title: VIP23.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP23.A


title: VIP20.A: prior to vaccination, pregnant

status: Public on Jan 31 2020

type: RNA

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

country: Germany

institute: Berlin Institute of Health, Charité Medical University of Berlin

description:
prior to vaccination, pregnant
VIP20.A

hyb_protocol: According to manufacturers instructions.

scan_protocol: Image analysis and data extraction were performed with Agilent's Feature Extraction software (version 11.5) to generate the raw expression data.

data_processing: Data analysis was performed in R version 3.6.0 (2019-04-26). Microarray data were pre-processed, normalised and analysed for differential expression using R package limma v3.41.15 13. The raw data were first background corrected using the normexp method. Background corrected signals were quantile normalised between arrays.

molecule: total RNA

organism: Homo sapiens

source_name: peripherial blood RNA prior to vaccination

label_protocol: Microarray experiments were performed as single-color hybridization, and RNA was labeled with the Low Input Quick-Amp Labeling Kit (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer, and labeled with cyanine 3-CTP by T7 in vitro transcription. After precipitation, purification and quantification, 0.75 μg labeled cRNA was fragmented and hybridized to custom whole genome human 8 × 60 K multipack microarrays (Agilent-048908) according to the supplier’s protocol (Agilent Technologies).

extract_protocol: Peripheral blood was drawn into PAXgene tubes (PreAnalytiX) and RNA was extracted on the automated QIAcube system (Qiagen) using the PAXgene Blood RNA kit (Qiagen) according to the manufacturer’s instructions. Quality control and quantification of isolated RNA was analyzed with an Agilent 2100 Bioanalyzer (Agilent Technologies) and a NanoDrop 1000 UV-Vis spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: After informed consent had been obtained the first study visit was arranged to take place between 16 and 32 weeks of pregnancy. At this visit all participants had a blood sample collected into a PAXgene tube followed by administration of 1 dose (0.5mls) Boostrix-IPV into the deltoid muscle of their non-dominant arm. A second blood sample was collected into a Paxgene tube 24 hours after vaccine administration and information collected about any adverse events which they had experienced.

tag: time

value: prior to vaccination

tag: tissue

value: peripheral blood

tag: timepoint

tag: status

value: pregnant


title: VIP15.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP15.B

source_name: peripherial blood RNA day 1 post vaccination

value: day 1 post vaccination


title: VIP16.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP16.B


title: VIP24.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP24.A


title: VIP25.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP25.A


title: VIP18.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP18.A


title: VIP21.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP21.A


title: VIP20.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP20.B


title: VIP17.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP17.A


title: VIP14.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP14.B


title: VIP28.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP28.B


title: VIP19.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP19.A


title: VIP27.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP27.B


title: VIP16.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP16.A


title: VIP26.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP26.B


title: VIP15.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP15.A


title: VIP14.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP14.A


title: VIP07.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP07.A


title: VIP13.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP13.A


title: VIP08.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP08.A


title: VIP09.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP09.A


title: VIP05.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP05.B


title: VIP04.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP04.B


title: VIP12.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP12.A


title: VIP03.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP03.B


title: VIP06.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP06.B


title: VIP09.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP09.B


title: VIP05.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP05.A


title: VIP08.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP08.B


title: VIP10.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP10.B


title: VIP04.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP04.A


title: VIP06.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP06.A


title: VIP13.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP13.B


title: SID_45: pregnant, placebo, group 4

status: Public on Jan 25 2020

description: Mouse muscle total RNA at site of injection, pregnant, placebo, group 4, sample SID_45

organism: Mus musculus

source_name: pregnant, placebo, group 4

label_protocol: RNA was labelled with a Low Input Quick Amp Labelling Kit (Agilent Technologies) according to the manufacturer’s instructions. Quantity and labelling efficiency were verified before hybridization

growth_protocol: Time mated and control female BALB/c mice of 6–8 weeks of age were purchased from Charles River (Southampton, UK).

extract_protocol: Small pieces of tissue (3 mm x 3 mm x 3 mm) were harvested and flash frozen in liquid nitrogen. Total RNA isolation (including microRNA (miRNA) species) was performed using the miRNeasy mini kit (Qiagen, UK), as described in the standard protocol for purification of miRNA and total RNA from tissues and cells. RNA, which was stored at −80°C until required for microarray hybridisation.

treatment_protocol: Animals received a single 50μl injection of Boostrix-IPV (equivalent to 1/10th of a human dose11) or PBS in their right hind leg quadricep muscle and were then culled 24hr after the immunisation. When each animal was culled, the injected muscle site was harvested and flash frozen in liquid nitrogen.

value: muscle

tag: vaccine

value: placebo

tag: group


title: VIP01.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP01.A


title: VIP01.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP01.B


title: VIP02.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP02.A


title: SID_41: pregnant, placebo, group 4

description: Mouse muscle total RNA at site of injection, pregnant, placebo, group 4, sample SID_41


title: VIP10.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP10.A


title: SID_35: pregnant, Boostrix, group 3

description: Mouse muscle total RNA at site of injection, pregnant, Boostrix, group 3, sample SID_35

source_name: pregnant, Boostrix, group 3

value: Boostrix


title: SID_43: pregnant, placebo, group 4

description: Mouse muscle total RNA at site of injection, pregnant, placebo, group 4, sample SID_43


title: SID_36: pregnant, Boostrix, group 3

description: Mouse muscle total RNA at site of injection, pregnant, Boostrix, group 3, sample SID_36


title: VIP03.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP03.A


title: SID_46: pregnant, placebo, group 4

description: Mouse muscle total RNA at site of injection, pregnant, placebo, group 4, sample SID_46


title: VIP02.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP02.B


title: SID_42: pregnant, placebo, group 4

description: Mouse muscle total RNA at site of injection, pregnant, placebo, group 4, sample SID_42


title: VIP07.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP07.B


title: FLHL-WT-Rep2_L12945

status: Public on May 13 2019

type: SRA

first: Christina

last: Paliou

address: Ihnestrasse 63-73

institute: Max Planck Institute for Molecular Genetics

description:
wild type
FLHL-WT_L12944-1-2_L12945_merged_MAPQ30.KR_10kb.WashU.txt
vC_WT_FLHL_chr5_28789001_28799000_Shh_promoter.5kb_norm.bedgraph

library_source: genomic

data_processing:
Library strategy: Capture Hi-C
Raw sequencing reads were preprocessed with cutadapt v1.15 (Martin, 2011) to trim potential low quality bases (-q 20 -m 25) and Illumina sequencing adapters (-a and -A option with Illumina TruSeq adapter sequences according to the cutadapt documentation) at the 3’ end of reads. Next, sequencing reads were mapped to reference genome mm9, filtered and deduplicated using the HiCUP pipeline v6.1.0 (Wingett et al., 2015) (no size selection, Nofill: 1, Format: Sanger). The pipeline was set up with Bowtie2 v2.3.4.1 (Langmead and Salzberg, 2012) for short read mapping. The trimming of sequencing adapters in the first step would not have been necessary, because potentially remaining sequencing adapter in reads from valid ligation products should also be removed by the truncation after ligation sites implemented in the HiCUP pipeline. In case replicates were available, they were combined after the processing with the HiCUP pipeline. Juicer command line tools v1.7.6 (Durand et al., 2016) was used to generate binned contact maps from valid and unique reads pairs with MAPQ≥30 and to normalize maps by Knights and Ruiz matrix balancing (Durand et al., 2016; Knight and Ruiz, 2013; Rao et al., 2014). For binning and normalization, only the genomic region chr5:27,800,001- 30,600,000 enriched in the DNA-capturing step was considered. Therefore, only reads pairs mapping to this region were kept, shifted by the offset of 27,800,000 bp and imported with Juicer tools using a custom chrom.sizes file which contained only the length of the enriched region (2.8 Mb). Afterwards, KR normalized maps, as well as raw count maps, were exported for 5 kb and 10kb resolution and coordinates were shifted back to their original values. Subtraction maps were generated from KR normalized maps, which were normalized in a pair-wise manner before subtraction. To account for differences between two maps in their distance-dependent signal decay, maps were scaled jointly across their sub-diagonals. Therefore, the values of each sub-diagonal of one map were divided by the sum of this sub-diagonal and multiplied by the average of these sums from both maps. Afterwards, the maps were scaled by 106 / total sum. cHiC maps of count values, as well as subtraction maps, were visualized as heatmaps in which values above the 97-th  percentile were truncated for visualization purposes.
In order to obtain more fine-grained interaction profiles for selected loci, we defined 10kb viewpoint regions and generated virtual Capture-C-like profiles based on the filtered, unique read-pairs that were also used for the cHiC maps. A read pair was considered in a profile, when it had a MAPQ≥30 and one read mapped to the defined viewpoint region, while the other read mapped outside of it. The reads outside of the viewpoint were counted per restriction fragment and read counts were binned afterwards to 1 kb bins. In case a fragment was overlapping more than one bin, the read count was distributed proportionally. Afterwards, the each binned profiles wasere smoothed by averaging over a running window of 5 bins and scaled by 103 / sum of all its counts in the enriched region on chr5. The viewpoint and a window ± 5kb around it were not considered for the computation of the scaling factor. The profiles were generated with custom Java code using htsjdk v2.12.0  (https://samtools.github.io/htsjdk/). Virtual Capture-C viepoint: Shh promoter (chr5:28,789,001-28,799,000)
Supplementary_files_format_and_content: bedgraph, txt

molecule: genomic DNA

source_name: Embryonic Limb Bud

growth_protocol: Limbs from 34-5 somite-stage (E10.5) mouse embryos were microdissected in PBS.

extract_protocol:
Tissues were homogenized in Collagenase solution, fixes with 2% FA at room temperature, 10 min and the cells were lysed in custom-made lysis buffer (10mM Tris pH7.5, 10mM NaCl, 5mM MgCl2, 0.1mM EGTA, Protease Inhibitor). Upon PBS wash, samples were snap-frozen and stored at -80°C. Samples were then digested with DpnII, re-ligated, de-crosslinked and purified.
The 3C-library was then sheared using a Covaris sonicator (duty cycle: 10%, intensity: 5, cycles per burst: 200, time: 2 cycles of 60 s each, set mode: frequency sweeping, temperature: 4 to 7 °C). Adaptors were added to the sheared DNA and amplified according to Agilent instructions for Illumina sequencing. The library was hybridized to the custom-designed SureSelect beads and indexed for sequencing (50 to 100 bp paired-end) following Agilent instructions.

