title: striatum tissue RNA rep 1

description:
processed data file: TRAP_rpkms.txt; ST_IN
ST_IN_GTCCGC_L004

source_name: striatum tissue RNA

extract_protocol:
Microglial RNA was isolated from the unbound fraction of TRAP in the striatum
cDNA was generated using Nugen Ovation V2 kit. Libraries were produced using TruSeq DNA Sample kit. Multiplexed libraries were directly loaded on NextSeq 500 (Ilumina) with High Output single read sequencing for 75 cycles.

value: Striatum tissue


title: striatum single nuclei RNA rep 2

status: Public on Jul 13 2018

type: SRA

city: New York

first: Pinar

last: Ayata

state: New York

address: 1425 Madison Ave

department: Neuroscience

country: USA

institute: Icahn School of Medicine at Mt Sinai

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St50
St_M50_AGGCAGAATAGATCGC_L001

library_source: transcriptomic

data_processing:
Raw sequencing data was processed using Illumina bcl2fastq2 Conversion Software v2.17.
Single end cDNA .fastq files were aligned using STAR (2.4.0a).
Aligned reads were mapped using featureCounts from the subread package (1.4.4)
Negative binomial model was implemented in edgeR (3.10.0) for single cell differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: peaks, RPKM

molecule: total RNA

organism: Mus musculus

source_name: striatum single nuclei RNA

extract_protocol:
Microglial nuclei were isolated using FACS. RNA was obtained from single nuclei using Fluidigm C1™ System
cDNA was prepared suing using SMARTer® Ultra™ Low RNA Kit for the Fluidigm C1™ System. Libraries were constructed using Nextera XT DNA Sample Preparation Kit.

treatment_protocol: Mice were treated with Tamoxifen at 4-6 weeks of age.

tag: strain background

tag: age

tag: genotype/variation

tag: tissue

value: Striatal microglia


title: cbMg TRAP 3mo Eed-ko rep 1

description:
processed data file: TRAP_rpkms.txt; X22_CB_ACAGTG_L001
22_CB_ACAGTG_L001

data_processing:
Raw sequencing data was processed using Illumina bcl2fastq2 Conversion Software v2.17.
Sequences were mapped using the TopHat2 package (v2.1.0)71.
Reads were counted using HTSeq-count (v0.6.0) against the Ensembl v67 annotation.
The read alignment, read counting, and quality assessment were done using SPEctRA.
The raw counts were processed through VST procedure using the DESeq2 package.
Genome_build: mm9
Supplementary_files_format_and_content: peaks, RPKM

source_name: cbMg TRAP 3mo Eed-ko

extract_protocol:
Microglial RNA was isolated from cerebellum using TRAP.
cDNA was generated using Nugen Ovation V2 kit. Libraries were produced using TruSeq DNA Sample kit. Multiplexed libraries were directly loaded on NextSeq 500 (Ilumina) with High Output single read sequencing for 75 cycles.

value: Cerebellar microglia


title: striatum single nuclei RNA rep 19

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St73
St_M73_AGGCAGAATAGATCGC_L001


title: cbMg TRAP 3mo control rep 2

description:
processed data file: TRAP_rpkms.txt; X72_CB_GTGAAA_L001
72_CB_GTGAAA_L001

source_name: cbMg TRAP 3mo control


title: striatum tissue RNA rep 2

description:
processed data file: TRAP_rpkms.txt; ctrl_UB_ST
ctrl_UB_ST_CAGATC_L001


title: cbMg TRAP 3mo control rep 1

description:
processed data file: TRAP_rpkms.txt; X77_CB_GTGAAA_L006
77_CB_GTGAAA_L006


title: stMg TRAP 3mo control rep 2

description:
processed data file: TRAP_rpkms.txt; X77_ST_GTGAAA_L007
77_ST_GTGAAA_L007

source_name: stMg TRAP 3mo control

extract_protocol:
Microglial RNA was isolated from striatum using TRAP.
cDNA was generated using Nugen Ovation V2 kit. Libraries were produced using TruSeq DNA Sample kit. Multiplexed libraries were directly loaded on NextSeq 500 (Ilumina) with High Output single read sequencing for 75 cycles.


title: striatum single nuclei RNA rep 3

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St54
St_M54_TAAGGCGACTCTCTAT_L001


title: cxMg H3K27me3_ChIP

description:
processed data file: H3K27me3 cxMg TSS 1kb.xlsx; K27_MGCX
H3K27_MGCX_NoIndex_L002

library_source: genomic

data_processing:
Raw sequencing data was processed using Illumina bcl2fastq2 Conversion Software v2.17.
Sequences were aligned with Bowtie (v2.2.0)
Only uniquely mapped reads were retained, and the alignments were subsequently filtered using the SAMtools package (v0.1.19)
Peak-calling was performed using MACS (v2.1.1)
Annotation of called peaks and differential regions to their genomic features was performed using region-analysis (v0.1.2)
Genome_build: mm10
Supplementary_files_format_and_content: peaks, RPKM

molecule: genomic DNA

source_name: cxMg H3K27me3_ChIP

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Cortical microglia

tag: chip antibody

value: H3K27me3 (Millipore; 07-449)


title: cxMg ChIP input

description:
processed data file: H3K27me3 cxMg TSS 1kb.xlsx; Input_MGCX
Input_MGCX_NoIndex_L003

source_name: cxMg ChIP input


title: stMg TRAP 3mo Eed-ko rep 1

description:
processed data file: TRAP_rpkms.txt; X24_ST_ACAGTG_L007
24_ST_ACAGTG_L007

source_name: stMg TRAP 3mo Eed-ko


title: stMg TRAP 3mo Eed-ko rep 2

description:
processed data file: TRAP_rpkms.txt; X22_ST_ACAGTG_L005
22_ST_ACAGTG_L005


title: cbMg TRAP 3mo Eed-ko rep 2

description:
processed data file: TRAP_rpkms.txt; X24_CB_ACAGTG_L006
24_CB_ACAGTG_L006


title: stMg TRAP 3mo control rep 1

description:
processed data file: TRAP_rpkms.txt; X72_ST_GTGAAA_L005
72_ST_GTGAAA_L005


