title: L90


title: L91

status: Public on Sep 30 2018

type: genomic

city: Hefei

first: Xuelei

last: Zhang

state: China

address: Science and teaching building, Meishan Road 81, Hefei230032, Anhui Province, China

department: Dermatology

country: China

institute: Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University

description: Genomic DNA extracted from whole blood was genotyped using Human610-Quad BeadChip (Illumina).

hyb_protocol: The whole genome genotyping was conducted at Chinese National Human Genome Center at Shanghai, China. Approximately 200ng of genomic DNA was used for genotyping analysis. Briefly, each sample was whole-genome amplified, fragmented, precipitated and resuspended in appropriate hybridization buffer.

scan_protocol: After hybridization, the BeadChip oligonucleotides were extended by a single labeled base,which was detected by fluorescence imaging with an Illumina Bead Array Reader.

label: not provided

molecule: genomic DNA

organism: Homo sapiens

source_name: Leprosy

label_protocol: not provided

extract_protocol: Genomic DNA was extracted from peripheral blood lymphocytes by standard procedures (Miller et al, 1988) using Flexi Gene DNA kits (QIAGEN, Germany)

tag: gender

value: Male

tag: tissue

value: Whole blood

tag: disease state

value: granulomatous disease


title: L92

data_processing: Genomic DNA extracted from whole blood was genotyped using Human610-Quad BeadChip (Illumina).


title: pNET_unph_mock_rep1

type: SRA

city: Guangzhou

first: Zhicheng

last: Dong

state: Guangdong

address: 230 Wai Huan Xi Road,Guangzhou Higher Education Mega Center

department: School of Life Sciences

institute: Guangzhou University

description: nascent RNA

library_source: transcriptomic

data_processing:
Library strategy: PNET-seq
After trimming of adapter and filtering of low quality data by Cutadapt v1.2.1, reads originating from rRNA were filtered by aligning against an index consisting of the 45S and 5S transcripts using STAR v2.5.3a and unmapped reads were subsequently aligned to the Arabidopsis genome TAIR10. Only uniquely mapped reads were retained, and the 5 coordinate of each read was used as the position of engaged polymerase.
genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include counts of engaged Pol II at each position on chromosome

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: The Arabidopsis (Col-0 ecotype) seeds were germinated and grown in 1/2 MS for 12 days at 20°C under 16 hour light/8 hour dark.

extract_protocol:
The tissue powder was solubilized in 30 ml lysis buffer (50 mM HEPES, pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 10% glycerol, 5 mM 2-mercaptoethanol, 2 μg/ml pepstatin A, 2 μg/ml aprotinin, 1 mM PMSF), mixed well and filtrated through 110 μm nylon mesh and a 40 μm cell strainer.  The nuclei were spanned down at 3,200 g for 20 min at 4°C, followed by two washes with HBB buffer (25 mM Tris–HCl, pH 7.6, 0.44 M sucrose, 10 mM MgCl2, 0.1% Triton-X, 10 mM 2-mercaptoethanol) and HBC buffer (20 mM Tris–HCl, pH 7.5, 352 mM sucrose, 8 mM MgCl2, 0.08% Triton-X, 8 mM 2-mercaptoethanol, 20% glycerol).
The obtained nuclei pellet were resuspended with 1 ml MNase buffer (20 mM Tris–HCl, pH 8.0, 5 mM NaCl, and 2.5 mM CaCl2) and digested with 20 U MNase (TaKaRa, 20U/μl) for 5 minutes at 37°C rotating at 1,400 rpm. Stopped the digestion by adding 40 μl 500 mM EDTA. Pol II-nascent RNA complex was released by mild sonication. Supernatants were collected by centrifuging at 16,000 g for 5 min at 4°C and Pol II complex were immunoprecipitated according to Nojima et al. [14]. The Pol II bond nascent RNAs were treated by T4 PNK on beads and extracted with 500μl TRIzol Reagent (Invitogen). The IP RNA was resolved on an 8% TBE-urea polyacrylamide gel and RNA with size from 35-100 nt was recovered. The 35-100 nt IP RNA was used to construct the NET-SEQ cDNA library with NEXTflex™ Small RNA-Seq Kit v3 (Bioo Scientific) according to the manual. The cDNA library was resolved in a non-denaturing 6% TBE polyacrylamide gel and size region 150-230 bp was recovered. cDNA library concentration was determined by Qubit QuantIT (Invitrogen) and kapa quantitative realtime PCR.

treatment_protocol: samples were treated with DMSO for one hour

tag: ecotype

value: seedling

tag: age

value: 12 days

tag: antibody

value: name:8WG16; Clonality:Monoclonal; Supplier:Abcam; Catalog number:Ab817


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: High Fat (sample 46)

type: RNA

city: Aberdeen

first: Claus

last: Mayer

address: Greenburn Road

country: United Kingdom

institute: Biomathematics & Statistics Scotland

description: Gene Expression in Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: High Fat

hyb_protocol: Hybridization of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: The raw data were pre-processed and normalized using the R/Bioconductor library gcrma

label: biotin

organism: Mus musculus

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix, as per the manufacturer's instructions.

growth_protocol: Male C57BL/6J mice were obtained from Charles River at three weeks of age and were maintained on normal lab chow. Mice were housed in pairs. At twelve weeks of age, all mice received control diet as a run-in for four weeks.

extract_protocol: Total RNA was extracted fwith TRIzol reagent (Invitrogen, Carlsbad, CA), treated with DNAse and purified on columns using the RNeasy Mini Kit (Qiagen, Venlo, The Netherlands). RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) with 6000 Nano Chips. RNA was judged as suitable only if samples showed intact bands of 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products.

treatment_protocol: Mice were maintained for 1 or 4 weeks on either a HFD (45% kCal from fat) or LFD (10% kCal from fat) ( composition based on D12451 and D12450B respectively Research Diets, NJ, US). The fat source in this experiment was palm oil instead of lard.  Diets were prepared by Research Diet Services (Wijk bij Duurstede, The Netherlands). Mice were then challenged with three intraperitoneal (IP) injections of recombinant mouse leptin (2 mg/kg body weight) (R&D Systems, Abingdon, UK) or vehicle at 24, 15 and approximately 3 hours prior to killing in the early morning.

tag: strain

value: male

value: 16 week old

tag: week

tag: treatment

value: lept

tag: diet

value: High Fat

value: hypothalamus


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: Low Fat (sample 44)

description: Gene Expression in Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: Low Fat

value: Low Fat


title: GRO_30_rep2

description: nascent RNA

data_processing:
Library strategy: GRO-seq
After trimming of adapter and filtering of low quality data by Cutadapt v1.2.1, reads originating from rRNA were filtered by aligning against an index consisting of the 45S and 5S transcripts using STAR v2.5.3a and unmapped reads were subsequently aligned to the Arabidopsis genome TAIR10. Only uniquely mapped reads were retained, and the 5 coordinate of each read was used as the position of engaged polymerase.
genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include counts of engaged Pol II at each position on chromosome

extract_protocol:
The fine seedling powder was solubilized in 30 ml extraction buffer (2 M hexylene glycol, 20 mM PIPES pH 7.0, 10 mM MgCl2, 5 mM 2-mercaptoethanol) and filtrated through 110 μm and 60 μm nylon mesh. Add triton X-100 into the lysates to the final concentration of 1% and leave on ice for 10 minutes. Cell fractionation was performed using a 30%-80% percoll gradient solution and nuclei were collected at the 30%-80% interface.
Breifly, nascent RNA was treated with T4 PNK (NEB) and followed by acidic phenol/chloroform purification. Phosphorylated nascent RNA was polyA tailed using E. coli Poly(A) Polymerase (NEB) and reverse transcribed by superscript III reverse transcriptase (Invitrogen) with RT primer (GRO-oligo2, synthesized by IDT DNA, 5’-/5Phos/GA TCG TCG GAC TGT AGA ACT CTG AAC /idSp/CC TTG GCA CCC GAG AAT TCC ATT TTT TTT TTT TTT TTT TTT VN-3’). Free RT primer was removed by Exonuclease I (Fermentas) and RNA was eliminated by alkaline hydrolysis. The resulted 1st-strand cDNA was resolved from a 10% TBE-urea polyacrylamide gel. The cDNA with size above120 nt was recovered and self-ligated using CircLigase (Epicentre). The circularized single-stranded cDNA was relinearized by APE 1 (NEB). The linearized cDNA was recovered again by a 10% TBE-urea polyacrylamide gel. The cDNA was PCR amplified by Kapa HiFi polymerase with the illumina compatible primers (Universal primer F 5’GAT CGT CGG ACT GTA GAA CTC TGA ACG TGT AGA TCT CGG TGG TCG CCG TAT CAT T 3’, Reverse Index primer R 5’CAA GCA GAA GAC GGC ATA CGA GAT NNNNNN GTG ACT GGA GTT CCT TGG CAC CCG AGA ATT CCA 3’, NNNNNN: index). The PCR reaction starts with a 30s denaturation at 94˚C, followed by 12-14 cycles of 10s denaturation at 94˚C, 15s annealing at 60˚C and 15s extension at 72˚C. The PCR product was resolved in a non-denaturing 8% TBE polyacrylamide gel and size region 200-330 bp was recovered. cDNA library concentration was determined by Qubit QuantIT (Invitrogen) and kapa quantitative realtime PCR according to the manual.

treatment_protocol: run-on assay was performed at a temprature of 30 oC


title: GRO_30_rep1

description: nascent RNA


title: GRO_22_rep2

description: nascent RNA

treatment_protocol: run-on assay was performed at a temprature of 22 oC


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: Low Fat (sample 45)


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: High Fat (sample 43)

description: Gene Expression in Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: High Fat


title: GRO_22_rep1

description: nascent RNA


title: L934


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: High Fat (sample 42)


title: pNET_unph_mock_rep2

description: nascent RNA


title: GRO-sar_rep2

description: nascent RNA

treatment_protocol: run-on assay was performed without sarkosyl


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: Low Fat (sample 41)

description: Gene Expression in Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: Low Fat

value: ctrl


title: L961


title: L954


title: GRO-sar_rep1

description: nascent RNA


title: pNET_Ser2P_rep1-2

description: nascent RNA

value: name:CMA602; Clonality:Monoclonal; Supplier:MBL Life science; Catalog number:MABI0602


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: Low Fat (sample 40)


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: High Fat (sample 38)

description: Gene Expression in Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: High Fat


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: High Fat (sample 39)


title: L964

value: Female


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: Low Fat (sample 37)

description: Gene Expression in Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: Low Fat


title: L93


title: L97


title: L98


title: L973


title: GRO-seq_rep1-2

description: nascent RNA


title: L982


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: Low Fat (sample 36)


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: Low Fat (sample 34)


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: Low Fat (sample 35)


title: L983


title: L985


title: L986


title: GRO-seq_rep2-2

description: nascent RNA


title: L99


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: Low Fat (sample 33)


title: L978


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: Low Fat (sample 32)


title: si-NRDE2-2 rep3

city: Oxford

first: Alan

last: Jiao

state: MA

address: Old Road Campus Research Building

institute: Ludwig Institute for Cancer Research, Oxford University

description:
cDNA
AJ6

data_processing:
Reads were aligned and quantified using STAR v2.5.1b
Differential expression was performed by DESeq2 v1.10.1
Data processing was performed as part of the VIPER analysis pipeline (https://bitbucket.org/cfce/viper/).
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing FPKM values for each sample

growth_protocol: MDA-MB-231 cells were grown in RPMI 1640 medium supplemented with 10% FBS and 5% Penicillin/Streptomycin, in 5% CO2 and at 37C

extract_protocol:
Total RNA was extracted 48h post-transfection using the mirVana RNA Isolation kit (Thermo Fisher) according to the manufacturer's protocol
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500ng of purified total RNA according to the manufacturer’s protocol

treatment_protocol: Cells were transfected with 20nM control or NRDE2-targeting siRNAs using lipofectamine RNAiMAX for 48h

tag: cell line

tag: cell type

value: Triple negative breast cancer cell line

tag: sirna

value: 20nM si-NRDE2-2 (Ambion s30064)


title: si-NRDE2-2 rep2

description:
cDNA
AJ5


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: High Fat (sample 30)


title: si-Control rep1

description:
cDNA
AJ1

value: 20nM si-Control (Ambion AM4611)


title: si-NRDE2-2 rep1

description:
cDNA
AJ4


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: Low Fat (sample 29)