tag: strain

tag: embryonic stage

tag: genotype

value: wild type


title: FLHL-WT-Rep1_L12944


title: SID_32: pregnant, Boostrix, group 3

description: Mouse muscle total RNA at site of injection, pregnant, Boostrix, group 3, sample SID_32


title: SID_24: control, placebo, group 2

description: Mouse muscle total RNA at site of injection, control, placebo, group 2, sample SID_24

source_name: control, placebo, group 2

value: control


title: H1_ESC_RNAseq_rep2

status: Public on Apr 16 2019

city: Worcester

first: Rene

last: Maehr

state: MA

address: 55 Lake Ave N

department: Program in Molecular Medicine

country: USA

institute: UMass Medical School

description: DiffExp_DESeq2_1_sampleGroup_vs_hESC_Rene_vs_hDE01.xlsx

library_source: transcriptomic

data_processing:
Base calling: fastq files were obtained from Illumina Basespace under default parameters.
Bulk RNA-seq data utilized in atacTFAP analysis were trimmed, aligned, quantified, filtered, and tested for differential expression as follows.
Trimming: raw reads were trimmed 5bp from the head orientation and to 55 bp at the tail.
Alignment: reads were aligned with salmon version 0.8.2 to human reference transcriptome version GRCH37 using default parameters and setting the flags -l A --posBias --gcBias --seqBias.
Quantification: Transcript and gene expression levels were quantified using the salmon output and the txImport R package.
Filtering: we removed all genes with less than 3 (20th percentile) or more than 27337.16 (99.5th  percetnile) reads across the dataset.
Differential expression analysis:  performed using DESeq2. Genes with a minimal expression level of 5 RPKM in at least 2 samples and a FDR threshold of 0.01 were considered as differentially expressed.
ATAC-seq and ChIP-seq data underwent alignment, read extension, peak calling, IDR-based filtering, and differential analysis as follows.
Extension: For ChIP-seq only, reads were extended to 200 bp.
Alignment: reads were aligned to the human reference genome hg19 using Bowtie 2 version 2.3.2 using default parameters and filtering duplicate reads.
Peak calling and IDR: MACS2 in combination with the IDR framework was used for peak calling and detection of regions of genomic enrichment using an IDR cutoff of 0.1.
Differential analysis: we used the R package diffbind in combination with DESeq2 for all IDR based peak sets, requiring no overlap of peaks across conditions and using a DBA score based quantification.
Note: paired-end: R1 is a barcode
For RNA-seq, ATAC-seq, and ChIP-seq data visualization, IGV tools {Thorvaldsdottir:2013iw} was used to generate .tdf files.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files are bed files containing peaks.  Also included is one Excel file with total RNA results from hESC and hEND. Peaks were not used for K27me3 data, so no bed files were used in the analysis.

source_name: Embryonic stem cells

growth_protocol: H1-AAVS1-TetOn-dCas9-KRAB hESCs were maintained in mTeSR1 on hES qualified matrigel-coated plates

extract_protocol:
ATAC-seq samples were processed according to Buenrostro et. al with slight modifications. Briefly, approximately 50,000 cells were pelleted at 750 x g for 15 minutes at 4oC. After the addition of lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAl CA-630), nuclei were pelleted at 750 x g for 15 minutes at 4oC and the supernatent was discarded. Transposase reaction was performed at 37oC for 30 minutes. The purified, tagmented DNA was amplified for 9-10 cycles and size selected using AMPure XP beads (Beckman Coulter, A63881) as follows: 0.55X volume of 2X concentrated AMPure beads was added to the amplified DNA and incubated for 5 minutes at room temperature. The supernatant, containing low-molecular weight DNA, was collected in a separate tube by removing the beads using a magnetic rack. 1X volume of AMPure beads was added to the supernatant and incubated for 5 min at room temperature. The beads were washed twice with 75% ethanol and then air dried. The final purified library was eluted in EB buffer and sequenced (paired-end, 75-75) on a NextSeq500 or Hi-Seq2000 platform.
Total RNA was isolated using Trizol Reagent (Invitrogen, 15596-018) according to the manufacturer’s instructions. For quantitative PCR analysis, 1 μg of total RNA was reverse-transcribed using SuperScript III First-Strand Synthesis System (Thermo, 18080051).
Bulk RNA-sequencing library preparation of H1 hESC and differentiated hEND was performed following a published protocol {Zhang:2012kc}. Briefly, 4 μg of total RNA was depleted of ribosomal RNA using Ribo-Zero rRNA Removal Kit (Epicentre, MRZH116) and then converted to cDNA. Final sequencing libraries were generated using dUTP (Thermo, R0133) incorporation and uracil-N-glycosylase (NEB, M0280) treatment to generate strand-specific RNA-seq libraries. The final libraries were sequenced at paired-end on a Hi-Seq2000 platform.

treatment_protocol: For perturbation experiments, H1-AAVS1-TetOn-dCas9-KRAB hESCs were transduced with individual gRNA lentiviral constructs and selected with puromycin for 72 hours. 48 hours prior to the start of differentiation, the selected cells were pooled and treated with 500 ng/mL doxycycline. The cells were then split for differentiation and differentiated along published protocols in the presence of 500 ng/mL doxycycline.

tag: assay

value: RNA

tag: treatment protocol

value: No guide

tag: chip antibody


title: H1_ESC_RNAseq_rep1


title: SID_22: control, placebo, group 2

description: Mouse muscle total RNA at site of injection, control, placebo, group 2, sample SID_22


title: FAIRE-seq of cell sample 1

status: Public on Jul 24 2019

city: Winnipeg

first: James

middle: Ronald

last: Davie

state: Manitoba

address: 745 Bannatyne Avenue, RM 333A

department: Biochemistry and Medical Genetics

country: Canada

institute: University of Manitoba

data_processing:
fastqc checked the  Miseq fastq data quality. The adapters were removal by cutadapt v1.11.
The sequence reads were mapped on Gal3 genome reference using bwa (v0.6.2) sampe module.
The peaks were called by Macs2 (v2.0.10)
Genome_build: Gal3
Supplementary_files_format_and_content: peaks.xls, chr, start, end, length, summit, tags, -10*log10(pvalue),fold_enrichment FDR(%)

organism: Gallus gallus

source_name: Erythrocyte cell

extract_protocol:
Chicken immature erythrocyte nuclei were treated with 0.6% formaldehyde and chromatin was sheared into 300-500 bp fragments. Phenol-Chloroform extraction was performed and DNA was purified from aqueous layer.
FAIRE-Seq library preparation was performed according to the NEBNext Ultra II DNA library preparation protocol. 50 ng of FAIRE DNA was end-repaired and dA-tailed. Ligation products were cleaned up and PCR enriched. Library was quantified by qPCR and normalized before sequencing.FAIRE DNA library was sequenced using the MiSeq platform and v3 sequencing reagents.

tag: cell type

value: Immature erythrocyte cells

tag: cell cycle phase

tag: breed

value: White leghorn

value: Bovan


title: SID_34: pregnant, Boostrix, group 3

description: Mouse muscle total RNA at site of injection, pregnant, Boostrix, group 3, sample SID_34


title: hES_H3K27me3_rep2

description: (no peak calls used)

value: Millipore, 07-454


title: SID_15: control, Boostrix, group 1

description: Mouse muscle total RNA at site of injection, control, Boostrix, group 1, sample SID_15

source_name: control, Boostrix, group 1


title: H1_ESC_H3K27ac_ChIPseq_rep2

value: Diagenode, C15410196


title: SID_12: control, Boostrix, group 1

description: Mouse muscle total RNA at site of injection, control, Boostrix, group 1, sample SID_12


title: SID_33: pregnant, Boostrix, group 3

description: Mouse muscle total RNA at site of injection, pregnant, Boostrix, group 3, sample SID_33


title: SID_14: control, Boostrix, group 1

description: Mouse muscle total RNA at site of injection, control, Boostrix, group 1, sample SID_14


title: H1_END_RNAseq_rep2

source_name: Definitive endoderm


title: H1_END_RNAseq_rep1


title: SID_13: control, Boostrix, group 1

description: Mouse muscle total RNA at site of injection, control, Boostrix, group 1, sample SID_13


title: H1_END_ATACseq_rep2

value: ATAC


title: S.pombe-epe1D(white)

status: Public on Apr 24 2019

city: Kobe

first: Atsushi

last: Matsuda

address: 588-2, Iwaoka, Iwaoka-cho, Nishi-ku

country: Japan

institute: National Institute of Information and Communications Technology

hyb_protocol: Hybridization was done by using the Gene Expression Hybridization Kit (Agilent Technologies) according to manufacturer's instructions except for amount of Cy3-labelled cRNA (37.5 ng was used for each hybridization). After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8 x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 micro-m, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software (ver 10.7.3.1, Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 038274_D_F_20120123) to obtain background subtracted and spatially detrended Processed Signal intensities. 6767 probes (including 56 control probes: indicated by “control” in the comment columns) are spotted multiply to fill 62976 spots in each array. A median of the gProcessedsignals of the spots for each probe was calculated to make a data set for 6767 probes. The median was normalized by the 75 percentile method (the value at 75% was set to 2500). When the average of the gIsWellAboveBG of the spots for each probe is higher than 0.55, the probe signal is considered more than the detection limit, ranked with “a” in the Rank columns. The values of probes that represent duplicated genes were divided by the number of duplicated genes to give corrected values in the Value columns (indicated by “corrected” in the comment columns). The values of probes that were cross-hybridized with paralogs were corrected with the correction probes (indicated as “correction” in the comment columns) as described in the supplemental file with GPL18374 to give corrected values in the Value columns (indicated by “corrected” in the comment columns). “combined” and “deleted” in the comment columns mean the genes were combined with other genes or deleted.
6767 probes (including 56 control probes) are spotted multiply to fill 62976 spots in each array. A median of the gProcessedsignals of the spots for each probe was calculated to make a data set for 6767 probes. The median was normalized by the 75 percentile method (the value at 75% was set to 2500.) to get the value in the Matrix sheet. ID_REF in the Matrix sheet match the identifiers in the SPOT ID column in the 038274_D_GEO_20120123.txt file. When the average of the gIsWellAboveBG of the spots for each probe is higher than 0.55, the probe signal is considered more than the detection limit, ranked with “a” in the Rank columns. The values of probes that represent duplicated genes were divided by the number of duplicated genes to give corrected values in the Corrected columns. The values of probes that were cross-hybridized with paralogs were corrected as described in the supplemental file with GPL18374 to give corrected values in the Corrected columns.