title: CRAC, HuD induced cells, rep 3

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

description: processed data file: HuD_RNA_interactome.txt

data_processing:
Library strategy: CRAC-seq
CRAC: adapter removal and collapse of duplicate reads (also with identical random barcode, marking PCR duplicates) were performed with hyb (https://github.com/gkudla/hyb). Reads were aligned to the mouse genome (GRCm38.p4) with Tophat (version 2.0.14), using the Gencode M6 transcript annotation as transcriptome guide. In order to detect CRAC binding sites, we developed and implemented a dedicated computational methodology (MAPAS, standing for Mutation And PWM Assisted Search) that takes advantage of cross-linking induced mutations, consisting primarily in deletions in our experiment, in order to localize candidate binding sites (similar in this step to CIMS, (Zhang and Darnell, 2011). After the integration of replicates, to increase specificity, we penalized locations with aligned reads and deletions in control experiments (noise subtraction and removal). For each of the remaining locations, we calculated a combined p-value based on a) the number of deletions, b) the number of aligned reads (coverage). P-values were empirically calculated from the genome-wide experimental distributions of coverage and number of deletions. Coverage and deletion p-values were combined with the Fisher method.  A pool of 753 sequences surrounding unique genomic locations with a combined p-value < 0.05 were selected to build a PWM (Positional Weight Matrix), hence used as a “seed” matrix to score to all the other candidate binding sites. To create the seed PWM, we defined a region spanning seven nucleotides around the deletion site. PWM analysis was performed with functions implemented in the Biostrings R package. The seed PWM was used to score all deletion sites and select high-confidence HuD bound sites. A PWM score threshold was chosen, based on the 95 percentile of scores obtained from random heptamers. HuD “high confidence” binding sites were selected among those with i) PWM score > PWM score threshold, ii) number of HuD deletions >= 3 (at least one for replicate), iii) number of aligned reads >= 6 (at least two for replicate).    POL-Seq and RNA-Seq: after quality control (FastQC) reads generated from each sample were aligned to the mouse genome (GRCm38.p4) with STAR (version 2.5.3a, --quantMode TranscriptomeSAM GeneCounts), using the Gencode M6 transcript annotation as transcriptome guide. Normalization with the TMM method and identification of genes with altered TE upon HuD overexpression were performed with the edgeR package.    3'end mRNA sequencing: after quality control (FastQC), reads generated from each sample were aligned to the mouse genome (GRCm38.p4) with STAR (version 2.5.3a, --quantMode TranscriptomeSAM GeneCounts), using the Gencode M6 transcript annotation as transcriptome guide. Polyadenylation site usage (pAu) values were determined counting the number of reads starting within 10 nucleotides from known polyadenylation sites. Normalization and differential polyadenylation analysis were performed with the edgeR package.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: HuD_APA_counts.txt: tab-delimited text file including transcript annotations (columns 1-10) and sample-specific counts of aligned reads starting within 10 nucleotides from the polyadenylation site.   HuD_RNA_interactome.txt: tab-delimited text file of HuD bound exonic RNA regions. The file contains the genomic coordinates (columns 1-4), binding analysis and annotation of the regions.  HuD_TOTPOL_counts.txt: tab-delimited text file including gene annotations (columns 1-7) and sample-specific counts of aligned reads.

growth_protocol: NSC-34 cells were grown in DMEM medium with 10% FBS, 100 U/ml penicillin streptomycin and 0.01 mM L-glutamine

extract_protocol:
CRAC: growing cells were UV crosslinked on ice with λ = 254 nm in Stratalinker 1800 (Stratagene). The cells were lysed and treated with DNase (Promega M610A). Cell lysates were incubated with HA agarose beads (26181 Pierce). Ribonucleoprotein complexes on HA beads were trimmed with 0.5 unit RNaseA+T1 mix (RNace-IT, Stratagene 400720-81) and HuD-RNA complexes were eluted. The eluate was incubated with Ni-NTA Agarose (Ni-NTA Superflow 50% suspension IBA 2-3206-010). RNAs bound to HuD were radiolabelled with 32P-γ-ATP and 3′ miRCat-33 linker ligation was performed. Then RNA ligase 1 and barcoded 5′ linker were added and the reaction mixture HuD-RNA complexes were eluted by incubation with NuPage-Eluition buffer. Protein-RNA complexes were resolved on a 4%–12% Bis-TrisNuPAGE gel (Life Technologies, NP0335) in NuPAGE SDS MOPS running buffer (Life Technologies, NP0001) and transferred to nitrocellulose membrane (GE Healthcare, AmershamHybond ECL). Air-dried membrane was exposed on film o.n. and the radioactive bands corresponding to the HuD complexes were cut out.    POL-Seq and RNA-Seq: cells were treated with cycloheximide and then lysed in 300μl of cold lysis buffer. The lysate was centrifuged at 4 °C for 5min at 20.000 g to pellet cell debris. The cytoplasmic lysates loaded on a linear 15–50% [w/v] sucrose gradient and centrifuged in a SW41Ti rotor (Beckman) for 1 h 40 min at 180.000 g at 4 °C in a Beckman Optima™ Optima XPN-100 Ultracentrifuge. Fractions of 1 ml of volume, were then collected monitoring the absorbance at 254 nm with the UA-6 UV/VIS detector (Teledyne Isco). Sucrose fractions corresponding to polysomes and total RNA were pooled together and the RNA was extracted with phenol/chloroform.    3'end mRNA sequencing: RNAs were isolated using Trizol reagent (Life Technologies) following the manufacturer’s instructions.
CRAC: RNA was extracted and reverse transcribed. cDNA was amplified and PCR products were precipitated, resuspended and separated on a 2.5% MetaPhoragarose (Lonza). After purification with Gel Extraction Kit with MinElute columns (QIAGEN) the samples were sequenced on Illumina HiSeq 2000 platform.     POL-Seq and RNA-Seq:  libraries were prepared with the Illumina TruSeq mRNA stranded Kit. Samples were sequenced on Illumina HiSeq 2500 platform.    3'end mRNA sequencing: libraries were prepared with the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit REV. Samples were sequenced on Illumina HiSeq 2500 platform.

treatment_protocol: CRAC: Trex-HuD NSC-34 and control Trex NSC-34 cells were induced for human HuD production with 10 μg/ml Tetracycline for 24 h.   POL-Seq, RNA-Seq and 3'end sequencing: Trex-HuD NSC-34 were induced for human HuD production with 2 μg/ml Tetracycline for 48 h.

