title: 559479A12 - 124_DFLO+14_Rep_N+S+_3 vs 80_DFLO_Rep_N+S+_3

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 Pea 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: 80_DFLO_Rep_N+S+_3 Cy5 / 124_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.

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.

organism: Lathyrus oleraceus

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 - NA

treatment_protocol: no treatment

value: 31.8day dev.stage (Boyes et al. Plant Cell 2001):boyes:6.00

value: 43.5day dev.stage (Boyes et al. Plant Cell 2001):boyes:6.50


title: 559479A09 - 82_DFLO_Rep_N+S+_2 vs 120_DFLO+14_Rep_N+S+_2

status: Public on Jan 01 2019

type: RNA

hyb_protocol: 120_DFLO+14_Rep_N+S+_2 Cy5 / 82_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.

molecule: total RNA

tag: age


title: 559479A10 - 120_DFLO+14_Rep_N+S+_2 vs 82_DFLO_Rep_N+S+_2

hyb_protocol: 82_DFLO_Rep_N+S+_2 Cy5 / 120_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: 559479A08 - 130_DFLO+14_Rep_N+S+_1 vs 72_DFLO_Rep_N+S+_1

hyb_protocol: 72_DFLO_Rep_N+S+_1 Cy5 / 130_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: mir-71(n4115) rep4

city: Cologne

first: Thorsten

last: Hoppe

address: Joseph-Stelzmann-Str. 26

department: Institut für Genetik

country: Germany

institute: CECAD Cologne and Institute for Genetics

hyb_protocol: Reversely transcribed RNAs were hybridized to Affymetrix EleGene 1.0 ST microarrays, according to the manufacturer's instructions.

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

data_processing: Raw data files were imported into Partek Genomics Suite software, version 6.6 (Partek Inc.) using RMA normalization.

label: biotin

organism: Caenorhabditis elegans

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: wildtype (N2) and mir-71(n4115) worms were synchronized by bleaching and grown until day 1 of adulthood. Food source: E. coli OP50

extract_protocol: The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen). RNA was subsequently purified using the RNeasy kit (Qiagen).

tag: genotype

value: day 1 of adulthood


title: 559479A07 - 72_DFLO_Rep_N+S+_1 vs 130_DFLO+14_Rep_N+S+_1

hyb_protocol: 130_DFLO+14_Rep_N+S+_1 Cy5 / 72_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: sov2_NP6070_rep1

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 mutant

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).

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: fertility phenotype

value: Fertile


title: 27_NGP_pA_C7

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

country: Belgium

institute: University Ghent

data_processing:
Alligment with STAR v2.5.3 :STAR --runThreadN 10 --outFileNamePrefix outdir --readFilesIn sample.fastq --genomeDir star_index --sjdbGTFfile gtf_index --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --twopassMode Basic --outSAMmultNmax 1 --outSAMprimaryFlag AllBestScore --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0
Quantification with Kallisto v0.43.1. For polyA: kallisto quant -t 10 -i kallisto_index --single -l 200 -s 20 -o outdir sample.fastq; For total: kallisto quant -t 10 -i kallisto_index –rf-stranded --single -l 200 -s 20 -o outdir sample.fastq
Genome_build: hg38
Supplementary_files_format_and_content: abundance.tsv output for kallisto

organism: Homo sapiens

source_name: cell line

extract_protocol:
Cells were lysed and cDNA was synthesized according to the SMARTer single cell total RNA sequencing protocol on script hub (Fluidigm).
polyA+ RNA-seq libraries were generated using the SMART-seq ultra low input RNA kit for the Fluidigm C1 system. Total RNA-seq libraries were generated using a single cell adapted SMARTer stranded total RNA-seq v2 kit pico input mammalian protocol.

tag: treatment

value: nutlin

tag: cell line

value: NGP

tag: mrna seq

value: polyA+


title: 559479A11 - 80_DFLO_Rep_N+S+_3 vs 124_DFLO+14_Rep_N+S+_3

hyb_protocol: 124_DFLO+14_Rep_N+S+_3 Cy5 / 80_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: 559479A05 - 80_DFLO_Rep_N+S+_3 vs 112_DFLO+14_Rep_N-S+_3

hyb_protocol: 112_DFLO+14_Rep_N-S+_3 Cy5 / 80_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.

