+KLF4) or BFP tagged Doxycycline inducible empty vector (shKlf4+EV) lentivirus. After 3 days, 100 ng/ml of Dox was added to cultures to induce Klf4 expression while control cultures received no Dox. Two days later, all shKlf4+KLF4 and shKlf4+EV cells with or without Dox treatment were collected for RNA extraction. Total RNA was extracted using an RNeasy mini kit (Qiagen, CA). RNA-seq libraries were prepared with the TruSeq sample preparation kit (Illumina, CA). ChIP-Seq: For ChIP-seq analyses, 1x107Â cells of the Akt transformed prostate stem cell line with endogenous Klf4 were fixed in PBS containing 1% of formaldehyde for 8 min at room temperature on a rotating platform. The reaction was quenched with 0.125M glycine for 5 min. After washing twice with cold PBS, cells were collected and the chromatin prepared according to the ChIP-IT High Sensitivity protocol (Active Motif, CA). Cell pellets were re-suspended in 10 ml of chromatin prep buffer supplemented with a proteinase inhibitor cocktail (PIC) and PMSF (100 ÂµM) and nuclei were extracted using a chilled Dounce homogenizer. Nuclei were re-suspended in ChIP buffer supplemented with PIC and PMSF (1 mM) and sonicated using a Diagenode Bioruptor 300 at maximum intensity and pulsed for 30 sec on and 30 sec off for 30 cycles. Prior to ChIP, chromatin size was confirmed by reverse-crosslinking of 2.5% of the input by incubation with 10 Âµg of RNAse for 30min at 37ÂºC followed by addition of 20 Âµg proteinase K and incubation for 30 min at 55ÂºC and 2 hours at 80ÂºC, making sure we had achieved an average length between 200-1200. Immunoprecipitation was performed overnight at 4C on 30 Î¼g of sheared chromatin using 4 Î¼g of KLF4 antibody. Chromatin samples were washed 5 times before reversing crosslinks. DNA was then extracted using in a DNA purification column (Active Motif, CA) and eluted in 37 Âµl of DNA Purification Elution Buffer (Active Motif, CA) for ChIP-seq analysis. Sample quality and DNA concentration was assessed by Qubit (Invitrogen, CA). ChIP-Seq libraries were made using the ThruPLEX DNA-seq kit (Rubicon Genomics, MI) using 200 pg of ChIP DNA or KAPA Hyper Prep kit (Kapa Biosystems, MA) using 1 ng of ChIP DNA. Libraries were size selected prior to PCR amplification using AMPure XP beads (Beckman Coulter, CA). Multiplexed libraries were run on an Illumina HiSeq 2500 instrument, Genome Analyzer using the 50-base pair single read method.

treatment_protocol: cells were cultured in 10-cm dishes and infected with virus for 7hr, virus was removed and replaced with fresh medium and after 20hr cells were re-infected as above and incubated for 2 additional days. Puromycin (5-8Î¼g/ml) was added to cells for 48hr and those that survived the selection were processed for experiments. For Dox inducible KLF4 experiments, KLF4 re-expressing cells (shKlf4+KLF4) and control empty vector (shKlf4+EV) cells were treated with Dox (10 ng/ml) for 48 hr before in vitro experiments or performing Western blots.

tag: cell ine

value: Akt (5MOI)

tag: lentivirus

value: shKlf4 (5MOI), BFP-tagged human KLF4 (5MOI)

tag: passage number

value: passage 3

value: mouse prostate stem cell line

tag: harvest time


title: shKlf4_ev_BFP_1negDox

value: shKlf4 (5MOI), BFP-tagged empty vector (5MOI)


title: shKlf4_KLF4_1negDox


title: shKlf4_ev_BFP_2negDox


title: shKlf4_2

value: shKlf4 (5MOI)

value: passage 6


title: shKlf4_1


title: shKlf4_KLF4_2negDox


title: shKlf4_KLF4_1posDox


title: RHS_1

value: scramble shRNA (5MOI)


title: shKlf4_ev_BFP_2posDox


title: Klf4_Ab

tag: antibody

value: Anti-KLF4 polyclonal Ab (R&D system, cat#AF3158)


title: Splenic-MZ-B-cell-072915

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

description:
FPKM_allsamples.txt
gene_exp.diff
Splenic_MZ_072915

data_processing:
The raw fastq files were mapped to whole mouse genome build MM9 using Tophat v2.1.0 with parameters --no-novel-juncs --no-coverage-search
Cufflinks program was used to measure relative abundance for genes in Fragments Per Kilobase of exon model per Million mapped fragments(FPKM)
Differential Expression analysis was done using Cuffdiff
Genome_build: MM9
Supplementary_files_format_and_content: Tab delimited files containing FPKM values for mouse refseq genes from Cufflinks
Supplementary_files_format_and_content: Tab delimited file containing log2FC from Cuffdiff

source_name: Splenic-MZ-B-cells

extract_protocol:
N/A
Total splenic B cells from 8-10 wk old mice were purified by negative selection using magnetic cell sorting (STEMCELL Technologies, Vancouver, BC, Canada) followed by sorting of specific subsets of B cells using FACS.  B cell purities were ~ 99% as determined by flow cytometry. Total RNA was isolated from sorted B cells using RNAqueous® −4PCR kit (Ambion, Austin, Tx).
Illumina kit, single end, not strand specific.

tag: strain

tag: tissue

value: spleen

value: B cells

tag: markers


title: input_IgG

value: Goat IgG (R&D system, AB-108-C)