tag: cell line

tag: sequencing method

value: CRAC

tag: condition

value: HuD induced


title: CRAC, CTRL cells, rep 3

value: control


title: CRAC, HuD induced cells, rep 2


title: CRAC, HuD induced cells, rep 1


title: CRAC, CTRL cells, rep 2


title: CRAC, CTRL cells, rep 1


title: bovine liver_ISe_biological rep5

type: RNA

city: Lexington

first: James

middle: C

last: Matthews

state: KY - Kentucky

address: 325 Cooper Drive

department: Animal and Food Sciences

institute: University of Kentucky

hyb_protocol: The biotinylated cRNAs were further fragmented and used as probes to hybridize the gene chips in the GeneChip Hybridization Oven 640 (Affymetrix).After hybridization, the chips were washed and stained on a GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The reaction image and signals were read with a GeneChip Scanner (GCS 3000, 7G; Affymetrix)

data_processing:
Data were collected using the GeneChip Operating Software (GCOS, version 1.2; Affymetrix). The raw expression intensity values from the GCOS were imported into Partek Genomics Suite software (PGS 7.17.0918; Partek Inc.). For GeneChip background correction, the algorithm of Robust Multichip Averaging adjusted with probe length and GC oligo contents was implemented. The background-corrected data were further converted into expression values using quantile normalization across all the chips and median polish summarization of multiple probes for each probe set.
BovGene-1_0-st.pgf
BovGene-1_0-st.mps

label: biotin

organism: Bos taurus

source_name: bovine liver, ISe

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Liver collected right after death of each animal

extract_protocol: Liver samples were collected from the mid-lower right lobe and placed in a foil pack, flash-frozen in liquid nitrogen, and stored at -80°C. Total RNA was extracted using TRIzol Reagent following the manufacturer’s instructions.

value: liver

tag: treatment

value: supplemented with sodium selenite


title: Tead1 icKO_biological rep2

city: Pittsburgh

first: Vijay

middle: K.

last: Yechoor

state: PA

address: 200 Lothrop Street, BST 1058W

institute: University of Pittsburgh

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (G48528) 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 by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8X60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 028005_D_F_20110614) to obtain background subtracted, spatially detrended Processed Signal intensities and quantile normalized.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Tead1 icKO_heart ventricle

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNAs were extracted and cleaned up using RNeasy Mini Kit (QIAGEN) according to manufacturer’s protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Heart ventricle tissues were excised from each mouse.

tag: genotype/background

value: inducible Tead1 icKO (Tead1F/F; Myh6-CreER)

tag: gender

value: male

value: Heart ventricle tissue


title: stMg ChIP input

data_processing:
Sequences were aligned with Bowtie (v2.2.0)
Only uniquely mapped reads were retained, and the alignments were subsequently filtered using the SAMtools package (v0.1.19)
Peak-calling was performed using MACS (v2.1.1)
Annotation of called peaks and differential regions to their genomic features was performed using region-analysis (v0.1.2)
Genome_build: mm9
Supplementary_files_format_and_content: peaks, RPKM

source_name: Striatal microglia

tag: antibody

value: none (input)


title: stMg H3K27me3 ChIP


title: bovine liver_OSe_biological rep4

source_name: bovine liver, OSe

value: supplemented with SEL-PLEX


title: bovine liver_ISe_biological rep6


title: cbMg ChIP input

source_name: Cerebellar microglia


title: bovine liver_ISe_biological rep1


title: bovine liver_ISe_biological rep3


title: bovine liver_ISe_biological rep2


title: Tead flox_biological rep1

source_name: Tead flox_heart ventricle

value: control; Tead1 flox


title: bovine liver_OSe_biological rep7


title: Tead flox_biological rep3


title: bovine liver_OSe_biological rep8


title: bovine liver_OSe_biological rep5


title: bovine liver_ISe_biological rep4


title: Tead1 icKO_biological rep1


title: Tead1 icKO_biological rep3


title: Tead flox_biological rep2


title: fog2_10036

city: Philadelphia

first: Colin

last: Conine

state: Pennsylvania

address: 421 Curie Blvd BRB 1213

department: Genetics and Neonatology

institute: UPenn Perelman SOM and CHOP

data_processing:
Reads were aligned to ce11 RefSeq using Bowtie software in a sequencial manner first to rRNAs to eliminate any reads coming from them and then aligned to the genome using RSEM. During RSEM duplicated reads were removed.
Genome_build: ce11 ws245
Supplementary_files_format_and_content: excel sheet with normalized gene counts

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: Animals were passaged by bleaching gravid worms and directly plating 125,000 eggs mixed with E. coli OP50 (washed and resuspended in M9 buffer to 0.33 mg/mL), therefore worms never experience starvation under these conditions. Strains were maintained on 150 x 15 mm petri dishes that contained standard nematode growth media (NGM) with modification [10g agarose + 7g agar instead of 17g agar]. Gravid animals were washed from plates with M9 buffer, collected in conical tubes and centrifuged at 2000 x g for 30 seconds. Next, the supernatant was removed and worms were treated with 10 mL of bleach solution [41:6:3 ddH2O, sodium hypochlorite (Fisher Chemical, SS290-1), 5M KOH, and kept on a rocking platform. Worms were spun down after 4 minutes and the supernatant was replaced with fresh bleach. This procedure was repeated one more time and the suspension was visually checked to ensure all worm bodies were dissolved. The suspension was centrifuged at 2000 x g for 30 seconds, bleach solution was removed, and embryos were washed with M9 buffer supplemented with PEG 3350 (0.5%, w/v) three times before use. In this study, M9 buffer was always supplemented with PEG 3350 (0.5%, w/v) unless noted otherwise. The density of embryos in M9 were determined by manual counting.

extract_protocol:
Single L1 animals were placed in 5 ul of a typical worm lysis buffer (40mM Tris pH7.5, 10mM EDTA, 200mM NaCl, 0.5% SDS, and 0.4ug/ul Proteinase K), incubated at 55° for 10 minutes, and then frozen at -20°C until use for RNA-sequencing.
single-L1 RNA-seq/Nextera kit

treatment_protocol: For L1s arrested at different densities eggs were reconsititued at 1, 5, 20, or 100 eggs/ul of M9 and hatched/arrested overnight.