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: High Fat (sample 27)


title: si-Control rep3

description:
cDNA
AJ3


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: High Fat (sample 31)


title: OAW42_Aza_E2

city: Grand Rapids

first: Peter

middle: A

last: Jones

state: MI

address: 333 Bostwick Ave

department: Center for Epigenetics

country: USA

institute: Van Andel Research Institute

description:
rRNA removal
OAW42 protein coding.txt

data_processing:
alignment using HISAT2
compute FPKM using featureCounts after splitting strands
base count output by RepeatMasker program to caculate base coverage of interspersed repeats and low complexity DNA sequences
Genome_build: hg19
Supplementary_files_format_and_content: txt containing FPKM of gene expression as output by featureCounts, and tsv containing base counts of repeatative elements

growth_protocol: A2780, CAOV3, PEO14, and OAW42 ovarian cancer cell lines were authenticated using the American Type Culture Collection (ATCC) human cell line authentication service. All cell lines were cultured according to standard mammalian tissue culture protocols using sterile technique. A2780 were maintained in McCoy’s 5A medium, PEO14 cells in Roswell Park Memorial Institute (RPMI) 1640 medium and CAOV3 and OAW42 in Dulbecco’s Modified Eagle Medium (DMEM). All media (from GIBCO) were supplemented with 10% fetal bovine serum (Sigma-Aldrich) and 1% penicillin/streptomycin (GIBCO). VenorTM GeM Mycoplasma Detection Kit (Sigma-Aldrich) was used every three months to confirm all cell lines were mycoplasma-free.

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Zymo Direct-Zol RNA mini prep kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared by the Genomic Services Laboratory (GSL) at HudsonAlpha Institute for Biotechnology using established protocols for directional RNA seq with ribosomal RNA reduction
Total RNA sequencing with ribosomal RNA depleted

treatment_protocol: A2780 and OAW42 cells were treated with 100 nM 5-aza-CdR for 48 h and subsequently 400 nM G9Ai for 72 h. CAOV3 and PEO14 cells were treated with two consecutive daily doses of 100 nM 5-aza-CdR for 48 h and subsequently a dose of 400 nM G9Ai for 72 h. Cells were harvested at day 5 after the start of the treatment.

value: human ovarian serous adenocarcinoma cell line

tag: replicates


title: OAW42_G9Ai_E2

description:
rRNA removal
OAW42 protein coding.txt

value: G9A inhibitor


title: OAW42_Combo_E2

description:
rRNA removal
OAW42 protein coding.txt

value: Combination


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: High Fat (sample 26)


title: si-Control rep2

description:
cDNA
AJ2


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: Low Fat (sample 24)

description: Gene Expression in Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: Low Fat


title: OAW42_PBS_E2

description:
rRNA removal
OAW42 protein coding.txt

value: PBS


title: OAW42_Combo

description:
rRNA removal
OAW42 protein coding.txt


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: Low Fat (sample 28)


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: High Fat (sample 23)


title: OAW42_PBS

description:
rRNA removal
OAW42 protein coding.txt


title: OAW42_G9ai

description:
rRNA removal
OAW42 protein coding.txt


title: P0 KO 2

city: Mishima

first: Yuzuru

last: Kato

state: Shizuoka

address: 1111 Yata

department: Division of Mammalian Development

country: Japan

institute: National Institute of Genetics

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 50 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: XX gonads at P0 (Elavl2 knockout)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.20 µg RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were housed in special pathogen free room

extract_protocol: Total RNAs were extracted by QIAGEN (Rneasey Mini Kit) according to the manufacture's protocol

treatment_protocol: Embryonic and newborn gonads were disected in ice-cold PBS and were immeadiately frozen in RNAlater (Ambion). Frozen tissues were stored at -80 degree until total RNA extraction.

value: female

value: ovary

tag: sample type

value: mixed

tag: developmental stage

value: newborn


title: P0 KO 3


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: Low Fat (sample 21)

value: male

value: 16 week old


title: PEO14_Aza_E2

description:
rRNA removal
PEO14 protein coding.txt

value: human high grade ovarian serous adenocarcinoma cell line


title: PEO14_Combo_E2

description:
rRNA removal
PEO14 protein coding.txt


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: Low Fat (sample 25)

value: lept

value: Low Fat

value: hypothalamus


title: P0 WT 3

source_name: XX gonads at P0 (wildtype)


title: PEO14_G9Ai_E2

description:
rRNA removal
PEO14 protein coding.txt


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: Low Fat (sample 20)

value: ctrl


title: P0 KO 1


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: High Fat (sample 19)

description: Gene Expression in Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: High Fat

value: High Fat


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: High Fat (sample 22)


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: High Fat (sample 18)


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: High Fat (sample 15)


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: Low Fat (sample 16)


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: Low Fat (sample 17)


title: E17.5 KO 2

source_name: XX gonads at E17.5 (Elavl2 knockout)

value: embryo


title: OAW42_Aza

description:
rRNA removal
OAW42 protein coding.txt

value: human ovarian serous adenocarcinoma cell line


title: P0 WT 1


title: P0 WT 2


title: PEO14_PBS_E2

description:
rRNA removal
PEO14 protein coding.txt


title: E17.5 WT 2

source_name: XX gonads at E17.5 (wildtype)


title: E17.5 KO 1


title: PEO14_Aza

description:
rRNA removal
PEO14 protein coding.txt


title: E17.5 WT 1


title: PEO14_G9ai

description:
rRNA removal
PEO14 protein coding.txt

value: G9A inhibitor


title: E17.5 WT 3


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: Low Fat (sample 14)


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: Low Fat (sample 13)


title: PEO14_PBS

description:
rRNA removal
PEO14 protein coding.txt


title: CAOV3_Combo_E2

description:
rRNA removal
CAOV3 protein coding.txt

value: Combination


title: E17.5 KO 3


title: CAOV3_Aza_E2

description:
rRNA removal
CAOV3 protein coding.txt


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: High Fat (sample 12)


title: E15.5 KO 3

source_name: XX gonads at E15.5 (Elavl2 knockout)


title: CAOV3_G9Ai_E2

description:
rRNA removal
CAOV3 protein coding.txt


title: DE442_S11

city: York

first: Katherine

last: Newling

address: Wentworth Way

department: Biology

institute: University of York

description:
sleuth_matrix_est_counts.txt
sleuth_test_results.txt

data_processing:
Illumina HiSeq 3000 sequencing
Reads were trimmed using Cutadapt v.1.8.3
Reads were pseudo-aligned to Rhodobacter Capsulatus SB1003 transcriptome using Kallisto 0.43.1
Differential expression anlaysis was performed by fitting linear models in Sleuth 0.29.0
Genome_build: SB1003 reference transcriptome (GenBank CP001313.1) and plasmid pRCB133 (GenBank CP001312.1)
Supplementary_files_format_and_content: sleuth_matrix_est_counts.txt: tab-delimited text file containing estimated count values from Kallisto quantification step; sleuth_test_results.tx: tab-delimted text file containing output from Sleuth linear modelingl looking at the effect of strain - p-values, qvalues, B values, std error of B values

organism: Rhodobacter capsulatus DE442

source_name: early stationary growth phase cells

growth_protocol: RCV medium  under anaerobic, photoheterotrophic conditions at 30℃

extract_protocol:
Cells were harvested at early stationary growth phase. Total RNA was purified using the NucleoSpin RNA Kit (Macherey-Nagel) and DNAseI treated on column according to the manufacturer’s protocol.
RNA yield was quantified and quality checked using a Nanodrop spectrophotometer and Aglient bioanalyser. Ribosomal RNA was removed from 1 µg good quality total RNA using the Ribo-Zero rRNA Removal Kit (Bacteria; Illumina). Libraries were then prepared from rRNA-depleted samples using the NEBNext RNA Ultra II Directional Library preparation kit for Illumina, with single 6 bp indices, according the manufacturer's guidelines for insert sizes of approximately 200 - 350 bp. Libraries were pooled at equimolar ratios, and the pool was sent for 2 x 150 base paired end sequencing on a HiSeq 3000 at the University of Leeds Next Generation Sequencing Facility.

tag: genotype/variation

value: GTA hyperproducer


title: DE442_S12


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: Low Fat (sample 10)

tag: gender


title: E15.5 KO 2

value: female

tag: tissue


title: Pregnant endometrium mare 4

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

data_processing:
Trimmomatic v.0.32.2, remove low quality bases from the 3′ end by sliding window approach (quality score 20 in average across 4 bases), headcrop of 2 bases, remove sequences below a minimal length of 30 nt after the trimming steps
HISAT2 v2.0.3, mapping to the equine genome sequence assembly
QuasR Qcount, generation of read count table for all annotated equine genes based on the NCBI GFF3 annotation file
Counts per million (CPM) per sample filtering tool (Chen et al. 2014), remove sequences with negligible read counts
Genome_build: EquCab2.0
Supplementary_files_format_and_content: tab-delimited text files, Readcounts_whole_endo.txt contains mapped read counts, CPM_Eca_endo_biopTrendedDisp.txt contains counts per million (cpm) values of the genes that passed the CPM filter

organism: Equus caballus

source_name: endometrium

growth_protocol: Samples were collected from 4 normal cycling Bavarian Warmblood mares belonging to the Bavarian principal and state stud of Schwaiganger, Germany.

extract_protocol:
Total RNA was isolated from the endometrial biopsy samples using Trizol® Reagent (Invitrogen GmbH, Karlsruhe, Germany) according to the manufacturer’s instructions. Quantity and purity of RNA were measured with a NanoDrop 1000 (PEQLAB Biotechnologie GMBH, Erlangen, Germany). Quality of total RNA was determined electrophoretically with an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). RNA integrity (RIN) values ranged from 8.3 to 9.2.
The mRNA-Seq sample preparation kit (Illumina, San Diego, USA) was used for preparation of RNA-Seq libraries. Library preparation followed the manufacturers instructions. Briefly, poly(A)-containing RNA was purified with oligo-dT-coated magnetic beads starting from 5 µg total RNA and fragmented under elevated temperature using divalent cations. The obtained cleaved RNA fragments were reverse transcribed to first strand cDNA using Superscript II reverse transcriptase (Invitrogen, Karlsruhe, Germany) and random primers, followed by second strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments underwent an end-repair process with T4 DNA polymerase, Klenow DNA polymerase and T4 Polynucleotide kinase, addition of a single ´A´-base, and ligation of adapters. Ligation products were subsequently separated on a 2% agarose gel (Biozym Phor Agarose, Biozym Scientific GmbH, Hess. Oldendorf, Germany) and a gel slice was cut out (X-Tracta, Biozym Scientific GmbH) in the 200 bp (±25 bp) range. After isolation of the DNA from the gel slice (QIAquick Gel Extraction Kit, Qiagen, Hilden, Germany), cDNA fragments were amplified through 15 cycles of PCR (Phusion DNA polymerase, New England Biolabs GmbH, Frankfurt a. Main, Germany) to generate the final sequencing libraries. Concentration of the cDNA fragments was estimated on an Agilent DNA 1000 chip (Agilent Technologies) and with the Qubit Fluorometer (Invitrogen).