title: shKlf4_ev_BFP_1posDox


title: Splenic-FO-IgD-Hi-B-cell-072915

description:
FPKM_allsamples.txt
gene_exp.diff
Splenic_FOIGD_HI_072915_G

source_name: Splenic-FO-IgD-Hi-B-cells

tag: cell type subset

value: IgD-HI


title: MZ-B-cell-080515

description:
FPKM_allsamples.txt
gene_exp.diff
MZ_080515

source_name: MZ-B-cells

value: MZ


title: MZ-B-cell-072815

description:
FPKM_allsamples.txt
gene_exp.diff
MZ_072815


title: FO-IgD-Lo-B-cell-080515

description:
FPKM_allsamples.txt
gene_exp.diff
FOIGD_LO_080515

source_name: FO-IgD-Lo-B-cells

value: IgD-LO


title: FO-IgD-Hi-B-cell-072815

description:
FPKM_allsamples.txt
gene_exp.diff
FOIGD_HI_072815_G

source_name: FO-IgD-Hi-B-cells


title: Splenic-FO-IgD-Lo-B-cell-072915

description:
FPKM_allsamples.txt
gene_exp.diff
Splenic_FOIGD_LO_072915

source_name: Splenic-FO-IgD-Lo-B-cells


title: FO-IgD-Lo-B-cell-072815

description:
FPKM_allsamples.txt
gene_exp.diff
FOIGD_LO_072815


title: FO-IgD-Hi-B-cell-080515

description:
FPKM_allsamples.txt
gene_exp.diff
FOIGD_HI_080515_G


title: Maf+/+ Il7rCre ATAC rep 2

city: Durham

first: Maria

last: Ciofani

state: NC

address: 207 Research Drive, 128 Jones Building

department: Integrative Immunobiology

institute: Duke University School of Medicine

data_processing:
Adapters and bases with Q < 20 were trimmed using TrimGalore! (cutadapt; v0.4.4).
Pared-end reads were aligned to the GENCODE GRCm38 (mm10) genome using bowtie2 (v2.3.4.1 ) with "--very-sensitive" settings
Duplicate reads were marked using Picard MarkDuplicates (v2.18.9) and excluded from subsequent analysis.
Reads overlapping ENCODE blacklisted regions were remove using bedtools intersect (v2.27.1)
Reads having an insert size > 175 bp were removed using a custom filter implemented in perl.
Visualization files were generated using deeptools (v3.1.2) bamCoverage with RPKM normalization (excluding chrX, chrY, and chrM during normalization)
Peaks were called using MACS2 (v2.1.1) with settings ‘callpeak –nomodel -f BAMPE -q 0.1’
Genome_build: mm10
Supplementary_files_format_and_content: RPKM-normalized bigWig files (for visualization) and called peak files (narrowPeak) from MACS2

source_name: Maf WT CD24+ CD45RBlo gd T cells

growth_protocol: Mice were maintained under specific pathogen-free conditions. Fetuses were harvested at embryonic day 17-18.

extract_protocol:
15 to 17 thousand CD4- CD8- TCRgd+ CD3e+ CD24+ CD45RBlo thymocytes were sort purified from pooled E17-E18 Maf+/+ Il7rCre and Maf fl/fl Il7rCre fetuses. The Omni-ATAC protocol was performed according to Corces et al (Nature Methods, 2017). Nuclei were subjected to Tn5 transposition (Illumina) and transposed DNA was purified using a Qiagen MinElute Kit prior to library amplification.
Transposed DNA fragments were amplified with Nextera PCR primers for a total of 9-11 cycles using NEBNext High-Fidelity Polymerase (NEB).

tag: strain background

value: C57Bl/6 (N5 backcross)

tag: developmetal stage

tag: genotype/variation

value: Maf WT

value: Fetal thymus

value: CD24+ CD45RBlo gd T cells


title: Maf fl/fl Il7rCre ATAC rep 2

source_name: Maf KO CD24+ CD45RBlo gd T cells

value: Maf KO


title: Maf+/+ Il7rCre ATAC rep 1


title: Maf fl/fl Il7rCre ATAC rep 1


title: RHS_2

value: Akt (5MOI)

value: mouse prostate stem cell line


title: Tumor6

city: Hangzhou

first: Tianhua

last: Zhou

state: Zhejiang

address: 866 Yuhangtang Road

department: School of Medicine

country: China

institute: Zhejiang University

description: Tumor tissue and its matched non-tumor tissue  from separate patients

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labelled ds-cDNA in NimbleGen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.

source_name: gastric caner tissue6

label_protocol: For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). 1 μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

extract_protocol: Total RNA was extracted and clean-up using the kit (TRIzol® Reagent,Invitrogen life technologies; RNasey Mini Kit,Qiagen; Dnase,EPICENTRE) following the manufacturer's recommendations.Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: Six fresh human gastric cancer tissues and their matched non-tumor tissues

value: stomach

tag: disease state

value: tumor


title: Tumor2

source_name: gastric caner tissue2


title: Non-tumor2(matched Tumor2)

source_name: gastric cancer non-tumor tissue2

value: non-tumor


title: Tumor3

source_name: gastric caner tissue3


title: Non-tumor5(matched Tumor5)

source_name: gastric cancer non-tumor tissue5


title: Non-tumor3(matched Tumor3)

source_name: gastric cancer non-tumor tissue3


title: Tumor1

source_name: gastric caner tissue1


title: Non-tumor1(matched Tumor1)

source_name: gastric cancer non-tumor tissue1


title: Tumor4

source_name: gastric caner tissue4


title: Non-tumor4(matched Tumor4)

source_name: gastric cancer non-tumor tissue4


title: T17p1_G8

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

institute: Janssen R&D

hyb_protocol: Following fragmentation, 1.875ug of cDNA was hybridized for 16 hr at 45oC on GeneChip HT HG-U133+ PM 96 array plates. GeneChips were washed and stained in the Affymetrix GeneChip Array Station.

scan_protocol: GeneChips were scanned using the GeneChipHT Scanner.

data_processing: The data was normalized by RMA using ArrayStudio version 9.

source_name: tissue biopsy

label_protocol: Target was prepared from 100ng total RNA using the NuGEN Ovation V2 kit, followed by NuGEN Encore biotin labeling module, using the manufacturer’s protocol.

extract_protocol: Total RNA was isolated with Qiagen's RNeasy mini kit according to the manufacturer’s instructions.

treatment_protocol: Mucosal biopsies (n=162) were collected 15 to 20 cm from the anal verge at screening during endoscopies from a subset of 87 patients who participated in the PURSUIT study. The Mayo score ranges from 0-12, with higher scores indicating more severe disease. More information on the score can be found at: http://www.globalrph.com/mayo_clinic_score.htm  Independent of the PURSUIT study , biopsies were also collected from 21 healthy normal subjects to serve as control.  Biopsies were immediately placed in RNAlater and subsequently stored at –80oC until RNA preparation.

value: colon mucosa

tag: subject

tag: disease

value: Ulcerative Colitis (UC)

tag: age

tag: treatment

value: Placebo

tag: visit

value: Week 6

value: No

tag: mayo score


title: T17p2_F2

value: Yes


title: Tumor5

source_name: gastric caner tissue5


title: T17p2_F5


title: T17p2_D2


title: T17p1_H11


title: Rorc(t) GFP/GFP KO RNAseq rep 4

description:
MC-157
processed data file: rorc_raw_counts.txt
RorcKO_rep4

data_processing:
Adapters and bases with Q < 20 were trimmed using TrimGalore! (cutadapt; v0.4.4).
Single-end reads were aligned to the GENCODE GRCm38 (mm10) genome using STAR (v2.6.0a) allowing no novel splice junctions (--alignSJoverhangMin 500) and keeping only uniquely-mapped reads (--outFilterMultimapNmax 1)
Reads were assigned to features in the GENCODE GRCm38 vM17 gene annotation using featureCounts (v1.6.2)
Genes having less than 2 counts per million were excluded and differential expression analysis was performed with edgeR (v3.22.3) using the exactTest method.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of raw read counts obtained from featureCounts, separate files for Maf and Rorc(t) experiments

source_name: Rorc KO CD25- CD27- gd T cells

extract_protocol:
RNA was extracted from 10-90 thousand FACS-purified CD27- CD25- TCRgd+ CD3e+ E17-18 fetal thymocytes cells using Trizol (Invitrogen), with the aqueous phase subjected to RNA purification using the RNeasy Plus Micro Kit (Qiagen).
Libraries were constructed from RNA using the Clontech SMARTer v3/v4 ultra-low input RNA-Seq kit (Takara Biosciences).