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.

value: 43.5day dev.stage (Boyes et al. Plant Cell 2001):boyes:6.00-6.50


title: sov2_KG00226_rep3


title: sov2_KG00226_rep2


title: 25_NGP_pA_C5


title: 26_NGP_pA_C6

value: vehicle


title: mir-71(n4115) rep2


title: mir-71(n4115) rep3


title: 559479A06 - 112_DFLO+14_Rep_N-S+_3 vs 80_DFLO_Rep_N+S+_3

hyb_protocol: 80_DFLO_Rep_N+S+_3 Cy5 / 112_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: 24_NGP_pA_C4


title: sov2_KG00226_rep1


title: 29_NGP_pA_C9


title: nos-Gal4_sov-RNAi_rep3

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

value: Sterile


title: 559479A04 - 110_DFLO+14_Rep_N-S+_2 vs 82_DFLO_Rep_N+S+_2

hyb_protocol: 82_DFLO_Rep_N+S+_2 Cy5 / 110_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: 23_NGP_pA_C3


title: 22_NGP_pA_C1


title: nos-Gal4_sov-RNAi_rep2


title: wildtype rep3

source_name: wildtype

value: wildtype


title: wildtype rep4


title: wildtype rep2


title: nos-Gal4_sov-RNAi_rep1

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


title: mir-71(n4115) rep1


title: 21_NGP_pA_B10


title: 559479A03 - 82_DFLO_Rep_N+S+_2 vs 110_DFLO+14_Rep_N-S+_2

hyb_protocol: 110_DFLO+14_Rep_N-S+_2 Cy5 / 82_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: 20_NGP_pA_B9


title: nos-Gal4_mCherry-RNAi_rep2

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


title: 559479A02 - 102_DFLO+14_Rep_N-S+_1 vs 72_DFLO_Rep_N+S+_1

hyb_protocol: 72_DFLO_Rep_N+S+_1 Cy5 / 102_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: 19_NGP_pA_B8


title: wildtype rep1


title: H37Rv ΔdosSΔdosT_0.2% Ace_Aer_Rep2

city: New Delhi

first: Jaya

middle: Sivaswami

last: Tyagi

state: Delhi

address: Ansari Nagar

department: Biotechnology

country: India

institute: All India Institute of Medical Sciences

description: Gene expression of Mycobacterium tuberculosis H37Rv ΔdosSΔdosT grown in 0.2% acetate under aerobic conditions

hyb_protocol: For all arrays, the Gene Expression Hybridization Kit (Agilent Technologies, 5188-5279) and associated protocols (G4140-90040) were used.

scan_protocol: Microarray slides were scanned using Agilent Microarray Scanner (G2565CA) with scan control software as per manufacturer's instructions (G2505-90020).

data_processing: Images were quantified using Agilent Feature Extraction Software (v10.5). Feature extracted raw data was analyzed using GeneSpring 13.0 - GX. Normalization of the data was done in GeneSpring GX using the 75th percentile shift.

organism: Mycobacterium tuberculosis H37Rv

source_name: H37Rv ΔdosSΔdosT_0.2% Ace_Aer

label_protocol: The samples were labeled using Low Input Quick Amp WT labeling kit (Agilent Technologies G4140-90042). For labeling, in the first step, 25 ng of native RNA was used to synthesize cDNA using random nucleotides having T7 promoter at their 5' ends. This was followed by synthesis of fluorescent cRNA by in vitro transcription using transcription mix containing T7 RNA Polymerase, Cy3 labeled CTP, NTP mix and buffer. The labeled cRNA was then purified using RNeasy columns (QIAGEN INC., USA).

growth_protocol: Mycobacterial stocks stored at – 80°C were first cultured in Middlebrook 7H9 medium containing 0.05 % Tyloxapol (Ty), 0.5 % Albumin, 0.75 % Dextrose and 0.085 % NaCl (ADS), referred to as 7H9Ty-ADS medium with shaking at 220 rpm at 37 °C in 50 mL tubes. The cells were then pelleted, given a wash with 7H9Ty and then resuspended in 7H9Ty-AS medium containing 0.2 % sodium acetate or 0.2 % glucose as the carbon source. After 2-3 subcultures, bacteria were grown to an O.D.595 of 0.2-0.3 under shaking conditions (220 rpm), at which time they were harvested for RNA isolation.

extract_protocol: For RNA isolation, samples in TRI were thawed on ice and 10 μl of polyacryl carrier (Molecular Research Center, USA) was added. The cells were then lysed in a Mini bead beater (Biospec, USA) using 0.1 mm zirconium/silica beads (4800 rpm, 3 pulses of 60 sec with intervals of one min on ice). The samples were incubated for 10 min at room temperature followed by centrifugation (13000 rpm, 4 °C for 10 min). Bromochloropropane (1/10th volume) was added and after shaking for 15 sec the sample was incubated at room temperature for 10 min for phase separation. The aqueous phase was separated by centrifugation (12,000 rpm, 4 °C for 15 min). 10 μl of polyacryl carrier was then added and the RNA in the aqueous phase was precipitated with isopropanol (0.6 volumes, for 30 min), centrifuged (12,000 rpm, 4 °C for 15 min), washed with 75 % ethanol, air-dried an then resuspended in water.

treatment_protocol: Bacteria were grown in 7H9Ty-AS containing either 0.2 % acetate or 0.2 % glucose as sole carbon source. For the hypoxia set-up, these cultures were incubated at 37 °C for 5 days undisturbed, followed by centrifugation, resuspension of the cells in 1 mL TRI solution and storage at -80 °C, followed by RNA isolation.

