title: 554228A03 - 15_DFLO_Veg_N+S+_2 vs 28_DFLO-14_Veg_N-S+_2

hyb_protocol: 28_DFLO-14_Veg_N-S+_2 Cy5 / 15_DFLO_Veg_N+S+_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: da-Gal4_sov-RNAi_rep2

status: Public on Jan 01 2019

type: SRA

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

country: USA

institute: NIDDK, NIH

description:
FBgn0014387; FBgn0029899
ERCC subpool: 78B
Analysis group: sov RNAi

library_source: transcriptomic

data_processing:
RNAseq librarires were sequenced on an Illumina HiSeq 2500 machine with base calling by CASAVA software (version 1.8.2, Illumina, San Diego, CA, USA).
RNAseq reads were mapped to the Drosophila melanogaster FlyBase r6.21 genome with Hisat2 (version 2.0.5., PMID: 25751142, -k 1 --rna-strandness R --dta).
Read counts for each attribute of the Drosophila melanogaster FlyBase r6.21 GTF file were determined with HTSeq-count (version 0.7.2., PMID:25260700). Spike-in ERCC and transposable element sequence locations were added to the FlyBase r6.21 GTF file. Transposable element sequence locations were extracted from the UCSC Genome Browser RepeatMasker track (PMID:29106570; Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-4.0.).
Genome_build: Drosophila melanogaster FlyBase release 6.21 genome.
Supplementary_files_format_and_content: txt files contain total read counts for each attribute of the Drosophila melanogaster FlyBase release 6.21 GTF file.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: Flies were raised on Fly Food B with 0.4% propionic acid and 0.15% tegosept (Labexpress, Ann Arbor, MI) at 25°C and constant light. Females of the desired genotype were collected post-eclosion and aged 4-5 days before tissue extraction.

extract_protocol:
15 ovaries were dissected in PBS and immediately transferred to ice cold PBS for each sample. Total RNA was extracted with a Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) according to manufacturer’s protocol.
PolyA RNA was isolated from 200 ng of total RNA and used to create RNAseq libraries according to PMID: 27599372. 10 pg of ERCC spike-in control RNAs (pools 78A or 78B) were added to each sample during library preparation (PMID: 21816910, PMID:22859977, PMID:27342544, PMID: 27512518).

tag: age

value: 4-5 days post-eclosion

tag: age cv

tag: tissue cv

tag: Sex

value: Female

tag: sex cv

tag: developmental stage

value: Adult

tag: developmental stage cv

tag: genotype

tag: fertility phenotype

value: Sterile


title: 554228A01 - 9_DFLO_Veg_N+S+_1 vs 26_DFLO-14_Veg_N-S+_1

type: RNA

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Transcriptome in leaves of Medicago truncatula plants during the remobilization process . Effect of a nitrogen deficiency on this process.Note that lower leaves correspond to vegetative leaves (FV) and upper leaves correspond to leaves of the reproductive part (FR).

hyb_protocol: 26_DFLO-14_Veg_N-S+_1 Cy5 / 9_DFLO_Veg_N+S+_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

molecule: total RNA

organism: Medicago truncatula

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: caulin leaf - non renseigné.

treatment_protocol: Name:Nitrogen deficiency - time course study - azote concentration,azote:. One experimental treatment was performed after the beginning of flowering: a treatment with a nitrogen deficiency. After this stage, treated plants weren’t supplied in nitrogen (without KNO3). However, a plant set was watered with the classical nutrient solution (N+) and therefore constituted a control group.

tag: medicago truncatula (a17)  -  dev.stage (boyes et al. plant cell 2001)

treatment_protocol: no treatment

value: first flowers buds visible


title: da-Gal4_sov-RNAi_rep1

description:
FBgn0014387; FBgn0029899
ERCC subpool: 78A
Analysis group: sov RNAi


title: da-Gal4_sov-RNAi_rep3


title: MM_Aza

city: Chicago

first: Shimeng

last: Liu

state: Illinois

address: 320 East Superior Street

institute: Northwestern University

description: 96h 5µM 5'-Aza

library_source: genomic

data_processing:
Adapters were trimmed using cutadapt
Trimmed reads were aligned to hg19 using default parameters
Peak calling was performed using HOMER
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using HOMER

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary uterine myometrial cells

growth_protocol: All cell-based assays were performed on primary cells isolated from fresh MM or LM tissue and cultured within two passages. Primary cells were cultured in DMEM/F12 1:1 (GIBCO/BRL, 11320-082) containing 10% (vol/vol) FBS in a humidified atmosphere in 5% (vol/vol) CO2 at 37 °C.

extract_protocol: Libraries were prepared according to Illumina's instructions.

treatment_protocol: Cells were treated with vehicle (DMSO) or 5 µM 5’-aza (Sigma-Aldrich, A3656) for 96h with medium refreshed every 24h.

tag: passages

value: Primary P0 cells

tag: treatment

value: 96h 5uM 5'-Aza

tag: fraction

value: MethylCap DNA


title: MM_Veh

description: 96h DMSO

value: 96h DMSO


title: da-Gal4_mCherry-RNAi_rep3

description:
FBgn0014387; FBgn0029899
ERCC subpool: 78B
Analysis group: control RNAi

value: Genotype:w[*]/y[1] sc[*] v[1]; P{w[+mW.hs]=GAL4-da.G32}UH1/P{y[+t7.7] v[+t1.8]=VALIUM20-mCherry}attP2

value: Fertile


title: LM_Aza

description: 96h 5µM 5'-Aza

source_name: Primary uterine leiomyoma cells


title: 555031A11 - 8_DFLO_Rep_N+S+_3 vs 33_DFLO-14_Rep_N+S+_3

hyb_protocol: 33_DFLO-14_Rep_N+S+_3 Cy5 / 8_DFLO_Rep_N+S+_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: flower bud - non renseigné.