organism: Schizosaccharomyces pombe

source_name: epe1 deleted cells (white colony) at exponentially-growing phase

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit, one-color including Cy3-CTP (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated as follows: the cell pellet was frozen with liquid nitrogen and thawed on ice. Cells were washed once with pre-chilled water. The cell pellet was resuspended in 720 micro-l of TES(10mM Tris pH7.5, 10mM EDTA pH8, 0.5% SDS) on ice. 720 micro-l of acidic phenol-chloroform was added to the cell suspension and mixed immediately. The sample was incubated at 65°C for 1 hour, and then placed on ice for 1 min. The sample was centrifuged for 15 min. at 14000rpm at 4°C. 700 micro-l of water phase of the sample was added to 700 micro-l of acidic phenol-chloroform prepared in a phase lock tube (MaXtractTM HighDensity 2ml Qiagen), then mixed. The sample was centrifuged for 5min at 14000rpm at 4°C. 700 micro-l of water phase of the sample was added to 700 micro-l of chloroform prepared in a new phase lock tube, then mixed. The tube was centrifuged for 5 min at 14000rpm at 4°C. Total RNA from the 500 micro-l of the water phase was purified by ethanol precipitation.

treatment_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium. Cells were incubated at 30°C and collected with filtration when they reached a density of 5x106 cells/ml.

value: epe1 deleted cells


title: SID_25: control, placebo, group 2

description: Mouse muscle total RNA at site of injection, control, placebo, group 2, sample SID_25


title: S.pombe-epe1D(red)

source_name: epe1 deleted cells (red colony) at exponentially-growing phase


title: S.pombe-wildtype

source_name: wildtype for epe1D at exponentially-growing phase

value: epe1 wild type


title: SID_23: control, placebo, group 2

description: Mouse muscle total RNA at site of injection, control, placebo, group 2, sample SID_23


title: SID_11: control, Boostrix, group 1

description: Mouse muscle total RNA at site of injection, control, Boostrix, group 1, sample SID_11


title: SID_21: control, placebo, group 2

description: Mouse muscle total RNA at site of injection, control, placebo, group 2, sample SID_21


title: H1_ESC_ATACseq_rep2


title: hES_H3K27me3_rep1

description: (no peak calls used)

value: Millipore, 07-453


title: H1_END_ATACseq_rep1


title: H1_ESC_ATACseq_rep1


title: H1_ESC_H3K27ac_ChIPseq_rep1


title: Input DNA of DU 145 (cross-linking with 1% formaldehyde)

status: Public on Feb 23 2018

data_processing:
XSQ files generated from SOLiD machine were mapped on human reference genome hg19 using LifeScope v2.5.1 software
ChIPseq workflow of LifeScope was used
Adaptor and barcode sequences were removed
MACS version 1.4.2. ChIP-seq file and control file:
-t DU145_UCHL1_1.bam -c DU145_Input_1.bam
-t DU145_UCHL1_2.bam -c DU145_Input_2.bam
-t Hek_UCHL1.bam -c Hek_Input.bam
effective genome size = 2.70e+09.
band width = 300; model fold = 10,30; pvalue cutoff = 1.00e-05.
Range for calculating regional lambda is: 1000 bps and 10000 bps
Genome_build: hg19
Supplementary_files_format_and_content: peak file

source_name: Prostate cancer cells

growth_protocol: DU 145 prostate cancer cells were grown in EMEM medium and HEK293T cells were grown in DMEM medium. All of the media were supplemented with 10% FBS and 1% antibiotic-antimycotic. The cells were grown at 37°C containing 5% CO2.

extract_protocol:
DU 145 and HEK293T cells were incubateded with 1% formaldehyde only or with a combination of 1mM DSP and 1% formaldehyde. The DNA was fragmented by sonication to approximately 200-300bp or by MNase digestion to obtain a majority of mononucleosomes. UCHL1 was immunoprecipitated by a mouse monoclonal antibody (R&D Systems).
The ChIPseq libraries were prepared according to the 5500 SOLiD fragment library protocol (Life technologies). The ChIP and input DNA size was analyzed by the high sensitivity DNA kit and 2100 Bioanalyzer (Agilent Technologies). Approximately 20 ng of ChIP DNA was end-repaired and size selected (100-250 bp). This was followed by dA tailing and ligation of SOLiD barcodes. Finally, DNA libraries were prepared by emulsion PCR (ePCR) and loaded onto the flowchip for sequencing by the SOLiD platform.

tag: cell line

value: Prostate cancer derived from brain metastatic site

tag: crosslinking

value: 1% formaldehyde


title: Input DNA of DU 145 (cross-linking with 1mM DSP and 1% formaldehyde)

value: 1mM DSP and 1% formaldehyde


title: Input DNA of HEK293T (cross-linking with 1mM DSP and 1% formaldehyde)

source_name: Embryonic kidney cells

value: Embryonic kidney (neuronal lineage) SV40 T antigen


title: UCHL1 ChIP DNA of DU 145 (cross-linking with 1mM DSP and 1% formaldehyde)

value: UCHL1 (R&D Systems:MAB6007)


title: UCHL1 ChIP DNA of HEK293T (cross-linking with 1mM DSP and 1% formaldehyde)


title: UCHL1 ChIP DNA of DU 145 (cross-linking with 1% formaldehyde)


title: S.pombe-rpb1-CTD-S2A / White-rep1

status: Public on Dec 13 2017

hyb_protocol: 50 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/micro-g cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 micro-l containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 micro-l of 2x GE hybridization buffer HI-RPM (Agilent) was added to the fragmentation mixture and hybridized to Agilent custom microarrays (8 x 15k format) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8 x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5 micro-m, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (ver 10.7.3.1, Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 028936_D_F_20100615) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: rpb1-CTD-S2A / White at exponentially-growing phase replicate 1

tag: medium

value: YES

tag: temperature

tag: genotype/variation

tag: colony color

value: white


title: S.pombe-rpb1-CTD-S7A / Pink-rep2

source_name: rpb1-CTD-S7A / Pink at exponentially-growing phase replicate 2

value: pink


title: BLCA_Cx_305

status: Public on Mar 13 2017

city: Lund

first: Pontus

last: Eriksson

state: Select:

address: Scheelevägen 2

department: Department of Clinical Sciences

country: Sweden

institute: Lund University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Bioconductor R package Affy. Probe intensities were normalized in labeling batches of 24 using RMA. Batches were combined and RMA normalized.
The file Processed_Data_Supplement.txt contains ready-to-use median centered gene expression data for 307 tumor samples, with EntrezID and GeneSymbol. Sample order is derived from ConsensusClusterPlus, performed on the top 50% variance genes (n=7031) and matches the Sjodahl 2017 publication. Metadata: CEL Filename, GEO_SampleName, Labeling Batch, Hybridisation Number, TURB Stage, TURB Grade, Lund 2012 Taxonomy By Centroid Correlation, ConsensusClusterPlus Cluster, Sjodahl 2017 mRNA-cluster/Phenotype, Publication Heatmap Order.

label: biotin

source_name: FFPE tissue specimen

label_protocol: SensationPlus FFPE Amplification and WT labeling kit

extract_protocol: High Pure FFPET RNA isolation kit (Roche)

tag: tissue

value: bladder cancer

tag: stage and grade

value: pT2   G3

tag: labeling batch


title: S.pombe-rpb1-CTD-S7A / Pink-rep1

source_name: rpb1-CTD-S7A / Pink at exponentially-growing phase replicate 1


title: S.pombe-rpb1-CTD-S2A / White-rep2

source_name: rpb1-CTD-S2A / White at exponentially-growing phase replicate 2


title: BLCA_Cx_178

value: pT2   G2


title: BLCA_Cx_234


title: BLCA_Cx_235


title: BLCA_Cx_198


title: S.pombe_wildtype_rep1

status: Public on Feb 04 2016

description: SAMPLE 1

data_processing:
The scanned images were analyzed with Feature Extraction Software (ver 10.7.3.1, Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 038274_D_F_20120123) to obtain background subtracted and spatially detrended Processed Signal intensities.
6767 probes (including 56 control probes: indicated by “control” in the comment columns) are spotted multiply to fill 62976 spots in each array. A median of the gProcessedsignals of the spots for each probe was calculated to make a data set for 6767 probes. The median was normalized by the 75 percentile method (the value at 75% was set to 2500.) to get the value in the Matrix sheet. ID_REF in the Matrix sheet match the identifiers in the SPOT ID column in the 038274_D_GEO_20120123.txt file. When the average of the gIsWellAboveBG of the spots for each probe is higher than 0.55, the probe signal is considered more than the detection limit, ranked with “a” in the Rank columns. The values of probes that represent duplicated genes were divided by the number of duplicated genes to give corrected values in the Value columns (indicated by “corrected” in the comment columns). The values of probes that were cross-hybridized with palalogs were corrected with the correction probes (indicated as “correction” in the comment columns) as described in the supplemental file with GPL183374 to give corrected values in the Value columns (indicated by “corrected” in the comment columns). “combined” and “deleted” in the comment columns mean the genes were combined with other genes or deleted.

source_name: wildtype_exponentially-growing phase

treatment_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium. Cells were incubated at 30°C and collected with filtration when they reached a density of 5x10^6 cells/ml.

value: wildtype

tag: growth stage

value: exponentially-growing phase


title: S.pombe_set2DC_rep1

description: SAMPLE 5

source_name: set2 C-terminal deleted cells_exponentially-growing phase

value: set2 C-terminal deleted


title: S.pombe_wildtype_rep2

description: SAMPLE 2


title: BLCA_Cx_204


title: BLCA_Cx_258


title: BLCA_Cx_244


title: BLCA_Cx_285


title: BLCA_Cx_118

value: pTx   G3


title: S.pombe_set2DC_rep2

description: SAMPLE 6


title: S.pombe_set2DSRI_rep2

description: SAMPLE 8

source_name: set2 C-terminal SRI domain deleted cells_exponentially-growing phase

value: set2 C-terminal SRI domain deleted


title: BLCA_Cx_130

value: pT2   Gx


title: BLCA_Cx_283


title: BLCA_Cx_306


title: S.pombe_set2DSRI_rep1

description: SAMPLE 7


title: S.pombe_set2D_rep1

description: SAMPLE 3

source_name: set2 deleted cells_exponentially-growing phase

value: set2 deleted


title: S.pombe_set2D_rep2

description: SAMPLE 4


title: BLCA_Cx_197


title: BLCA_Cx_134

value: pT3   G3


title: SE-DNAseq of cell sample sC

status: Public on Jan 01 2016

description: oldSE

data_processing:
Library strategy: F1-seq
XSQ files generated from SOLiD machine were mapped on reference genome gal3 using LifeScope v2.5.1 software
genomic resequencing frag workflow of LifeScope was used with defult settings of 2-mismatch penelty
Adaptor and barcode sequences were removed
mapped bam files were converted to bed files by bamtobed
domain peaks were called using the bed files  by SICER_V1.1 program with window 1K and gab 1k settings
Genome_build: galGal3
Supplementary_files_format_and_content: domain text, chr,start, end, island score

source_name: Erythrocyte cell

extract_protocol:
Chicken immature erythrocyte nuclei were incubated with micrococcal  nuclease, and chromatin fragments soluble in a low ionic strength solution containing 10 mM  EDTA were recovered in fraction SE. Chromatin fraction SE was made 150mM in NaCl, and  chromatin fragments from the salt-soluble fraction (S150) were size-resolved on a Bio-Gel A-  1.5m column to isolate the F1 fraction containing polynucleosomes. DNA from SE and  the chromatin fractions were isolated with phenol/chloroform followed by a DNA purification step using commercially available PCR purification kit (Qiagen).
Genomic DNA libraries  were prepared according to the 5500 SOLiD fragment library protocol (Life technologies). 5 ug of sheared genomic DNA  were end-repaired and size selected (100-250bp), followed by dA tailing, ligation of SOLiD barcodes and library PCR amplification. Libraries were subjected to emulsion PCR (ePCR) and loaded on the flowchip for sequencing.