tag: genotype/variation

value: ΔdosSΔdosT


title: 559479A01 - 72_DFLO_Rep_N+S+_1 vs 102_DFLO+14_Rep_N-S+_1

hyb_protocol: 102_DFLO+14_Rep_N-S+_1 Cy5 / 72_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: H37Rv ΔdosSΔdosT_0.2% Glu_Aer_Rep2

description: Gene expression of Mycobacterium tuberculosis H37Rv ΔdosSΔdosT grown in 0.2% glucose under aerobic conditions

source_name: H37Rv ΔdosSΔdosT_0.2% Glu_Aer


title: H37Rv ΔdosSΔdosT_0.2% Ace_Aer_Rep1


title: nos-Gal4_mCherry-RNAi_rep1

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


title: 558223A12 - 167_DFLO+27_Veg_N+S+_3 vs 123_DFLO+14_Veg_N+S+_3

hyb_protocol: 123_DFLO+14_Veg_N+S+_3 Cy5 / 167_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.


title: 558223A11 - 123_DFLO+14_Veg_N+S+_3 vs 167_DFLO+27_Veg_N+S+_3

hyb_protocol: 167_DFLO+27_Veg_N+S+_3 Cy5 / 123_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: 558223A10 - 169_DFLO+27_Veg_N+S+_2 vs 119_DFLO+14_Veg_N+S+_2

hyb_protocol: 119_DFLO+14_Veg_N+S+_2 Cy5 / 169_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: 17_NGP_pA_B6


title: c587-Gal4_sov-RNAi_rep3


title: nos-Gal4_mCherry-RNAi_rep3


title: c587-Gal4_sov-RNAi_rep2


title: 558223A09 - 119_DFLO+14_Veg_N+S+_2 vs 169_DFLO+27_Veg_N+S+_2

hyb_protocol: 169_DFLO+27_Veg_N+S+_2 Cy5 / 119_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: 16_NGP_pA_B5


title: H37Rv ΔdosSΔdosT_0.2% Glu_Aer_Rep1


title: 18_NGP_pA_B7


title: 558223A08 - 171_DFLO+27_Veg_N+S+_1 vs 129_DFLO+14_Veg_N+S+_1

hyb_protocol: 129_DFLO+14_Veg_N+S+_1 Cy5 / 171_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: c587-Gal4_sov-RNAi_rep1


title: 558223A07 - 129_DFLO+14_Veg_N+S+_1 vs 171_DFLO+27_Veg_N+S+_1

hyb_protocol: 171_DFLO+27_Veg_N+S+_1 Cy5 / 129_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: H37Rv_0.2% Ace_Hyp_Rep2

description: Gene expression of Mycobacterium tuberculosis H37Rv grown in 0.2% acetate under hypoxic conditions

source_name: H37Rv_0.2% Ace_Hyp

value: wild type


title: c587-Gal4_mCherry-RNAi_rep3

value: Genotype:P{w[+mW.hs]=GawB}C587, w[*]/y[1] sc[*] v[1]; P{y[+t7.7] v[+t1.8]=VALIUM20-mCherry}attP2


title: 558223A06 - 153_DFLO+27_Veg_N-S+_3 vs 111_DFLO+14_Veg_N-S+_3

hyb_protocol: 111_DFLO+14_Veg_N-S+_3 Cy5 / 153_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.


title: H37Rv_0.2% Ace_Hyp_Rep1


title: H37Rv_0.2% Ace_Aer_Rep2

description: Gene expression of Mycobacterium tuberculosis H37Rv grown in 0.2% acetate under aerobic conditions

source_name: H37Rv_0.2% Ace_Aer


title: 14_NGP_pA_B3


title: 13_NGP_pA_B2


title: c587-Gal4_mCherry-RNAi_rep1


title: c587-Gal4_mCherry-RNAi_rep2


title: 558223A05 - 111_DFLO+14_Veg_N-S+_3 vs 153_DFLO+27_Veg_N-S+_3

hyb_protocol: 153_DFLO+27_Veg_N-S+_3 Cy5 / 111_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: 558223A04 - 151_DFLO+27_Veg_N-S+_2 vs 109_DFLO+14_Veg_N-S+_2

hyb_protocol: 109_DFLO+14_Veg_N-S+_2 Cy5 / 151_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: NP6070_w1118_rep3