value: Rorc KO

tag: cell type

value: CD25- CD27- gd T cells


title: T17p2_G8


title: T17p1_B7


title: T17p1_A6


title: T17p1_H12


title: T17p2_B3


title: T17p1_A9


title: T17p1_F9


title: T17p2_F3


title: T17p2_H6


title: T17p1_H6


title: T17p1_H7


title: Rorc(t)+/+ RNAseq rep 4

description:
MC-156
processed data file: rorc_raw_counts.txt
RorcWT_rep4

source_name: Rorc WT CD25- CD27- gd T cells

value: Rorc WT


title: Rorc(t) GFP/GFP KO RNAseq rep 3

description:
MC-155
processed data file: rorc_raw_counts.txt
RorcKO_rep3

value: Fetal thymus


title: Rorc(t)+/+ RNAseq rep 2

description:
MC-152
processed data file: rorc_raw_counts.txt
RorcWT_rep2


title: Rorc(t) GFP/GFP KO RNAseq rep 2

description:
MC-153
processed data file: rorc_raw_counts.txt
RorcKO_rep2


title: T17p2_H3


title: Rorc(t) GFP/GFP KO RNAseq rep 1

description:
MC-151
processed data file: rorc_raw_counts.txt
RorcKO_rep1


title: Rorc(t)+/+ RNAseq rep 1

description:
MC-150
processed data file: rorc_raw_counts.txt
RorcWT_rep1


title: Rorc(t)+/+ RNAseq rep 3

description:
MC-154
processed data file: rorc_raw_counts.txt
RorcWT_rep3


title: Disome12_RPF

city: Boston

first: James

middle: Christopher

last: Taggart

state: MA

address: 200 Longwood Avenue

department: Systems Biology

institute: Harvard Medical School

description: ribosome protected mRNA

data_processing:
Library strategy: Ribo-Seq
Raw fastq files were trimmed of poly(A) or adapter sequences using Cutadapt with parameters –u 1 (or -u 3 for samples prepared with SMARTer smRNA-seq kit) and –m 24. Nucleotides are removed from the 5' end of reads to address non-template addition during reverse transcription and template switching.
Trimmed reads were aligned to reference transcriptome using tophat v1.4.1 using parameters –G --no_novel-juncs --transcriptome-only –N 1
Genome_build: sacCer3
Supplementary_files_format_and_content: wiggle files contain positions offset by +13 nucleotides and counts of mapped 5' ends.

organism: Saccharomyces cerevisiae

source_name: Budding yeast

growth_protocol: Overnight cultures were grown from a single colony in selective synthetic complete medium and back-diluted to OD590 = 0.002 in 500 mL YPD. Culture were grown in shaking 2.8L flasks at 30°C until OD590 reached 0.5.

extract_protocol:
Ribosome protected fragments were dephosphorylated at the 3’ end and cDNA was synthesized using the SMARTer smRNA-Seq kit (Clontech). cDNAs were depleted of rRNA-derived fragments by selective hybridization to biotinylated oligonucleotides. cDNA was then PCR amplified.
Cell lysis was performed as described in detail previously (Li et al., Cell 2014), with the following modifications. 500 mL of cell culture was rapidly filtered at 30C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal spatula, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 25 mL canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. Lysates were treated with RNase I and ribosome protected fragments were isolated by hot phenol extraction. Ribosome protected fragments were size selected by gel extraction.


title: Disome13_RPF

description: ribosome protected mRNA


title: Disome16_RPF

description: ribosome protected mRNA


title: Disome15_RPF

description: ribosome protected mRNA


title: Disome10_RPF

description: ribosome protected mRNA


title: T17p1_E2


title: T17p1_G4


title: T17p2_E4


title: T17p1_C11


title: T17p2_D6

value: Week 0


title: T17p1_C6


title: T17p2_H2


title: Disome9_RPF

description: ribosome protected mRNA


title: T17p1_D12


title: T17p2_E3


title: T17p1_B4


title: T17p1_G12


title: T17p1_B3


title: T17p1_G6


title: Disome2_RPF

description: ribosome protected mRNA


title: Disome11_RPF

description: ribosome protected mRNA


title: T17p2_E5


title: T17p2_E2


title: DisomeWT_rep2_RPF

description: ribosome protected mRNA

value: DisomeWT


title: Disome1_RPF

description: ribosome protected mRNA


title: Endo A1 [JCZ_33]

city: Montpellier

first: Laurent

last: MANCHON

address: 1919 Route de Mende

institute: CNRS

description:
JCZ_33
FACS-sorted Endoderm precursors
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking

data_processing:
Sequencing quality control: Image analysis and base calling were performed using the HiSeq Control Software 3.3.76 and Real-Time Analysis component 2.7.6. Demultiplexing was performed using Illumina's sequencing analysis software bcl2fastq2.17 v2.17.1.14. The quality of the data was assessed using the Illumina pipeline. The Illumina pipeline estimates the reads quality according to the percentage of bases having a base quality value greater or equal to 30 (Q30), i.e., less than 1 error in 1000 bases.
Our RNA treatment uses the trimmomatic package to remove bases that correspond to the standard Illumina adapters. Trimmomatic will look for seed matches (<16 bases) allowing a defined number of mismatches. In case of single end reads, whenever the seed alignment occurs, the entire alignment is scored. The trimming options used are: seedMismatches is set at 2 and simpleClipThreshold is at 5, the remaining reads are called "clean reads" and stored as FASTQ format.
Alignments have been performed using TopHat tool from Tuxedo package against human GRCh37 reference genome. Tophat is a splice-aware aligner that uses bowtie aligner to align the data before counting the reads that have mapped to all the genes. TopHat outputs were stored in BAM files (accepted_hits.bam typically) which contain all the alignments. Then read alignments are assembled by Cufflinks to produce a transcriptome annotation for the genome. The next step is performed by Cuffdiff, which tests for differential expression of genes and transcripts between the conditions using a rigorous statistical analysis.
To compute expression estimation, normalization and comparison we used Cufflinks and Cuffdiff programs. Cufflinks is a program that assembles aligned RNA-Seq reads into transcripts, estimates their abundances, and tests for differential expression and regulation transcriptome-wide. Cufflinks builds the minimum number of transcripts to explain all candidate splice sites. It then measures transcript abundances in Fragments Per Kilobase of exon per Million fragments mapped (FPKM), which is analogous to single-read "RPKM". Cuffdiff then uses the Cufflinks transcript quantification engine to calculate gene and transcript expression levels in more than one condition and tests them for significant differences. It can find differentially expressed genes and transcripts, as well as genes that are being differentially regulated at the transcriptional and post-transcriptional levels.
Genome_build: GRCh37
Supplementary_files_format_and_content: *_tracking: Matrix tables of raw counts and normalized counts per sample (tab delimited) with a first column for gene/isoform ID identification. The next column corresponds to the raw read counts (non-normalized) or normalized counts (fpkm) per sample.

source_name: Endoderm precursors

growth_protocol: Human-induced Pluripotent Stem Cells H9 Line (SBI, System Biosciences) were maintained on matrigel (BD Biosciences) or on Vitronectin (Stemcell Technologies) with chemically defined mTeSR (Stemcell Technologies) medium. Cultures were passaged by enzymatic dissociation using dispase or Gentle Cell Dissociation Reagent (Stemcell Technologies).