title: 555031A12 - 33_DFLO-14_Rep_N+S+_3 vs 8_DFLO_Rep_N+S+_3

hyb_protocol: 8_DFLO_Rep_N+S+_3 Cy5 / 33_DFLO-14_Rep_N+S+_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: da-Gal4_mCherry-RNAi_rep2

description:
FBgn0014387; FBgn0029899
ERCC subpool: 78A
Analysis group: control RNAi


title: LM_Veh

description: 96h DMSO


title: M22 rna-seq

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

description:
M22
RNA-seq data for Male chorionic villus sample M22.
processed data file: genecounts.txt

data_processing:
Align to genome with STAR.
Count reads mapping to genes with featureCounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: genecounts.txt: Tab-delimited text file

source_name: Chorionic villus

extract_protocol:
CVS tissue was thawed on ice with 600 μl of RTL Plus lysis buffer (QIAGEN) and 1% β-mercaptoethanol added to each sample. Cells were homogenized by passing at least 10 times through single-use needles with decreasing gauge (22G, 25G, then 27G) attached to a 1 mL sterile, RNase-free syringe. The homogenates were loaded onto AllPrep spin columns and the remainder of the protocol was performed following manufacturer instructions. DNA and RNA were extracted using the commercial AllPrep DNA/RNA Extraction Mini Kit (QIAGEN) for RNA-seq. RNA was eluted with 30 μl of the kit-provided RNase-free water at room temperature, then the elution was passed through the column a second time to increase RNA yield. DNA was eluted with 100 μl of the kit-provided EB buffer warmed to 70°C.
RNA-Seq libraries were constructed from 200 ng of total RNA using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kits (Illumina, Carlsbad, CA). Constructed libraries contained RNAs >200 nt (both unpolyadenylated and 140 polyadenylated) and were depleted of cytoplasmic and mitochondrial rRNAs.

tag: tissue

value: Chorionic villus

value: Male

tag: gestational age


title: da-Gal4_mCherry-RNAi_rep1


title: M21 rna-seq

description:
M21
RNA-seq data for Male chorionic villus sample M21.
processed data file: genecounts.txt

value: other


title: Night-Shift, ID543, 12PM

city: Birmingham

first: Karen

middle: L.

last: Gamble

state: Alabama

address: 1720 7th Ave S

department: Psychiatry

institute: University of Alabama at Birmingham

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised with GenomeStudio (Illumina)

label: biotin

source_name: PBMC isolated

label_protocol: cDNA was incubated with in vitro transcription (IVT) components including the biotin labeled uracil and T7 RNA polymerase

extract_protocol: RNA was extracted with Trizol reagent and samples were DNase I (Invitrogen™) treated according to manufacturer’s protocol. cDNA was synthesized from previously isolated RNA with SuperScript™ VILO™ MasterMix (Invitrogen™) according to manufacturer’s protocol.

tag: work shift

value: Night-Shift

tag: time of sample


title: Kr[If-1] + Phenotype Total mRNA Biological Repeat 2

city: Charleston

first: Vamsi

last: Gangaraju

address: 173 Ashley Ave

institute: Medical University of South Carolina

data_processing:
RNA fragments were aligned to dm3 transcriptome and transposon consensus sequences using Bowtie 2 and quantified using RSEM.
Differential expression analysis was conducted using EBSeq
Genome_build: dm6
Supplementary_files_format_and_content: excel file with results from RSEM. Includes FPKM values of all biological repeats.

source_name: Head

extract_protocol:
Total RNA was isolated from 10 heads using TRIzol (Thermo Fisher Scientific) and mRNA sequencing was performed as described elsewhere (J Biol Chem 292, 6039-6046). RNA integrity was verified on an Agilent 2200 TapeStation (Agilent Technologies, Palo Alto, CA). 100-200 ng of total RNA was used to prepare RNA-Seq libraries using the TruSeq RNA Sample Prep kit following the protocol described by the manufacturer (Illumina, San Diego, CA). Please note that polyA containing RNA was first purfied prior to the library preparation step. Single end sequencing (1X50 cycles) was performed on an Illumina HiSeq2500. Sequencing was performed at Hollings Cancer Center Genomics Core Lab at MUSC.
RNA libraries were prepared using TruSeq RNA Sample Prep Kit after selecting for polyA RNA

tag: gender


title: Night-Shift, ID543, 9AM

description: replicate 1

tag: group

value: Fasted


title: Night-Shift, ID543, 12AM

description: replicate 1


title: 555031A10 - 41_DFLO-14_Rep_N+S+_2 vs 16_DFLO_Rep_N+S+_2

hyb_protocol: 16_DFLO_Rep_N+S+_2 Cy5 / 41_DFLO-14_Rep_N+S+_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Kr[If-1] + Phenotype Total mRNA Biological Repeat 1


title: Night-Shift, ID959, 6AM

description: replicate 1


title: 555031A07 - 10_DFLO_Rep_N+S+_1 vs 39_DFLO-14_Rep_N+S+_1

hyb_protocol: 39_DFLO-14_Rep_N+S+_1 Cy5 / 10_DFLO_Rep_N+S+_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 555031A09 - 16_DFLO_Rep_N+S+_2 vs 41_DFLO-14_Rep_N+S+_2

hyb_protocol: 41_DFLO-14_Rep_N+S+_2 Cy5 / 16_DFLO_Rep_N+S+_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 555031A08 - 39_DFLO-14_Rep_N+S+_1 vs 10_DFLO_Rep_N+S+_1

hyb_protocol: 10_DFLO_Rep_N+S+_1 Cy5 / 39_DFLO-14_Rep_N+S+_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Kr[If-1] No Phenotype Total mRNA Biological Repeat 2


title: Night-Shift, ID959, 12AM

description: replicate 1


title: Night-Shift, ID959, 3AM

description: replicate 1


title: Night-Shift, ID959, 3PM

description: replicate 1


title: Night-Shift, ID959, 9PM

description: replicate 1


title: Kr[If-1] No Phenotype Total mRNA Biological Repeat 1


title: M19 rna-seq

description:
M19
RNA-seq data for Male chorionic villus sample M19.
processed data file: genecounts.txt


title: 555031A05 - 8_DFLO_Rep_N+S+_3 vs 25_DFLO-14_Rep_N-S+_3

hyb_protocol: 25_DFLO-14_Rep_N-S+_3 Cy5 / 8_DFLO_Rep_N+S+_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Night-Shift, ID959, 9AM

description: replicate 1


title: M17 rna-seq

description:
M17
RNA-seq data for Male chorionic villus sample M17.
processed data file: genecounts.txt


title: Night-Shift, ID959, 12PM

description: replicate 1


title: M16 rna-seq

description:
M16
RNA-seq data for Male chorionic villus sample M16.
processed data file: genecounts.txt


title: 555031A03 - 16_DFLO_Rep_N+S+_2 vs 29_DFLO-14_Rep_N-S+_2

hyb_protocol: 29_DFLO-14_Rep_N-S+_2 Cy5 / 16_DFLO_Rep_N+S+_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 555031A06 - 25_DFLO-14_Rep_N-S+_3 vs 8_DFLO_Rep_N+S+_3

hyb_protocol: 8_DFLO_Rep_N+S+_3 Cy5 / 25_DFLO-14_Rep_N-S+_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: M18 rna-seq