tag: strain

value: Bovan

tag: develomental stage

value: G0 phase Immature erythrocyte cells

tag: layer

value: White leghorn

tag: isolation protocol

value: DNA isolated from EDTA soluble chromatin

tag: chromatin

value: EDTA soluble total chromatin


title: BLCA_Cx_73


title: F1-DNAseq of cell sample sC

value: DNA isolated from 150mM Salt soluble chromatin fraction 1

value: Transcriptionally active chromatin fraction 1 (F1)


title: SE-DNAseq of cell sample sB

description: NewSE


title: BLCA_Cx_82

value: bladder cancer

value: pT1   G3


title: F1-DNAseq of cell sample sB


title: F1-DNAseq of cell sample sA


title: BLCA_Cx_241

value: pT2   G3


title: Nuclear RNAseq of cell sample s2

data_processing:
XSQ files generated from SOLiD machine were mapped on reference genome gal3 using LifeScope v2.5.1 software
whole.transcriptome.pe workflow of LifeScope was used with 2 mismatch penalty settings
Adaptor and barcode sequences were removed
read counts and rpkm against gal3 refGenes UCSC annotation were calculated by WT count module of LifeScope v2.5.1
Genome_build: galGal3
Supplementary_files_format_and_content: TEXT, gene ID, chr, strand, start, end, count, length, RPKM, exon#,-expr-exons(>10 reads), Transcripts

molecule: nuclear RNA

extract_protocol:
RNA from immature erythrocyte cells were isolated using RNeasy plus mini kit (Qiagen) following manufacturer's instruction. DNase digestion was performed (Promega) to remove any genomic DNA in the purified RNA.
SOLiD Total RNA-Seq kit was used to prepare whole transcriptome libraries. RNA quality and integrity was assessed using the RNA pico Kit and 2000 Bioanalyzer  (Agilent technologies). 4-6 ug of Total RNA was subjected to rRibosomal depletion (RiboMinus eukaryote system v2, Life technologies) followed by RNAse III fragmentation, adaptor hybridization and reverse transcription. Reversed transcribed DNA was size selected and PCR amplified. Libraries were sequenced in a multiplex manner, pooling two libraries per lane.


title: Total RNAseq of cell sample s2


title: Nuclear RNAseq of cell sample s1


title: Total RNAseq of cell sample s1


title: H3K4me3ChIPseq of cell sample sD

data_processing:
XSQ files generated from SOLiD machine were mapped on reference genome gal3 using LifeScope v2.5.1 software
Fastq sequences with 76bp generated by Miseq were trimmed off the first 3 bases and the last 2 bases and mapped onto reference genome by bowtie-0.12.8.
ChIPseq workflow of LifeScope was used
Adaptor and barcode sequences were removed
peaks were called using the bed files  by MACS1.4 program
peak  pvalue cutoff = 1.00e-05
Genome_build: galGal3
Supplementary_files_format_and_content: peaks.xls, chr, start, end, length, summit, tags, -10*log10(pvalue),fold_enrichment FDR(%)

extract_protocol:
Chicken immature erythrocyte nuclei were treated  with 0.5% formaldehyde and chromatin was sheared into 200bp fragments. Immunoprecipitation was performed with respective antibody.
ChIPSeq library preparation was performed according to the NEBNext ChIP-Seq library preparation protocol. 20 ng of ChIP DNA was end-repaired and dA-tailed. Ligation products were size selected and PCR enriched. Libraries were quantified by qPCR,normalized and pulled to 10 nM before sequencing.

tag: antibody information


title: H3K27ac of cell sample sD


title: H3K27ac of cell sample sD (MiSeq)

extract_protocol:
Chicken immature erythrocyte nuclei were treated  with 0.5% formaldehyde and chromatin was sheared into 200bp fragments. Immunoprecipitation was performed with respective antibody.
ChIPSeq library preparation was performed according to the NEBNext ChIP-Seq library preparation protocol. 20 ng of ChIP DNA was end-repaired and dA-tailed. Ligation products were size selected and PCR enriched. Libraries were quantified by qPCR,normalized and pulled to 10 nM before sequencing.ChIP DNA and Input libraries were sequenced using the MiSeq platform and v3 sequencing reagents.


title: Input DNA of cell sample sD


title: S.pombe-wildtype-in-1/100xN-EMM2-continuous-rep2

status: Public on Oct 22 2015

hyb_protocol: Hybridization was done by using the Gene Expression Hybridization Kit (Agilent Technologies) according to manufacturer's instructions except for amount of Cy3-labelled cRNA (37.5 ng was used for each hybridization except for the 1/8, 1/12, 1/20 dilution experiments. 75ng, 50ng, and 30ng cRNA were used for 1/8, 1/12 and 1/20 experiments respectively.). After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

data_processing: The scanned images were analyzed with Feature Extraction Software (ver 10.7.3.1, Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 038274_D_F_20120123) to obtain background subtracted and spatially detrended Processed Signal intensities. 6767 probes (including 56 control probes: indicated by "control" in the comment columns) are spotted multiply to fill 62976 spots in each array. A median of the gProcessedsignals of the spots for each probe was calculated to make a data set for 6767 probes. The median was normalized by the 75 percentile method (the value at 75% was set to 2500). When the average of the gIsWellAboveBG of the spots for each probe is higher than 0.55, the probe signal is considered more than the detection limit, ranked with "a" in the Rank columns. The values of probes that represent duplicated genes were divided by the number of duplicated genes to give corrected values in the Value columns (indicated by "corrected" in the comment columns). The values of probes that were cross-hybridized with paralogs were corrected with the correction probes (indicated as "correction" in the comment columns) as described in the supplemental file with GPL18374 to give corrected values in the Value columns (indicated by "corrected" in the comment columns). "combined" and "deleted" in the comment columns mean the genes were combined with other genes or deleted.  The ID_REF in the data table matches the identifiers in the SPOT ID column in the 038274_D_GEO_20120123.txt file.

source_name: wildtype in 1/100xN-EMM2 continuous culture replicate 2

extract_protocol: Total RNA was isolated as follows: the cell pellet was frozen with liquid nitrogen. The frozen cell pellet was suspended in 500 µl of TES (10 mM Tris pH 7.5, 10 mM EDTA pH 8, 0.5% SDS) on ice. 500 µl of acidic phenol-chloroform was added to the cell suspension and mixed immediately. The sample was incubated at 65°C for 1 hour, and then placed on ice for 1 min. The sample was transferred to a phase lock tube (MaXtractTM HighDensity 2 ml Qiagen) and was centrifuged for 5 min at 14,000 rpm at 4°C. 500 µl of water phase of the sample was added to 500 µl of acidic phenol-chloroform in a new phase lock tube, then mixed. The sample was centrifuged for 5 min at 14,000 rpm at 4°C. 500 µl of water phase of the sample was added to 500 µl of chloroform prepared in a new phase lock tube, then mixed. The tube was centrifuged for 5 min at 14,000 rpm at 4°C. Total RNA was purified from the water phase by ethanol precipitation. After resolving the RNA pellet in a fixed volume of water, the concentration of the isolated RNA was measured with the spectrophotometer ND-1000 (NanoDrop Technology). A small portion of the isolated RNA was also analyzed with the BIO-analyzer 2100 (Agilent) to check its purity and composition of RNA species.

treatment_protocol: S. pombe cells were incubated at 30°C in YES or 33°C in EMM2 liquid media for batch culture, and collected with filtration when they reached a density of 5x106 cells/ml. For continous culture, after 72 hours in EMM2 with high or low nitrogen at 30°C, cells were harvested with filtration.

value: wild type

tag: culture

value: continuous


title: S.pombe-wildtype-in-1/100xN-EMM2-continuous-rep3

source_name: wildtype in 1/100xN-EMM2 continuous culture replicate 3


title: S.pombe-wildtype-in-EMM2-batch-1/16-rep2

source_name: wildtype in EMM2 batch culture replicate 2


title: S.pombe-wildtype-in-EMM2-batch-1/16-rep3

source_name: wildtype in EMM2 batch culture replicate 3


title: S.pombe-wildtype-in-1xN-EMM2-continuous-rep2

source_name: wildtype in 1xN-EMM2 continuous culture replicate 2


title: S.pombe-wildtype-in-1xN-EMM2-continuous-rep4

source_name: wildtype in 1xN-EMM2 continuous culture replicate 4


title: S.pombe-wildtype-in-YES-batch-1/16

source_name: wildtype in YES batch culture: hibridization with 1/16 dilution

value: YES


title: S.pombe-wildtype-in-1xN-EMM2-continuous-rep3

source_name: wildtype in 1xN-EMM2 continuous culture replicate 3


title: S.pombe-wildtype-in-1xN-EMM2-continuous-rep1

source_name: wildtype in 1xN-EMM2 continuous culture replicate 1


title: S.pombe-wildtype-in-1/100xN-EMM2-continuous-rep1

source_name: wildtype in 1/100xN-EMM2 continuous culture replicate 1


title: S.pombe-wildtype-in-EMM2-batch-1/16-rep1

source_name: wildtype in EMM2 batch culture replicate 1


title: S.pombe-wildtype-in-YES-batch-1/12

data_processing: The scanned images were analyzed with Feature Extraction Software (ver 10.7.3.1, Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 038274_D_F_20120123) to obtain background subtracted and spatially detrended Processed Signal intensities. 6767 probes (including 56 control probes: indicated by "control" in the comment columns) are spotted multiply to fill 62976 spots in each array. A median of the gProcessedsignals of the spots for each probe was calculated to make a data set for 6767 probes. The median was normalized by the 75 percentile method (the value at 75% was set to 2500). When the average of the gIsWellAboveBG of the spots for each probe is higher than 0.55, the probe signal is considered more than the detection limit, ranked with "a" in the Rank columns. The values of probes that represent duplicated genes were divided by the number of duplicated genes to give corrected values in the Value columns (indicated by "corrected" in the comment columns). The values of probes that were cross-hybridized with paralogs were corrected with the correction probes (indicated as "correction" in the comment columns) as described in the supplemental file with GPL18374 to give corrected values in the Value columns (indicated by "corrected" in the comment columns). "combined" and "deleted" in the comment columns mean the genes were combined with other genes or deleted.