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


title: 11_NGP_pA_A11


title: 15_NGP_pA_B4


title: 12_NGP_pA_A12


title: 10_NGP_pA_A10


title: H37Rv_0.2% Ace_Aer_Rep1


title: 9_NGP_pA_A9


title: NP6070_w1118_rep1


title: NP6070_w1118_rep2


title: H37Rv_0.2% Glu_Hyp_Rep2

description: Gene expression of Mycobacterium tuberculosis H37Rv grown in 0.2% glucose under hypoxic conditions

source_name: H37Rv_0.2% Glu_Hyp


title: H37Rv_0.2% Glu_Hyp_Rep1


title: 8_NGP_pA_A8


title: 558223A02 - 149_DFLO+27_Veg_N-S+_1 vs 101_DFLO+14_Veg_N-S+_1

hyb_protocol: 101_DFLO+14_Veg_N-S+_1 Cy5 / 149_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: 558223A03 - 109_DFLO+14_Veg_N-S+_2 vs 151_DFLO+27_Veg_N-S+_2

hyb_protocol: 151_DFLO+27_Veg_N-S+_2 Cy5 / 109_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: BDI642: Submergence Bio 2

city: Newark

first: Karl

last: Franke

state: Delaware

address: 15 Innovation Way

department: Plant and Soil Sciences

institute: University of Delaware

data_processing:
Adapters were trimmed from reads.
PARE reads were mapped to their appropriate genome using bowtie 0.12.7
PARE libraries were normalized to TP10M
RNAseq reads were mapped to the Brachypodium genome using STAR 2.5.3a with ENCODE standard settings.
RNAseq libraries were normalized using RSEM 1.2.31
Genome_build: Brachypodium distachyon JGI v3.1
Genome_build: Panicum virgatum JGI v4.1
Genome_build: Sorghum bicolor JGI v3.1.1
Supplementary_files_format_and_content: RNAseq proccessed data files are RSEM normalized gene counts. PARE processed data files indicate the prominence of PARE reads mapping to predicted miRNA target sites.

organism: Brachypodium distachyon

source_name: Above ground tissue

growth_protocol: Seeds were germinated in soil and the plants were grown in a growth chamber at a constant 20°C, under a 20 h-light, 4 h-dark cycle. Leaf, stem, and panicle tissues were harvested from six-week old plants. Leaf tissue was the blade of first and second leaf from the top, not including the leaf sheath. Stem tissue was harvested from just above the first top node to just below the second node, including both nodes as well as the leaf sheath of the second leaf. Panicle tissue was harvested from plants with immature, unfertilized flowers from the tip of the spikelet to just above, but not including, the panicle node at approximately 10 h into the subjective day. To collect root tissue, seeds were husked, surface-sterilized with a 50% bleach solution, rinsed with sterile water, and germinated on half-strength Murashige and Skoog (MS) medium containing 0.2% (w/v) Phytagel in sterile plastic boxes. Root tissue was harvested from three-week old plants from the tip of the root to just below, but not including the seed.

extract_protocol:
RNAs were isolated using Trizol reagent (Molecular Research Center).
PARE libraries were constructed as described (German et al., 2008). RNA-seq libraries were constructed using the ScriptSeq RNA-Seq Library Preparation Kit from Illumina (Cat#SSV21124) and sequenced using Illumina HiSeq 2500.

tag: strain

tag: stress

value: Submergence

tag: tissue

value: Above ground tissue


title: BDI643: Heat Bio 1

value: Heat


title: NP6070_sov2_rep2

value: 4-5 days post-eclosion


title: H37Rv_0.2% Glu_Aer_Rep2

description: Gene expression of Mycobacterium tuberculosis H37Rv grown in 0.2% glucose under aerobic conditions

source_name: H37Rv_0.2% Glu_Aer


title: 558223A01 - 101_DFLO+14_Veg_N-S+_1 vs 149_DFLO+27_Veg_N-S+_1

hyb_protocol: 149_DFLO+27_Veg_N-S+_1 Cy5 / 101_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: 558222A11 - 124_DFLO+14_Rep_N+S+_3 vs 168_DFLO+27_Rep_N+S+_3

hyb_protocol: 168_DFLO+27_Rep_N+S+_3 Cy5 / 124_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.

value: 43.5day dev.stage (Boyes et al. Plant Cell 2001):boyes:6.50


title: 558222A10 - 170_DFLO+27_Rep_N+S+_2 vs 120_DFLO+14_Rep_N+S+_2

hyb_protocol: 120_DFLO+14_Rep_N+S+_2 Cy5 / 170_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: BDI644: Heat Bio 2


title: 7_NGP_pA_A7


title: 558222A12 - 168_DFLO+27_Rep_N+S+_3 vs 124_DFLO+14_Rep_N+S+_3

hyb_protocol: 124_DFLO+14_Rep_N+S+_3 Cy5 / 168_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: 6_NGP_pA_A6


title: 558222A09 - 120_DFLO+14_Rep_N+S+_2 vs 170_DFLO+27_Rep_N+S+_2

hyb_protocol: 170_DFLO+27_Rep_N+S+_2 Cy5 / 120_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: BDI640: Cold Bio 2

value: Cold


title: NP6070_sov2_rep1

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

value: Female

value: Adult

value: Fertile


title: NP6070_NP6070_rep3


title: H37Rv_0.2% Glu_Aer_Rep1

hyb_protocol: For all arrays, the Gene Expression Hybridization Kit (Agilent Technologies, 5188-5279) and associated protocols (G4140-90040) were used.