description:
M18
RNA-seq data for Male chorionic villus sample M18.
processed data file: genecounts.txt


title: M15 rna-seq

description:
M15
RNA-seq data for Male chorionic villus sample M15.
processed data file: genecounts.txt


title: M20 rna-seq

description:
M20
RNA-seq data for Male chorionic villus sample M20.
processed data file: genecounts.txt


title: Night-Shift, ID395, 3AM

description: replicate 1


title: Night-Shift, ID395, 3PM

description: replicate 1


title: Night-Shift, ID395, 6PM

description: replicate 1


title: M13 rna-seq

description:
M13
RNA-seq data for Male chorionic villus sample M13.
processed data file: genecounts.txt


title: M14 rna-seq

description:
M14
RNA-seq data for Male chorionic villus sample M14.
processed data file: genecounts.txt


title: Night-Shift, ID395, 6AM

description: replicate 1


title: Night-Shift, ID395, 12PM

description: replicate 1


title: 555031A04 - 29_DFLO-14_Rep_N-S+_2 vs 16_DFLO_Rep_N+S+_2

hyb_protocol: 16_DFLO_Rep_N+S+_2 Cy5 / 29_DFLO-14_Rep_N-S+_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Night-Shift, ID395, 12AM

description: replicate 1


title: 555031A02 - 27_DFLO-14_Rep_N-S+_1 vs 10_DFLO_Rep_N+S+_1

hyb_protocol: 10_DFLO_Rep_N+S+_1 Cy5 / 27_DFLO-14_Rep_N-S+_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 554377A12 - 64_DFLO-27_Veg_N+S+_3 vs 32_DFLO-14_Veg_N+S+_3

hyb_protocol: 32_DFLO-14_Veg_N+S+_3 Cy5 / 64_DFLO-27_Veg_N+S+_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: medicago truncatula (a17)  - age


title: 555031A01 - 10_DFLO_Rep_N+S+_1 vs 27_DFLO-14_Rep_N-S+_1

hyb_protocol: 27_DFLO-14_Rep_N-S+_1 Cy5 / 10_DFLO_Rep_N+S+_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 554377A08 - 59_DFLO-27_Veg_N+S+_1 vs 38_DFLO-14_Veg_N+S+_1

hyb_protocol: 38_DFLO-14_Veg_N+S+_1 Cy5 / 59_DFLO-27_Veg_N+S+_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Day-Shift, ID672, 6AM

description: replicate 1

tag: Sex

value: Day-Shift


title: 554377A11 - 32_DFLO-14_Veg_N+S+_3 vs 64_DFLO-27_Veg_N+S+_3

hyb_protocol: 64_DFLO-27_Veg_N+S+_3 Cy5 / 32_DFLO-14_Veg_N+S+_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: M12 rna-seq

description:
M12
RNA-seq data for Male chorionic villus sample M12.
processed data file: genecounts.txt


title: 122B: nephroureterectomy from patient 40

city: Burlington

first: Travis

last: Sullivan

state: MA

address: 41 Mall Rd.

institute: Lahey Hospital & Medical Center

description: sample name: 122B

data_processing:
Non-normalized data are the Cq values computed by the Bio-Rad CFX themal cycler software, no adjustment to baseline backgrounds were made
Each microRNA of interest was normalized to the global mean within each sample.  The global mean was calculated only using microRNA with a Cq<37 detected in all 35 samples.   2^-deltaCq, where deltaCq = (Cq_Target − Cq_global_mean).  All Cq values >37 were set to 40.
Fold change (delta delta Ct) values were not computed for this dataset
normalized data matrix reports normalized signal (against each samples global mean).

label: SYBR Green

source_name: upper tract urothelial carcinoma

label_protocol: cDNA and RT-PCR were performed using the miRCURY LNA miRNA PCR Human Arrays I&II, currently provided by Qiagen formerly from Exiqon, following the manufacturer's recommendations. Catalog number for the array is: 339322

extract_protocol: Total RNA was isolated using the Ambion RecoverAll Total Nucleic Acid Isolation Kit for FFPE following the manufacturer's recommendations

tag: tissue preparation

value: FFPE

value: upper tract urothelial carcinoma

tag: grade/ invasive

value: high/ non-invasive


title: 554377A10 - 67_DFLO-27_Veg_N+S+_2 vs 40_DFLO-14_Veg_N+S+_2

hyb_protocol: 40_DFLO-14_Veg_N+S+_2 Cy5 / 67_DFLO-27_Veg_N+S+_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Night-Shift, ID395, 9AM

description: replicate 1

value: Female


title: 554377A09 - 40_DFLO-14_Veg_N+S+_2 vs 67_DFLO-27_Veg_N+S+_2

hyb_protocol: 67_DFLO-27_Veg_N+S+_2 Cy5 / 40_DFLO-14_Veg_N+S+_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 40B: nephroureterectomy from patient 4

description: sample name: 40B

value: low/ non-invasive


title: 4B: nephroureterectomy from patient 49

description: sample name: 4B


title: M10 rna-seq

description:
M10
RNA-seq data for Male chorionic villus sample M10.
processed data file: genecounts.txt


title: 554377A06 - 55_DFLO-27_Veg_N-S+_3 vs 24_DFLO-14_Veg_N-S+_3

hyb_protocol: 24_DFLO-14_Veg_N-S+_3 Cy5 / 55_DFLO-27_Veg_N-S+_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: medicago truncatula (a17)  - harvest date


title: M09 rna-seq

description:
M09
RNA-seq data for Male chorionic villus sample M09.
processed data file: genecounts.txt


title: 49B: nephroureterectomy from patient 28

description: sample name: 49B


title: 554377A04 - 57_DFLO-27_Veg_N-S+_2 vs 28_DFLO-14_Veg_N-S+_2

description: Transcriptome in leaves of Medicago truncatula plants during the remobilization process . Effect of a nitrogen deficiency on this process.Note that lower leaves correspond to vegetative leaves (FV) and upper leaves correspond to leaves of the reproductive part (FR).