extract_protocol:
Total RNA extraction was performed according to the Qiagen miRNeasy kit. RNA concentrations were determined using Qubit fluorometric quantification and purity by the RNA 6000 Bioanalyzer kit (Agilent).
RNA-Seq libraries were constructed with the TruSeq stranded mRNA sample preparation (Low throughput protocol) kit and TruSeq Small RNA protocol from Illumina. The first step of the pipeline is transcripts purification by depleting abundant ribosomal RNAs with specific RiboZero kit. 3 μg of high quality total RNA was eluted in 10 μL RNase-free water for the construction of the libraries. All samples were supplied at the same concentration of 300 ng/μL and were DNase treated. The Illumina TruSeq Small RNA protocol is optimized to target small RNAs with 5’-monophosphate. This option is required for samples with unknown 5’-phosphorylation status. The final cDNA libraries were validated with a Fragment Analyzer (Advanced Analytical, Ankeny, IA) and quantified with a KAPA qPCR kit (Kapa Biosystems, Wilmington, MA). Having passed quality control, the libraries were sequenced on Illumina HiSeq 4000.

treatment_protocol: Endoderm differentiation was induced in Advanced RPMI (Invitrogen), 0.5% FBS (Hyclone), Activin A (100 ng/ml) (R&D) and WNT3A (50 ng/ml) (R&D). HUES64-derived hepatoblasts (dHep) were induced by culturing day 5 endoderm in RPMI media containing B27 (1X), FGF2 (10ng/ml) (Millipore) and BMP4 (20 ng/ml) (R&D) for five days, and collected after 10 days total of differentiation. Mesoderm differentiation was induced by the addition of media consisting of in DMEM/F12 (Life Technologies), 0.5% FBS (Hyclone), Activin A (100ng/ml) (R&D) (for the first 24 hours only), BMP4 (100 ng/ml) (R&D), VEGF (100 ng/ml) (R&D) and FGF2 (20 ng/ml) (Millipore). Ectoderm differentiation was induced using A83-01 (2um) (Tocris), PNU 74654 (2um) (Tocris) and Dorsomorphin (2um) (Tocris), DMEM/F12 (Life Technologies) containing 15% Knock serum replacer (Life Technologies).

tag: cell line

value: Endoderm precursors

tag: development stage

value: Endoderm

value: Differentiation protocol


title: Endo A2 [JCZ_34]

description:
JCZ_34
FACS-sorted Endoderm precursors
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking


title: T17p1_H5


title: Meso A1 [JCZ_31]

description:
JCZ_31
FACS-sorted Endoderm precursors
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking

source_name: Mesoderm precursors

value: Mesoderm precursors

value: Mesoderm


title: Ecto A2 [JCZ_30]

description:
JCZ_30
FACS-sorted Endoderm precursors
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking

source_name: Ectoderm precursors

value: Ectoderm precursors

value: Ectoderm


title: Meso A2 [JCZ_32]

description:
JCZ_32
FACS-sorted Endoderm precursors
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking


title: T17p2_A3

value: colon mucosa

value: Ulcerative Colitis (UC)

value: Placebo


title: H99 0.5 kGy sample_1

source_name: H99 0.5 kGy sample

value: wild type

tag: exposesd to

value: γ-radiation (0.5 kGy)


title: T17p2_D4

tag: tissue

value: No


title: T17p1_A3

value: Yes


title: T17p1_A7


title: eiF4A3 A1 [JCZ_27]

description:
JCZ_27
Human induced pluripotent stem cells
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking

source_name: eIF4A3 shRNA transduction

value: Stem Cells

value: Pluripotency

value: shRNA transduction + doxycycline induction


title: Ecto A1 [JCZ_29]

description:
JCZ_29
FACS-sorted Endoderm precursors
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking


title: T17p2_C2

value: Week 0


title: T17p1_E9


title: T17p1_G7


title: U2AF1 B2 [JCZ_24]

description:
JCZ_24
Human induced pluripotent stem cells
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking

source_name: U2AF1 shRNA transduction


title: NCBP1 A2 [JCZ_26]

description:
JCZ_26
Human induced pluripotent stem cells
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking

source_name: NCBP1 shRNA transduction


title: NCBP1 A1 [JCZ_25]

description:
JCZ_25
Human induced pluripotent stem cells
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking


title: eiF4A3 A2 [JCZ_28]

description:
JCZ_28
Human induced pluripotent stem cells
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking


title: U2AF1 B1 [JCZ_23]

description:
JCZ_23
Human induced pluripotent stem cells
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking


title: T17p2_F9


title: U2AF1 A2 [JCZ_22]

description:
JCZ_22
Human induced pluripotent stem cells
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking


title: Sc +Dox A1 [JCZ_19]

description:
processed data file: JCZ_19
Human induced pluripotent stem cells
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking

source_name: Scramble shRNA Control transduction

value: Scramble shRNA Control transduction + doxycycline


title: Sc +Dox A2 [JCZ_20]

description:
JCZ_20
Human induced pluripotent stem cells
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking


title: U2AF1 A1 [JCZ_21]

description:
JCZ_21
Human induced pluripotent stem cells
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking


title: T17p1_E8


title: T17p1_F4


title: Dif 10j A2 [JCZ_18]

description:
processed data file: JCZ_18
10 days differentiated human induced pluripotent stem cells
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking

source_name: Differentiation 10 days

value: Ectoderm, Mesoderm and Endoderm precursors

value: Three germ layers precursors

value: KOSR Differentiation protocol


title: T17p1_F8


title: T17p1_D2


title: T17p1_H8


title: Dif 10j A1 [JCZ_17]

description:
processed data file: JCZ_17
10 days differentiated human induced pluripotent stem cells
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking


title: T17p1_B6


title: T17p1_G11


title: T17p1_H2


title: T17p2_G9


title: Colon-NHC-UC_C2

value: Healthy


title: T17p2_G2


title: Colon-NHC-UC_F4


title: iPS wt 5j A1 [JCZ_15]

description:
processed data file: JCZ_15
Human induced pluripotent stem cells
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking

source_name: human induced pluripotent stem cells WT


title: iPS wt 5j A2 [JCZ_16]

description:
processed data file: JCZ_16
Human induced pluripotent stem cells
Small RNA
Single end (50bp)
processed data file: JCZ_15-34_genes.count_tracking.txt
processed data file: JCZ_15-34_genes.fpkm_tracking
processed data file: JCZ_15-34_isoforms.count_tracking.txt
processed data file: JCZ_15-34_isoforms.fpkm_tracking


title: Colon-NHC-UC_E4


title: T17p2_F8


title: eiF4A3 A1 [JCZ_13]

description:
processed data file: JCZ_13
Human induced pluripotent stem cells
Paired-end (2x150bp)
processed data file: JCZ_1-14_genes.count_tracking.txt
processed data file: JCZ_1-14_genes.fpkm_tracking
processed data file: JCZ_1-14_isoforms.count_tracking.txt
processed data file: JCZ_1-14_isoforms.fpkm_tracking


title: eiF4A3 A2 [JCZ_14]