title: NP6070_sov2_rep3


title: NP6070_NP6070_rep2


title: 4_NGP_pA_A4

value: NGP

value: polyA+


title: BDI641: Submergence Bio 1


title: 558222A08 - 172_DFLO+27_Rep_N+S+_1 vs 130_DFLO+14_Rep_N+S+_1

hyb_protocol: 130_DFLO+14_Rep_N+S+_1 Cy5 / 172_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: BDI638: Control Bio 2


title: NP6070_NP6070_rep1


title: 3_NGP_pA_A3

value: vehicle


title: BDI637: Control Bio 1


title: NP6070_KG00226_rep3


title: 5_NGP_pA_A5

value: nutlin


title: BDI639: Cold Bio 1


title: NP6070_KG00226_rep2


title: BDI634b: Drought Bio 2

value: Drought


title: 1_NGP_pA_A1


title: 558222A07 - 130_DFLO+14_Rep_N+S+_1 vs 172_DFLO+27_Rep_N+S+_1

hyb_protocol: 172_DFLO+27_Rep_N+S+_1 Cy5 / 130_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: BDI633b: Drought Bio 1


title: 558222A06 - 154_DFLO+27_Rep_N-S+_3 vs 112_DFLO+14_Rep_N-S+_3

hyb_protocol: 112_DFLO+14_Rep_N-S+_3 Cy5 / 154_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.

value: 43.5day dev.stage (Boyes et al. Plant Cell 2001):boyes:6.00-6.50


title: 558222A05 - 112_DFLO+14_Rep_N-S+_3 vs 154_DFLO+27_Rep_N-S+_3

hyb_protocol: 154_DFLO+27_Rep_N-S+_3 Cy5 / 112_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: BDI544: Heat Bio#2

data_processing:
Library strategy: PARE-seq
Adapters were trimmed from reads.
PARE reads were mapped to their appropriate genome using bowtie 0.12.7
PARE libraries were normalized to TP10M
RNAseq reads were mapped to the Brachypodium genome using STAR 2.5.3a with ENCODE standard settings.
RNAseq libraries were normalized using RSEM 1.2.31
Genome_build: Brachypodium distachyon JGI v3.1
Genome_build: Panicum virgatum JGI v4.1
Genome_build: Sorghum bicolor JGI v3.1.1
Supplementary_files_format_and_content: RNAseq proccessed data files are RSEM normalized gene counts. PARE processed data files indicate the prominence of PARE reads mapping to predicted miRNA target sites.


title: NP6070_KG00226_rep1


title: KG00226_w1118_rep3

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


title: BDI542: Cold Bio#2


title: KG00226_w1118_rep2


title: KG00226_w1118_rep1


title: 2_NGP_pA_A2


title: THP1 TRIPZ-shRUVBL2 NO DOX-3 DAY 2

city: London

first: Owen

last: Williams

address: 30 Guilford Street

department: Cancer section

country: United Kingdom

institute: UCL GOS ICH

description:
EAM223
processed data file: DAY2_NODOX_vs_DOX_fold_change.csv

data_processing:
All tools in the analysis were invoked through the Galaxy Project for NGS analysis, as follows:
Fastq was demultiplexed and generated using Illumina bcl2fastq v2.19 before pre-processing (trimmomatic) to remove adapter read-through and poor quality sequences.
Pre-processed data were then aligned to the genome (UCSC hg38) with Bowtie 2 and deduplicated using Picard.
Reads-per-transcript were counted by FeatureCounts, before differential expression analysis by SARTools, a DESeq2 wrapper.
Genome_build: hg38
Supplementary_files_format_and_content: *_NODOX_vs_DOX_fold_change.csv: Comma-separated text files include average count values for each sample.

growth_protocol: THP1 cells (monocyte cell line) (ATCC, Manassas, VA, USA) were maintained in culture in RPMI 1640 medium containing 10% fetal bovine serum, 100 units/ml penicillin and 100 ug/ml streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted with RNeasy Plus Mini Kit according to manufacturer's instructions.
Indexed RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA v2 protocols.

treatment_protocol: TRIPZ-shRUVBL2 transduced THP1 cells were treated with either medium only or 1 μg/ml Doxycycline for 4 days.

tag: cell type

value: monocyte cell line

tag: shRNA

value: RUVBL2-specific inducible shRNA

tag: agent

tag: time point

value: day 2


title: BDI514: Drought Bio#2

value: Above ground tissue


title: THP1 TRIPZ-shRUVBL2 NO DOX-2 DAY 2

description:
EAM203
processed data file: DAY2_NODOX_vs_DOX_fold_change.csv


title: THP1 TRIPZ-shRUVBL2 DOX-1 DAY 2

description:
EAM194
processed data file: DAY2_NODOX_vs_DOX_fold_change.csv

value: doxycycline


title: THP1 TRIPZ-shRUVBL2 DOX-3 DAY 2

description:
EAM224
processed data file: DAY2_NODOX_vs_DOX_fold_change.csv


title: BDI507: Cold Bio#1


title: THP1 TRIPZ-shRUVBL2 NO DOX-1 DAY 2

description:
EAM193
processed data file: DAY2_NODOX_vs_DOX_fold_change.csv


title: 558222A04 - 152_DFLO+27_Rep_N-S+_2 vs 110_DFLO+14_Rep_N-S+_2

description: Transcriptome in leaves of Pea 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: 110_DFLO+14_Rep_N-S+_2 Cy5 / 152_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.