hyb_protocol: 28_DFLO-14_Veg_N-S+_2 Cy5 / 57_DFLO-27_Veg_N-S+_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 554377A07 - 38_DFLO-14_Veg_N+S+_1 vs 59_DFLO-27_Veg_N+S+_1

hyb_protocol: 59_DFLO-27_Veg_N+S+_1 Cy5 / 38_DFLO-14_Veg_N+S+_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 554377A05 - 24_DFLO-14_Veg_N-S+_3 vs 55_DFLO-27_Veg_N-S+_3

hyb_protocol: 55_DFLO-27_Veg_N-S+_3 Cy5 / 24_DFLO-14_Veg_N-S+_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: M11 rna-seq

description:
M11
RNA-seq data for Male chorionic villus sample M11.
processed data file: genecounts.txt


title: Day-Shift, ID672, 9PM

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol


title: Day-Shift, ID672, 3AM

description: replicate 1


title: M08 rna-seq

description:
M08
RNA-seq data for Male chorionic villus sample M08.
processed data file: genecounts.txt


title: 118B: nephroureterectomy from patient 61

description: sample name: 118B


title: M07 rna-seq

description:
M07
RNA-seq data for Male chorionic villus sample M07.
processed data file: genecounts.txt


title: 28B: nephroureterectomy from patient 75

description: sample name: 28B


title: M06 rna-seq

description:
M06
RNA-seq data for Male chorionic villus sample M06.
processed data file: genecounts.txt


title: 75B: nephroureterectomy from patient 112

description: sample name: 75B


title: 77B: nephroureterectomy from patient 93

description: sample name: 77B


title: M05 rna-seq

description:
M05
RNA-seq data for Male chorionic villus sample M05.
processed data file: genecounts.txt


title: Day-Shift, ID672, 12PM

description: replicate 1


title: M04 rna-seq

description:
M04
RNA-seq data for Male chorionic villus sample M04.
processed data file: genecounts.txt


title: 554377A03 - 28_DFLO-14_Veg_N-S+_2 vs 57_DFLO-27_Veg_N-S+_2

hyb_protocol: 57_DFLO-27_Veg_N-S+_2 Cy5 / 28_DFLO-14_Veg_N-S+_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 93B: nephroureterectomy from patient 82

description: sample name: 93B


title: M03 rna-seq

description:
M03
RNA-seq data for Male chorionic villus sample M03.
processed data file: genecounts.txt


title: 554251A12 - 65_DFLO-27_Rep_N+S+_3 vs 33_DFLO-14_Rep_N+S+_3

hyb_protocol: 33_DFLO-14_Rep_N+S+_3 Cy5 / 65_DFLO-27_Rep_N+S+_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 74B: nephroureterectomy from patient 35

description: sample name: 74B


title: M02 rna-seq

description:
M02
RNA-seq data for Male chorionic villus sample M02.
processed data file: genecounts.txt


title: Day-Shift, ID843, 6AM

description: replicate 1


title: 61B: nephroureterectomy from patient 51

description: sample name: 61B


title: 554377A02 - 52_DFLO-27_Veg_N-S+_1 vs 26_DFLO-14_Veg_N-S+_1

hyb_protocol: 26_DFLO-14_Veg_N-S+_1 Cy5 / 52_DFLO-27_Veg_N-S+_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: F17 rna-seq

description:
F17
RNA-seq data for Female chorionic villus sample F17.
processed data file: genecounts.txt


title: M01 rna-seq

description:
M01
RNA-seq data for Male chorionic villus sample M01.
processed data file: genecounts.txt


title: F16 rna-seq

description:
F16
RNA-seq data for Female chorionic villus sample F16.
processed data file: genecounts.txt


title: 51B: nephroureterectomy from patient 84

description: sample name: 51B


title: 124B: nephroureterectomy from patient 113

description: sample name: 124B


title: Day-Shift, ID672, 6PM

description: replicate 1


title: 8B: nephroureterectomy from patient 53

description: sample name: 8B


title: F15 rna-seq

description:
F15
RNA-seq data for Female chorionic villus sample F15.
processed data file: genecounts.txt


title: 554251A10 - 68_DFLO-27_Rep_N+S+_2 vs 41_DFLO-14_Rep_N+S+_2

hyb_protocol: 41_DFLO-14_Rep_N+S+_2 Cy5 / 68_DFLO-27_Rep_N+S+_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 35B: nephroureterectomy from patient 29

description: sample name: 35B


title: 554251A11 - 33_DFLO-14_Rep_N+S+_3 vs 65_DFLO-27_Rep_N+S+_3

hyb_protocol: 65_DFLO-27_Rep_N+S+_3 Cy5 / 33_DFLO-14_Rep_N+S+_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Day-Shift, ID672, 9AM

description: replicate 1


title: F14 rna-seq

description:
F14
RNA-seq data for Female chorionic villus sample F14.
processed data file: genecounts.txt


title: 554377A01 - 26_DFLO-14_Veg_N-S+_1 vs 52_DFLO-27_Veg_N-S+_1

hyb_protocol: 52_DFLO-27_Veg_N-S+_1 Cy5 / 26_DFLO-14_Veg_N-S+_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Day-Shift, ID843, 3PM

description: replicate 1


title: 554251A06 - 56_DFLO-27_Rep_N-S+_3 vs 25_DFLO-14_Rep_N-S+_3

hyb_protocol: 25_DFLO-14_Rep_N-S+_3 Cy5 / 56_DFLO-27_Rep_N-S+_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 554251A09 - 41_DFLO-14_Rep_N+S+_2 vs 68_DFLO-27_Rep_N+S+_2

hyb_protocol: 68_DFLO-27_Rep_N+S+_2 Cy5 / 41_DFLO-14_Rep_N+S+_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 554251A08 - 60_DFLO-27_Rep_N+S+_1 vs 39_DFLO-14_Rep_N+S+_1

hyb_protocol: 39_DFLO-14_Rep_N+S+_1 Cy5 / 60_DFLO-27_Rep_N+S+_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Day-Shift, ID843, 3AM

description: replicate 1


title: 554251A07 - 39_DFLO-14_Rep_N+S+_1 vs 60_DFLO-27_Rep_N+S+_1

hyb_protocol: 60_DFLO-27_Rep_N+S+_1 Cy5 / 39_DFLO-14_Rep_N+S+_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 84B: nephroureterectomy from patient 122

description: sample name: 84B


title: Day-Shift, ID672, 3PM

description: replicate 1


title: 554251A04 - 58_DFLO-27_Rep_N-S+_2 vs 29_DFLO-14_Rep_N-S+_2

hyb_protocol: 29_DFLO-14_Rep_N-S+_2 Cy5 / 58_DFLO-27_Rep_N-S+_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 78B: nephroureterectomy from patient 39

description: sample name: 78B


title: Day-Shift, ID843, 9PM

description: replicate 1


title: Day-Shift, ID843, 6PM

description: replicate 1


title: Day-Shift, ID843, 12AM

description: replicate 1


title: 29B: nephroureterectomy from patient 109

description: sample name: 29B


title: F12 rna-seq

description:
F12
RNA-seq data for Female chorionic villus sample F12.
processed data file: genecounts.txt