treatment_protocol: Follicular development and ovulation were monitored routinely by daily transrectal palpation and ultrasound examination. When mares developed an ovarian follicle of approximately 35 mm in diameter, accompanied by prominent endometrial edema, they were treated with 1500 IU human chorionic gonadotropin i.v. (Ovogest®, Intervet Deutschland GmbH, Unterschleissheim, Germany) to induce ovulation. All mares were inseminated artificially with >500 x 10^6 freshly collected, progressively motile, extended spermatozoa from one fertile stallion. Insemination was performed 24 h after induction of ovulation and was repeated if ovulation had not occurred after 48 h. Endometrial samples were obtained by transcervical biopsy. Samples were collected on day 12 after flushing of the uterus. Pregnancy was proved by ultrasonographic detection of an embryonic vesicle in the uterine lumen before flushing. Embryos were flushed transcervically without sedation using up to four times 1.5 l pre-warmed and sterile filtered phosphate buffered saline (DPBS, Lonza Verviers Sprl, Verviers, Belgium). The fluid was recovered directly into sterile glass bottles and subsequently, if necessary, filtered with an embryo filter system. For determination of peripheral plasma progesterone concentrations, blood samples were collected in EDTA tubes from the jugular vein on day 0 and directly after biopsy. In order to analyse tissue composition, the biopsy samples were cut transversely into six equal and plane-parallel slices. For quantitative stereological analyses, every second slice was transferred into embedding capsules. The remaining pieces of the biopsy samples were immediately transferred into vials containing 4 ml RNAlater (Ambion, Huntingdon, Cambridgeshire, UK) for mRNA expression analysis. The vials were cooled on ice and incubated overnight at 4°C. Samples were stored at -80°C until further processing.

tag: day of pregnancy or estrous cycle

value: Day 12 of pregnancy


title: Pregnant endometrium mare 3


title: DE442_S10


title: E15.5 KO 1

value: ovary

value: mixed


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: Low Fat (sample 6)

value: male


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: Low Fat (sample 9)

value: 16 week old


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: High Fat (sample 11)


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: High Fat (sample 7)


title: CAOV3_PBS_E2

description:
rRNA removal
CAOV3 protein coding.txt

value: human high grade ovarian serous adenocarcinoma cell line

value: PBS


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: High Fat (sample 8)


title: Pregnant endometrium mare 2


title: E15.5 WT 1

source_name: XX gonads at E15.5 (wildtype)


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: Low Fat (sample 5)

value: Low Fat


title: DE442_S09


title: E15.5 WT 3


title: Pregnant endometrium mare 1


title: E15.5 WT 2


title: CAOV3_Combo

description:
rRNA removal
CAOV3 protein coding.txt


title: CAOV3_Aza

description:
rRNA removal
CAOV3 protein coding.txt


title: Control endometrium mare 4

value: Day 12 of estrous cycle


title: DE442_S08


title: DE442_S07


title: CAOV3_G9ai

description:
rRNA removal
CAOV3 protein coding.txt


title: DE442_S06


title: Control endometrium mare 2


title: Control endometrium mare 3


title: DE442_S05


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: High Fat (sample 3)

value: ctrl

value: hypothalamus


title: Control endometrium mare 1


title: A2780_Combo_E2

description:
rRNA removal
A2780 protein coding.txt

value: human ovarian carcinoma cell line


title: CAOV3_PBS

description:
rRNA removal
CAOV3 protein coding.txt


title: A2780_Aza_E2

description:
rRNA removal
A2780 protein coding.txt


title: A2780_G9Ai_E2

description:
rRNA removal
A2780 protein coding.txt


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: High Fat (sample 4)

value: High Fat


title: A2780_PBS_E2

description:
rRNA removal
A2780 protein coding.txt


title: A2780 Combo

description:
rRNA removal
A2780 protein coding.txt


title: A2780 Aza

description:
rRNA removal
A2780 protein coding.txt


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: Low Fat (sample 1)


title: Treated with DSF+C23, rep 3

city: Belfast

first: Shi-qi

last: An

address: Lisburn Road

institute: Queen's University Belfast

hyb_protocol: Following fragmentation, cRNA were hybridized  on GeneChip P. aeruginosa Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip 3000 7G scanner

data_processing: Biomedical Genomics Workbench 4

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa airway infection treated with DSF+C23

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA

growth_protocol: P.aeruginosa strains were grown in LB at 37°C overnight.

extract_protocol: RNA was isolated from airway homogenate pellets using Trizol according to the manufacturer's instructions. Samples were treated with DNAse, then rRNA was removed from 1 to 5 μg of total RNA using the RiboZero kit for Gram-negative bacteria. rRNA-depleted samples were concentrated by EtOH precipitation. cDNA synthesis and hybridization to Affymetrix GeneChip P. aeruginosa genome arrays.

treatment_protocol: Infected animals as described above were euthanized 24 h post-infection.

tag: host strain

tag: host strain gener

tag: infection tissue

value: mouse lung

tag: bacteria infection

value: P. aeruginosa in vivo infection

tag: treated with

tag: time point

value: 24 h post-infection


title: Treated with DSF+C23, rep 2

value: female


title: Treated with DSF+C23, rep 1


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: Low Fat (sample 2)

tag: strain

tag: age

tag: week

tag: treatment

tag: diet


title: Treated with DSF, rep 3

source_name: Pseudomonas aeruginosa airway infection treated with DSF

value: DSF


title: A2780 G9Ai

description:
rRNA removal
A2780 protein coding.txt

tag: cell line

tag: cell type

value: G9A inhibitor

tag: replicates


title: Treated with DSF, rep 1


title: Caco-2 cells 240 minutes after infection by the C. jejuni cas9 deletion strain (delta_Cj1523), rep2

city: Wageningen

last: van Baarlen

address: De Elst 1

department: Animal Sciences

country: Netherlands

institute: Wageningen University

description: After 240 minutes of Caco-2 cell infection with Campylobacter jejuni cas9 deletion strain, Caco-2 cells were incubated with TriZol reagents until lysis was complete, then RNA extraction and purification were performed. RNA was extracted from a single well of a 6-well microtiter plate.

hyb_protocol: Labelled samples were hybridised on Affymetrix GeneChip Human Gene 1.1 ST arrays, provided in plate format. Hybridisation, washing and scanning of the array plates were performed on an Affymetrix GeneTitan Instrument, according to the manufacturer's recommendations. Detailed protocols can be found in the Affymetrix WT Terminal Labelling and Hybridisation User Manual (part no. 702808 revision 4), and are also available upon request.

scan_protocol: The Human Gene 1.1 ST array was scanned on an Affymetrix GeneChip 3000 7G scanner. Detailed methods are described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual, Revision 3, from Affymetrix.

data_processing: Packages from the Bioconductor project (Gentleman et al., 2004) integrated in an in-house developed on-line management and analysis database for multiplatform microarray experiments (Lin et al., J Integr Bioinform. 2011 Jul 21;8(2):160. doi: 10.2390/biecoll-jib-2011-160) were used for analysing the scanned Affymetrix arrays.

source_name: Caco-2 cell line, C. jejuni cas9 deletion strain, 240 minutes

label_protocol: The Ambion WT Expression kit (Life Technologies, cat. no. 4411974), in conjunction with the Affymetrix GeneChip WT Terminal Labelling kit (Affymetrix, Santa Clara, CA; cat. no. 900671), was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction.

growth_protocol: Human intestinal epithelial cell line Caco-2 (human epithelial colorectal adenocarcinoma cells) were maintained in Dulbecco's modified Eagle's medium (DMEM) (Thermo Fisher Scientific, Bleiswijk, The Netherlands) supplemented with 10% fetal bovine serum (FBS) (Thermo Fisher Scientific), 100 U/ml penicillin, 100 µg/ml streptomycin and 1% non-essential amino acids (NEAA) (Thermo Fisher Scientific). The cells were cultured in a 75-cm2 flask (Greiner Bio-one, Alphen aan den Rijn, The Netherlands) at 37°C and 5% CO2 in a humidified air incubator.

extract_protocol: At each assay time point, 1 ml of TRIzol® reagent (Ambion Life Technologies) was added to the appropriate wells and total RNA was extracted from the Caco-2 cells following the manufacturer's protocol. The extracted, air-dried RNA was resuspended in 100 µl MilliQ water and further purified and desalted using Qiagen RNeasy Mini Kit spin columns, following the manufacturer's instructions to make it suitable for microarray hybridizations. RNA quantity and quality were assessed spectrophotometrically via a NanoDrop device (ND-1000, NanoDrop Technologies, Wilmington, DE, USA) and with 6000 Nano chips via a Bioanalyzer 2100 device (Agilent, Santa Clara, CA, USA), respectively.

treatment_protocol: To investigate the transcriptome of Caco-2 cells infected with C. jejuni strains, cells were seeded in 6-well plates (Greiner Bio-one) at a density of 1.0 x 10[exp5] cells per well. Cells were allowed to grow to confluence for 19 days and infected; 3 biological replicates (3 different wells) were used per C. jejuni strain per time point. In total, in addition to the t=0 time point at which incubation with bacteria or medium-only (the control) was carried out, 5 time points of RNA extraction were used (30, 60, 120, 180, 240 minutes after infection), rationally chosen based on an earlier study (Louwen et al., 2012).

value: epithelial colorectal adenocarcinoma cell line

tag: infection

tag: timepoint

value: 240 minutes after infection


title: 72h

city: Nanjing

first: Heng

last: Liu

address: No. 123 Tian Fei Xiang, Mo Chou Road

department: Department of Pediatrics

institute: Nanjing Maternity and Child Health Care Hospital

description: Tübingenz

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to z10 whole genome using bwa 0.7.5a-r405 with parameters "mem -T 19".
CircRNA prediction of sequencing results by CIRI algorithm v1.1.
SRPBM (Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads (units in billion)/read length) used to normalize the expression of circRNAs.
For differential expression analysis of circRNAs, raw counts of reads that spanned a particular head-to-tail junction were analyzed using edgeR package (version 3.12.1) with TMM normalization in generalized linear model. The Trimmed Mean of M-values (TMM) normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change (FC) ≥2 and p< 0.05.
Genome_build: z10
Supplementary_files_format_and_content: tab-delimited text files include SRPBM values and junction reads for each Sample.

organism: Danio rerio

source_name: Embryo

extract_protocol:
Total RNA was isolated using the standard TRIzol (Invitrogen) protocol
Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit (Life Technology). The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio-analyzer. Strand-specific libraries were constructed by following the manufacturer’s instructions (Illumina)

treatment_protocol: Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability, UV disinfects and aerates the recycled water.The embryos were obtained after spontaneous mating from sexually mature wild-type (WT) adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development.

tag: tissue

value: Embryo

value: 72 hpf

tag: developmental stage

value: incubation

value: Tubingenz

tag: genotype

value: WT


title: 24h

description: Tübingenz

value: 24 hpf

value: segmentation


title: 4.5h

description: Tübingenz

value: 4.5 hpf

value: blastula


title: 8h

description: Tübingenz

value: 8 hpf

value: gastrula


title: 48h

description: Tübingenz

value: 48 hpf

value: throat


title: Treated with DSF, rep 2

tag: host strain

tag: host strain gener

value: female

tag: infection tissue

value: mouse lung

value: P. aeruginosa in vivo infection

value: DSF

value: 24 h post-infection


title: Caco-2 cells 240 minutes after infection by the C. jejuni wild-type strain (11168), rep2

description: After 240 minutes of Caco-2 cell infection with Campylobacter jejuni strain 11168, Caco-2 cells were incubated with TriZol reagents until lysis was complete, then RNA extraction and purification were performed. RNA was extracted from a single well of a 6-well microtiter plate.