tag: age


title: THP1 TRIPZ-shRUVBL2 DOX-2 DAY 2

description:
EAM204
processed data file: DAY2_NODOX_vs_DOX_fold_change.csv


title: BDI493: Submergence Bio#2

value: Submergence


title: BDI508: Submergence Bio#1


title: BDI491: Heat Bio#1

value: Heat


title: 558222A03 - 110_DFLO+14_Rep_N-S+_2 vs 152_DFLO+27_Rep_N-S+_2

hyb_protocol: 152_DFLO+27_Rep_N-S+_2 Cy5 / 110_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: KG00226_sov2_rep1

value: 4-5 days post-eclosion

tag: age cv

tag: tissue cv

tag: Sex

tag: genotype


title: KG00226_NP6070_rep3

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

value: Female

tag: sex cv

tag: developmental stage

tag: developmental stage cv

tag: fertility phenotype


title: 558222A01 - 102_DFLO+14_Rep_N-S+_1 vs 150_DFLO+27_Rep_N-S+_1

hyb_protocol: 150_DFLO+27_Rep_N-S+_1 Cy5 / 102_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: THP1 TRIPZ-shRUVBL2 DOX-3 DAY 4

description:
EAM-14
processed data file: DAY4_NODOX_vs_DOX_fold_change.csv

tag: cell line

value: day 4


title: THP1 TRIPZ-shRUVBL2 NO DOX-3 DAY 4

description:
EAM-13
processed data file: DAY4_NODOX_vs_DOX_fold_change.csv


title: KG00226_sov2_rep2

value: Adult

value: Fertile


title: KG00226_NP6070_rep2


title: THP1 TRIPZ-shRUVBL2 DOX-2 DAY 4

description:
EAM-12
processed data file: DAY4_NODOX_vs_DOX_fold_change.csv


title: BDI381: Root Bio#2

source_name: Root

tag: strain

value: Root


title: KG00226_sov2_rep3


title: THP1 TRIPZ-shRUVBL2 NO DOX-2 DAY 4

description:
EAM-11
processed data file: DAY4_NODOX_vs_DOX_fold_change.csv


title: KG00226_NP6070_rep1


title: BDI289: Stem Bio#2

source_name: Stem

tag: stress

value: Stem


title: 557917A11 - 79_DFLO_Veg_N+S+_3 vs 123_DFLO+14_Veg_N+S+_3

hyb_protocol: 123_DFLO+14_Veg_N+S+_3 Cy5 / 79_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: 43.5day dev.stage (Boyes et al. Plant Cell 2001):boyes:6.50

value: 31.8day dev.stage (Boyes et al. Plant Cell 2001):boyes:6.00


title: THP1 TRIPZ-shRUVBL2 DOX-1 DAY 4

description:
EAM-10
processed data file: DAY4_NODOX_vs_DOX_fold_change.csv


title: KG00226_KG00226_rep3


title: 557917A10 - 119_DFLO+14_Veg_N+S+_2 vs 81_DFLO_Veg_N+S+_2

hyb_protocol: 81_DFLO_Veg_N+S+_2 Cy5 / 119_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: BDI288: Leaf Bio#2

source_name: Leaf

tag: tissue

value: Leaf


title: 557917A12 - 123_DFLO+14_Veg_N+S+_3 vs 79_DFLO_Veg_N+S+_3

hyb_protocol: 79_DFLO_Veg_N+S+_3 Cy5 / 123_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: 558222A02 - 150_DFLO+27_Rep_N-S+_1 vs 102_DFLO+14_Rep_N-S+_1

hyb_protocol: 102_DFLO+14_Rep_N-S+_1 Cy5 / 150_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.

value: 43.5day dev.stage (Boyes et al. Plant Cell 2001):boyes:6.00-6.50


title: KG00226_KG00226_rep1


title: KG00226_KG00226_rep2


title: BDI284: Drought Bio#1

value: Drought


title: BDI287: Panicle Bio#2

source_name: Panicle

value: Panicle


title: BDI490b: Control Bio#2

value: Above ground tissue


title: 557917A08 - 129_DFLO+14_Veg_N+S+_1 vs 71_DFLO_Veg_N+S+_1

hyb_protocol: 71_DFLO_Veg_N+S+_1 Cy5 / 129_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: 557917A09 - 81_DFLO_Veg_N+S+_2 vs 119_DFLO+14_Veg_N+S+_2

hyb_protocol: 119_DFLO+14_Veg_N+S+_2 Cy5 / 81_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: Dfsov_w1118_rep3