title: Day-Shift, ID843, 12PM

description: replicate 1


title: 554251A05 - 25_DFLO-14_Rep_N-S+_3 vs 56_DFLO-27_Rep_N-S+_3

hyb_protocol: 56_DFLO-27_Rep_N-S+_3 Cy5 / 25_DFLO-14_Rep_N-S+_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: F11 rna-seq

description:
F11
RNA-seq data for Female chorionic villus sample F11.
processed data file: genecounts.txt


title: F13 rna-seq

description:
F13
RNA-seq data for Female chorionic villus sample F13.
processed data file: genecounts.txt


title: 53B: nephroureterectomy from patient 107

description: sample name: 53B


title: F10 rna-seq

description:
F10
RNA-seq data for Female chorionic villus sample F10.
processed data file: genecounts.txt


title: 39B: nephroureterectomy from patient 2

description: sample name: 39B

value: high/ invasive


title: Day-Shift, ID550, 6AM

description: replicate 1


title: F09 rna-seq

description:
F09
RNA-seq data for Female chorionic villus sample F09.
processed data file: genecounts.txt


title: 109B: nephroureterectomy from patient 117

description: sample name: 109B


title: 107B: nephroureterectomy from patient 118

description: sample name: 107B


title: Day-Shift, ID843, 9AM

description: replicate 1


title: 554251A02 - 53_DFLO-27_Rep_N-S+_1 vs 27_DFLO-14_Rep_N-S+_1

description: Transcriptome in leaves of Medicago truncatula plants during the remobilization process . Effect of a nitrogen deficiency on this process.Note that lower leaves correspond to vegetative leaves (FV) and upper leaves correspond to leaves of the reproductive part (FR).

hyb_protocol: 27_DFLO-14_Rep_N-S+_1 Cy5 / 53_DFLO-27_Rep_N-S+_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Day-Shift, ID550, 12AM

description: replicate 1


title: 2B: nephroureterectomy from patient 25

description: sample name: 2B


title: Day-Shift, ID550, 9PM

description: replicate 1


title: 554251A01 - 27_DFLO-14_Rep_N-S+_1 vs 53_DFLO-27_Rep_N-S+_1

hyb_protocol: 53_DFLO-27_Rep_N-S+_1 Cy5 / 27_DFLO-14_Rep_N-S+_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: F08 rna-seq

description:
F08
RNA-seq data for Female chorionic villus sample F08.
processed data file: genecounts.txt


title: 554251A03 - 29_DFLO-14_Rep_N-S+_2 vs 58_DFLO-27_Rep_N-S+_2

hyb_protocol: 58_DFLO-27_Rep_N-S+_2 Cy5 / 29_DFLO-14_Rep_N-S+_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Day-Shift, ID550, 6PM

description: replicate 1


title: F06 rna-seq

description:
F06
RNA-seq data for Female chorionic villus sample F06.
processed data file: genecounts.txt


title: F07 rna-seq

description:
F07
RNA-seq data for Female chorionic villus sample F07.
processed data file: genecounts.txt


title: F05 rna-seq

description:
F05
RNA-seq data for Female chorionic villus sample F05.
processed data file: genecounts.txt


title: 554228A11 - 7_DFLO_Veg_N+S+_3 vs 32_DFLO-14_Veg_N+S+_3

hyb_protocol: 32_DFLO-14_Veg_N+S+_3 Cy5 / 7_DFLO_Veg_N+S+_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: first flowers buds visible


title: 554228A12 - 32_DFLO-14_Veg_N+S+_3 vs 7_DFLO_Veg_N+S+_3

hyb_protocol: 7_DFLO_Veg_N+S+_3 Cy5 / 32_DFLO-14_Veg_N+S+_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Day-Shift, ID550, 3PM

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol


title: Day-Shift, ID550, 12PM

description: replicate 1


title: 25B: nephroureterectomy from patient 22

description: sample name: 25B


title: Day-Shift, ID550, 9AM

description: replicate 1


title: 554228A09 - 15_DFLO_Veg_N+S+_2 vs 40_DFLO-14_Veg_N+S+_2

hyb_protocol: 40_DFLO-14_Veg_N+S+_2 Cy5 / 15_DFLO_Veg_N+S+_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 554228A08 - 38_DFLO-14_Veg_N+S+_1 vs 9_DFLO_Veg_N+S+_1

hyb_protocol: 9_DFLO_Veg_N+S+_1 Cy5 / 38_DFLO-14_Veg_N+S+_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: F04 rna-seq

description:
F04
RNA-seq data for Female chorionic villus sample F04.
processed data file: genecounts.txt


title: 22B: nephroureterectomy from patient 74

description: sample name: 22B


title: 554228A07 - 9_DFLO_Veg_N+S+_1 vs 38_DFLO-14_Veg_N+S+_1

hyb_protocol: 38_DFLO-14_Veg_N+S+_1 Cy5 / 9_DFLO_Veg_N+S+_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: F03 rna-seq

description:
F03
RNA-seq data for Female chorionic villus sample F03.
processed data file: genecounts.txt


title: 112B: nephroureterectomy from patient 12

description: sample name: 112B

value: low/ invasive


title: 554228A10 - 40_DFLO-14_Veg_N+S+_2 vs 15_DFLO_Veg_N+S+_2

hyb_protocol: 15_DFLO_Veg_N+S+_2 Cy5 / 40_DFLO-14_Veg_N+S+_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: F02 rna-seq

description:
F02
RNA-seq data for Female chorionic villus sample F02.
processed data file: genecounts.txt


title: FA (IB6_B2)

city: Tempe

first: Ben

last: Readhead

state: AZ

address: 797 E. Tyler Street

institute: ASU-Banner Neurodegenerative Disease Research Center

data_processing: We used the R software package, Limma, and the neqc function to perform background subtraction using the negative control probes, and quantile normalization using both positive and negative control probes.

label: Biotin

source_name: Keratinocytes

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays (Thermo Fisher Scientific)

growth_protocol: HaCat human keratinocytes were grown in DMEM supplemented with 10 % Fetal Bovine Serum and 1 X Pen/Strep

extract_protocol: RNA was extracted using EZNA Total RNA Kit I  (Omega Bio-tek, GA, USA)  exactly according to the manufacturer's  instructions . The RNA quality and concentration was analyzed using Nanodrop  spectrophotometer.