source_name: Caco-2 cell line, C. jejuni wild-type strain, 240 minutes

value: epithelial colorectal adenocarcinoma cell line

value: C. jejuni wild-type strain (11168)

value: 240 minutes after infection


title: Caco-2 cells 240 minutes after infection by the C. jejuni cas9 deletion strain (delta_Cj1523), rep3


title: Caco-2 cells 240 minutes after infection by the C. jejuni cas9 deletion strain (delta_Cj1523), rep1


title: A2780 PBS

description:
rRNA removal
A2780 protein coding.txt

value: human ovarian carcinoma cell line

value: PBS


title: Wild type, rep 3

source_name: Pseudomonas aeruginosa airway infection

tag: bacteria infection

tag: time point


title: Wild type, rep 2


title: Wild type, rep 1


title: Caco-2 cells 240 minutes after infection by the C. jejuni wild-type strain (11168), rep3


title: Caco-2 cells 180 minutes after infection by the C. jejuni cas9 deletion strain (delta_Cj1523), rep3

description: After 180 minutes of Caco-2 cell infection with Campylobacter jejuni cas9 deletion strain, Caco-2 cells were incubated with TriZol reagents until lysis was complete, then RNA extraction and purification were performed. RNA was extracted from a single well of a 6-well microtiter plate.

source_name: Caco-2 cell line, C. jejuni cas9 deletion strain, 180 minutes

value: 180 minutes after infection


title: Caco-2 cells 180 minutes after infection by the C. jejuni cas9 deletion strain (delta_Cj1523), rep2


title: JM3334_S11: TFEB/TFE3 RAW264.7 MEFs 8h Etoposide rep 2

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,
then mapped to mm10 whole genome using HISAT2 aligner
count tables were generated using featureCounts (http://bioinf.wehi.edu.au/featureCounts/)

source_name: RAW264.7 macrophage cell line

growth_protocol: Null and CRISPR TFEB/TFE3 DKO RAW264.7 were grown were grown in DMEM with high glucose, GlutaMAX, sodium pyruvate and supplemented with 10% fetal bovine serum

extract_protocol:
RNA was isolated from samples with the PureLink RNA Mini Kit (Thermo Fisher 12183018A) or RNeasy Plus Mini Kit (QIAGEN 74134). Genomic DNA was removed from RNA preparations by DNAse digestion using QIAGEN RNAse-free DNAse Set (QIAGEN 79254)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were untreated (control) or treated with 100 microMolar Etoposide for 8 hours

value: RAW264.7 macrophage cell line

value: CRISPR TFEB/TFE3 DKO


title: JM3334_S10: TFEB/TFE3 RAW264.7 MEFs 8h Etoposide rep 1


title: JM3334_S7: Null RAW264.7 8h Etoposide rep 1


title: JM3334_S6: TFEB/TFE3 DKO RAW264.7 Control rep 3


title: TIG1 fibroblasts with siRNY1 & SeV_OSKM_d3_rep1

city: Kyoto

first: Satoshi

last: Gojo

address: 465 Kajii-cho, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

description: Gene expression in TIG-1 fibroblasts with siRNY1 & SeV_OSKM at d3_rep1

hyb_protocol: Hybridization and washing steps were using Gene Expression Wash Pack (Agilent Technology) according to the manufacturer's instructions.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using DNA MicroArray Scanner (Agilent Technologies).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software version 9.5.3 and further analyzed using GeneSpring GX software version 11.0.2. Data were normalized to the 75 th percentile (median).

source_name: Human Fibroblasts, d3, siRNY1, SeV_OSKM, replicate 1

label_protocol: 250 ng of total RNA was labelled with Cy3 using the Low RNA Fluorecent Linear Amplification Kit PLUS, One-Color (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: TIG-1 fibroblasts was grown in DMEM with 10% FBS and 1% antibiotics.

extract_protocol: Total RNA was extracted from each samples using the TRIzol Reagent (Life technologies, Inc.) and Direct-zol™ RNA MiniPrep Kit (Zymo Research)

treatment_protocol: Cells (1e5/well in 6 well plate) were seeded and transfected siRNAs using RNAiMAX reagent. Next day, cells were transduced OSKM using CytoTune-iPS 1.0 or 2.0. Three days after infection, cells were harvested for Microarray analysis.

value: TIG1 fibroblasts

tag: sirna


title: JM3334_S9: Null RAW264.7 8h Etoposide rep 3


title: JM3334_S8: Null RAW264.7 8h Etoposide rep 2


title: TIG1 fibroblasts with siNeg & SeV_OSKM_d3_rep1

description: Gene expression in TIG-1 fibroblasts with siNeg & SeV_OSKM at d3_rep1

source_name: Human Fibroblasts, d3, siNeg, SeV_OSKM, replicate 1

value: siNegative control


title: JM3334_S12: TFEB/TFE3 RAW264.7 MEFs 8h Etoposide rep 3


title: Caco-2 cells 180 minutes after infection by the C. jejuni cas9 deletion strain (delta_Cj1523), rep1


title: Caco-2 cells 30 minutes after infection by the C. jejuni wild-type strain (11168), rep2

description: After 30 minutes of Caco-2 cell infection with Campylobacter jejuni strain 11168, Caco-2 cells were incubated with TriZol reagents until lysis was complete, then RNA extraction and purification were performed. RNA was extracted from a single well of a 6-well microtiter plate.

source_name: Caco-2 cell line, C. jejuni wild-type strain, 30 minutes

value: 30 minutes after infection


title: TIG1 fibroblasts with siRNY1 & SeV_OSKM_d3_rep2

description: Gene expression in TIG-1 fibroblasts with siRNY1 & SeV_OSKM at d3_rep2

source_name: Human Fibroblasts, d3, siRNY1, SeV_OSKM, replicate 2


title: TIG1 fibroblasts with siNeg & SeV_OSKM_d3_rep2

description: Gene expression in TIG-1 fibroblasts with siNeg & SeV_OSKM at d3_rep2

source_name: Human Fibroblasts, d3, siNeg, SeV_OSKM, replicate 2


title: Caco-2 cells 30 minutes after infection by the C. jejuni wild-type strain (11168), rep3


title: Caco-2 cells 240 minutes after infection by the C. jejuni wild-type strain (11168), rep1


title: Caco-2 cells 120 minutes after infection by the C. jejuni cas9 deletion strain (delta_Cj1523), rep2

description: After 120 minutes of Caco-2 cell infection with Campylobacter jejuni cas9 deletion strain, Caco-2 cells were incubated with TriZol reagents until lysis was complete, then RNA extraction and purification were performed. RNA was extracted from a single well of a 6-well microtiter plate.

source_name: Caco-2 cell line, C. jejuni cas9 deletion strain, 120 minutes

value: 120 minutes after infection


title: Caco-2 cells 120 minutes after infection by the C. jejuni cas9 deletion strain (delta_Cj1523), rep1


title: TIG1 fibroblasts without any treatment_rep1

description: Gene expression in TIG-1 fibroblasts without any treatment_rep1

source_name: Human Fibroblasts, replicate 1


title: TIG1 fibroblasts without any treatment_rep2

description: Gene expression in TIG-1 fibroblasts without any treatment_rep2

source_name: Human Fibroblasts, replicate 2


title: Caco-2 cells 120 minutes after infection by the C. jejuni cas9 deletion strain (delta_Cj1523), rep3


title: Caco-2 cells 30 minutes after infection by the C. jejuni wild-type strain (11168), rep1


title: HEK 293 cell, control

city: Chiba

first: Yuki

last: Sawai

address: 1-8-1 Inohana,  Chuo-ku

department: Department of Oral Science

institute: Graduate School of Medicine, Chiba University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: HEK 293 cell, control

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: RNA samples (50 ng) from HaCaT and HEK 293 cell, which passed quality control by a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Inc. Wilmington, DE USA), was analyzed by an Agilent SurePrint G3 Human GE microarray (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: All of cells were grown and maintained in Dulbecco's modified Eagle medium/DMEM (Sigma) supplemented with 10% fetal bovine serum and 50 units/mL penicillin and streptomycin at 37 °C, 5% CO2 in humidified atmosphere.

value: HEK 293


title: JM3334_S5: TFEB/TFE3 DKO RAW264.7 Control rep 2


title: JM3334_S4: TFEB/TFE3 DKO RAW264.7 Control rep 1


title: JM3334_S3: Null RAW264.7 Control rep 3


title: JM1793_S11: TFEB/TFE3 DKO MEFs 8h Etoposide rep 2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,
then mapped to mm10 whole genome using HISAT2 aligner
count tables were generated using featureCounts (http://bioinf.wehi.edu.au/featureCounts/)
Genome_build: mm10

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Null and CRISPR TFEB/TFE3 DKO MEFs were grown were grown in DMEM with high glucose, GlutaMAX, sodium pyruvate and supplemented with 10% fetal bovine serum

value: Mouse Embryonic Fibroblasts


title: JM1793_S9: Null MEFs 8h Etoposide rep 3


title: Pregnant stroma mare U

data_processing:
Trimmomatic v.0.32.2, remove low quality bases from the 3′ end by sliding window approach (quality score 28 in average across 4 bases), remove sequences below a minimal length of 50 nt after the trimming steps
FastqMcf sequence quality filtering and clipping (Galaxy Version 1.0); removal of remaining adapter sequences and sequences below a minimal length of 50 nt after adapter clip
FastUniq v1.1, removal of PCR duplicates
HISAT2 v2.0.3, mapping to the equine genome sequence assembly
QuasR Qcount, generation of read count table for all annotated equine genes based on the NCBI GFF3 annotation file
Counts per million (CPM) per sample filtering tool (Chen et al. 2014), remove sequences with negligible read counts
Genome_build: EquCab2.0
Supplementary_files_format_and_content: tab-delimited text files, Readcounts.txt contains mapped read counts, CPM_Eca_endo_all_dedup_TrendedDisp.txt contains counts per million (cpm) values of the genes that passed the CPM filter, CPM_Eca_endo_sel_TrendedDisp.txt contains counts per million (cpm) values of the genes that passed the CPM filter for selected samples

source_name: endometrium

growth_protocol: Endometrium biopsies for the isolation of specific endometrial cell types were collected from 6 healthy cycling warmblood mares belonging to the University of Zurich, Clinique for Animal Reproduction Medicine, Switzerland. All the experiments with animals were conducted with the permission of the veterinary inspection office of the Kanton Zurich (permission no. 24/2014) and the degree of severity corresponded to grade 1.