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


title: 557917A07 - 71_DFLO_Veg_N+S+_1 vs 129_DFLO+14_Veg_N+S+_1

hyb_protocol: 129_DFLO+14_Veg_N+S+_1 Cy5 / 71_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: LY19Y646F_RNA-seq_rep3

city: Lausanne

first: Giovanni

last: Ciriello

address: Rue du Bugnon 27

department: Department of Computational Biology

country: Switzerland

institute: University of Lausanne

data_processing:
Raw reads were aligned to hg19 and coordinate-sorted using STAR (v2.5.3a, parameters: --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000 --outSAMtype BAM SortedByCoordinate)
Gene-level expression was estimated as FPKM with Cufflinks (v2.2.1, default parameters)
Gene-level fold changes of FPKMs between LY19WT and LY19Y646F were computed with CuffMerge and CuffDiff (v2.2.1, default parameters)
Genome_build: hg19
Supplementary_files_format_and_content: Gene-level lists of transcripts with location, gene annotation (if available) and FPKM value

source_name: Lymphoma B-cell immortalized cell line

growth_protocol: Cell lines were propagated in sterile incubators at 37°C, 5% CO2, grown in RPMI (Life Technologies) supplemented with 10% fetal bovine serum (Life Technologies) and 1% antibiotic.

extract_protocol:
RNA was isolated using TRIzol/Chloroform followed by RNA purification using RNeasy spin columns (Qiagen 74104). RNA profile quality was assessed using the TapeStation 4200.
Libraries were prepared using the TruSeq stranded mRNA LT preparation, starting from 2500ng RNA, according to Illumina protocol 15031047 Rev. E (internal exp code ECX028). Libraries were sequenced using the NextSeq500 platform with 400 million reads and SE reads of 85 nucleotides.

treatment_protocol: Cell lines were untreated

value: constitutive expression EZH2-Y646F (CMV promoter)

tag: cell line passages


title: LY19Y646F_RNA-seq_rep2


title: Dfsov_w1118_rep2


title: 557917A05 - 79_DFLO_Veg_N+S+_3 vs 111_DFLO+14_Veg_N-S+_3

hyb_protocol: 111_DFLO+14_Veg_N-S+_3 Cy5 / 79_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.


title: THP1 TRIPZ-shRUVBL2 NO DOX-1 DAY 4

description:
EAM-9
processed data file: DAY4_NODOX_vs_DOX_fold_change.csv

tag: cell type

value: monocyte cell line

tag: shRNA

value: RUVBL2-specific inducible shRNA


title: Dfsov_w1118_rep1

value: 4-5 days post-eclosion


title: LY19Y646F_RNA-seq_rep1


title: LY19WT_RNA-seq_rep3

value: EZH2-wild type


title: BDI283: Control Bio#1


title: 557917A04 - 109_DFLO+14_Veg_N-S+_2 vs 81_DFLO_Veg_N+S+_2

hyb_protocol: 81_DFLO_Veg_N+S+_2 Cy5 / 109_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: Dfsov_sov2_rep3

value: Female

value: Sterile


title: LY19WT_RNA-seq_rep2


title: Dfsov_sov2_rep2

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

value: Adult


title: LY19WT_RNA-seq_rep1


title: H9 ESCs_Aba-seq

city: santa barbara

first: Guojing

last: Liu

state: CA

address: 552 University Rd

institute: University of California, santa barbara

library_source: genomic

data_processing:
library strategy: Aba-seq
NextSeq RTA version 2.4.11 software used for basecalling
First, sequences with correct barcodes were extracted.  These sequences were mapped to the hg19 genome build using bwa v0.7.15 with parameters aln -q 0 -n 0.04 -k 2 -l 200 -t 8 -B 6.  PCR duplicates were removed using SAMtools v.1.5.
A custom Perl script was used to identify 5hmC sites from the sam files. This code is available on request.
Genome_build: hg19 version
Supplementary_files_format_and_content: Ensemble gene id and normalized 5hmc level per gene (bin size is from 1kb upstream to 1kb downstream of protein coding genes, normalized by total number CG sites per bin size)