source_name: wildtype in YES batch culture: hibridization with 1/12 dilution


title: Mll2_WT_Cg1_57

status: Public on Sep 13 2015

city: New York

first: Laura

last: Pasqualucci

state: NY

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

hyb_protocol: Fragmented and labeled cDNA was hybridized to Affymetrix MG430.2 arrays using the Affymetrix HWS kit, Standard Array (49 Format) for 16 hours. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G, connected to Command Console software.

data_processing: Raw expression values were normalized using the Robust Multiarray Averaging (RMA) algorithm. For GSEA analysis, multiple probes corresponding to the same gene are collapsed with maximum t-statistic.

label: Biotin

label_protocol: 3.75ug of amplified cDNA was biotin-labeled with the Encore® Biotin Module (NuGEN) according to the manufacturer's instructions

growth_protocol: Mice (8-12 week old) were immunized with SRBC (day 0: 1X10^8 cells; d5:1X10^9 cells) and sacrificed at d12 for analysis.

extract_protocol: Total RNA was isolated using the Total RNA isolation NucleoSpin RNA XS kit (NACHEREY-NAGEL) according to the user's manual. Twenty nanograms of RNA from each sample were then reverse transcribed and amplified using the Ovation RNA Amplification System (NuGEN)

treatment_protocol: Single cell suspensions prepared from the spleen of immunized mice were processed with the mouse B-cell isolation kit (Miltenyi Biotec), and germinal center B cells (B220+CD95+PNA+) were sorted from individual mouse samples by fluorescence-activated cell sorting

tag: strain background

tag: age

value: 2-3 months

tag: gender

value: female

tag: genotype

value: Mll2fl/fl Cg1-Cre

value: spleen

tag: cell type


title: Mll2_WT_CD19_146

value: male

value: Mll2fl/fl CD19-Cre

value: germinal center B cells (B220+CD95+PNA+)


title: Mll2_WT_CD19_123


title: S.pombe-wildtype-in-YES-batch-1/20

source_name: wildtype in YES batch culture: hibridization with 1/20 dilution

tag: genotype/variation

tag: medium

tag: temperature


title: S.pombe-wildtype-in-YES-batch-1/8

source_name: wildtype in YES batch culture: hibridization with 1/8 dilution


title: Mll2_WT_Cg1_44

tag: tissue


title: Mll2_WT_Cg1_47


title: Mll2_HET_Cg1_49


title: S.pombe-wildtype-in-1/100xN-EMM2-continuous-rep4

source_name: wildtype in 1/100xN-EMM2 continuous culture replicate 4


title: Mll2_HET_Cg1_67


title: Mll2_HET_Cg1_63


title: Mll2_KO_Cg1_60


title: Mll2_KO_Cg1_42


title: Mll2_HET_CD19_119


title: Mll2_KO_Cg1_58


title: Mll2_WT_CD19_117


title: Mll2_HET_CD19_124


title: Mll2_HET_CD19_118


title: Mll2_KO_CD19_161


title: Mll2_KO_CD19_121


title: Mll2_KO_CD19_132


title: S.pombe-wildtype-in-YES-batch-1/16


title: Monocyte_male_29_TB

status: Public on Aug 25 2015

type: genomic

description: Monocyte from TB patient (male, age 29 years)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan with standard recommended Illumina scanner setting

data_processing:
Genomestudio 2011.1 (methylationmodule 1.9.0)
normalized Average Beta (to internal controls like recommended by Illumina, no background subtraction)

label: Cy5 and Cy3

label_protocol: standard Illumina Protocol for HumanMethylation450

extract_protocol: DNA was isolated using  TRIzol® reagent (Life Technologies Corporation) according to manufacturer's instructions. Quality and quantity of nucleic acids were determined by electrophoresis and spectrophotometry.

treatment_protocol: Patients presenting with TB symptoms (TB, n=8) were recruited on the day of diagnosis, and subsequently, LTBI participants (LTBI, n=8) were recruited to match the patients' age and gender.  Granulocytes and monocytes were sequentially separated from peripheral blood by magnetic beads (MACS, Miltenyi Biotec GmbH, CD15+ and CD14+, respectively) according to manufacturer's instructions.

value: Monocyte

tag: study group

value: TB patient

tag: matched pair id

tag: subject id


title: Monocyte_male_50_TB

description: Monocyte from TB patient (male, age 50 years)


title: Monocyte_male_23_TB

description: Monocyte from TB patient (male, age 23 years)


title: Monocyte_male_45_TB

description: Monocyte from TB patient (male, age 45 years)


title: Monocyte_female_NA_TB

description: Monocyte from TB patient (female, age not known)

source_name: Monocyte,female,NA,TB


title: Neutrophil_male_49_HHC

description: Neutrophil from household contact (male, age 49 years)

value: Neutrophil

value: household contact


title: Neutrophil_male_37_HHC

description: Neutrophil from household contact (male, age 37 years)


title: Monocyte_male_52_TB

description: Monocyte from TB patient (male, age 52 years)


title: Neutrophil_male_42_HHC

description: Neutrophil from household contact (male, age 42 years)


title: Neutrophil_male_23_TB

description: Neutrophil from TB patient (male, age 23 years)


title: Neutrophil_female_NA_TB

description: Neutrophil from TB patient (female, age not known)

source_name: Neutrophil,female,NA,TB


title: Monocyte_female_18_TB

description: Monocyte from TB patient (female, age 18 years)


title: Neutrophil_female_19_TB

description: Neutrophil from TB patient (female, age 19 years)


title: Monocyte_male_49_HHC

description: Monocyte from household contact (male, age 49 years)


title: Monocyte_male_28_TB

description: Monocyte from TB patient (male, age 28 years)


title: Neutrophil_male_50_TB

description: Neutrophil from TB patient (male, age 50 years)


title: Neutrophil_female_21_HHC

description: Neutrophil from household contact (female, age 21 years)


title: Neutrophil_male_28_TB

description: Neutrophil from TB patient (male, age 28 years)


title: Monocyte_female_21_HHC

description: Monocyte from household contact (female, age 21 years)


title: Neutrophil_female_22_HHC

description: Neutrophil from household contact (female, age 22 years)


title: Neutrophil_female_18_TB

description: Neutrophil from TB patient (female, age 18 years)


title: Monocyte_male_24_HHC

description: Monocyte from household contact (male, age 24 years)


title: Monocyte_female_22_HHC

description: Monocyte from household contact (female, age 22 years)


title: Neutrophil_male_45_TB

description: Neutrophil from TB patient (male, age 45 years)


title: Neutrophil_male_52_TB

description: Neutrophil from TB patient (male, age 52 years)


title: Monocyte_male_37_HHC

description: Monocyte from household contact (male, age 37 years)


title: Neutrophil_male_24_HHC

description: Neutrophil from household contact (male, age 24 years)


title: Monocyte_female_19_TB

description: Monocyte from TB patient (female, age 19 years)


title: Monocyte_male_42_HHC

description: Monocyte from household contact (male, age 42 years)


title: Monocyte_male_38_TB

description: Monocyte from TB patient (male, age 38 years)


title: CTRL012M

status: Public on Aug 22 2015

description: Cell specific transcriptome from blood monocytes isolated from a household contact, male

hyb_protocol: After precipitation, purification and quantification of the labeling reactions, 1.25µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies). Washing of the hybridizations was done with the SSPE wash protocol according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.0.1.1, Agilent Technologies) using the protocol GE1_1100_Jul11 according the supplier's recommendations. The raw intensity files were read into limma / BioConductor (gProcessedSignal column) and normalized using the quantile method. Intensities were averaged for identical probes and control probes were removed.

label_protocol: Total RNA was labeled with the single-color Quick amp Labeling Kit (Agilent Technologies) according to manufacturer’s instructions.

extract_protocol: Total RNA (tRNA) was isolated using TRIzol® reagent (Life Technologies Corporation) according to manufacturer's instructions. Quality and quantisty of nucleic acids were determined by electrophoresis and spectrophotometry.

value: monocytes


title: TB007M

description: Cell specific transcriptome from blood monocytes isolated from a TB patient, male


title: TB005M

source_name: Cell specific transcriptome from blood monocytes isolated from a TB patient, male


title: TB007N

description: Cell specific transcriptome from blood granulocytes isolated from a TB patient, male

value: granulocytes


title: CTRL012N

description: Cell specific transcriptome from blood granulocytes isolated from a household contact, male


title: TB005N

source_name: Cell specific transcriptome from blood granulocytes isolated from a TB patient, male


title: CTRL009M

source_name: Cell specific transcriptome from blood monocytes isolated from a household contact, male


title: CTRL003M

description: Cell specific transcriptome from blood monocytes isolated from a household contact, female


title: TB015N

description: Cell specific transcriptome from blood granulocytes isolated from a TB patient, female


title: TB015M

description: Cell specific transcriptome from blood monocytes isolated from a TB patient, female


title: TB011N

source_name: Cell specific transcriptome from blood granulocytes isolated from a TB patient, female


title: CTRL009N

source_name: Cell specific transcriptome from blood granulocytes isolated from a household contact, male


title: CTRL003N

description: Cell specific transcriptome from blood granulocytes isolated from a household contact, female


title: TB010N


title: CTRL010M

source_name: Cell specific transcriptome from blood monocytes isolated from a household contact, female


title: TB001N


title: TB011M

source_name: Cell specific transcriptome from blood monocytes isolated from a TB patient, female


title: CTRL010N

source_name: Cell specific transcriptome from blood granulocytes isolated from a household contact, female


title: CTRL002N


title: Neutrophil_male_32_HHC

description: Neutrophil from household contact (male, age 32 years)


title: CTRL008N


title: TB001M


title: Monocyte_female_23_HHC

description: Monocyte from household contact (female, age 23 years)


title: Monocyte_male_23_HHC

description: Monocyte from household contact (male, age 23 years)


title: Neutrophil_female_23_HHC

description: Neutrophil from household contact (female, age 23 years)


title: Neutrophil_male_23_HHC

description: Neutrophil from household contact (male, age 23 years)


title: CTRL002M


title: TB005M

description: Cell specific microRNA transcriptome from blood monocytes isolated from a household contact, female