description:
processed data file: JCZ_14
Human induced pluripotent stem cells
Paired-end (2x150bp)
processed data file: JCZ_1-14_genes.count_tracking.txt
processed data file: JCZ_1-14_genes.fpkm_tracking
processed data file: JCZ_1-14_isoforms.count_tracking.txt
processed data file: JCZ_1-14_isoforms.fpkm_tracking


title: Colon-NHC-UC_C4


title: Colon-NHC-UC_B4


title: U2AF1 B1 [JCZ_9]

description:
JCZ_9
Human induced pluripotent stem cells
Paired-end (2x150bp)
processed data file: JCZ_1-14_genes.count_tracking.txt
processed data file: JCZ_1-14_genes.fpkm_tracking
processed data file: JCZ_1-14_isoforms.count_tracking.txt
processed data file: JCZ_1-14_isoforms.fpkm_tracking


title: U2AF1 B2 [JCZ_10]

description:
processed data file: JCZ_10
Human induced pluripotent stem cells
Paired-end (2x150bp)
processed data file: JCZ_1-14_genes.count_tracking.txt
processed data file: JCZ_1-14_genes.fpkm_tracking
processed data file: JCZ_1-14_isoforms.count_tracking.txt
processed data file: JCZ_1-14_isoforms.fpkm_tracking


title: NCBP1 A1 [JCZ_11]

description:
processed data file: JCZ_11
Human induced pluripotent stem cells
Paired-end (2x150bp)
processed data file: JCZ_1-14_genes.count_tracking.txt
processed data file: JCZ_1-14_genes.fpkm_tracking
processed data file: JCZ_1-14_isoforms.count_tracking.txt
processed data file: JCZ_1-14_isoforms.fpkm_tracking


title: U2AF1 A1 [JCZ_7]

description:
JCZ_7
Human induced pluripotent stem cells
Paired-end (2x150bp)
processed data file: JCZ_1-14_genes.count_tracking.txt
processed data file: JCZ_1-14_genes.fpkm_tracking
processed data file: JCZ_1-14_isoforms.count_tracking.txt
processed data file: JCZ_1-14_isoforms.fpkm_tracking


title: U2AF1 A2 [JCZ_8]

description:
JCZ_8
Human induced pluripotent stem cells
Paired-end (2x150bp)
processed data file: JCZ_1-14_genes.count_tracking.txt
processed data file: JCZ_1-14_genes.fpkm_tracking
processed data file: JCZ_1-14_isoforms.count_tracking.txt
processed data file: JCZ_1-14_isoforms.fpkm_tracking


title: Sc +Dox A2 [JCZ_6]

description:
JCZ_6
Human induced pluripotent stem cells
Paired-end (2x150bp)
processed data file: JCZ_1-14_genes.count_tracking.txt
processed data file: JCZ_1-14_genes.fpkm_tracking
processed data file: JCZ_1-14_isoforms.count_tracking.txt
processed data file: JCZ_1-14_isoforms.fpkm_tracking

value: Scramble shRNA Control transduction + doxycycline induction


title: Colon-NHC-UC_F1

value: colon mucosa


title: Colon-NHC-UC_D4


title: Colon-NHC-UC_C1


title: Colon-NHC-UC_B1


title: Colon-NHC-UC_A1


title: NCBP1 A2 [JCZ_12]

description:
processed data file: JCZ_12
Human induced pluripotent stem cells
Paired-end (2x150bp)
processed data file: JCZ_1-14_genes.count_tracking.txt
processed data file: JCZ_1-14_genes.fpkm_tracking
processed data file: JCZ_1-14_isoforms.count_tracking.txt
processed data file: JCZ_1-14_isoforms.fpkm_tracking


title: T17p1_C4

value: Ulcerative Colitis (UC)

value: Week 6


title: Dif 10j A2 [JCZ_4]

description:
JCZ_4
10 days differentiated human induced pluripotent stem cells
Paired-end (2x150bp)
processed data file: JCZ_1-14_genes.count_tracking.txt
processed data file: JCZ_1-14_genes.fpkm_tracking
processed data file: JCZ_1-14_isoforms.count_tracking.txt
processed data file: JCZ_1-14_isoforms.fpkm_tracking


title: Dif 10j A1 [JCZ_3]

description:
JCZ_3
10 days differentiated human induced pluripotent stem cells
Paired-end (2x150bp)
processed data file: JCZ_1-14_genes.count_tracking.txt
processed data file: JCZ_1-14_genes.fpkm_tracking
processed data file: JCZ_1-14_isoforms.count_tracking.txt
processed data file: JCZ_1-14_isoforms.fpkm_tracking


title: Sc +Dox A1 [JCZ_5]

description:
JCZ_5
Human induced pluripotent stem cells
Paired-end (2x150bp)
processed data file: JCZ_1-14_genes.count_tracking.txt
processed data file: JCZ_1-14_genes.fpkm_tracking
processed data file: JCZ_1-14_isoforms.count_tracking.txt
processed data file: JCZ_1-14_isoforms.fpkm_tracking


title: Colon-NHC-UC_H4


title: iPS wt 5j A2 [JCZ_2]

description:
JCZ_2
Human induced pluripotent stem cells
Paired-end (2x150bp)
processed data file: JCZ_1-14_genes.count_tracking.txt
processed data file: JCZ_1-14_genes.fpkm_tracking
processed data file: JCZ_1-14_isoforms.count_tracking.txt
processed data file: JCZ_1-14_isoforms.fpkm_tracking


title: Colon-NHC-UC_F2


title: iPS wt 5j A1 [JCZ_1]

description:
processed data file: JCZ_1
Human induced pluripotent stem cells
Paired-end (2x150bp)
processed data file: JCZ_1-14_genes.count_tracking.txt
processed data file: JCZ_1-14_genes.fpkm_tracking
processed data file: JCZ_1-14_isoforms.count_tracking.txt
processed data file: JCZ_1-14_isoforms.fpkm_tracking


title: Colon-NHC-UC_B2


title: Colon-NHC-UC_G1


title: Colon-NHC-UC_H1


title: Dengue Infected, Rep2

city: San Francisco

first: Nevan

middle: J

last: Krogan

state: CA California

address: 1700 4th Street, 308 Byers Hall, Box 2530

institute: University of California, San Francisco

description: Dengue infected for RNA-seq

data_processing:
Samples were sequenced on the Illumina HiSeq 4000.
Base-calling was performed using Illumina real time analysis and bcl2fastq was used to create fastq files
Resulting sequence data were Q33 quality filtered. Interferon stimulated genes significantly increased in expression following DENV infection were identified by Tophat2 and Cuffdiff analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Text file of differentially expressed genes

source_name: Huh7 cells

growth_protocol: Huh7 cells were grown to ~80% confluency in 15cm dishes

extract_protocol:
Cells were scraped, washed two times with cold PBS, and lysed in Trizol, RNA was purified using Rneasy columns (Life Technologies), and mRNA was enriched using PolyA purification beads (BioO) according to manufacturer protocols
Library preparation for next generation sequencing was done using a stranded RNA-seq library preparation kit (KAPA) according to manufacturer recommendations.