tag: developmental stage

value: L1 larvae

tag: strain

tag: l1 arrest density

value: 100 egg/ul


title: fog2_10038


title: fog2_10037


title: bovine liver_OSe_biological rep6


title: bovine liver_OSe_biological rep3


title: fog2_10035


title: fog2_10032


title: fog2_10027


title: fog2_10031


title: fog2_10026


title: fog2_10024


title: bovine liver_OSe_biological rep1


title: cbMg H3K27me3 ChIP


title: fog2_10023


title: fog2_10025


title: fog2_10022


title: bovine liver_MIX_biological rep6

source_name: bovine liver, MIX

value: supplemented with 1:1 blend of sodium selenite and SEL-PLEX


title: fog2_10021


title: bovine liver_OSe_biological rep2


title: fog2_10034


title: fog2_10033


title: fog2_10018


title: fog2_10017


title: bovine liver_MIX_biological rep3


title: bovine liver_MIX_biological rep2


title: bovine liver_MIX_biological rep7


title: fog2_10016


title: bovine liver_MIX_biological rep4


title: fog2_10028


title: bovine liver_MIX_biological rep1


title: fog2_10014


title: fog2_10015


title: bovine liver_MIX_biological rep5


title: fog2_10012


title: Dorsal_Hippocampus_Male_Stress_14_Days_Rep 3

city: Independencia

first: Wladimir

middle: Antonio

last: Corrales

address: Olivos 1007

department: Biochemistry and Molecular Biology

country: Chile

institute: Universidad de Chile

description: RNA < 200 nt

hyb_protocol: Each sample was then hybridized under standardized conditions (16 h at 48°C) in a hybridization oven (Affymetrix) and array slides were stained with streptavidin/phycoerythrin and washed according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip® Operating Software (AGCC; Version 3.2).

data_processing: To analyze the microarray datasets, two tools were utilized: 1) Differential Expression Analysis using LIMMA-Bioconductor with R software (www.rproject.org) and 2) the Analysis in Partek® Genomics Suite™ (Partek, Inc., St. Louis, MO, USA). For both tools, a single log scale normalized expression measure was obtained for each probe set after background correction and normalization between samples with RMA algorithm. In order to evaluate the quality of the microarray data and to identify any unusual data in the array slides, several plots (Box plots, density plots, MA plots) were generated for both raw and normalized data. For the method based in R software, the statistical significance P value of the log ratio for each probe was determined by a modification of the standard t-test by using an empirical Bayesian approach. For Partek, analysis of variance (ANOVA) was used to identify differentially expressed probes. Probes that had P< 0.05 were considered to be differentially expressed between experimental groups and controls. Among the significant probes, only rat miRNA probes were kept. To further refine the selection of significant genes, common significant genes found with the two biostatistical tools were used for downstream analysis. Heat maps were generated using BioConductor package HeatPlus. Dendrograms of samples (columns) and genes (row) were generated by hierarchical clustering. Color scale was from 3-fold lower (log2-fold= -1.585) than the mean (blue) to 3-fold higher (log2-fold= 1.585) than the mean (red).

organism: Rattus norvegicus

source_name: dorsal hippocampus

label_protocol: Purified RNAs (< 200 nt) were labeled using the Affymetrix FlashTagTMBiotin HSR kit, according to the manufacturer’s protocol

extract_protocol: The dorsal hippocampi relative to bregma -3.10 to -4.44 mm coordinates (Paxinos, 1982) were rapidly dissected at 4°C and frozen under liquid N2 and kept at -80°C until processing for RNA isolation and protein extract. Purified RNAs from dorsal hippocampi of the rat were isolated as we have previously described (Castaneda et al., 2015) by using the RNeasy Mini Kit, that allows the separation of RNAs according to their size (RNAs <200 nt and >200 nt). RNA concentration and purity were determined at OD260/280 and samples with an absorbance ratio between 1.8 and 2.0 were chosen. RNA integrity was evaluated by nondenaturing agarose gel electrophoresis

treatment_protocol: Prior to the experimental procedures, rats were handled once per day for a one-week period, during the light phase of the photoperiod cycle. In the case of the stress experimental group, the rats were housed in a group of 3-4 rats and maintained in the experimental room. The stress procedure was conducted between 9:00 and 12:00, as previously reported (Pacheco et al., 2017). In brief, the rats were introduced in transparent acrylic tubes (25 x 8 cm) during 2.5 h during 7 days (n=9) or 14 days (n=17). During the restraint, animals were placed in a cage in groups of 3-4 rats. After this procedure, the stressed group of animals was placed in the home cage with new bedding.

tag: Sex

value: stress, 14 days

value: adult

value: two months old

value: dorsal hippocampus


title: Dorsal_Hippocampus_Male_Stress_14_Days_Rep 4

description: RNA < 200 nt


title: fog2_10013


title: fog2_2036

value: 20 egg/ul


title: fog2_10011


title: fog2_2038


title: fog2_2033


title: fog2_2035


title: Dorsal_Hippocampus_Male_Stress_14_Days_Rep 2

description: RNA < 200 nt


title: fog2_2031


title: fog2_2028


title: Dorsal_Hippocampus_Male_Stress_14_Days_Rep 1

description: RNA < 200 nt


title: fog2_2027


title: fog2_2024


title: Dorsal_Hippocampus_Male_Stress_7_Days_Rep 1

description: RNA < 200 nt

value: stress, 7 days


title: fog2_2026


title: fog2_2025


title: Dorsal_Hippocampus_Male_Control_Rep 3

description: RNA < 200 nt

value: control


title: fog2_2023


title: Dorsal_Hippocampus_Male_Stress_7_Days_Rep 2

description: RNA < 200 nt


title: fog2_2022


title: fog2_2037


title: fog2_2021


title: Dorsal_Hippocampus_Male_Control_Rep 2

description: RNA < 200 nt


title: Dorsal_Hippocampus_Male_Stress_7_Days_Rep 3

description: RNA < 200 nt


title: fog2_2017


title: Dorsal_Hippocampus_Male_Control_Rep 1

description: RNA < 200 nt


title: fog2_2012


title: fog2_2013


title: fog2_2015


title: fog2_538

value: 5 egg/ul


title: fog2_2011


title: fog2_536


title: fog2_537


title: fog2_535


title: fog2_533


title: fog2_532


title: fog2_2016


title: fog2_531


title: fog2_527


title: fog2_528


title: Gr1lo monocytes, no latex beads, rep2

city: Saint Louis

first: Gwendalyn

last: Randolph

state: MO

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

description:
Gr1lo_no_latex_2
mRNA

hyb_protocol: Hybridization was performed as previously described (Grabner et al., 2009). Microarray was performed on an Affymetrix GeneChip 430 2.0.