extract_protocol:
Laser capture microdissection (LCM)  Stained frozen sections (10 µm) were prepared using a microtome cryostat CryoStar NX50 (Histocom AG, Zug, Switzerland) on PEN-Membrane Glass Slides®, and Arcturus® HistoGene® Frozen Section Staining Kit (Applied Biosystems). The collection of luminal epithelium (LE), glandular epithelium (GE) and stromal areas (S) was performed using an ArcturusXT® Laser Capture Microdissection instrument.  RNA isolation, quantification and quality control   RNA isolation was performed with the Arcturus PicoPureTM RNA Isolation Kit (Thermo Fisher Scientific, Darmstadt, Germany). Concentration of the RNA was measured with a QuantusTM Fluorometer (Promega; sensitivity 390 pg RNA/ml using QuantiFluor® RNA Dye). Quality was analyzed by the use of the Agilent 2100 Bioanalyzer (Eukaryote Total RNA Pico Assay), which estimates the concentration of the RNA sample and provides a quality score (RNA integrity number, RIN).
For the generation of RNA-Seq libraries from LCM samples, the Ovation® Single Cell RNA-Seq System (NuGEN Technologies, Inc., European office, Leek, The Netherlands) was used starting from 1 ng total RNA. Since for a number of libraries the concentration of the obtained cDNA fragments was too low (Agilent Bioanalyzer DNA High Sensitivity assay), an additional amplification was performed with the KAPA HiFi Library Amplification Kit (Axon Lab AG, Baden, Switzerland). Single-end reads (125 bp) were generated on an Illumina HiSeq 2500 instrument running multiplexed libraries on two lanes of one flow cell.

treatment_protocol: The mares were monitored for signs of estrus using a LOGIQ e ultrasound equipment (GE Healthcare, Glattbrugg, Switzerland). When a follicle of at least 35 mm diameter was detected in conjunction with a uterine edema, a single dose of 1500 IU human choriogonadotropin (hCG) was applied to induce ovulation (day -2). The mares were randomly assigned to one of the experimental cycles: control cycle or pregnancy. If assigned to the pregnancy cycle the mare was inseminated with fresh cooled semen one day before ovulation (day -1). To induce luteolysis at the end of the experiment, prostaglandin F2 alpha (PGF2a) was applied on day 12. During the experimental days (-2 to 12) ultrasound images of both uterus and ovaries were recorded and blood samples for measurement of progesterone were collected. On day 12, endometrial samples were obtained by performing a uterine biopsy. After a longitudinal cut of the biopsy, one half was fixated in formalin for histological examination and the other half was snap-frozen in a cryo-embedding matrix (OCT = optimal cutting temperature) in liquid nitrogen and stored at -80°C.

tag: day of pregnancy or estrous cycle

value: Day 12 of pregnancy

tag: endometrial cell type/compartment

value: stroma


title: PEO14_Combo

description:
rRNA removal
PEO14 protein coding.txt

value: human high grade ovarian serous adenocarcinoma cell line

tag: treatment

value: Combination


title: JM1793_S10: TFEB/TFE3 DKO MEFs 8h Etoposide rep 1


title: JM3334_S1: Null RAW264.7 Control rep 1


title: JM3334_S2: Null RAW264.7 Control rep 2


title: Caco-2 cells 120 minutes after infection by the C. jejuni wild-type strain (11168), rep3

description: After 120 minutes of Caco-2 cell infection with Campylobacter jejuni strain 11168, Caco-2 cells were incubated with TriZol reagents until lysis was complete, then RNA extraction and purification were performed. RNA was extracted from a single well of a 6-well microtiter plate.

source_name: Caco-2 cell line, C. jejuni wild-type strain, 120 minutes

tag: cell line

value: epithelial colorectal adenocarcinoma cell line

value: C. jejuni wild-type strain (11168)


title: HEK 293 cell, 1.63µM cetuximab

source_name: HEK 293 cell, 1.63µM cetuximab


title: Pregnant luminal epithelium mare U

value: luminal epithelium


title: JM1793_S8: Null MEFs 8h Etoposide rep 2


title: JM1793_S7: Null MEFs 8h Etoposide rep 1


title: Caco-2 cells 120 minutes after infection by the C. jejuni wild-type strain (11168), rep2

tag: cell type


title: HaCaT cell, control

source_name: HaCaT cell, control

value: HaCaT


title: Pregnant luminal epithelium mare M


title: Caco-2 cells 60 minutes after infection by the C. jejuni cas9 deletion strain (delta_Cj1523), rep2

description: After 60 minutes of Caco-2 cell infection with Campylobacter jejuni cas9 deletion strain, Caco-2 cells were incubated with TriZol reagents until lysis was complete, then RNA extraction and purification were performed. RNA was extracted from a single well of a 6-well microtiter plate.

source_name: Caco-2 cell line, C. jejuni cas9 deletion strain, 60 minutes

value: 60 minutes after infection


title: Caco-2 cells 60 minutes after infection by the C. jejuni cas9 deletion strain (delta_Cj1523), rep3


title: Caco-2 cells 120 minutes after infection by the C. jejuni wild-type strain (11168), rep1


title: HaCaT cell, 1.63µM cetuximab

source_name: HaCaT cell, 1.63µM cetuximab


title: Caco-2 cells 180 minutes after infection by the C. jejuni wild-type strain (11168), rep1

description: After 180 minutes of Caco-2 cell infection with Campylobacter jejuni strain 11168, Caco-2 cells were incubated with TriZol reagents until lysis was complete, then RNA extraction and purification were performed. RNA was extracted from a single well of a 6-well microtiter plate.

source_name: Caco-2 cell line, C. jejuni wild-type strain, 180 minutes

value: 180 minutes after infection


title: JM1793_S6: TFEB/TFE3 DKO MEFs Control rep 3

value: CRISPR TFEB/TFE3 DKO


title: Caco-2 cells 180 minutes after infection by the C. jejuni wild-type strain (11168), rep3


title: Caco-2 cells 180 minutes after infection by the C. jejuni wild-type strain (11168), rep2


title: JM1793_S12: TFEB/TFE3 DKO MEFs 8h Etoposide rep 3


title: Pregnant stroma mare M


title: JM1793_S5: TFEB/TFE3 DKO MEFs Control rep 2


title: Caco-2 cells 60 minutes after infection by the C. jejuni cas9 deletion strain (delta_Cj1523), rep1


title: Caco-2 cells 60 minutes after infection by the C. jejuni wild-type strain (11168), rep2

description: After 60 minutes of Caco-2 cell infection with Campylobacter jejuni strain 11168, Caco-2 cells were incubated with TriZol reagents until lysis was complete, then RNA extraction and purification were performed. RNA was extracted from a single well of a 6-well microtiter plate.

source_name: Caco-2 cell line, C. jejuni wild-type strain, 60 minutes


title: Pregnant luminal epithelium mare B


title: Pregnant glandular epithelium mare U

value: glandular epithelium


title: Pregnant glandular epithelium mare M


title: JM1793_S3: Null MEFs Control rep 3


title: JM1793_S2: Null MEFs Control rep 2


title: Caco-2 cells 60 minutes after infection by the C. jejuni wild-type strain (11168), rep3


title: Pregnant luminal epithelium mare C


title: JM1793_S1: Null MEFs Control rep 1


title: Pregnant glandular epithelium mare B


title: Control stroma mare B

value: Day 12 of estrous cycle


title: Control stroma mare M


title: SB1003_S04

organism: Rhodobacter capsulatus SB 1003

source_name: early stationary growth phase cells

tag: genotype/variation

value: wild type


title: Liver TAZ-S89A SAM24306538

city: South San Francisco

first: Matthew

middle: T

last: Chang

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech

data_processing:
Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.
Genome_build: GRCm38
Supplementary_files_format_and_content: Entrez Gene IDs, counts and nRPKM statistics.

molecule: polyA RNA

source_name: RNA from YAP/TAZ-mutant liver cancer mouse cell lines

extract_protocol: Total RNA was extracted as per manufacturerâ€™s protocol (Qiagen RNeasy kit) Quality control of samples was done to determine RNA quantity and quality prior to their processing by RNA-seq. The concentration of total RNA samples was determined using NanoDrop 8000 (Thermo Scientific). The integrity of RNA samples was determined using 2100 Bioanalyzer (Agilent Technologies).

value: Liver

tag: mutation


title: Caco-2 cells 30 minutes after infection by the C. jejuni cas9 deletion strain (delta_Cj1523), rep2

description: After 30 minutes of Caco-2 cell infection with Campylobacter jejuni cas9 deletion strain, Caco-2 cells were incubated with TriZol reagents until lysis was complete, then RNA extraction and purification were performed. RNA was extracted from a single well of a 6-well microtiter plate.

source_name: Caco-2 cell line, C. jejuni cas9 deletion strain, 30 minutes

tag: infection

tag: timepoint

value: 30 minutes after infection


title: Liver TAZ-S89A SAM24306539

tag: tissue


title: Liver YAP-S127A SAM24294302


title: Caco-2 cells 60 minutes after infection by the C. jejuni wild-type strain (11168), rep1


title: Caco-2 cells 30 minutes after infection by the C. jejuni cas9 deletion strain (delta_Cj1523), rep1


title: Caco-2 cells 30 minutes after infection by the C. jejuni cas9 deletion strain (delta_Cj1523), rep3


title: JM1793_S4: TFEB/TFE3 DKO MEFs Control rep 1

value: Mouse Embryonic Fibroblasts

tag: genotype


title: Control luminal epithelium mare U


title: SB1003_S02

description:
sleuth_matrix_est_counts.txt
sleuth_test_results.txt


title: SB1003_S01


title: Liver YAP-S127A SAM24294303


title: Liver YAP-S127A SAM24294304


title: Control luminal epithelium mare M


title: Pregnant glandular epithelium  mare C

value: Day 12 of pregnancy


title: Caco-2 cells at t=0, uninfected, rep2

description: At the start of the infection series (t=0) the growth medium of the Caco-2 cells was refreshed and cells were incubated with TriZol reagents until lysis was complete, then RNA extraction and purification were performed. RNA was extracted from a single well of a 6-well microtiter plate.

source_name: Caco-2 cell line, uninfected, 0 minutes

value: 0 minutes


title: Control luminal epithelium mare J


title: Liver TAZ-S89A SAM24294310


title: SB1003_S03


title: Control luminal epithelium mare C


title: Caco-2 cells at t=0, uninfected, rep1


title: MiRNA_OSKM-TIG-1 whole_d0_02

data_processing: See manufacturer's website (http://www.nanostring.com/products/miRNA). We processed all data using nSolver analysis software version 2.5.

source_name: MiRNA_OSKM-TIG-1 whole_d0_02

value: TIG-1 fibroblasts

tag: agent

value: OSKM

tag: fraction

value: Whole

value: day 0


title: Control luminal epithelium mare B

value: luminal epithelium


title: Liver TAZ-S89A SAM24294308


title: Caco-2 cells at t=0, uninfected, rep3

value: epithelial colorectal adenocarcinoma cell line


title: MiRNA_OSKM-TIG-1 whole_d0_01

hyb_protocol: See manufacturer's website (http://www.nanostring.com/products/miRNA)

source_name: MiRNA_OSKM-TIG-1 whole_d0_01


title: Control glandular epithelium mare M


title: Liver YAP-S5A SAM24294318


title: Control glandular epithelium  mare C


title: Liver YAP-S5A SAM24294317


title: Liver YAP-S5A SAM24294319


title: MiRNA_OSKM-TIG-1 DDX6-IP_d3_02

scan_protocol: See manufacturer's website (http://www.nanostring.com/products/miRNA)

source_name: MiRNA_OSKM-TIG-1 DDX6-IP_d3_02

value: day 3


title: MiRNA_OSKM-TIG-1 whole_d3_01

source_name: MiRNA_OSKM-TIG-1 whole_d3_01

label_protocol: See manufacturer's website (http://www.nanostring.com/products/miRNA)