treatment_protocol: At 70% confluency, cells were pre-treated with 1 μM PI3K  inhibitor LY294002 for 6 hrs followed by 1 μM of glucocorticoid fluocinolone acetonide ( FA ) for additional 24 h (IB4 and IB8) or were treated with 1 μM of FA alone for 24 h (IB2 and IB6) or LY294002 alone 1 μM x 24 hrs  (IB3 and IB7). Control cells were treated with DMSO (vehicle control IB1 and IB5).

tag: cell line

value: HaCat

tag: cell type

value: Keratinocytes

value: FA

tag: batch


title: F01 rna-seq

description:
F01
RNA-seq data for Female chorionic villus sample F01.
processed data file: genecounts.txt

value: Chorionic villus


title: 30B: nephroureterectomy from patient 8

description: sample name: 30B


title: FA (IB2_B2)


title: 82B: nephroureterectomy from patient 124

description: sample name: 82B


title: 117B: nephroureterectomy from patient 77

description: sample name: 117B


title: 126B: nephroureterectomy from patient 126

description: sample name: 126B


title: 57B: nephroureterectomy from patient 78

description: sample name: 57B


title: Control (IB1_B2)

value: Untreated


title: HCCLM3-control-3

city: Shanghai

first: Yi

last: Yang

address: 180 Feng Lin Road

country: China

institute: Liver Cancer Institute, Zhongshan Hospital, Fudan University

description: LncRNA expression after up-/down- hnRNPAB in cell

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled RNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, USA) in hybridization oven (Cat#G2545A, Agilent technologies, USA). After 17 hours hybridization, slides were washed.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, USA) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, USA).

data_processing:
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, USA).
91 hnRNPAB-regulated lncRNAs overlapped all four groups (HepG2-control VS HepG2-hnRNPAB, P<0.05; PLC/PRF/5-control VS PLC/PRF/5-hnRNPAB, P<0.05; MHCC97H-control VS MHCC97H-sh-hnRNPAB, P<0.05; HCCLM3-control VS HCCLM3-sh-hnRNPAB, P<0.05)

source_name: mock lentiviral vectors，replicate-3

label_protocol: RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, USA).

growth_protocol: All cell lines were cultured with high-glucose Dulbecco’s modified eagle medium (DMEM) added with 10% fetal bovine serum, penicillin/streptomycin, at 37°C under 5% CO2 in incubator.

extract_protocol: RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions. RNA quality was inspected by electro phoresis using Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, USA), purified by RNeasy micro Kit (Cat#74004, QIAGEN, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, Germany).

treatment_protocol: HCCLM3 and MHCC97H cells transfected with hU6-MCS-CBh-gcGFP-IRES-puromycin-shRNA-hnRNPAB lentiviral vectors and hU6-MCS-CBh-gcGFP-IRES-puromycin-shRNA-mock lentiviral vectors. PLC/PRF/5 and HepG2 cells transfected with Ubi-MCS-SV40-EGFP-IRES-puromycin-hnRNPAB lentiviral vectors and Ubi-MCS-SV40-EGFP-IRES-puromycin-mock lentiviral vectors.

value: HCC

tag: metastasis

value: high

tag: hnrnpab

value: NC


title: 48B: nephroureterectomy from patient 57

description: sample name: 48B


title: 31B: nephroureterectomy from patient 48

description: sample name: 31B


title: FA.LY294002 (IB8_B1)

tag: treatment


title: HCCLM3-sh-hnRNPAB-1

source_name: hnRNPAB knockdown，replicate-1

value: down


title: HCCLM3-control-2

source_name: mock lentiviral vectors，replicate-2


title: HCCLM3-sh-hnRNPAB-3

source_name: hnRNPAB knockdown，replicate-3


title: LY294002 (IB7_B1)


title: MHCC97H-control-3


title: HCCLM3-sh-hnRNPAB-2

source_name: hnRNPAB knockdown，replicate-2


title: HCCLM3-control-1

source_name: mock lentiviral vectors，replicate-1


title: Control (IB5_B2)


title: Control (IB5_B1)


title: FA.LY294002 (IB4_B1)


title: MHCC97H-control-2


title: 113B: nephroureterectomy from patient 31

description: sample name: 113B

value: FFPE

tag: tissue


title: MHCC97H-control-1


title: 12B: nephroureterectomy from patient 30

description: sample name: 12B

value: upper tract urothelial carcinoma


title: FA (IB2_B1)


title: LY294002 (IB3_B1)


title: melanoma_patient [9248223051_R03C01]

type: genomic

city: Barcelona

first: joan anton

last: Puig Butille

address: Villarroel 170

country: Spain

institute: Hospital Clínic

hyb_protocol: Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html

data_processing:
Germline genomic DNA was genotyped using HumanOmni2.5-8v1 Genotyping BeadChips (Illumina). The .idat files were processed using the Genotyping Module of the GenomeStudio 2011.1 software package (Illumina Inc., San Diego CA 92122, U.S.A.) with default settings according to the manufacturer's user guide. The required manifest and cluster files were downloaded from http://support.illumina.com/array/downloads.html.
Genotype: AA,AB,BB,or NC (no call)

label: Cy5, Cy3

extract_protocol: Germline genomic DNA was extracted from blood samples using the salting out method or saliva samples using DNA Genotek kits

tag: status

value: male

tag: ethnicity

value: Caucasian

tag: subject group

value: melanoma patient belonging to a melanoma-prone family

value: Blood


title: melanoma_patient [9248223051_R02C01]

scan_protocol: Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html

tag: gender

value: female


title: Control (IB1_B1)


title: melanoma_patient [9248223051_R01C01]

label_protocol: Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html


title: MHCC97H-sh-hnRNPAB-2


title: melanoma_patient [9248223037_R04C01]


title: melanoma_patient [9248223035_R08C01]


title: no_melanoma [9248223035_R07C01]

value: individual belonging to a melanoma-prone family who has not developed melanoma


title: si_4_E_R3

city: Macau

first: Edwin

last: Cheung

state: Macau

address: Taipa

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

description: Replicate 3

hyb_protocol: cRNA was hybridized onto HumanHT-12 v4 Expression BeadChip (Illumina) using standerd protocol.