scan_protocol: Chip scanning was performed as previously described (Grabner et al., 2009).

data_processing: R packages 'oligo' and 'limma' were used to read, normalize by rma function (log2-scale), access QC and perform DE from the microarray expression data. Gene set enrichment analysis with 'fgsea' package was used to identify pathway enrichments in hallmark and canonical pathways. Benjamini-Hochberg correction was used to correct p-value for multiple comparisons.

source_name: blood monocytes

label_protocol: RNA amplification and direct labeling were performed as previously described (Grabner et al., 2009).

extract_protocol: RNA was extracted from sorted cells by TRIzol and RNeasy mRNA isolation kit (Qiagen).

treatment_protocol: Classical Ly-6C hi monocytes were labeled with beads 3 days after intravenous injection of 250 μl clodronate-loaded liposomes (clodronateliposomes.org). 1 μm Fluoresbrite green fluorescent (YG) plain microspheres (Polysciences Inc., Warrington, PA) diluted 1:4 in sterile PBS were administered i.v. Nonclassical Ly-6C lo monocytes were labeled with beads similarly, but without the use of clodronate-loaded liposomes (Potteaux et al., 2011). Labeling efficiency of blood monocytes was verified by flow cytometry 1 day after labeling.

tag: strain/background

tag: cell type

value: Gr1 low monocytes

value: no latex beads


title: fog2_526


title: fog2_525


title: fog2_521


title: fog2_523


title: fog2_522


title: Gr1lo monocytes, with latex beads, rep2

description:
Gr1lo_latex_2
mRNA

value: male

value: with latex beads


title: Gr1hi monocytes, no latex beads, rep2

description:
Gr1hi_no_latex_2
mRNA

value: Gr1 high monocytes


title: Gr1lo monocytes, no latex beads, rep1

description:
Gr1lo_no_latex_1
mRNA


title: fog2_518


title: Gr1hi monocytes, no latex beads, rep1

description:
Gr1hi_no_latex_1
mRNA


title: fog2_517


title: Gr1hi monocytes, with latex beads, rep2

description:
Gr1hi_latex_2
mRNA


title: Gr1hi monocytes, with latex beads, rep1

description:
Gr1hi_latex_1
mRNA


title: fog2_516


title: MCF7_RNAseq

description: transcriptome profiling of MCF-7 cells

data_processing:
For RIBO-seq data, Raw reads were processed by removing 5’ adapters, discarding reads shorter than 20 nucleotides and trimming the first nucleotide (using Trimmomatic v0.36). Reads mapping on rRNAs and tRNAs (downloaded from the SILVA rRNA and the Genomic tRNA databases respectively) were removed. RIBO-seq and RNA-seq reads were aligned to the human transcriptome (Ensembl v81, corresponding to GENCODE 23) with Bowtie2 (v2.2.6) employing the default settings. All reads aligning to the very same region were collapsed to avoid potential PCR duplicates, and only strand-specific reads were kept. The number of reads was determined with samtools idxstats.
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: MCF7_count_table.txt: tab-delimited text file including transcript annotation (columns 1-8) and sample-specific counts of aligned reads

organism: Homo sapiens

source_name: MCF-7 cells, transcriptome profiling (RNA_seq)

growth_protocol: MCF-7 breast carcinoma cells were uses in the study.

extract_protocol:
Total RNA was extracted from cytoplasmic lysates with acid-phenol:chloroform:isoamylalcohol and isopropanol precipitation and ribosomal RNA was removed with Ribo-Zero rRNA Removal Kit (Illumina): Libraries were prepared using the TruSeq RNA Library Prep Kit (Illumina) following the manufacturer's instructions.
Cells (1.5 x 10^6) were seeded in 10 cm cell culture dishes and kept in culture until reaching 80% confluency. Prior to lysis, cycloheximide (10 μg/mL) was added to the culture that was incubated in this condition at 37°C for 4 min. The dishes were then rinsed with ice cold PBS supplemented with 10 μg/ml cycloheximide and lysated with 150 μl of polysomes lysis buffer (10 mM NaCl, 10 mM MgCl2, 10 mM, TRIS/HCl-pH 7.5, 1% Triton X-100, 2 U/μl RNAse inhibitor, 1M DTT, 1% Na deoxycholate). The lysates were incubated for 5’ in ice, vortexed and centrifuged for 5’ at 14.000rpm at 4°C to precipitate cellular debris, nuclei and mitochondria. The supernatants have been stored at -80°C before the libraries preparation.

treatment_protocol: Cells were maintained in culture at 37°C with 5% of CO2 in Dulbecco’s Modified Eagle’s Medium (DMEM) with 4.5 g/l glucose supplemented with 2 mM glutamine, 10% Fetal Bovine Serum, 100 U/ml penicillin e 100 mg/ml streptomycin.

tag: rna fraction

value: cytoplasmic RNA


title: fog2_515

value: L1 larvae


title: fog2_514


title: fog2_513


title: MCF7_RIBOseq

description: ribosome profiling of MCF-7 cells

source_name: MCF-7 cells, ribosome profiling (RIBO_seq)

extract_protocol:
Cytoplasmic lysates were digested with 5 Units of ARTseq Nuclease for each A260 of lysate at room temperature for 45 minutes. The RNA was treated with Ribo-Zero rRNA Removal Kit (Illumina) to remove ribosomal RNA contamination and the Ribosome Protected Fragments (RPFs) were then extracted with acid-phenol:chloroform:isoamylalcohol and isopropanol precipitation and size seNGS libraries were prepared starting from RPFs using the ARTseq Ribosome Profiling Kit – Mammalian (Epicentre) following the standard protocol.
Cells (1.5 x 10^6) were seeded in 10 cm cell culture dishes and kept in culture until reaching 80% confluency. Prior to lysis, cycloheximide (10 μg/mL) was added to the culture that was incubated in this condition at 37°C for 4 min. The dishes were then rinsed with ice cold PBS supplemented with 10 μg/ml cycloheximide and lysated with 150 μl of polysomes lysis buffer (10 mM NaCl, 10 mM MgCl2, 10 mM, TRIS/HCl-pH 7.5, 1% Triton X-100, 2 U/μl RNAse inhibitor, 1M DTT, 1% Na deoxycholate). The lysates were incubated for 5’ in ice, vortexed and centrifuged for 5’ at 14.000rpm at 4°C to precipitate cellular debris, nuclei and mitochondria. The supernatants have been stored at -80°C before the libraries preparation.