title: Control glandular epithelium mare B


title: MiRNA_OSKM-TIG-1 DDX6-IP_d0_02

source_name: MiRNA_OSKM-TIG-1 DDX6-IP_d0_02


title: MiRNA_OSKM-TIG-1 DDX6-IP_d3_01

source_name: MiRNA_OSKM-TIG-1 DDX6-IP_d3_01


title: MiRNA_OSKM-TIG-1 DDX6-IP_d0_01

source_name: MiRNA_OSKM-TIG-1 DDX6-IP_d0_01


title: MiRNA_OSKM-TIG-1 whole_d3_02

source_name: MiRNA_OSKM-TIG-1 whole_d3_02


title: Liver TAZ-S89A SAM24294309


title: Control glandular epithelium mare U

source_name: endometrium


title: rotator cuff muscle sample 5

status: Public on Sep 29 2018

city: New York

first: Christopher

middle: L

last: Mendias

state: NY

address: 535 E 70th St

institute: Hospital for Special Surgery

library_source: genomic

data_processing:
QC: We employed FASTQC (version 0.11.3) to assess the overall quality of each sequenced sample and identify specific reads and regions that may benefit from trimming. We employed TrimGalore (version 0.4.0) to trim low-quality bases (quality score lower than 20), adapter sequences (stringency 6) and end-repair bases from the 3’ end of reads.
Aligment: For alignment and methylation calling we employed Bismark (version 0.14.3), an integrated alignment and methylation call program that performs unbiased alignment (by converting residual cytosines to thymines prior to alignment in both reads and reference). Briefly, we aligned reads to the reference genome (UCSC mm10 from iGenomes) using Bowtie2 (version 2.2.1) with default parameters settings, except for maximum number of mismatches in seed alignment (N) set to 1, and length of seed substrings (L) set to 20. Methylation calls were reported for all nucleotides with a read depth of at least 10 sites with >500 read depth were removed due to the likelihood that they are biased by duplicates from PCR amplification.
QC_2: We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
Normalization and Quantitation: We used the methylSig R package (0.4.4) to assess the overall quality of methylation calls and coverage. We then employed it to identify differentially methylated positions, as well as regions, by tiling the methylation data across windows of 25 bases. In addition, we used information from nearby CpG sites to improve variance estimates (local window size of 200 bases).
Differential Expression: For each pairwise comparison methylSig uses a beta- binomial approach to calculate differential methylation statistics, accounting for variation among replicates within each group. We adjusted the p-values for multiple testing using the FDR approach, and considered sites to be differentially methylated when they had a percent change in methylation of at least 20% and a qvalue smaller than 0.05. Finally, we annotated sites and regions using UCSC Genome Browser’s annotations for CpG islands, promoters and other genic regions.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files containing Bismark cytosine methylation calls for each sample, .xls file of basic alignment statistics and methylation statistics for each sample, pdf file of glossary of column headers in stats file

source_name: tdTomato-positive satellite cells from rotator cuff muscle

growth_protocol: Cells were not grown in culture prior to ERRBS analysis

extract_protocol:
Muscles underwent enzymatic digestion, and cells were isolated with a series of centrifugation, resuspension, and filtering steps. Muscle satellite cells were then isolated based on tdTomato fluorescenece with fluorescence activated cell sorting
single-end sequencing

treatment_protocol: Cells were not treated prior to ERRBS analysis. Mice from which these cells were obtained were treated with tamoxifen to induce tdTomato expression in muscle satellite cells prior to muscle harvest to allow for isolation of these cells via fluorescence activated cell sorting.

value: rotator cuff muscle

value: satellite cells


title: rotator cuff muscle sample 2


title: rotator cuff muscle sample 4


title: rotator cuff muscle sample 1


title: gastrocnemius muscle sample 5

source_name: tdTomato-positive satellite cells from gastrocnemius muscle

value: gastrocnemius muscle


title: gastrocnemius muscle sample 2


title: gastrocnemius muscle sample 3


title: gastrocnemius muscle sample 1


title: White_Blood_Cell-N.S19

city: Yongin-si

first: Junnam

last: Lee

address: Green Cross Genome, Green Cross Laboratories-3rd floor . 107 Ihyeon-ro 30 beon-g

country: South Korea

institute: GreenCross genome

hyb_protocol: DNA was processed as follows. Restriction digested, PCR amplified, fragmented, labeled and hybridized using agents (Affymetrix Hyb Buffer Part1-4) according to the manufacturer`s instructions.

scan_protocol: The arrays were then washed using Affymetrix Fluidics Stations, and scanned using the GeneChip Scanner 3000.

data_processing: The array image was acquired using Affymetrix GeneChip® Command Console (AGCC version 4.0.0.1567). Data processing and analysis (CEL file generation, smoothing and segmentation) were used Chromosome Analysis Suite (version 2.1.0.16).

label: Biotin

source_name: Human_WBC (WhiteBloodCell)

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: Genomic DNA was extracted from white blood cell from peripheral blood using the Chemagic DNA Blood Kit (200 µl). Extracted DNA quality and quantity were estimated using a Nanodrop Spectrophotometer.

value: White blood cells

tag: gender

value: Female

tag: phenotype

value: Normal

tag: diagnosis


title: White_Blood_Cell-N.S18


title: White_Blood_Cell-N.S1


title: White_Blood_Cell-N.S14


title: White_Blood_Cell-N.S5


title: White_Blood_Cell-N.S11


title: White_Blood_Cell-val.S30

value: Mental delay and/or physical disability


title: White_Blood_Cell-N.S13


title: White_Blood_Cell-N.S7


title: White_Blood_Cell-N.S10


title: White_Blood_Cell-N.S3


title: White_Blood_Cell-val.S29

value: Male


title: White_Blood_Cell-N.S6


title: White_Blood_Cell-N.S2


title: White_Blood_Cell-S29

value: Jacob's syndrome


title: White_Blood_Cell-N.S16


title: White_Blood_Cell-N.S15


title: White_Blood_Cell-N.S20


title: White_Blood_Cell-val.S27


title: White_Blood_Cell-val.S31


title: White_Blood_Cell-val.S26


title: White_Blood_Cell-val.S28


title: White_Blood_Cell-N.S9


title: White_Blood_Cell-N.S8


title: White_Blood_Cell-N.S12


title: White_Blood_Cell-val.S34


title: White_Blood_Cell-N.S17


title: White_Blood_Cell-val.S32


title: White_Blood_Cell-val.S25


title: White_Blood_Cell-val.S24


title: White_Blood_Cell-val.S20


title: White_Blood_Cell-val.S16


title: White_Blood_Cell-val.S23


title: White_Blood_Cell-N.S4


title: White_Blood_Cell-val.S33


title: White_Blood_Cell-val.S18


title: White_Blood_Cell-val.S17


title: White_Blood_Cell-val.S13


title: White_Blood_Cell-val.S11


title: White_Blood_Cell-val.S14


title: White_Blood_Cell-val.S8


title: White_Blood_Cell-val.S4

value: 9p13.2q21.31 deletion


title: White_Blood_Cell-val.S6

value: 15q11.2 duplication


title: White_Blood_Cell-val.S12


title: White_Blood_Cell-val.S19


title: White_Blood_Cell-val.S7

value: Xp11.4p11.3 deletion


title: White_Blood_Cell-val.S9


title: White_Blood_Cell-val.S3

value: 7q11.21 deletion


title: White_Blood_Cell-val.S1

value: Cri-du-chat


title: Psojae_PsDAMT3-KO_rep1

first: Haidong

last: Shu

state: Jiangsu

address: Weigang NO.1

department: Department of Plant Pathology

institute: Nanjing Agricultural University

data_processing:
Clean reads were aligned to Psojae v1.1 and Pinfestans whole genome using hisat2 v2.1.0 with default parameters
FPKM were calculated using stringtie v1.3.3b with default parameters
Genome_build: Psojae v1.1 and ASM14294v1
Supplementary_files_format_and_content: gtf files include FPKM,TPM,and coverage values for each Sample …

organism: Phytophthora sojae

source_name: mycelium

growth_protocol: V8 medium

extract_protocol:
RNA were extracted using OMEGA total RNA Kit I (Cat.#:R6834-04)
Library followed the standard Illumina protocol

value: psdamt3 mutant

tag: strain

value: mycelium

tag: age


title: Psojae_PsDAMT3-KO_rep2


title: White_Blood_Cell-val.S2

value: 6q25.3 deletion


title: Psoaje_WT_rep2

value: wild type


title: White_Blood_Cell-S28

value: Klinefelter


title: White_Blood_Cell-val.S5

value: 9q subtelomeric deletion


title: Psoaje_WT_rep1


title: White_Blood_Cell-S26

value: White blood cells

value: Turner syndrome


title: Psoaje_WT_rep3


title: EP_TCF_3: wing disc tissue ap>YAP/Yki+dTcf/Pan-RNAi

city: Copenhagen

first: Diana

last: Andrejeva

address: Blegdamsvej 3

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

hyb_protocol: According to manufacturer's protocol

scan_protocol: According to manufacturer's protocol

data_processing: Microarray data analysis was performed using R (3.5.0) (https://www.r-project.org/). Intensity signals were normalized and log2 transformed using “oligo” (1.44.0) package (http://www.bioconductor.org/packages/release/bioc/html/oligo.html). Control, background and spike-in probes were removed from further analysis. Probe sets that did not map to known genes, as well as genes whose expression was below background detection threshold in at least 3 samples were also filtered out. Threshold was defined as median expression of anti-genomic (background hybridization) probe intensity’s.

organism: Drosophila melanogaster

label_protocol: According to manufacturer's protocol

growth_protocol: Wing discs dissected 7 days after transgene induction - for more details see M and Ms in the article.

extract_protocol: Total RNA of the wing disc tissue was isolated using TRIzol® reagent.

value: wing disc

value: YAP/Yki+dTcf/Pan-RNA RNAi


title: White_Blood_Cell-val.S21

value: Female

value: Mental delay and/or physical disability

value: Normal


title: Psojae_PsDAMT3-KO-input_rep1

data_processing:
Clean reads were aligned to Psojae v1.1 and Pinfestans whole genome using bowtie2 v2.3.3.1 with parameter -N 1
Peaks were called using SICER v1.1 with sh SICER.sh . IP_file Input_file . species 1 200 100 0.74 200 .01
Bedtools was used to compute overlap peaks of two replicates
Genome_build: Psojae v1.1 and ASM14294v1

extract_protocol:
DNA were extracted using TIANGEN DNASeure Plant Kit (Cat.#DP320-03) and then treated with RNase A overnight. gDNA was sonicated to 200-400bp and denatured.
Denatured DNA fragments were IPed using antibody (Synaptic Systems: #202003). Library was prepared using VAHTSTM Turbo DNA Library Prep Kit for Illumina (Cat.#N102) and VAHTSTM Multiplex Oligos set 1 for Illumina (Cat.#N302-01).

tag: chip antibody


title: EP_TCF_1: wing disc tissue ap>YAP/Yki+dTcf/Pan-RNAi


title: Psojae_PsDAMT3-KO-MeDIP-seq_rep3


title: Psojae_PsDAMT3-KO-input_rep2


title: White_Blood_Cell-val.S22


title: White_Blood_Cell-S25

value: Male

value: Xq28 duplication


title: EP_TCF_2: wing disc tissue ap>YAP/Yki+dTcf/Pan-RNAi


title: EP_Control_3: wing disc tissue ap>YAP/Yki

description: wing disc tissue ap>YAP/Yki

source_name: wing disc tissue ap>YAP/Yki

value: YAP/Yki


title: EP_Control_2: wing disc tissue ap>YAP/Yki

description: wing disc tissue ap>YAP/Yki


title: Psojae_PsDAMT3-KO-MeDIP-seq_rep1


title: Psojae_PsDAMT3-KO-MeDIP-seq_rep2


title: White_Blood_Cell-S27


title: EP_Control_1: wing disc tissue ap>YAP/Yki

description: wing disc tissue ap>YAP/Yki


title: White_Blood_Cell-val.S15


title: Psojae_WT_input_rep2


title: Psojae_WT_input_rep1


title: Psojae_WT_MeDIP-seq_rep1


title: White_Blood_Cell-S20

value: Leri-Weill dyschondrostosis


title: Pinfestans_WT_rep1

organism: Phytophthora infestans


title: ATAC-Seq AW6

city: Beijing

first: Bofeng

address: Haidian District

department: School of Life Science

institute: Tsinghua University

data_processing:
Basecalls performed using CASAVA version 1.8
ATAC-seq reads were aligned to the hg19 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
Peak calling was using MACS1(1.4.2), with arguments --nolambda --nomodel
Genome_build: hg19
Supplementary_files_format_and_content: The bedGraph files counted by the number of reads falling into 100bp bin in the genome.  The peak bed files were generated by MACS1.