treatment_protocol: Cells were incubated media or DENV2 16681 at an MOI of 3 for 1 hour at 37C, infection was allowed to progress for 18 hours

tag: virus

tag: time point

value: 18 hours


title: Dengue Infected, Rep3

description: Dengue infected for RNA-seq


title: Dengue Infected, Rep1

description: Dengue infected for RNA-seq


title: Colon-NHC-UC_D1


title: Colon-NHC-UC_A2


title: T17p1_E11

value: golimumab


title: Mock, Rep3

description: Mock infection control for RNA-seq

value: Mock


title: Colon-NHC-UC_D2


title: Colon-NHC-UC_G4


title: Colon-NHC-UC_E1


title: Colon-NHC-UC_A4


title: Mock, Rep1

description: Mock infection control for RNA-seq


title: NS5 IFN ChIP, Rep3

description: Leo1 ChIP for NS5 interferon treatment

data_processing:
Input and ChIP samples were sequenced on the Illumina HiSeq 4000.
Base-calling was performed using Illumina real time analysis and bcl2fastq was used to create fastq files
Resulting sequence data were Q33 quality filtered, collapsed for duplicate reads and aligned using Bowtie (Langmead et al., 2009) with options set to disregard reads that map to multiple locations.
Following alignment, ChIP peaks were called using MACS2 and default parameters with broadpeak calling turned on.
Peaks were merged into single bed file using bedtools merge
Counts were quantified using bedtools coverage, normalized to input
Genome_build: hg19
Supplementary_files_format_and_content: BED file of peak, text files of tag counts

growth_protocol: Huh7 cells expressing GFP or dengue virus NS5 were grown to ~80% confluency in 15cm dishes

extract_protocol:
Cells were scraped, washed two times with cold PBS, and lysed in Cell Lysis Buffer (5mM HEPES-KOH pH 7.9, 85 mM KCl, 0.5% IGEPAL CA-630, 0.5 mM phenylmethane sulfonyl fluoride and cOmplete Protease Inhibitor Cocktail (Roche)). Nuclei were pelleted at 600 g for 10 minutes and lysed with Nuclei Lysis Buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 0.5 mM phenylmethane sulfonyl fluoride and cOmplete Protease Inhibitor Cocktail (Roche)). Chromatin shearing by water bath sonication (Diagenode Bioruptor) was optimized to produce ~200-300 nucleotide fragments, and protein concentration was quantified by Bradford Assay (Thermo Fisher). Chromatin was immunoprecipated overnight at 4C using 500g chromatin and 5g of anti-LEO1 antibody. To purifiy antibody-bound chromatin, 50L of Protein A Dynabeads (Thermo Fisher) were added and incubated at 4C for one hour. Dynabead-bound ChIP samples were washed two times with ChIP Dilution Buffer (50mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA and 1% Triton X-100), two times with ChIP High Salt Dilution Buffer (50 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA and 1% Triton X-100), and one time with LiCl Wash Buffer (50 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% IGEPAL CA-630 and 0.5% sodium deoxycholate) for five minutes each before being eluted. Samples were reverse crosslinked at 65C overnight and treated with RNAseA (Fermentas) and ProteinaseK (Fermentas). DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Library preparation for next generation sequencing was done using NextFLEX ChIP-seq Library Preparation Kit (BioO Scientific) according to manufacturer recommendations.

treatment_protocol: Cells were incubated with 31.25 U/mL of interferon-beta for 18 hours, or left untreated, cells were fixed with 1% formaldehyde for five minutes and quenched with 125mM glycine for five minutes

tag: protein expressed

value: interferon beta


title: NS5 IFN Input, Rep3

description: Input control for NS5 interferon treatment


title: NS5 IFN ChIP, Rep2

description: Leo1 ChIP for NS5 interferon treatment


title: NS5 IFN ChIP, Rep1

description: Leo1 ChIP for NS5 interferon treatment


title: T17p1_C9

value: Yes


title: NS5 IFN Input, Rep1


title: NS5 IFN Input, Rep2


title: NS5 Mock ChIP, Rep3

description: Leo1 ChIP for NS5 mock treatment

value: mock


title: NS5 Mock Input, Rep3

description: Input control for NS5 mock treatment


title: Mock, Rep2

description: Mock infection control for RNA-seq


title: NS5 Mock ChIP, Rep2

description: Leo1 ChIP for NS5 mock treatment


title: T17p1_D6


title: T17p2_E7


title: T17p2_D5


title: T17p1_F3


title: NS5 Mock Input, Rep2

description: Input control for NS5 mock treatment


title: T17p2_A9


title: T17p1_H9

value: No


title: T17p2_B2


title: T17p2_E9


title: T17p1_A2


title: T17p2_C9


title: NS5 Mock ChIP, Rep1

description: Leo1 ChIP for NS5 mock treatment


title: NS5 Mock Input, Rep1

description: Input control for NS5 mock treatment


title: GFP IFN ChIP, Rep3

description: Leo1 ChIP for GFP interferon treatment

value: GFP


title: GFP IFN ChIP, Rep2

description: Leo1 ChIP for GFP interferon treatment


title: GFP IFN Input, Rep3

description: Input control for GFP interferon treatment


title: GFP IFN Input, Rep2


title: Disome8_RPF

description: ribosome protected mRNA

tag: strain


title: T17p1_G2


title: GFP IFN ChIP, Rep1

description: Leo1 ChIP for GFP interferon treatment


title: G08T2

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

description: Ribo and Globin depleted library

data_processing:
Basecalls performed using CASAVA version 1.8.2
Trimming performed with Trimmomatic v0.35, with following parameters: MINLEN:40, AVGQUAL:25 and TRAILING:15
Trimmed reads aligned to GRCh38 using STAR v.2.5.2b using as reference transcript the gencode (v.25) primary assembly gene transfer file (GTF).
Gene counting performed on files including only uniquely mapped fragments using featurecounts v1.5.1 with custom parameters: --minOverlap 5; only both reads, no multimapping.
Genome_build: GRCh38
Supplementary_files_format_and_content: excel file including raw counts for each sample (columns) across 58906 genes (rows) [counts matrix]

source_name: Not Responder T2 patient10

extract_protocol:
Peripheral blood was collected in EDTA tubes at T1 and T2 and stored at -20°C after adding 400µl of 2X Denaturing solution (Ambion, USA).Total RNA was extracted from 800 µl of blood with MirVana Paris Kit and treated with Turbo DNA-free Kit (Ambion, USA). RNA Quality was assessed on Agilent Bioanalyzer with the RNA 6000 Nano Kit (Agilent, Santa Clara, CA) and samples were considered suitable for processing if RNA Integrity Number was greater than 7.5
Sequencing libraries were prepared with the TruSeq Stranded Total RNA with Ribo-Zero Globin Kit (Illumina, San Diego, CA) using 800 ng of total RNA

value: Whole blood cells collected from patient after septic shock

tag: patient

tag: timepoint

tag: clinical classification

value: NR


title: G08T1

description: Ribo and Globin depleted library

source_name: Not Responder T1 patient10


title: GFP Mock ChIP, Rep3

description: Leo1 ChIP for GFP mock treatment


title: GFP Mock Input, Rep3

description: Input control for GFP mock treatment


title: Wild-type sample_3

city: Seoul

first: Kihoon

last: Han

address: 73, Inchon-ro, Seongbuk-gu

department: Neuroscience

institute: Korea University College of Medicine

data_processing:
Transcript abundance was estimated with Salmon(v0.9.1) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.0) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.19.11).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Wild-type brain