molecule: genomic DNA

source_name: H9 Human Embryonic Stem Cell

growth_protocol: H9 ESCs are grown in mTeSR1 medium on matrigel-coated plates

extract_protocol:
~50,000 cells were suspended in 10 µL of lysis buffer (100 µg Qiagen Protease, 0.04% Triton X-100, 1x NEB CutSmart buffer) and incubated at 50 °C for 15 h, 75 °C for 20 min and 80 °C for 5 min.
Then 10 µL of 1x NEB CutSmart buffer, 10 U NEB T4-BGT, 2.5x NEB UDP-Glucose was added to glucosylate 5-hmC sites in the genome, and the sample was incubated at 37 °C for 16 h.  Next, 10 µL of protease mix (100 µg Qiagen Protease, 1x NEB CutSmart) was added and incubated at 50 °C for 5 h, 75 °C for 20 min and 80 °C for 5 min.  10 µL of digestion mix (10 U AbaSI, 1x NEB CutSmart) was added and incubated at 25°C for 2 h, and 65 °C for 20 min.  Next, 1 µL of 0.5 µM ds-adaptor was added, followed by 9 µL of ligation mix (2,000 U T4 DNA Ligase, 1x T4-ligase buffer, 3.33 mM ATP) and each sample was incubated at 16 °C for 16 h.  The ds-adaptor sequences are described in scAba-seq (Mooijman et al., 2016).  DNA clean-up was then performed with 0.825x Agencourt Ampure XP beads and eluted in 25 µL of nuclease-free water.  The samples were vacuum centrifuged to a volume 8 µL.  12 uL of in vitro transcription mix was added (2 µL of each ribonucleotide, 2 µL of T7 buffer, 2 µL T7 enzyme mix) and incubated at 37 °C for 13 h.  Library preparation starting from amplified RNA was performed as described in the CEL-Seq2 protocol with the following minor modifications (Hashimshony et al., 2016).  RNA was fragmented by adding 5 µL of fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500mM KOAc, 150 mM MgOAc) at 94 °C for 2 min and immediately placed on ice. 2.5 µL of fragmentation stop buffer (0.5 M EDTA) was added to quench the reaction.  Next, RNA clean-up was performed using 0.825x Agencourt RNAClean beads and finally resuspended in 22 µL of nuclease-free water.  Thereafter, all library preparation steps were performed as described in the CEL-Seq2 protocol (Hashimshony et al., 2016).

value: humna Embryonic Stem Cells (hESCs)

tag: passage

tag: growing condition


title: Dfsov_sov2_rep1

tag: age

tag: age cv


title: Dfsov_KG00226_rep3

tag: tissue cv

tag: Sex


title: MM_Aza_input

city: Chicago

first: Shimeng

state: Illinois

address: 320 East Superior Street

institute: Northwestern University

description: 96h 5µM 5'-Aza

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

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: Fregmented genomic DNA


title: Dfsov_KG00226_rep2

source_name: ovary

tag: sex cv

tag: developmental stage

tag: developmental stage cv

tag: genotype

tag: fertility phenotype


title: 557917A02 - 101_DFLO+14_Veg_N-S+_1 vs 71_DFLO_Veg_N+S+_1

hyb_protocol: 71_DFLO_Veg_N+S+_1 Cy5 / 101_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.

value: 31.8day dev.stage (Boyes et al. Plant Cell 2001):boyes:6.00


title: 557917A03 - 81_DFLO_Veg_N+S+_2 vs 109_DFLO+14_Veg_N-S+_2

hyb_protocol: 109_DFLO+14_Veg_N-S+_2 Cy5 / 81_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.

value: 43.5day dev.stage (Boyes et al. Plant Cell 2001):boyes:6.50


title: MM_Veh_input

description: 96h DMSO

value: 96h DMSO


title: 554228A06 - 24_DFLO-14_Veg_N-S+_3 vs 7_DFLO_Veg_N+S+_3

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: 7_DFLO_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.

organism: Medicago truncatula

growth_protocol: caulin leaf - non renseigné.

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

value: first flowers buds visible


title: 554228A05 - 7_DFLO_Veg_N+S+_3 vs 24_DFLO-14_Veg_N-S+_3

hyb_protocol: 24_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.


title: 557917A01 - 71_DFLO_Veg_N+S+_1 vs 101_DFLO+14_Veg_N-S+_1

hyb_protocol: 101_DFLO+14_Veg_N-S+_1 Cy5 / 71_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.

value: 43.5day dev.stage (Boyes et al. Plant Cell 2001):boyes:6.00-6.50


title: 554228A04 - 28_DFLO-14_Veg_N-S+_2 vs 15_DFLO_Veg_N+S+_2

hyb_protocol: 15_DFLO_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: LM_Aza_input

description: 96h 5µM 5'-Aza

source_name: Primary uterine leiomyoma cells


title: Night-Shift, ID543, 6AM

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)

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: Dfsov_KG00226_rep1


title: Night-Shift, ID543, 6PM

description: replicate 1


title: Night-Shift, ID543, 9PM

description: replicate 1


title: Night-Shift, ID543, 3AM

description: replicate 1


title: LM_Veh_input

description: 96h DMSO


title: 554228A02 - 26_DFLO-14_Veg_N-S+_1 vs 9_DFLO_Veg_N+S+_1

hyb_protocol: 9_DFLO_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: 557917A06 - 111_DFLO+14_Veg_N-S+_3 vs 79_DFLO_Veg_N+S+_3

hyb_protocol: 79_DFLO_Veg_N+S+_3 Cy5 / 111_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: Night-Shift, ID543, 3PM

description: replicate 1