source_name: human embryonic stem cell_Activin A_and_Wnt3a

growth_protocol: For feeder-free culture condition, H1 cells were cultured on Matrigel (BD Biosciences)-coated plate with N2B27 chemically defined medium (DMEM/F-12 supplemented with N2, B27, 1 mM L-glutamine, 0.1 mM nonessential amino acids, 0.1 mM β-mercaptoethanol, and 20 ng/ml recombinant human bFGF)

extract_protocol:
After dissociation with Accutase, embryonic stem cells were washed with PBS and incubated in lysis buffer.
ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al. with slightly modification

treatment_protocol: For mesendoderm differentiation, H1 cells were maintained on Matrigel-coated plate with N2B27-bFGF chemically defined medium to about 50-60% confluence, and then differentiation was induced in B27 chemically defined medium (DMEM/F-12, B27, 1 mM L-glutamine, 0.1 mM nonessential amino acids) supplemented with Activin A (25ng/ml), Wnt3a (25 ng/ml), or Activin A plus Wnt3a (25 ng/ml for each). Control group was cultured in parallel with differention group with growth protocol

tag: differentiation status

value: early stage of mesendoderm differentiation


title: Pinfestans_WT_rep2

value: mycelium


title: White_Blood_Cell-S23

value: Duchenne Muscular Dystrophy


title: White_Blood_Cell-S17

value: Down syndrome


title: White_Blood_Cell-val.S10


title: Pinfestans_WT_MeDIP-seq_rep2

value: wild type


title: White_Blood_Cell-S22

value: Xp21 deletion


title: ATAC-Seq A6

source_name: human embryonic stem cell_Activin A

tag: cell line


title: Psojae_WT_MeDIP-seq_rep2


title: ATAC-Seq Control

source_name: human embryonic stem cell_control


title: Pinfestans_WT_input


title: White_Blood_Cell-S19

tag: cell type

value: White blood cells

value: Phelan-Mcdermid


title: Pinfestans_WT_MeDIP-seq_rep1


title: ATAC-Seq W6

source_name: human embryonic stem cell_Wnt3a


title: White_Blood_Cell-S24


title: White_Blood_Cell-S18

value: DiGeorge syndrome


title: White_Blood_Cell-S15


title: White_Blood_Cell-S14

value: Miller-Dieker


title: White_Blood_Cell-S13

value: Female


title: C2C12_pat1_rep2

status: Public on Sep 28 2018

first: Zhonglin

last: Tang

address: No. 2 Yuanmingyuan West Road, Beijing, 100193, P.R.China,

department: Institute of Animal Science

institute: Chinese Academy of Agricultural Sciences

description: C2C12 cells transfected with pcDNA3.1,sample2

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: slides were scanned with the Agilent DNA Microarray Scanner. Data was extracted using Agilent Feature Extraction software. Normalization was performed using Agilent GeneSpring GX 11.5.1.

data_processing: Data analysis was performed using Agilent GeneSpring GX 11.5.1 software.

source_name: C2C12 cell transfected with pcDNA3.1, rep2

label_protocol: Total RNA was labeled with Cy3 using the Agilent One-Color Quick Amp Labeling Protocol

growth_protocol: The mouse C2C12 myoblast was cultured in Dulbecco's modiﬁed Eagle's medium (DMEM) with high glucose (Gibco, Invitrogen, Carlsbad, CA, USA), supplemented with 10% fetal bovine serum (Gibco, Invitrogen, Carlsbad, CA, USA) and 1% glutamine, incubated at 5% CO2 and 37°C.

extract_protocol: Total RNA was isolated using the TRIzol Reagent (Invitrogen, Carlsbad, CA, USA).  Genomic DNA was removed by DNase I (Qiagen, Beijing, China).mRNA was purified from total RNA after removal of rRNA. Integrity and concentration of RNA was assessed after RNA extraction and prior to sample labeling.

treatment_protocol: Briefly, the C2C12 cells transfected with pcDNA3.1, pcDNA3.1-MEG3, siRNA or the negative control were seeded into 96-well plates in triplicate (2×103 cells/well). The cell proliferation assay was performed by adding 10 µl of the Cell-Counting Kit-8 (CCK-8) solution and incubated at 37˚C for 1h.

tag: time

value: 72 h after transfection

tag: transfection


title: C2C12_MEG3_overexpression_rep2

description: C2C12 cells transfected with pcDNA3.1-MEG3,sample2

source_name: MEG3 Overexpression, C2C12 myoblast cell line, rep2


title: C2C12_pat1_rep3

description: C2C12 cells transfected with pcDNA3.1,sample3

source_name: C2C12 cell transfected with pcDNA3.1, rep3


title: C2C12_MEG3_overexpression_rep3

description: C2C12 cells transfected with pcDNA3.1-MEG3,sample3

source_name: MEG3 Overexpression, C2C12 myoblast cell line, rep3


title: C2C12_MEG3_overexpression_rep1

description: C2C12 cells transfected with pcDNA3.1-MEG3,sample1

source_name: MEG3 Overexpression, C2C12 myoblast cell line, rep1


title: C2C12_MEG3_knockdown_rep1

description: C2C12 cells transfected with siRNA,sample1

source_name: MEG3 knockdown, C2C12 myoblast cell line, rep1

value: siRNA


title: White_Blood_Cell-S16

value: Mental delay and/or physical disability

value: Edward syndrome


title: White_Blood_Cell-S11

value: Male

value: 15q11-13 duplication


title: C2C12_MEG3_knockdown_rep2

description: C2C12 cells transfected with siRNA,sample2

source_name: MEG3 knockdown, C2C12 myoblast cell line, rep2


title: C2C12_pat1_rep1

description: C2C12 cells transfected with pcDNA3.1,sample1

source_name: C2C12 cell transfected with pcDNA3.1, rep1


title: White_Blood_Cell-S9

value: 9q subtelomeric deletion


title: White_Blood_Cell-S12

value: Prader-Willi syndrome


title: C2C12_control_rep1

description: C2C12 cells transfected with the negative control, sample1

source_name: Negative control,C2C12 myoblast cell line, rep1

value: negative control


title: C2C12_MEG3_knockdown_rep3

description: C2C12 cells transfected with siRNA,sample3

source_name: MEG3 knockdown, C2C12 myoblast cell line, rep3


title: Myo4 = SID6698

city: Heidelberg

first: Sören

last: Meyer

address: Im Neuenheimer Feld 410

country: Germany

institute: University Hospital Heidelberg

data_processing:
Sequencing on Illumina HiSeq2000
Transcript analysis of raw read files mapped with STAR v2.4.1c5
read counts generated with subread's feature counts program 6
DGE analysis performed with EdgeR
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Biopsy of LV from patient with myocarditis

extract_protocol:
biopsies were obtained during cardiac catheterization (standard protocol)
Libraries were generated using TruSeq Stranded Total RNA sample Preparation Kit with Ribo-Zero Human/Mouse/Rat from Illumina

value: apical part of free LV wall

tag: cardiac disease

value: myocarditis

value: heart


title: Myo3 = SID6697


title: Myo2 = SID6696


title: White_Blood_Cell-S8

source_name: Human_WBC (WhiteBloodCell)

value: White blood cells

value: Williams syndrome


title: DCM11 = SID5665

source_name: Biopsy of LV from patient with DCM

value: Dilated cardiomyopathy


title: C2C12_control_rep3

description: C2C12 cells transfected with the negative control,sample3

source_name: Negative control,C2C12 myoblast cell line, rep3


title: Confront Theanine 2

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

institute: Akita Prefectural University

description: 3 month

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Normalized by using Supernorm (Skylight-biotech); https://www.ncbi.nlm.nih.gov/pubmed/14718068

source_name: 1 day after confrontation

label_protocol: Total RNA was processed to synthesize biotinylated cRNA using One-Cycle Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA, USA)

growth_protocol: Mice at 4 weeks of age were housed in a group of six in a cage for 5 days to habituate them to novel conditions. The mice were then divided into two groups, namely confrontationally and group housed. In brief, for confrontational housing, a standard polycarbonate cage was divided into two identical subunits by a stainless-steel partition.

extract_protocol: Total RNA was extracted from the hippocampus using an RNeasy Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Two mice were housed in the partitioned cage for 1 month to establish territorial consciousness (single housing); then the partition was removed to expose the mice to the confrontational stress, and subsequently, the two mice cohabited in the same cage (confrontational housing).

tag: background strain

value: AKR/J (however, it may also have been crossed with ddY or other lines).

tag: group

value: Confront Theanine

value: brain hippocampus


title: Confront Theanine 1

description: 3 month

tag: tissue


title: Confront Water 2

description: 3 month

value: Confront Water


title: White_Blood_Cell-S21

value: Female

value: Mental delay and/or physical disability

value: steroid sulfatase enzyme deficiency


title: DCM10 = SID5661


title: Single Water 1

description: 3 month

source_name: control

value: Single Water


title: DCM8 = SID5659


title: Confront Water 1

description: 3 month


title: Single Theanine 1

description: 3 month

value: Single Theanine


title: Myo1 = SID6695


title: White_Blood_Cell-S3

value: 3p deletion


title: DCM4 = SID5655


title: DCM5 = SID5656


title: DCM3 = SID5654


title: White_Blood_Cell-S7

value: Male

value: Sotos syndrome


title: DCM2 = SID5653

value: apical part of free LV wall


title: Myo5 = SID6820

value: myocarditis

value: heart


title: White_Blood_Cell-S10

value: White blood cells

value: Potocki-Shaffer


title: Single Water 2

description: 3 month

value: AKR/J (however, it may also have been crossed with ddY or other lines).


title: DCM6 = SID5657

value: Dilated cardiomyopathy


title: Single Theanine 2

description: 3 month

value: brain hippocampus


title: pRB+ rep 2

city: Boston

last: Oser

address: 450 Brookline Avenue, Mayer 457

institute: Dana-Farber Cancer Institute

data_processing:
Basecalls
For RNA-Seq: gene counts were done using STAR (v2.5.1b) {Dobin A., etal (2013), Bioinformatics 29: 15.} and normalized gene counts (RPKM) were calculated using Cufflinks (v2.2.1) {Trapnell C., etal (2010), Nat. Biotech. 28: 511.}. Analysis was performed using the VIPER snakemake pipeline {Cornwell M., etal (2018), BMC Bioinformatics 19: 135.}
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-Seq, cufflinks file shows normalized RPKM values.

source_name: NCI-H82 cells

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen #74106) per the manufacturer's instructions
Libraries were constructed as per the manufacturers instructions. For RNASeq: 500 ng RNA was used with the Illumina stranded total RNASeq protocol; whereas, for ChIP-Seq the Illumina Nextera protocol was used.