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit  (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Sample Preparation Guide)

value: hypothalamus

value: 10 to 12 week

tag: genotype

value: WT


title: T17p1_D10

source_name: tissue biopsy

tag: subject

tag: disease

tag: age


title: T17p1_B12

tag: treatment

tag: visit

tag: mayo score


title: Wild-type sample_1


title: T17p1_C2


title: GFP Mock ChIP, Rep2

description: Leo1 ChIP for GFP mock treatment


title: Transgenic sample_3

source_name: Transgenic brain

value: TG


title: T17p2_C4

value: colon mucosa


title: T17p1_D3

value: Ulcerative Colitis (UC)


title: T17p2_C8

value: Week 6


title: T17p1_F10


title: T17p1_C5


title: T17p1_G5


title: Transgenic sample_2


title: GFP Mock Input, Rep2

description: Input control for GFP mock treatment


title: Transgenic sample_1


title: GFP Mock ChIP, Rep1

description: Leo1 ChIP for GFP mock treatment


title: Maf+/+ Il7rCre RNAseq rep 2

description:
MC-S50.
processed data file: maf_raw_counts.txt
MafWT_rep2

source_name: Maf WT CD25- CD27- gd T cells

tag: strain background

value: C57Bl/6 (N5 backcross)

tag: genotype/variation

value: Maf WT

tag: developmetal stage

value: Fetal thymus

tag: cell type

value: CD25- CD27- gd T cells


title: GFP IFN Input, Rep1

value: interferon beta


title: T17p1_F6

tag: tissue

value: golimumab


title: T17p1_A1

value: No


title: Wild-type sample_2


title: Maf fl/fl Il7rCre RNAseq rep 1

description:
MC-S28
processed data file: maf_raw_counts.txt
MafKO_rep1

source_name: Maf KO CD25- CD27- gd T cells

value: Maf KO


title: T17p1_C1

value: Yes


title: GFP Mock Input, Rep1

description: Input control for GFP mock treatment

tag: protein expressed

value: GFP

value: mock


title: Maf+/+ Il7rCre RNAseq rep 1

description:
MC-S27
processed data file: maf_raw_counts.txt
MafWT_rep1


title: T17p1_F12


title: T17p1_E5


title: T17p2_A8


title: Maf fl/fl Il7rCre RNAseq rep 2

description:
MC-S51
processed data file: maf_raw_counts.txt
MafKO_rep2


title: WM8 siASAH1

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: RNA extracted from WM8 cells after transfection with siRNA against ASAH1

hyb_protocol: Agilent : 600.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and differential analysis using Limma package in R / Bioconductor.

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Total RNAs were extracted using TRIzol reagent (Invitrogen)

value: Skin Malignant Melanoma

tag: cell line

tag: rin number

tag: sirna


title: T17p1_E4


title: T17p1_F7


title: T17p2_F1


title: T17p2_H5


title: PC-2_CD19-/CD138+

city: Gaithersburg

first: Christopher

last: Groves

state: MD

address: One MedImmune Way

institute: MedImmune

description: Gene expression data from FACS purified human bone-marrow CD19-/CD138+ cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133 Plus 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

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

data_processing: The data were processed and analyzed in R with frma package

source_name: FACS purified human bone marrow CD19-/CD138+ cells

label_protocol: Biotinylated cRNA were prepared according MessageAmp™ Premier RNA Amplification Kit procedure

extract_protocol: Zymo miniprep kit

treatment_protocol: Untreated BM cells were stained w mAbs and sorted by FACS. The populations from BM were identified by CD27, CD38, CD19, CD20, and CD138. ASC were defined as CD38hiCD27+CD138+ and either CD19+ or CD19-. B cells were non-ASC CD19+ and either CD20+ or CD20-.

tag: marker

value: Bone Marrow


title: WM3912 siASAH1

description: RNA extracted from WM3912 cells after transfection with siRNA against ASAH1


title: T17p1_D9


title: PC-1_CD19-/CD138+


title: HuBM_CD19-_CD138+_9-16


title: PC-2_CD19+/CD138+

description: Gene expression data from FACS purified human bone-marrow CD19+/CD138+ cells

source_name: FACS purified human bone marrow CD19+/CD138+ cells


title: Cha_M2_2011_Cy3

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

institute: IRHS

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532 and 635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. Pair-data files were extracted from the scanned images using DEVA 1.2.1 software (Roche).

data_processing: Statistical analyses were performed using R version 2.14.1 (R Development Core Team, 2011) and the package LIMMA 3.10.1 (Smyth G.K., 2005) from the Bioconductor project. Data were normalized by the lowess method from LIMMA.

source_name: Chantecler apple fruit flesh, 2 months after cold storage, 2011

label_protocol: 200ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized.

growth_protocol: Fruits were harvested at INRA, Angers (Experimental unit of Bois L'Abbé-La Rétuziére).

extract_protocol: Derived from the apple tissues RNA extraction method (Gasic et al., 2004) and pine tree RNA isolation method (Chang et al., 1993)

treatment_protocol: Cold storage at 1°C, after harvest.

value: Fruit

tag: tissue compartment

value: Parenchyma

tag: cultivar

value: Chantecler

tag: genotype

value: Wild-type

tag: developmental stage at harvest

value: Harvested at optimum maturity

value: Cold storage for 60 days after harvest


title: WM8 siCtl

description: RNA extracted from WM8 cells after transfection with siRNA control

value: siControl


title: T17p2_B4

value: colon mucosa

tag: subject

tag: disease

value: Ulcerative Colitis (UC)

tag: age

tag: treatment

value: Week 6


title: T17p2_A5

value: golimumab

tag: visit

value: No

tag: mayo score


title: PC-1_CD19+/CD138+ (2)


title: Cha_M2_2011_Cy5


title: 501Mel siCtl

description: RNA extracted from 501Mel cells after transfection with siRNA control


title: HuBM_CD19-_CD138+_9-17


title: PC-1_CD19-/CD138+ (2)


title: Gol_re_2013_cin_Cy5

source_name: Golden delicious apple fruit flesh, at harvest, 2013

value: Golden delicious


title: Kan_M2_2011_Cy3

source_name: Kanzi apple fruit flesh, 2 months after cold storage, 2011

value: Kanzi


title: PC-1_CD19+/CD138+


title: T17p1_B11

value: Yes


title: 501Mel siASAH1

description: RNA extracted from 501Mel cells after transfection with siRNA against ASAH1