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.0.1.1, Agilent Technologies) using the protocol GE1_1100_Jul11 according the supplier's recommendations. The raw intensity files were read into limma / BioConductor, background corrected using the normexp method and normalized using the quantile method. Intensities were averaged for identical probes and control probes were removed.


title: TB007M

source_name: Cell specific microRNA transcriptome from blood monocytes isolated from a household contact, female


title: CTRL004N


title: TB008M


title: TB002M

description: Cell specific microRNA transcriptome from blood monocytes isolated from a household contact, male


title: TB008M


title: CTRL012M

description: Cell specific microRNA transcriptome from blood monocytes isolated from a TB patient, female


title: TB011M

source_name: Cell specific microRNA transcriptome from blood monocytes isolated from a household contact, male


title: TB001M


title: TB010N

description: Cell specific microRNA transcriptome from blood granulocytes isolated from a household contact, female


title: CTRL009M

source_name: Cell specific microRNA transcriptome from blood monocytes isolated from a TB patient, female


title: TB015M


title: CTRL010M

description: Cell specific microRNA transcriptome from blood monocytes isolated from a TB patient, male


title: CTRL002M


title: CTRL008M

description: Cell specific transcriptome from blood monocytes isolated from a household contact, male


title: CTRL005N


title: TB002N


title: TB008N

description: Cell specific transcriptome from blood granulocytes isolated from a TB patient, male


title: CTRL004M


title: Neutrophil_female_39_HHC

description: Neutrophil from household contact (female, age 39 years)


title: TB002M


title: CTRL005M

description: Cell specific transcriptome from blood monocytes isolated from a household contact, female


title: CTRL005M

source_name: Cell specific microRNA transcriptome from blood monocytes isolated from a TB patient, male


title: Monocyte_male_32_HHC

description: Monocyte from household contact (male, age 32 years)


title: TB007N

source_name: Cell specific microRNA transcriptome from blood granulocytes isolated from a household contact, female


title: Monocyte_female_39_HHC

description: Monocyte from household contact (female, age 39 years)


title: TB005N


title: TB015N

description: Cell specific microRNA transcriptome from blood granulocytes isolated from a household contact, male


title: CTRL010N

description: Cell specific microRNA transcriptome from blood granulocytes isolated from a TB patient, male


title: CTRL003N

source_name: Cell specific microRNA transcriptome from blood granulocytes isolated from a TB patient, male


title: CTRL003M


title: TB010M


title: CTRL005N


title: CTRL004N

description: Cell specific microRNA transcriptome from blood granulocytes isolated from a TB patient, female


title: TB001N


title: TB002N

source_name: Cell specific microRNA transcriptome from blood granulocytes isolated from a household contact, male


title: CTRL004M


title: TB008N


title: CTRL009N

source_name: Cell specific microRNA transcriptome from blood granulocytes isolated from a TB patient, female


title: CTRL012N


title: TB011N


title: CTRL002N


title: CTRL008N


title: CTRL008M


title: S.pombe-H3-K36A-rep2

status: Public on Jul 27 2015

data_processing:
The scanned images were analyzed with Feature Extraction Software (ver 10.7.3.1, Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 038274_D_F_20120123) to obtain background subtracted and spatially detrended Processed Signal intensities.
6767 probes (including 56 control probes: indicated by “control” in the comment columns) are spotted multiply to fill 62976 spots in each array. A median of the gProcessedsignals of the spots for each probe was calculated to make a data set for 6767 probes. The median was normalized by the 75 percentile method (the value at 75% was set to 2500). When the average of the gIsWellAboveBG of the spots for each probe is higher than 0.55, the probe signal is considered more than the detection limit, ranked with “a” in the Rank columns. The values of probes that represent duplicated genes were divided by the number of duplicated genes to give corrected values in the Value columns (indicated by “corrected” in the comment columns). The values of probes that were cross-hybridized with paralogs were corrected with the correction probes (indicated as “correction” in the comment columns) as described in the supplemental file with GPL183374 to give corrected values in the Value columns (indicated by “corrected” in the comment columns). For strains deleted for the hhf1 and hhf3 genes, however, we assigned surrogate values to hhf1 and hhf3 because the signals are obviously produced by cross hybridization with mRNA of hhf2. “combined” and “deleted” in the comment columns mean the genes were combined with other genes or deleted.

source_name: histone H3 mutant K36A at exponentially-growing phase replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the LowInput QuickAmp Labeling Kit, one-color including Cy3-CTP (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated and measured as follows: the cell pellet was frozen with liquid nitrogen. The frozen cell pellet was suspended in 500 μl of TES (10 mM Tris pH 7.5, 10 mM EDTA pH 8, 0.5% SDS) on ice. 500 μl of acidic phenol-chloroform was added to the cell suspension and mixed immediately. The sample was incubated at 65°C for 1 hour, and then placed on ice for 1 min. The sample was transferred to a phase lock tube (MaXtractTM HighDensity 2 ml Qiagen) and was centrifuged for 5 min at 14,000 rpm at 4°C. 500 μl of water phase of the sample was added to 500 μl of acidic phenol-chloroform in a new phase lock tube, then mixed. The sample was centrifuged for 5 min at 14,000 rpm at 4°C. 500 μl of water phase of the sample was added to 500 μl of chloroform prepared in a new phase lock tube, then mixed. The tube was centrifuged for 5 min at 14,000 rpm at 4°C. Total RNA was purified from the water phase by ethanol precipitation. After resolving the RNA pellet in a fixed volume of water, the concentration of the isolated RNA was measured with the spectrophotometer ND-1000 (NanoDrop Technology). A small portion of the isolated RNA was also analyzed with the BIO-analyzer 2100 (Agilent) to check its purity and composition of RNA species.

value: histone H3 mutant K36A


title: S.pombe-wildtype-for-set2D-rep1

data_processing: The scanned images were analyzed with Feature Extraction Software (ver 10.7.3.1, Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 038274_D_F_20120123) to obtain background subtracted and spatially detrended Processed Signal intensities. 6767 probes (including 56 control probes: indicated by “control” in the comment columns) are spotted multiply to fill 62976 spots in each array. A median of the gProcessedsignals of the spots for each probe was calculated to make a data set for 6767 probes. The median was normalized by the 75 percentile method (the value at 75% was set to 2500). When the average of the gIsWellAboveBG of the spots for each probe is higher than 0.55, the probe signal is considered more than the detection limit, ranked with “a” in the Rank columns. The values of probes that represent duplicated genes were divided by the number of duplicated genes to give corrected values in the Value columns (indicated by “corrected” in the comment columns). The values of probes that were cross-hybridized with paralogs were corrected with the correction probes (indicated as “correction” in the comment columns) as described in the supplemental file with GPL183374 to give corrected values in the Value columns (indicated by “corrected” in the comment columns). For strains deleted for the hhf1 and hhf3 genes, however, we assigned surrogate values to hhf1 and hhf3 because the signals are obviously produced by cross hybridization with mRNA of hhf2. “combined” and “deleted” in the comment columns mean the genes were combined with other genes or deleted.

source_name: wildtype for set2D at exponentially-growing phase replicate 1

value: wildtype (for set2 deletion)


title: S.pombe-wildtype-for-H3-K36R-rep2

source_name: wildtype for histone H3 mutant K36R at exponentially-growing phase replicate 2

value: wildtype (for histone H3 mutant K36R)


title: S.pombe-H3-K36R-rep2

source_name: histone H3 mutant K36R at exponentially-growing phase replicate 2

value: YES

value: histone H3 mutant K36R


title: S.pombe-H3-K36A-rep1

source_name: histone H3 mutant K36A at exponentially-growing phase replicate 1


title: S.pombe-wildtype-for-set2D-rep2

source_name: wildtype for set2D at exponentially-growing phase replicate 2


title: S.pombe-wildtype-for-H3-K36R-rep1

source_name: wildtype for histone H3 mutant K36R at exponentially-growing phase replicate 1


title: S.pombe-set2D-rep1

source_name: set2 deleted cells at exponentially-growing phase replicate 1

value: set2 deletion


title: TB010M

description: Cell specific transcriptome from blood monocytes isolated from a TB patient, male


title: S.pombe-set2D-rep2

source_name: set2 deleted cells at exponentially-growing phase replicate 2


title: B250-1_Naive

status: Public on Mar 24 2015

city: Aalborg

first: Rasmus

middle: Froberg

last: Brøndum

address: Sdr. Skovvej 15

department: Department of Haematology

country: Denmark

institute: Aalborg University Hospital

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B250-1_Naive_(HG-U133_Plus_2).CEL

hyb_protocol: Following the Appendix VI.A. From the User guide: Encore™Biotin Module Catalog #4200-12,4200-60 from NuGEN

scan_protocol: Gene Chips were scanned using the Affymetrix GeneChip scanner 3000 7G

data_processing: Data were analyzed using R version 3.0.2  and several R and Bioconductor packages. The .CEL-files were pre-processed using the Robust Multichip Average procedure (RMA) as implemented in the just.rma function from the Bioconductor package affy. All RMA-normalised arrays passed the statistical quality control provided by the function arrayQualityMetrics in the R-package arrayQualityMetrics.