scan_protocol: BeadChips were scanned with the iScanner (Illumina)

data_processing:
Data was normalized by quantile normalization
www.arrayanalysis.org computed the normalized signal intensity

source_name: LNCAP Cells

label_protocol: RNA was converted to cRNA using the TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip (Epibio)

growth_protocol: LNCaP cells were maintained in hormone satrved condition (RPMI media without phenole red + 10% charcole dextran treated FBS) for 72 hours before treatment

extract_protocol: Toatal RNA was isolated by Qiagen Rneasy kit

treatment_protocol: LNCaP cells were consicutively transfected twice with with 5nM of dsiRNA every 24 hours and after 48 hours of last trasfection, cells were treated with 10nM of DHT or ETOH for 12 hours

value: LNCAP Cells

tag: agent

value: ETOH


title: MHCC97H-sh-hnRNPAB-3


title: melanoma_patient [9248223035_R04C01]


title: si_1_E_R3

description: Replicate 3


title: melanoma_patient [9248223035_R05C01]


title: si_4_D_R3

description: Replicate 3

value: DHT


title: melanoma_patient [9248223035_R03C01]


title: PLC/PRF/5-hnRNPAB-2

source_name: hnRNPAB overexpression，replicate-2

value: low

value: up


title: PLC/PRF/5-control-2

value: HCC


title: PLC/PRF/5-control-1


title: melanoma_patient [9248223035_R01C01]


title: PLC/PRF/5-hnRNPAB-3

source_name: hnRNPAB overexpression，replicate-3


title: si_4_D_R2

description: Replicate 2


title: PLC/PRF/5-control-3


title: NC_D_R3

description: Replicate 3

value: control


title: no_melanoma [9248223026_R08C01]

value: individual belonging to a melanoma-prone family who has not developed melanoma, but with diagnostic of other cancer


title: si_1_D_R3

description: Replicate 3


title: HepG2-control-2

value: NC


title: si_4_E_R2

description: Replicate 2


title: FA (IB6_B1)

value: HaCat

value: Keratinocytes

value: FA


title: si_1_D_R2

description: Replicate 2


title: HepG2-control-1


title: NC_D_R2

description: Replicate 2


title: no_melanoma [9248223026_R07C01]

value: male

value: Caucasian


title: NC_E_R3

description: Replicate 3


title: HepG2-hnRNPAB-3


title: melanoma_patient [9248223026_R06C01]

value: melanoma patient belonging to a melanoma-prone family

value: Blood


title: melanoma_patient [9248223025_R07C01]

value: female


title: NC_E_R2

description: Replicate 2

value: LNCAP Cells


title: HepG2-control-3


title: pTpA_3E5_YPD_R9

city: Cambridge

first: Carl

middle: G

last: de Boer

address: 415 Main St

institute: The Broad Institute

description: 20160503_average_promoter_ELs_per_seq_atLeast100Counts.txt.gz

data_processing:
The paired reads representing both sides of the promoter sequence were aligned using the overlapping sequence in the middle, constrained to have 40 (+/-15) bp of overlap, and discarding any reads that failed to align well within these constraints.
Promoters were aligned to themselves using Bowtie2 (72) to identify clusters of related sequences, merging these clusters and taking the sequence with the most reads as the “true” promoter sequence for each cluster.
Mean expression level for each promoter (as in the processed files) was taken as the average of the bins, weighted by the number of times the promoter was observed in each bin. Here, bin labels are in the reverse order of expression (i.e. they reflect RFP/YFP).  Note that Abf1TATA sorting bin 16 (R4) was accidentally pooled with part of bin 11 (R9) and so was left out of all analyses and the processed data.
Genome_build: R64
Supplementary_files_format_and_content: compressed text files containing promoter sequences and their corresponding expression levels

organism: Saccharomyces cerevisiae

source_name: Random promoter library

growth_protocol: Libraries were transformed into yeast (strain Y8205) using the lithium acetate method, starting with 1L of yeast harvested at an OD of 0.3-0.4 , ensuring a complexity of at least 1E8 was achieved (with the exception of the high-quality pTpA library where a dilution series was performed to achieve the desired complexity). The yeast were then grown in SD-Ura for two days, diluting the media by 1:4 three times during this period.  Media was then changed to YPD, growing for at least 5 generations prior to cell sorting. For YPGly and YPGal experiments, the same pTpA transformation was used and the culture was grown for at least 8 generations (due to the change in carbon source). In the final 10 hours of growth prior to cell sorting, the cultures were allowed to grow continuously in log phase, never achieving an OD above 0.6, by diluting in fresh media.  All cultures were grown in a shaker incubator, at 30C and approximately 250 RPM.

extract_protocol:
Plasmids were isolated using Qiagen spin miniprep kits, as adapted for yeast according to the manufacturer's website. Cells were sorted by the log ratio of RFP to YFP signal (using mCherry and GFP absorption/emission) on a Beckman-Coulter MoFlo Astrios, using 18 uniform bins, done in three batches of six bins each. We note that the FACS configuration varied between experiments (e.g. different laser intensities), resulting in different baseline expression values. Post sort, cells were spun down and resuspended in SC-Ura (supplemented with 1% Gal for Gal sort) and grown for 2-3 days, shaking at 30C.
The plasmids were then isolated, the promoter region amplified, Nextera adaptors and multiplexing indices added, and the resulting libraries sequenced paired-end, 76 bp each, using 150 cycle kits so that complete coverage of the promoter could be achieved, including overlap in the center.

treatment_protocol: Prior to sort, yeast were spun down, washed once in ice-cold PBS, and then suspended in ice-cold PBS and kept on ice until cell sorting.

tag: media

value: YPD

tag: libraryid


title: pTpA_3E5_YPD_R7


title: pTpA_3E5_YPD_R8


title: si_1_E_R2

description: Replicate 2

value: ETOH


title: melanoma_patient [9248223025_R06C01]


title: pTpA_3E5_YPD_R6


title: MHCC97H-sh-hnRNPAB-1

value: high

value: down


title: melanoma_patient [6264550107_R07C01]

description: melanoma patient belonging to a melanoma-prone family

tag: subject status

value: blood


title: HepG2-hnRNPAB-1

source_name: hnRNPAB overexpression，replicate-1

value: HCC

value: low

value: up


title: pTpA_3E5_YPD_R5


title: no_melanoma [6285545091_R03C01]

description: individual belonging to a melanoma-prone family who has not developed melanoma


title: no_melanoma [6285545091_R01C01]

value: individual belonging to a melanoma-prone family who has not developed melanoma


title: pTpA_3E5_YPD_R4


title: pTpA_3E5_YPD_R3


title: melanoma_patient [6285545076_R07C01]


title: pTpA_3E5_YPD_R2


title: no_melanoma [6285545076_R03C01]


title: si_4_E_R1

description: Replicate 1


title: HepG2-hnRNPAB-2


title: melanoma_patient [6285545056_R08C01]


title: NC_D_R1

description: Replicate 1

value: control

value: DHT


title: pTpA_3E5_YPD_R19


title: melanoma_patient [6285545056_R07C01]


title: si_1_D_R1

description: Replicate 1


title: si_1_E_R1

description: Replicate 1


title: NC_E_R1

description: Replicate 1


title: pTpA_3E5_YPD_R17


title: human Tregs_stimulated_NRP1KD_4

city: Oxford

first: Ruud

last: van Stiphout

address: Old Road Campus Research Building

country: United Kingdom

institute: University of Oxford

description: Sample 26

data_processing: The data were normalised using quantile normalisation with R-package LIMMA (normalizeQuantiles)

source_name: human peripheral blood

label_protocol: biotinylation

growth_protocol: 16-day Treg expansion protocol with anti-CD3/anti-CD28 beads and interleukin-2 (see Hester et al (2012) Low‐Dose Rapamycin Treatment Increases the Ability of Human Regulatory T Cells to Inhibit Transplant Arteriosclerosis In Vivo. American Journal of Transplantation).