treatment_protocol:
doxycycline protocol: NCI-H82 pTripZ RB1 cells were plated at 100,000 cells/mL in 8 mls of complete media in petri dishes and grown in the presence or absence of DOX (at 0.5 μg/mL) for 96 hours on petri dishes changing the media and DOX at 48 hours.
AZD2811 protocol: NCI-H82 pTripz RB1 cells were plated at 100,000 cells/mL and grown in the presence or absence of DOX (at 0.5 μg/ml) for 48 hours and then treated with AZD2811 (32 nM) or DMSO for an additional 48 hours.

value: NCI-H82 cells

value: Small cell lung cancer cells

tag: doxycycline treatment

value: YES (pRB+)

value: NO


title: pRB- AZD1152 rep 2

value: NO (pRB-)

value: YES


title: pRB+ AZD1152 rep 2


title: pRB- rep 2


title: DCM1 = SID5652


title: pRB- AZD1152 rep 1


title: pRB- rep 1


title: White_Blood_Cell-S6

value: Mental delay and/or physical disability

value: 5q14.3 deletion


title: C2C12_control_rep2

description: C2C12 cells transfected with the negative control, sample2

source_name: Negative control,C2C12 myoblast cell line, rep2

value: 72 h after transfection

value: negative control


title: DCM7 = SID5658

value: apical part of free LV wall


title: pRB+ rep 1


title: DCM9 = SID5660

value: heart


title: White_Blood_Cell-S2

value: White blood cells

value: Female

value: Albright


title: White_Blood_Cell-S5

value: Wolf-Hirschhorn


title: White_Blood_Cell-S4

value: Male

value: 3q13 deletion


title: White_Blood_Cell-S1

value: 1q44 deletion


title: WT2

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Tophat with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR package of R.
Genome_build: mm9
Supplementary_files_format_and_content: RPKM

source_name: Day 4 uterus

extract_protocol:
Uteri were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time point

value: pregnant day 4

value: Uterus


title: WT1


title: Kidney_1

city: Stanford

first: Alina

last: Isakova

address: 318 Campus drive

department: Bioengineering

institute: Stanford University

data_processing:
Illumina BaseSpace software used for demultiplexing
Sequenced reads were trimmed for adaptor sequence, and mapped to mm10 whole genome using STAR v2.5.1 (Dobin et al., 2013) with the following parameters --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --alignIntronMax 1 --outMultimapperOrder Random --clip3pAdapterSeq TGGAATTCTC --clip3pAdapterMMp 0.1
Transcript counts were calculated using a FeatureCounts, featureCounts -a Mus_musculus.GRCm38.90.gtf -M –primary -s 0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts Sample

source_name: Kidney_Small non-coding RNA

extract_protocol:
Upon collection, tissue samples were submerged and preserved at -80C in RNAlater stabilization solution (ThermoFisher cat # AM7021) until further processing. Total RNA was isolated from ~ 100 mg of tissue using Qiagen miRNeasy mini kit (cat # 217004) and the Qiagen tissue lyser using 5 mm stainless steel beads. RNA integrity was assesses using Agilent Bioanalyzer using RNA 6000 pico kit (Agilent Technologies cat # 5067-1513). Short RNA libraries were prepared following the Illumina TruSeq Small RNA Library Preparation kit (cat # RS-200-0012, RS-200-0024, RS-200-0036, RS-200-0048) according to the manufacturer’s protocol and size-selected using Pippin Prep 3% Agarose Gel Cassette (Safe Science) in a range 135 bp – 210 bp. Samples were pooled in batches of 48 and sequenced using the Illumina Illumina NextSeq 500 instrument in a single-read, 75-base mode.
Short RNA libraries were prepared following the Illumina TruSeq Small RNA Library Preparation kit (cat # RS-200-0012, RS-200-0024, RS-200-0036, RS-200-0048) according to the manufacturer’s protocol and size-selected using Pippin Prep 3% Agarose Gel Cassette (Safe Science) in a range 135 bp – 210 bp. Samples were pooled in batches of 48 and sequenced using the Illumina Illumina NextSeq 500 instrument in a single-read, 75 -base mode.

tag: genotype

value: WT

value: adult, 3 months old

value: Kidney

tag: molecule subtype

value: sRNA


title: Kidney_12


title: Kidney_14


title: Kidney_13


title: pool wt 50d

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

country: Spain

institute: IIB

hyb_protocol: In Situ Hybridization Kit Plus (Agilent technologies) protocols

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.0).

data_processing: Agilent Feature Extraction Software (v 10.0) was used for background subtraction and LOWESS normalization.

source_name: Total RNA

label_protocol: RNA was labeled and array hybridized us ing the Low RNA Linear Amplification Kit and the In Situ Hybridization Kit Plus (Agilent technologies, Wilmington, DE) respectively.

growth_protocol: The feeder-independent E14 mouse embryonic stem (ES) and human embryonic kidney 293T cell lines were used in this study. E14 cells (a gift from T. Rodriguez, Imperial College, London) were grown on 0,1% gelatincoated flasks in GMEM supplemented with 10% FCS, NEAA, L-Glutamine, pyruvate, β-mercaptoethanol (all from Gibco) and 1,000 U/ml LIF (Millipore), and splitted 1:8 or 1:10 every 2–3 days using Trypsin-EDTA (Invitrogen) (Smith, 1991; Cambray et al, 2012). 293T cells were cultured in DMEM supplemented with 10% FCS, L-Glutamine and antibiotics, and divided 1:10 or 1:20 every 2-3 days using Trypsin-EDTA (Invitrogen). Both cell lines were maintained at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol: RNA was isolated using RNAesy Extraction Kit (QIAGen, Germany).

tag: developmental stage

value: E14 mouse embryonic stem (ES)

value: Stem cells

source_name: Pool from all cellular conditions


title: tpa wt 90d


title: clp end+/- 90d


title: clp wt 90d


title: DONOR 3_TSLP 12H

city: Paris

first: Lucia

last: Pattarini

address: 26 rue D' Ulm

country: France

institute: Institut Curie

description: CD40 33

hyb_protocol: After fragmentation, 20 ug of cRNA were hybridized on a U133 plus 2.0 gene  for 16 hours

scan_protocol: Gene ship were analyzed using the GCS3000 from Affyemtrix

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: DC_20 hrs in control medium plus TSLP, washed, and cultured for 12 hrs in new medium

label_protocol: 50 ng of total RNA were amplified using Affymetrix double amplification protocol

growth_protocol: Human primary dendritic cells were facs sorted (CD3, CD14, CD16, CD19)-, CD11c+, CD4+ and cultured at 1x10^6 cells/ml  in RPMI medium plus 10%FBS, 1% pen strep

extract_protocol: Total mRNA was extracted using the Quiagen RNAeasy micro kit #74004 according to manufacturer protocol

treatment_protocol: rhTSLP 50 ng/ml, LPS 1 ug/ml, rhCD40L 1 mg/ml

tag: donor

value: DONOR 3

value: primary blood Dendritic cells

tag: pre-treated in

value: control medium plus TSLP for 20hrs

tag: treated

value: for 12 hours in new medium


title: clp end +/- 50d


title: end +/- 90 d


title: clp wt 50d


title: Kidney_11

tag: strain

tag: age


title: DONOR 3_TSLP 12H CD40L

description: CD40 34

source_name: DC_20 hrs in control mediumplus TSLP, washed, and cultured for 12 hrs with rCD40L

tag: cell type

value: control mediumplus TSLP for 20hrs

value: for 12 hours with rCD40L


title: pool wt 90


title: end+/- 50d


title: tpa end +/- 90d


title: Kidney_10


title: DONOR 3_LPS 12H

description: CD40 35

source_name: DC_20 hrs in control medium plus LPS, washed, and cultured for 12 hrs in new medium

value: control medium plus LPS for 20hrs


title: DONOR 3_MED 12H

description: CD40 31

source_name: DC_20 hrs in control medium, washed, and cultured for 12 hrs in new medium

value: control medium for 20hrs


title: DONOR 3_LPS 12H CD40L

description: CD40 36

source_name: DC_20 hrs in control medium plus LPS, washed, and cultured for 12 hrs with rCD40L


title: DONOR 3_MED 12H CD40L

description: CD40 32

source_name: DC_20 hrs in control medium, washed, and cultured for 12 hrs with rCD40L


title: tpa end +/- 50d


title: Intestine_9

source_name: Intestine_Small non-coding RNA

value: Intestine


title: DONOR 3_LPS 6H CD40L

description: CD40 30

source_name: DC_20 hrs in control medium plus LPS, washed, and cultured for 6 hrs with rCD40L

value: for 6 hours with rCD40L


title: DONOR 3_LPS 6H

description: CD40 29

source_name: DC_20 hrs in control medium plus LPS, washed, and cultured for 6 hrs in new medium

value: for 6 hours in new medium


title: DONOR 3_TSLP 6H CD40L

description: CD40 28

source_name: DC_20 hrs in control mediumplus TSLP, washed, and cultured for 6 hrs with rCD40L


title: Intestine_7

value: WT


title: Intestine_8

value: adult, 3 months old


title: Intestine_6


title: Intestine_4


title: Intestine_5


title: Intestine_3


title: Intestine_1


title: Intestine_14


title: DONOR 3_TSLP 6H

description: CD40 27

source_name: DC_20 hrs in control medium plus TSLP, washed, and cultured for 6 hrs in new medium


title: DONOR 3_MED 6H CD40L

description: CD40 26

source_name: DC_20 hrs in control medium, washed, and cultured for 6 hrs with rCD40L


title: DONOR 2_LPS 12H CD40L

description: CD40 24

value: DONOR 2


title: Intestine_2

value: sRNA


title: Intestine_13


title: DONOR 3_MED 6H

description: CD40 25

source_name: DC_20 hrs in control medium, washed, and cultured for 6 hrs in new medium


title: Intestine_10


title: DONOR 2_LPS 12H

description: CD40 23


title: Heart_8

source_name: Heart_Small non-coding RNA

value: Heart


title: Heart_5


title: DONOR 2_TSLP 12H CD40L

description: CD40 22


title: DONOR 2_TSLP 12H

description: CD40 21


title: DONOR 2_MED 12H CD40L

description: CD40 20


title: DONOR 2_LPS 6H CD40L

description: CD40 18


title: Heart_7


title: DONOR 2_TSLP 6H CD40L

description: CD40 16


title: Heart_9


title: DONOR 2_MED 12H

description: CD40 19


title: Heart_3


title: DONOR 2_TSLP 6H

description: CD40 15


title: Heart_2


title: DONOR 2_MED 6H

description: CD40 13


title: DONOR 2_LPS 6H

description: CD40 17


title: DONOR 2_MED 6H CD40L

description: CD40 14


title: Heart_1


title: Heart_4


title: DONOR 1_LPS 12H

description: CD40 11

value: DONOR 1


title: DONOR 1_LPS 12H CD40L

description: CD40 12


title: Heart_13


title: Heart_14


title: tpa wt 50d

value: E14 mouse embryonic stem (ES)

value: Stem cells


title: DONOR 1_MED 12H CD40L

description: CD40 8

value: primary blood Dendritic cells


title: DONOR 1_TSLP 12H CD40L

description: CD40 10


title: Heart_12


title: Heart_11


title: Brain_8

source_name: Brain_Small non-coding RNA

value: Brain


title: DONOR 1_TSLP 12H

description: CD40 9

value: control medium plus TSLP for 20hrs

value: for 12 hours in new medium


title: Brain_9


title: Brain_7


title: DONOR 1_LPS 6H

description: CD40 5

value: control medium plus LPS for 20hrs


title: DONOR 1_LPS 6H CD40L

description: CD40 6


title: DONOR 1_TSLP 6H CD40L

description: CD40 4

value: control mediumplus TSLP for 20hrs


title: Brain_6