title: fog2_512


title: Gene Expression in Atxn3-KO MEFs Replicate 1

city: Ann Arbor

first: Henry

middle: L

last: Paulson

state: MI

address: 1500 E Medical Center Dr

department: Department of Neurology

institute: University of Michigan

hyb_protocol: Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: Data was analyzed using the limma and affy bioconductor packages implemented in the R-statistical environment version 2.12.0. RMA was used to fit log2 transformed expression values

label_protocol: Biotinylated aRNA were prepared according to the Ambion Premier kit protocol from 250 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion)

extract_protocol: RNA was isolated using RNeasy mini Kits (Qiagen, Valencia, CA)

tag: genotype/variation

value: MEF


title: fog2_511


title: Gene Expression in Atxn3-WT MEFs Replicate 3


title: Gene Expression in Atxn3-KO MEFs Replicate 3


title: DY11T3 (re-do from batch1)

city: Stanford

first: Dian

last: Yang

address: B261 Beckman Center, 1291 Welch Rd.

institute: Stanford University

data_processing:
We used Kallisto (Bray et al. 2016) to quantify expression. We kept only transcripts with max TPM value greater than 1 in at least one sample and with standard deviation greater than 1.
We performed the asinh() transformation to variance stabilize the data.
We used SVA (Leek & Storey 2007) to remove batch effects from the data.
fit a linear model (lmFit in R) modeling metastatic effect
rank genes in order of evidence for differential expression using an empirical Bayes method. We only compared genes with non-zero variance.
Genome_build: mm10
Supplementary_files_format_and_content: CMV_samples_TPM_pre_Merge.txt (Batch1_CMV TKO tumor samples TPM)
CGRP _samples_TPM_pre_Merge.txt (Batch2_CGRP TKO tumor samples TPM)
comp1_CMV_primary_v_CMV_met_data_corrected_no_sva_top_hits.txt (CMV_primary_tumor_vs_CMV_metastasis)
comp2_CMV_primary_v_CGRP_primary_data_corrected_no_sva_top_hits.txt (CMV_primary_tumor_vs_CGRP_primary_tumor)
comp3_CMV_primary_v_CGRP_all_data_corrected_no_sva_top_hits.txt (CMV_primary_tumor_vs_CGRP_all_tumors(primary+met))
comp4_CGRP_primary_tumor_vs_coo_metastasis_data_corrected_no_sva_top_hits.txt (CGRP_primary_v_CGRP_met)

source_name: primary tumor from the CMV TKO model (re-do from batch1)

growth_protocol: All murine SCLC samples are prepared fresh from tumor bearing mice

extract_protocol:
Qiagen Allprep DNA/RNA kit
[Reverse transcription and amplification protocol] Nugen Ovation v2 kit
Illumina TruSeq v2 kit

tag: tissue

value: liver metastasis

tag: genotype

tag: expression vector

value: Ad-CMV-Cre


title: Gene Expression in Atxn3-WT MEFs Replicate 1


title: Gene Expression in Atxn3-KO MEFs Replicate 2


title: fog2_148

value: 1 egg/ul


title: fog2_145


title: DY53L1 (re-do from batch1)

source_name: liver metastasis from the CMV TKO model (re-do from batch1)

value: lung tumor


title: fog2_151


title: fog2_142


title: G6L3

source_name: liver metastasis from the CGRP TKO model

value: Ad-CGRP-Cre


title: fog2_139


title: DY4T1 (re-do from batch1)


title: fog2_133


title: fog2_130


title: Wild type Brain

city: Iowa City

first: Brad

last: Amendt

state: Iowa

address: 100 Bowen Science Building

department: Anatomy and Cell Biology

institute: University of Iowa

description: Gene expression data from tissue of wild type brain

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Algorithm: ExpressionStat 5.0

source_name: Wild type Brain

label_protocol: Standard Affymetrix protocol

growth_protocol: All mice were housed at the University of Iowa, Program of Animal Resources and were handled in accordance with the principles and procedures specified in the Guide for the Care and Use of Laboratory Animals.

extract_protocol: miRNeasy Mini Kit from Qiagen was used to extract RNA from mouse tissues.

treatment_protocol: Mouse heads were dissected in phosphate-buffered saline (PBS),  brain, mandible and maxilla tisuse were manually seperated using scissors.

value: Brain

tag: age

value: postnatal Day 0

value: Wild type


title: Wild type Mandible & Maxilla

description: Gene expression data from tissue of wild type mandible and Maxilla

source_name: Wild type Mandible & Maxilla

value: Mandible & Maxilla


title: Gr1lo monocytes, with latex beads, rep1

description:
Gr1lo_latex_1
mRNA

value: Gr1 low monocytes

tag: condition


title: Gene Expression in Atxn3-WT MEFs Replicate 2


title: leukocytes_Se-adeq_replicate 11

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description:
Se-adeq_repl11
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturer's procedure using 2x Hybridization buffer (Agilent). Samples were applied to 44K microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 60C for 17 hours at 4rpm rotation. After hybridization, slides were washed sequentially with a SSPE wash procedure according to Agilent's recommendations.

scan_protocol: Scanned with a ScanArray Express HT scanner (Perkin Elmer).

data_processing: Images were quantified using ArrayVision 8.0 (GE Healthcare life sciences). Median density values and median background values of each spot were extracted for both the experimental samples (Cy5) and the reference pool samples (Cy3). Subsequently, quality control was performed for each microarray based on raw data and all arrays passed. Spots with a mean signal higher than twice the background value over all arrays and both channels were considered to be expressed. Data was normalized according to Pellis et al. (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

source_name: splenic leukocytes

label_protocol: 500 ng of purified individual total RNA was used for cDNA synthesis, split in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent linear amplification protocol, as described previously by van Schothorst et al. (Anal Biochem 2007;363:315-7). All Cy3-labeled samples were used for the reference pool.