source_name: Naive B-cells_ human tonsil

label_protocol: Encore™Biotin Module Catalog #4200-12,4200-60 from NuGEN following the User Guide

extract_protocol: B-cell subpopulations FACS from frozen tonsils into lysis buffer and mRNA purified using µMACS mRNA Isolation Kits fra Miltenyi cat.no 130-075-201. mRNA was amplified using WT-Ovation™Pico RNA Amplification System Version 1.0 Catalog #3300-12, 3300-60 fra NuGEN iflg. User Guide cat.#MO1113 Version 1

value: human healthy tonsils

value: Naive B-cells


title: B249-1_Naive

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B249-1_Naive_(HG-U133_Plus_2).CEL


title: B238-3_Centroblast

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B238-3_Centroblast_(HG-U133_Plus_2).CEL

source_name: Centroblast B-cells_human tonsil

value: Centroblast B-cells


title: B250-3_Centroblast

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B250-3_Centroblast_(HG-U133_Plus_2).CEL


title: B238-5_Plasmablast

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B238-5_Plasmablast_(HG-U133_Plus_2).CEL

source_name: Plasmablast B-cells_human tonsil

value: Plasmablast B-cells


title: B249-5_Plasmablast

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B249-5_Plasmablast_(HG-U133_Plus_2).CEL


title: B250-2_Centrocyte

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B250-2_Centrocyte_(HG-U133_Plus_2).CEL

source_name: Centrocyte B-cells_human tonsil

value: Centrocyte B-cells


title: B237-5_Plasmablast

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B237-5_Plasmablast_(HG-U133_Plus_2).CEL


title: B250-4_Memory

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B250-4_Memory_(HG-U133_Plus_2).CEL

source_name: Memory B-cells_human tonsils

value: Memory B-cells


title: B237-1_Naive

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B237-1_Naive_(HG-U133_Plus_2).CEL


title: B236-5_Plasmablast

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B236-5_Plasmablast_(HG-U133_Plus_2).CEL


title: B236-2_Centrocyte

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B236-2_Centrocyte_(HG-U133_Plus_2).CEL


title: B249-2_Centrocyte

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B249-2_Centrocyte_(HG-U133_Plus_2).CEL


title: B235-1_Naive

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B235-1_Naive_(HG-U133_Plus_2).CEL


title: B234-3_Centroblast

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B234-3_Centroblast_(HG-U133_Plus_2).CEL


title: B236-4_Memory

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B236-4_Memory_(HG-U133_Plus_2).CEL


title: B238-2_Centrocyte

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B238-2_Centrocyte_(HG-U133_Plus_2).CEL


title: B235-2_Centrocyte

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B235-2_Centrocyte_(HG-U133_Plus_2).CEL


title: B236-3_Centroblast

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B236-3_Centroblast_(HG-U133_Plus_2).CEL


title: B235-3_Centroblast

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B235-3_Centroblast_(HG-U133_Plus_2).CEL


title: B249-4_Memory

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B249-4_Memory_(HG-U133_Plus_2).CEL


title: B234-4_Memory

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B234-4_Memory_(HG-U133_Plus_2).CEL


title: B235-4_Memory

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B235-4_Memory_(HG-U133_Plus_2).CEL


title: B235-5_Plasmablast

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B235-5_Plasmablast_(HG-U133_Plus_2).CEL


title: B249-3_Centroblast

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B249-3_Centroblast_(HG-U133_Plus_2).CEL


title: B234-1_Naive

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B234-1_Naive_(HG-U133_Plus_2).CEL


title: B233-5_Plasmablast

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B233-5_Plasmablast_(HG-U133_Plus_2).CEL


title: B234-5_Plasmablast

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B234-5_Plasmablast_(HG-U133_Plus_2).CEL


title: B234-2_Centrocyte

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B234-2_Centrocyte_(HG-U133_Plus_2).CEL


title: B233-3_Centroblast

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B233-3_Centroblast_(HG-U133_Plus_2).CEL


title: H8

description: l1_e1_H8_a8_U133 Plus 2.0.CEL

hyb_protocol: Included in the label protocol; Kit1 or Kit2

source_name: diagnostic diffuse large B-cell lymphoma sample

label_protocol:
Kit1: Biotinylated cRNA were prepared using the GeneChip Expression 3’ amplification One-cycle Target Labeling (#P/N 900493, Affymetrix) from 5 ug total RNA using manual P/N 702232 Rev.2.
Kit2: Biotinylated cRNA were prepared using the GeneChip 3' IVT Express Kit (#P/N901229, Affymetrix) from 100 ng total RNA using manual P/N702646 Rev.4.

extract_protocol: Total RNA was purified from frozen diagnostic DLBCLs by homogenizing the sample in Trizol and incubating for 5 minutes at RT. 200µl chloroform was added and incubated 2 minutes at RT, the mixture was centrifuged at 12,000 g for 10 minutes at 4°C. The aqueous phase was transferred to a new tube and 100 % ethanol added in 1.25X the volume. Mix well and transfer to mirVANA columns (#1561, Ambion) and follow the manufacturer’s instruction from this point.

treatment_protocol: Diagnostic samples of diffuse large B-cell lymphoma (DLBCL)

value: diffuse large B-cell lymphoma (DLBCL)

tag: label protocol

tag: mutational status of gene myd88 (na=not analyzed)

value: WT

tag: mutational status of gene ezh2

tag: mutational status of gene cd79b

tag: abc/gcb/nc subclass

value: ABC

tag: the probability of belonging to abc/gcb/nc subclass

tag: bagsclass

value: Plasmablast

tag: experimental protocol

tag: probability of belonging to the listed bags group

tag: the regs probability of resistance towards cyclophosphamide/mafosfamide (c)

tag: the regs probability of resistance towards doxorubicin (h)

tag: the regs probability of resistance towards vincristine (o)


title: B233-4_Memory

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B233-4_Memory_(HG-U133_Plus_2).CEL

tag: cell type


title: H60

description: l1_e1_H60_a59_U133 Plus 2.0.CEL

tag: tissue

value: Mutation

value: GCB

value: Centrocyte


title: H58

description: l1_e1_H58_a57_U133 Plus 2.0.CEL

value: Unclassified


title: H55

description: l1_e1_H55_a54_U133 Plus 2.0.CEL


title: H59

description: l1_e1_H59_a58_U133 Plus 2.0.CEL

value: Memory


title: H6

description: l1_e1_H6_a6_U133 Plus 2.0.CEL


title: H51

description: l1_e1_H51_a50_U133 Plus 2.0.CEL


title: S.pombe-H3-K36R-rep1

source_name: histone H3 mutant K36R at exponentially-growing phase replicate 1

tag: medium

value: YES

tag: temperature

tag: genotype/variation

value: histone H3 mutant K36R


title: H50

description: l1_e1_H50_a49_U133 Plus 2.0.CEL

tag: label protocol

value: Centroblast


title: B233-1_Naive

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B233-1_Naive_(HG-U133_Plus_2).CEL

value: human healthy tonsils

value: Naive B-cells


title: H56

description: l1_e1_H56_a55_U133 Plus 2.0.CEL

tag: mutational status of gene myd88 (na=not analyzed)


title: H7

description: l1_e1_ H7_a7_U133 Plus 2.0.CEL

tag: mutational status of gene ezh2


title: H52

description: l1_e1_H52_a51_U133 Plus 2.0.CEL

tag: mutational status of gene cd79b


title: H54

description: l1_e1_H54_a53_U133 Plus 2.0.CEL

tag: abc/gcb/nc subclass


title: H9

description: l1_e1_H9_a9_U133 Plus 2.0.CEL

tag: the probability of belonging to abc/gcb/nc subclass


title: B233-2_Centrocyte

description:
Gene expression data from B-cell subpopulations FACS from human healthy tonsils
B233-2_Centrocyte_(HG-U133_Plus_2).CEL


title: H48

description: l1_e1_H48_a47_U133 Plus 2.0.CEL

tag: bagsclass


title: H446

tag: experimental protocol


title: H47

description: l1_e1_H47_a46_U133 Plus 2.0.CEL

tag: probability of belonging to the listed bags group


title: H57

description: l1_e1_H57_a56_U133 Plus 2.0.CEL

tag: the regs probability of resistance towards cyclophosphamide/mafosfamide (c)


title: H53

description: l1_e1_H53_a52_u133 Plus 2.0.CEL

tag: the regs probability of resistance towards doxorubicin (h)


title: H46

description: l1_e1_H46_a45_U133 Plus 2.0.CEL

tag: the regs probability of resistance towards vincristine (o)


title: H44

description: l1_e1_H44_a43_U133 Plus 2.0.CEL


title: H49

description: l1_e1_H49_a48_U133 Plus 2.0.CEL


title: H43

description: l1_e1_H43_a42_U133 Plus 2.0.CEL


title: H42

description: l1_e1_H42_a41_U133 Plus 2.0.CEL


title: H41

description: l1_e1_H41_a40_U133 Plus 2.0.CEL


title: H35

description: l1_e1_H35_a34_U133 Plus 2.0.CEL


title: H45


title: H37

description: l1_e1_H37_a36_U133 Plus 2.0.CEL


title: H36

description: l1_e1_H36_a35_U133 Plus 2.0.CEL


title: H33

description: l1_e1_H33_a32_U133 Plus 2.0.CEL


title: H31

description: l1_e1_H31_a30_U133 Plus 2.0.CEL


title: H3

description: l1_e1_H3_a3_U133 Plus 2.0.CEL


title: H4

description: l1_e1_H4_a4_U133 Plus 2.0.CEL


title: H38

description: l1_e1_H38_a37_U133 Plus 2.0.CEL


title: H295


title: H296


title: H25

description: l1_e1_H25_a24_U133 Plus 2.0.CEL


title: H19

description: l1_e1_H19_a18_U133 Plus 2.0.CEL


title: H2


title: H20

description: l1_e1_H20_a19_U133 Plus 2.0.CEL


title: H21

description: l1_e1_H21_a20_U133 Plus 2.0.CEL


title: H29

description: l1_e1_H29_a28_U133 Plus 2.0.CEL


title: H30

description: l1_e1_H30_a29_U133 Plus 2.0.CEL


title: H28

description: l1_e1_H28_a27_U133 Plus 2.0.CEL


title: H15

description: l1_e1_H15_a15_U133 Plus 2.0.CEL


title: H13

description: l1_e1_H13_a13_U133 Plus 2.0.CEL


title: H23

description: l1_e1_H23_a22_U133 Plus 2.0.CEL


title: H34

description: l1_e1_H34_a33_U133 Plus 2.0.CEL


title: H22

value: Naive


title: H14


title: H11

description: l1_e1_H11_a11_U133 Plus 2.0.CEL


title: H10

description: l1_e1_H10_a10_U133 Plus 2.0.CEL


title: H12


title: H18

description: l1_e1_H18_a17_U133 Plus 2.0.CEL


title: H24

description: l1_e1_H24_a23_U133 Plus 2.0.CEL


title: H1

description: l1_e1_H1_a1_U133 Plus 2.0.CEL


title: WT_d00_e0_vs_KO_d00_e0

status: Public on Sep 02 2014

hyb_protocol: After precipitation, purification and quantification, 1.25Âµg labeled samples were mixed and hybridized according to the supplierâ€™s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5Âµm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1.1, Agilent Technologies). The probe-level normalized/processed data are included in the LogRatio column of the Agilent Feature Extraction files (ie, normalized log10 Cy5/Cy3 ratios).