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Mini kit

treatment_protocol: lentivirus-mediated transduction with pLKO1 vector (TRC consortium) encoding either shRNA against NRP1 (human neuropilin-1 gene) or scrambled control

value: Tregs

tag: shRNA

tag: biological replicate (donor)

tag: stimulation condition

value: 72hrs with anti-CD3/anti-CD28 beads & IL-2

tag: cell subtype


title: human Tregs_stimulated_NRP1KD_3

description: Sample 24

tag: cell type


title: human Tregs_stimulated_control vector pLKO1_4

description: Sample 25


title: pTpA_3E5_YPD_R16


title: melanoma_patient [6285545056_R02C01]

value: Caucasian

value: melanoma patient belonging to a melanoma-prone family


title: pTpA_3E5_YPD_R15


title: no_melanoma [6285545054_R06C01]

value: female


title: human Tregs_stimulated_NRP1KD_2

description: Sample 22


title: pTpA_3E5_YPD_R13


title: melanoma_patient [6285545054_R04C01]


title: no_melanoma [6285545025_R07C01]

value: male


title: pTpA_3E5_YPD_R18

value: YPD


title: pTpA_3E5_YPD_R11


title: no_melanoma [6285545056_R05C01]


title: pTpA_3E5_YPD_R12


title: no_melanoma [6285545054_R02C01]


title: pTpA_3E5_YPD_R14


title: Msa1-TAP_replicate

city: New York

first: Kaustav

last: Mukherjee

address: 1 Gustave Levy Place

institute: Mount Sinai Medical Center

description: Msa1-TAP CLIP-Seq

data_processing:
STAR (Dobin et al) reads aligned to S. pombe genome
Samtools – sort and index sam file to generate bam file
Deeptools – to generate bigwig file from bam file
Homer – peak calling, peak annotation, and enrichment analysis
Genome_build: ASM294v2.26
Supplementary_files_format_and_content: bigWig files containing CLIP-Seq coverage scores

organism: Schizosaccharomyces pombe

source_name: yeast

growth_protocol: cells were grown on YES media with supplements at 30C till they reached log phase. They were then harvested, washed and put on ME media to induce meiosis. Samples were taken at 4,5,6 hours and pelleted. The pellet was washed with lysis buffer and flash frozen in liquid nitrogen and stored in -80C

extract_protocol:
Pellets were thawed on ice, suspended in 400ul lysis buffer and lysed by bead beating using Zirconia beads. The lysate was clarified by centrifugation. After immunoprecipitation, RNA was extracted by phenol:chloroform extraction and ethanol precipitation
Nugen Ovation Universal kit (part # 0343-32) was used to prepare libraries using dUTP and random hexamers/polyA combination to make strand-specific cDNA. cDNA was sonicated and end repaired. 5’ and 3’ sequencing adapters were added and libraries were amplified for 12 cycles

tag: mating type

tag: tap tag

tag: growth condition

value: nitrogen starved ME media 4h


title: no_melanoma [6285545054_R03C01]

tag: tissue


title: si_4_D_R1

description: Replicate 1

tag: cell line

value: LNCAP Cells

tag: treatment


title: PLC/PRF/5-hnRNPAB-1

tag: metastasis

tag: hnrnpab


title: melanoma_patient [6285545025_R02C01]

tag: ethnicity

tag: gender

tag: subject group


title: human Teffs_unstimulated_NRP1-KD_1

description: Sample 14

value: Teffs

value: 72hrs no beads


title: human Tregs_stimulated_control vector pLKO1_2

description: Sample 21


title: Mei2-TAP_replicate

description: Mei2-TAP CLIP-Seq


title: human Teffs_unstimulated_NRP1-KD_3

description: Sample 20


title: human Tregs_unstimulated_NRP1-KD_5

description: Sample 12


title: pTpA_3E5_YPD_R10

tag: media

tag: libraryid


title: human Tregs_stimulated_control vector pLKO1_3

description: Sample 23

tag: shRNA

tag: biological replicate (donor)


title: human Tregs_unstimulated_control vector pLKO1_5

description: Sample 11

tag: stimulation condition

tag: cell subtype


title: human Teffs_unstimulated_control vector pLKO1_2

description: Sample 15

tag: cell type


title: human Tregs_unstimulated_NRP1-KD_4

description: Sample 10


title: human Teffs_unstimulated_control vector pLKO1_3

description: Sample 19


title: human Tregs_unstimulated_control vector pLKO1_4

description: Sample 9


title: human Teffs_unstimulated_NRP1-KD_2

description: Sample 16


title: Msa1-TAP

description: Msa1-TAP CLIP-Seq

tag: mating type

tag: tap tag


title: melanoma_patient [6285545021_R06C01]

tag: subject status

tag: tissue

value: blood


title: human Teffs_unstimulated_control vector pLKO1_1

description: Sample 13


title: no_melanoma [6264550114_R07C01]


title: Mei2-TAP

description: Mei2-TAP CLIP-Seq

tag: growth condition


title: untagged

description: untagged control CLIP-Seq


title: no_melanoma [6264550114_R08C01]


title: melanoma_patient [6285545021_R03C01]


title: no_melanoma [6285545025_R01C01]


title: no_melanoma [6285545025_R03C01]


title: melanoma_patient [6264550114_R05C01]


title: melanoma_patient [6264550114_R04C01]


title: no_melanoma [6264550114_R02C01]


title: no_melanoma [6264550112_R08C01]


title: melanoma_patient [6264550114_R01C01]


title: no_melanoma [6264550114_R06C01]


title: human Tregs_unstimulated_control vector pLKO1_3

description: Sample 7


title: human Tregs_stimulated_control vector pLKO1_1

description: Sample 5


title: no_melanoma [6264550112_R07C01]