value: Skin Malignant Melanoma


title: WM3912 siCtl

description: RNA extracted from WM3912 cells transfection with siRNA control


title: BdB_re_2012_Cy3

source_name: Belle de Boskoop apple fruit flesh, at harvest, 2012

value: Belle de Boskoop


title: Kan_M2_2011_Cy5

value: Fruit


title: Els_re_2012_Cy5

source_name: Elstar apple fruit flesh, at harvest, 2012

value: Parenchyma

value: Elstar


title: Els_re_2012_Cy3

value: Wild-type


title: BdB_re_2012_Cy5

value: Harvested at optimum maturity


title: T17p2_H1


title: HuBM_CD19+_CD138+ (no.1)

value: Bone Marrow


title: T17p1_D1


title: Gol_M2_2013_cin_Cy3

source_name: Golden delicious apple fruit flesh, 2 months after cold storage, 2013

value: Cold storage for 60 days after harvest


title: T17p2_G7

value: colon mucosa


title: HuBM_CD19+_CD138+_9-17


title: Gol_M2_2013_cin_Cy5


title: Gol_re_2013_cin_Cy3


title: Gol_re_2012_cin_Cy3

source_name: Golden delicious apple fruit flesh, at harvest, 2012


title: Gol_M2_2012_cin_Cy5

source_name: Golden delicious apple fruit flesh, 2 months after cold storage, 2012


title: HuBM_CD19+_CD138+_9-16


title: HuBM_CD19+_CD138+_9-23


title: Gol_M2_2012_cin_Cy3


title: HuBM_PC CD19+_CD138+


title: T17p1_H3

value: Ulcerative Colitis (UC)


title: Gra_re_2012_cin_Cy5

source_name: Granny Smith apple fruit flesh, at harvest, 2012

value: Granny Smith


title: Gra_re_2012_cin_Cy3


title: Gra_M2_2012_cin_Cy5

source_name: Granny Smith apple fruit flesh, 2 months after cold storage, 2012


title: Gra_M2_2012_cin_Cy3


title: Gra_M2_2011_cin_Cy3

source_name: Granny Smith apple fruit flesh, 2 months after cold storage, 2011


title: Gra_re_2011_cin_Cy5

source_name: Granny Smith apple fruit flesh, at harvest, 2011


title: T17p1_D8

source_name: tissue biopsy

value: golimumab

value: Week 6


title: PC-2_CD19+/CD20-

description: Gene expression data from FACS purified human bone-marrow CD19+/CD20- cells

source_name: FACS purified human bone marrow CD19+/CD20- cells


title: T17p1_G10

value: No


title: T17p1_B8


title: Gra_M2_2011_cin_Cy5


title: T17p1_F1


title: HuBM CD19+_CD138+


title: Gra_re_2011_cin_Cy3


title: T17p1_D7


title: H07_M1_2012_Cy3

source_name: H074 apple fruit flesh, 1 month after cold storage, 2012

value: Hybride H074

value: Cold storage for 30 days after harvest


title: HuBM_CD19+_CD20- (no.2)


title: HuBM_CD19+_CD20-_YL_11-11


title: W05_M1_2012_Cy5

source_name: W055 apple fruit flesh, 1 month after cold storage, 2012

value: Hybride W055


title: HuBM_CD19+_CD20-_9-23


title: HuBM_CD19+_CD20-_9-17


title: H07_M1_2012_Cy5


title: W05_M1_2012_Cy3


title: T17p1_H10

value: Yes


title: T17p2_D1


title: W05_M1_2011_Cy5

source_name: W055 apple fruit flesh, 1 month after cold storage, 2011

value: Fruit


title: H07_M1_2011_Cy3

source_name: H074 apple fruit flesh, 1 month after cold storage, 2011

value: Parenchyma


title: HuBM_CD19+_CD20-_9-16


title: T17p1_A5


title: V00_M2_2012_Cy5

source_name: V002 apple fruit flesh, 2 months after cold storage, 2012

value: Hybride V002


title: H07_M1_2011_Cy5

value: Wild-type


title: T17p1_B10


title: HuBM_CD19+_CD20-


title: T17p1_B9

value: Week 0


title: W05_M1_2011_Cy3

value: Harvested at optimum maturity


title: H08_M2_2012_Cy3

source_name: H088 apple fruit flesh, 2 months after cold storage, 2012

value: Hybride H088

value: Cold storage for 60 days after harvest


title: T17p2_C7

value: colon mucosa

value: Ulcerative Colitis (UC)


title: H08_M2_2011_Cy3

source_name: H088 apple fruit flesh, 2 months after cold storage, 2011


title: H08_M2_2011_Cy5


title: HuBM_CD19+_CD20+_YL_11-11

description: Gene expression data from FACS purified human bone-marrow CD19+/CD20+ cells

source_name: FACS purified human bone marrow CD19+/CD20+ cells

value: Bone Marrow


title: V00_M2_2011_Cy5

source_name: V002 apple fruit flesh, 2 months after cold storage, 2011


title: T17p1_D11

value: golimumab


title: HuBM_CD19+_CD20+_9-23


title: T17p1_F11


title: V00_M2_2012_Cy3


title: HuBM_CD19+_CD20+_9-17


title: V00_M1_2012_Cy5

source_name: V002 apple fruit flesh, 1 month after cold storage, 2012


title: H08_M2_2012_Cy5


title: Gol_re_2012_cin_Cy5

source_name: Golden delicious apple fruit flesh, at harvest, 2012

value: Golden delicious


title: H08_M1_2012_Cy3

source_name: H088 apple fruit flesh, 1 month after cold storage, 2012


title: H08_M1_2012_Cy5


title: T17p2_B9


title: HuBM_CD19+_CD20+


title: HuBM_CD19+_CD20+ (no.2)


title: V00_M1_2012_Cy3


title: V00_M1_2011_Cy5

source_name: V002 apple fruit flesh, 1 month after cold storage, 2011


title: T17p2_D8


title: T17p2_D9


title: H08_M1_2011_Cy3

source_name: H088 apple fruit flesh, 1 month after cold storage, 2011


title: T17p1_F5


title: H08_re_2012_Cy3

source_name: H088 apple fruit flesh, at harvest, 2012


title: T17p1_C12

source_name: tissue biopsy


title: H08_M1_2011_Cy5


title: T17p2_D7


title: V00_M2_2011_Cy3


title: H08_re_2012_Cy5


title: H08_re_2011_Cy3

source_name: H088 apple fruit flesh, at harvest, 2011


title: H08_re_2011_Cy5


title: T17p2_H8


title: V00_re_2011_Cy3

source_name: V002 apple fruit flesh, at harvest, 2011


title: V00_M1_2011_Cy3


title: V00_re_2012_Cy5

source_name: V002 apple fruit flesh, at harvest, 2012


title: T17p2_C5


title: V00_re_2012_Cy3


title: V00_re_2011_Cy5


title: ChIP-seq from omental fat pad (ENCLB331IQP)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR968GYD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR968GYD
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB331IQP
size range: 200-600

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens female adult (53 years) omental fat pad tissue

tag: antibody

value: Control

value: omental fat pad

value: tissue

tag: description

value: EnTEX:Adipose - Visceral (Omentum)

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

value: adult

value: 53 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Kristin Ardlie

tag: link

value: ENCBS368SNX at ENCODE; https://www.encodeproject.org/ENCBS368SNX/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/