label_protocol: Total RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7-promotor primer and the resulting cRNA was labeled either with Cyanine 3-CTP or Cyanine 5-CTP.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier. Briefly, samples were homogenized in 1 ml TRIzol, shock frozen and stored at â€“80Â°C. The homogenates were thawed and further processed for total RNA isolation as described by the manufacturer.

tag: day

tag: strain

tag: genotype

tag: experimental run

value: KO


title: WT_d21_eX_vs_KO_d21_eX

value: eX


title: WT_d00_eX_vs_KO_d00_eX


title: WT_d00_e0_vs_WT_d21_e9


title: KO_d00_eX_vs_WT_d00_eX


title: KO_d21_eX_vs_WT_d21_eX


title: KO_d00_eX_vs_KO_d21_eX


title: KO_d21_e8_vs_WT_d21_e9


title: KO_d21_e8_vs_KO_d00_e0


title: KO_d00_e0_vs_WT_d00_e0


title: WT_d21_e8_vs_WT_d00_e0


title: WT_d00_eX_vs_WT_d21_eX


title: WT_d21_eX_vs_WT_d00_eX


title: KO_d21_eX_vs_KO_d00_eX


title: biopsy_ID: P45-01

status: Public on Jan 07 2014

city: Oslo

first: Marianne

last: Brodtkorb

address: Ullernchausseen 70

department: Institute for Cancer Research, The Norwegian Radium Hospital

country: Norway

institute: Oslo University Hospital

description: Fresh frozen tumor tissue sample

hyb_protocol: cRNA was fragmented and hybridized according to the manufacturer's (Affymetrix) guidelines

scan_protocol: GeneChips were scanned using a standard scanning protocol recommended by the manufacturer (Affymetrix)

data_processing: Quantile normalization of gene expression data from each individual array was performed using the GCOS/Expression Console

source_name: follicular lymphoma

label_protocol: cRNA was produced and labeled with biotin according to the manufacturer's (Affymetrix) guidelines

extract_protocol: total RNA was extracted from fresh frozen whole tissue sections using the Stratagene Absolute RNA Miniprep Kitaccording to manufacturer's guidelines

tag: tissue

value: Tumor (lymph node)


title: biopsy_ID: P07-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P17-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P04-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P42-03

description: Fresh frozen tumor tissue sample

source_name: DLBCL 50% and FL 50%


title: biopsy_ID: P34-03

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P14-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P36-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P12-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P24-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P16-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P06-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P23-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P44-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P19-03

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P08-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P19-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P09-03

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P01-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P21-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P34-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P09-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P37-03

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P34-04

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P13-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P08-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P37-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P22-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P42-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P39-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P24-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P07-03

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P33-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P29-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P34-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P23-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P08-03

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P47-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P11-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P45-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P41-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P05-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P46-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P16-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P15-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P46-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P36-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P27-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P47-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P26-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P06-02

description: Fresh frozen tumor tissue sample

source_name: DLBCL


title: biopsy_ID: P32-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P05-03

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P09-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P18-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P12-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P07-02

description: Fresh frozen tumor tissue sample

source_name: DLBCL 10% and FL 90%


title: biopsy_ID: P19-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P39-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P14-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P11-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P01-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P40-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P22-03

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P18-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P26-03

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P31-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P41-02

description: Fresh frozen tumor tissue sample

source_name: DLBCL 30% and FL 70%


title: biopsy_ID: P16-03

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P31-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P29-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P33-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P04-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P10-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P38-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P27-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P38-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P10-02

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P21-01

description: Fresh frozen tumor tissue sample


title: S.pombe-caf4D-rep1

status: Public on Jun 27 2012

data_processing: The scanned images were analyzed with Feature Extraction Software (ver 10.7.3.1, Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 028936_D_F_20100615) to obtain background subtracted and spatially detrended Processed Signal intensities. 5589 probes (including 60 control probes) are spotted multiply to fill 15744 spots in each array. A geometric mean of the gProcessedsignals of the spots for each probe was calculated to make a data set for 5589 probes. The logarithm of the geometric mean to the base 2 was normalized by the 75 percentile method (the value at 75% was set to 0.) to get the value in the Matrix sheet. These processing was done by GeneSpring software. ID_REF in the Matrix sheet match the identifiers in the SPOT ID column in the 028936_D_GEO_20110527.txt file.

source_name: caf4 deleted cells at exponentially-growing phase replicate 1

tag: genotype/variation

tag: medium

tag: temperature


title: S.pombe-not2D-rep2

source_name: not2 deleted cells at exponentially-growing phase replicate 2


title: S.pombe-not3D-rep2

source_name: not3 deleted cells at exponentially-growing phase replicate 2


title: S.pombe-caf4D-rep2

source_name: caf4 deleted cells at exponentially-growing phase replicate 2


title: S.pombe-not3D-rep1

source_name: not3 deleted cells at exponentially-growing phase replicate 1


title: S.pombe-wildtype-rep1

source_name: wildtype at exponentially-growing phase replicate 1

value: wild type


title: S.pombe-not2D-rep1

source_name: not2 deleted cells at exponentially-growing phase replicate 1


title: biopsy_ID: P42-01

description: Fresh frozen tumor tissue sample


title: biopsy_ID: P13-02

description: Fresh frozen tumor tissue sample


title: S.pombe-dcr1D-rep2

status: Public on Aug 31 2013

description: SAMPLE 4

data_processing:
The scanned images were analyzed with Feature Extraction Software (ver 10.7.3.1, Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 028936_D_F_20100615) to obtain background subtracted and spatially detrended Processed Signal intensities.
5589 probes (including 60 control probes) are spotted multiply to fill 15744 spots in each array. A geometric mean of the gProcessedsignals of the spots for each probe was calculated to make a data set for 5589 probes. The geometric mean was normalized by the 75 percentile method (the value at 75% was set to 2500.) to get the value in the Matrix sheet. ID_REF in the Matrix sheet match the identifiers in the SPOT ID column in the 028936_D_GEO_20110527.txt file. When the average of the gIsWellAboveBG of the spots for each probe is higher than 0.55, the probe signal is considered more than the detection limit, ranked with “a” in the Rank columns.

value: dcr1 deleted

tag: growth temperature


title: S.pombe-med20D-pink-rep1

description: SAMPLE 13

source_name: med20 deleted_pink colony_exponentially-growing phase

value: med20 deleted


title: S.pombe-pmc6D-white-rep1

description: SAMPLE 7

source_name: pmc6 deleted_white colony_exponentially-growing phase

value: pmc6 deleted


title: S.pombe-med20D-white-rep2

description: SAMPLE 12

source_name: med20 deleted_white colony_exponentially-growing phase


title: S.pombe-wildtype-rep2

source_name: wildtype at exponentially-growing phase replicate 2


title: S.pombe-wildtype-for-dcr1D-rep1

description: SAMPLE 1

source_name: wildtype for dcr1D_exponentially-growing phase

value: wild type (for dcr1D)


title: S.pombe-wildtype-for-dcr1D-rep2

description: SAMPLE 2


title: S.pombe-med20D-pink-rep2

description: SAMPLE 14


title: S.pombe-dcr1D-rep1

description: SAMPLE 3


title: S.pombe-pmc6D-pink-rep1

description: SAMPLE 9

source_name: pmc6 deleted_pink colony_exponentially-growing phase


title: S.pombe-pmc6D-white-rep2

description: SAMPLE 8


title: S.pombe-med20D-white-rep1

description: SAMPLE 11


title: S.pombe-wildtype-for-pmc6d-med20D-rep1

description: SAMPLE 5

source_name: wildtype for pmc6D and med20D_exponentially-growing phase

value: wild type (for pmc6D, med20D)


title: S.pombe-pmc6D-pink-rep2

description: SAMPLE 10


title: S.pombe-wildtype-for-pmc6d-med20D-rep2

description: SAMPLE 6


title: Gene expression upon nitrogen starvation, 3hrs (D223)

status: Public on Sep 29 2009

description: Comparing between vegetatively-growing control cells (Cy3) and cells at each time point after nitrogen starvation (Cy5).

hyb_protocol: The labeled targets were added to the hybridization solution to contain an equal amount of the Cy3 and Cy5, and then were hybridized onto DNA on the microarray, using Genomic solutions GeneTac Hybridization Station, for four hours at 40°C in Genomic solutions GeneTac Hyb buffer 120microl (including 42% formamide ). The slides after hybridization were washed in the following sequence: (1) 2xSSC 0.1%SDS at 40°C for 5min, (2) 0.2xSSC at 25°C for 1min, and (3) 0.1xSSC at 25°C for 1min.

scan_protocol: Microarrays were scanned using an ArraywoRx arrayscanner, and the acquired data was analyzed by a SoftwoRx software (Applied Precision, Inc., Seattle, WA). Fluorescent intensity in each spot circle (150microm diameter) was measured by Softworx tracker.

data_processing: Measured fluorescent intensity, I, was corrected as follows to give a corrected intensity, C:C = I-M,  (for I>M+2s), C = I*2s/(M+2s),  (for I<M+2s) where M and s are an average and a standard deviation of I of negative control spots for each wave length respectively. When I = M+2s, that is C=2s, it was set to be a detection limit. When C for either Cy3 or Cy5 or both were greater than 2s, the values were considered to be effective data. VALUE (Expression ratio r') of the each effective detection spot obtained thus was scaled as follows: r'=r-m, r=logR(base is 2), R=(Ccy5/Ccy3), m is an average of r of all effective detection spots.

molecule: polyA RNA

source_name: L972, 3hrs after nitorogen starvation

label_protocol: The polyA-RNA (3-6microg) was labeled by CyScribe Post-Labeling Kit (Amasham Pharmacia) with Cy5 with Oligo dT primer.

extract_protocol: Total RNA was isolated by acid phenol methods described in http://www.sanger.ac.uk/PostGenomics/S_pombe/, and then polyA-RNA was purified by Oligotex-dT30<super>mRNA purification kit (Takara).

treatment_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium to grow to 5x(the 6th power of 10)cell/ml at 30°C. After two washes in EMM2-N (EMM2 depleted of nitrogen sources), cells were transferred to EMM2-N and further incubated at 30°C. Cells were collected at each time point after the nitrogen starvation.

tag: L972 h- wild type

source_name: L972, logarithmically growing

label_protocol: The polyA-RNA (3-6microg) was labeled by CyScribe Post-Labeling Kit (Amasham Pharmacia) with Cy3 with Oligo dT primer.

treatment_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium. Cells were collected at 5x(the 6th power of 10)cell/ml at 30｡C.