extract_protocol: Total RNA was isolated from whole cell pellets of splenic leukocytes suspended in 800 μl of cold Trizol (Invitrogen, Karlsruhe, Germany) and homogenized with a TissueLyser (Qiagen, Hilden, Germany) and RNeasy Mini kit (Qiagen), quantified using Nanodrop (IsoGen Life Science) and qualified using Bioanalyzer 2100 (Agilent). All samples had a RIN-number above 9.0.

treatment_protocol: Male C57BL/6J mice (3–4 wk of age) from Charles River (Sulzfeld, Germany) were randomly assigned to the selenium-deficient or selenium-adequate group (12 mice per group) with free access to food and water. The selenium-adequate diet (Se-adeq) was produced by mixing selenomethionine (Acros, Geel, Belgium) into the selenium-deficient diet (Se-def; No. C1045 with 50% carbohydrates, 17% protein, 5% fat, 4% fibre, and mixture of micronutrients; Altromin, Lage, Germany) containing 0.086mg Se/kg (Riese et al., Endocrinology 2006) to yield a selenium content of 0.15 mg/kg corresponding to the dietary reference intake for mice. Diets were fed as powder for 6wk until mice were killed in the non-fasted state. Animals were anesthetized with isofluran and blood with heparinized capillaries by puncture of the retroorbital plexus. Anesthetized animals were killed by cervical dislocation. Spleens were removed aseptically, placed on a sterile microscope slide and crushed with the end of a 6-ml syringe plunger. Released cells were diluted in 5ml of cell culture medium (RPMI with 5% fetal calf serum; Gibco, Karlsruhe, Germany). Clumps were dispersed by drawing and expelling the suspension repeatedly through a 6-ml syringe with a 20-gauge needle. A 100-μmmesh was used to remove clumps and particles and to receive a single cell suspension. The mesh was rinsed with 5 ml RPMI. After centrifugation (5 min, 200g) and washing with 10 ml RPMI, erythrocytes were lysed for 5 min in 5 ml of ammonium chloride lysis buffer (0.15 mol/L NH4Cl, 10 mmol/L KHCO3, 0.1 mmol/L Na2EDTA, pH 7.4). Thereafter, 15 ml of balanced salt solution containing 0.2% bovine serum albumin was added, and the suspension was centrifuged for 5 min at 200g. The pellet was suspended in 1 ml phosphate-buffered saline (PBS) and transferred into a 2-ml tube. Thirty microliters of the suspension was smeared on microscope slides and dried on air for counting. The cells of the remaining suspension were pelleted (5 min, 200g) and washed with 1 ml PBS. The pellet was frozen at−80°C until RNA isolation. As determined with May–Grünwald–Giemsa staining, the leukocyte population was independent of the selenium status and on average was composed of 79% lymphocytes, 18% granulocytes and 2% monocytes.

value: 9 or 10 weeks

value: splenic leukocytes

tag: treatment

value: selenium-adequate diet

value: mix of selenium-deficient and selenium-adequate diets


title: fog2_136


title: G6L2


title: FoxO6-/- Mandible & Maxilla

description: Gene expression data from tissue of FoxO6-/- mandible and Maxilla

source_name: FoxO6-/- Mandible & Maxilla

value: FoxO6 -/-


title: fog2_127

value: L1 larvae


title: G6L1


title: G6T2

source_name: primary tumor from the CGRP TKO model


title: fog2_124


title: fog2_118


title: fog2_121


title: fog2_115


title: FoxO6-/- Brain

description: Gene expression data from tissue of FoxO6-/- brain

source_name: FoxO6-/- Brain


title: leukocytes_Se-adeq_replicate 09

description:
Se-adeq_repl09
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: male


title: G6T1


title: leukocytes_Se-adeq_replicate 08

description:
Se-adeq_repl08
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: N2-10038

value: 100 egg/ul


title: leukocytes_Se-adeq_replicate 12

description:
Se-adeq_repl12
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: leukocytes_Se-adeq_replicate 07

description:
Se-adeq_repl07
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: G3L3

value: liver metastasis


title: N2-10037


title: N2-10036


title: G3L2


title: N2-10033


title: N2-10034


title: N2-10035


title: G3T2


title: N2-10031


title: leukocytes_Se-adeq_replicate 04

description:
Se-adeq_repl04
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: leukocytes_Se-adeq_replicate 05

description:
Se-adeq_repl05
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: leukocytes_Se-adeq_replicate 06

description:
Se-adeq_repl06
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: G2L2


title: leukocytes_Se-adeq_replicate 10

description:
Se-adeq_repl10
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: N2-10027


title: fog2_112

value: 1 egg/ul


title: G2L1


title: N2-10026


title: leukocytes_Se-adeq_replicate 02

description:
Se-adeq_repl02
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: N2-10025


title: N2-10024


title: G2T2

value: lung tumor


title: N2-10023


title: N2-10022


title: N2-10021


title: leukocytes_Se-adeq_replicate 03

description:
Se-adeq_repl03
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: leukocytes_Se-adeq_replicate 01

description:
Se-adeq_repl01
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: G2T1

value: Ad-CGRP-Cre


title: G1T2


title: N2-10018


title: N2-10028


title: N2-10017


title: G1T1


title: N2-10016


title: N2-10015


title: N2-10014


title: leukocytes_Se-def_replicate 11

description:
Se-def_repl11
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: selenium-deficient diet


title: leukocytes_Se-def_replicate 08

description:
Se-def_repl08
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: N2-10013


title: leukocytes_Se-def_replicate 10

description:
Se-def_repl10
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: N2-10012


title: N2-10011


title: leukocytes_Se-def_replicate 06

description:
Se-def_repl06
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: leukocytes_Se-def_replicate 04

description:
Se-def_repl04
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: leukocytes_Se-def_replicate 05

description:
Se-def_repl05
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: leukocytes_Se-def_replicate 09

description:
Se-def_repl09
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: N2-2038

value: 20 egg/ul


title: leukocytes_Se-def_replicate 07

description:
Se-def_repl07
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: N2-2037


title: leukocytes_Se-def_replicate 03

description:
Se-def_repl03
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: N2-2035


title: leukocytes_Se-def_replicate 02

description:
Se-def_repl02
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: leukocytes_Se-def_replicate 12

description:
Se-def_repl12
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Healthy donor 1 CD40L

city: Darlinghurst

first: Stuart

last: Tangye

state: NSW

address: 384 Victoria St

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

description: RNA from normal transitional B cells stimulated with CD40L alone

hyb_protocol: 3 µg fragmented, biotin labelled ss-cDNA was hybridised to Affymetrix Human Gene Array version 2.1ST. Samples were hybridised to arrays for 16 hours at 45°C in the Affymetrix GeneTitan Instrument

scan_protocol: Arrays were washed and scanned on the Affymetrix GeneTitanand Affymetrix GC3000 scanner instrument as per manufacturers protocol

data_processing: Bioconductor packages implemented in the R statistical computing environment, version 3.4.1.  The file normalized_data_with_all_control_probesets.txt contains the log2 RMA data for all probe sets including control probe sets. The sample data tables include a subset of the control probe sets found on platform GPL23159.

source_name: transitional B cells from normal donors

label_protocol: 1 ng of total RNA was used as input for the amplification and labelling of samples using the Affymetrix WT Pico Kit

growth_protocol: Human transitional B cells were cultured in RPMI1640 containing 10% FCS for 4 days

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: B cells were stimulated with recombinant CD40 ligand alone or together with IL-21 (50 ng/mL)

value: transitional B cells

tag: diagnosis

value: healthy/normal


title: Healthy donor 3 CD40L/IL21

description: RNA from normal transitional B cells stimulated with CD40L + IL-21


title: N2-2032


title: WT5_L004

city: Los Angeles

first: Xia

address: 610 Charles E. Young Drive East

institute: UCLA

data_processing:
HISAT was used to align the RNA-Seq reads against the Rattus norvegicus genome to discover the locations from which the reads originated and to determine the transcript sites.
StringTie was used to assemble the RNA-seq alignments into potential transcripts.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) for each transcript were obtained by Ballgown tool and used as the expression measure.
Genome_build: UCSC version rn6
Supplementary_files_format_and_content: Transcription abundances in terms of the FPKM measure of the expressed transcripts in each sample were obtained by using Ballgown R tool.

source_name: Hypothalamus

growth_protocol: Twenty-four Male Sprague–Dawley rats (Charles River Laboratories, Inc., Wilmington, MA) approximately 2 months old were housed in polyacrylic cages and maintained under standard housing conditions (room temperature 22–24C) with 12 h light/dark cycle. All experiments were performed in accordance with the United States National Institutes of Health Guide for the Care and Use of Laboratory Animals. The animal studies and experimental procedures were approved by the University of California at Los Angeles Chancellor's Animal Research Committee (ARC).

extract_protocol:
RNA was extracted from hypothalamus tissue using Qiagen AllPrep DNA/RNA mini kit.
Libraries were constructed according to instructions of TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold kit.

treatment_protocol: All animals were subjected to either sham or fluid percussion injury (FPI). After 1 week of injury animals were tested for glucose tolerance (GTT) and were sacrificed immediately by decapitation. Body weight, food intake, water intake and calorie intake were measured throughout the study.

value: Male

value: Sprague-Dawley

value: TBI


title: leukocytes_Se-def_replicate 01

description:
Se-def_repl01
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

tag: gender

value: 9 or 10 weeks

value: splenic leukocytes


title: PIK3CD patient 1 CD40L/IL21

description: RNA from PIK3CD GOF transitional B cells stimulated with CD40L + IL-21

source_name: transitional B cells from PIK3CD GOF patients

value: PIK3CD GOF (APDS)


title: PIK3CD patient 1 CD40L

description: RNA from PIK3CD GOF transitional B cells stimulated with CD40L


title: PIK3CD patient 2 CD40L/IL21


title: Healthy donor 4 CD40L/IL21


title: WT5_L003


title: Healthy donor 2 CD40L/IL21


title: colon_Se-def_replicate 12

source_name: colon

extract_protocol: Colon tissue was ground under liquid nitrogen. In total, 20–30mg powder were suspended in 800 mL of cold Trizol (Invitrogen, Karlsruhe, Germany), homogenized with a tissue lyzer (Qiagen, Hilden, Germany), and RNA isolated using the Trizol protocol and RNeasy mini columns (Qiagen). RNA was quantified using Nanodrop (IsoGen Life Science) and qualified using Bioanalyzer 2100 (Agilent). All samples had a RIN-number of at least 9.0.

treatment_protocol: Male C57BL/6J mice (3–4 wk of age) from Charles River (Sulzfeld, Germany) were randomly assigned to the selenium-deficient or selenium-adequate group (12 mice per group) with free access to food and water. The selenium-adequate diet was produced by mixing selenomethionine (Acros, Geel, Belgium) into the selenium-deficient diet (No. C1045 with 50% carbohydrates, 17% protein, 5% fat, 4% fibre, and mixture of micronutrients; Altromin, Lage, Germany) containing 0.086mg Se/kg (Riese et al., Endocrinology 2006) to yield a selenium content of 0.15 mg/kg corresponding to the dietary reference intake for mice. Diets were fed as powder for 6wk until mice were killed in the non-fasted state. Animals were anesthetized with isofluran and blood was withdrawn from the retro-orbital plexus. Anesthetized animals were killed by cervical dislocation. Plasma and tissues freeze clamped in liquid nitrogen were stored at -80C.

value: colon

value: mix of selenium-deficient and selenium-adequate diets

tag: sample type

value: reference pool


title: PIK3CD patient 3 CD40L/IL21


title: colon_Se-def_replicate 11

value: male


title: N2-2028

source_name: L1 larvae

tag: developmental stage

value: L1 larvae


title: N2-2031

tag: strain


title: patient 436

type: genomic

city: Amsterdam

first: Fleur

last: Peters

address: Meibergdreef 9

institute: Amsterdam UMC (AMC)

hyb_protocol: Isolated genomic DNA (500 ng) was treated with sodium bisulphite using the EZ-96 DNA methylation kit (Zymo Research, Irvine, CA, USA). Hybridization was performed following manufacturer’s instructions. DNA methylation of CpGs was measured by the Illumina HumanMethylation450K BeadChip using the manufacturer’s protocol (Illumina, Inc., San Diego, CA, USA).

scan_protocol: Array was scanned using the iScan BeadChip scanner according to Illumina protocol.

data_processing: All data pre-processing and statistical analysis were performed in R software version 3.2.5. Raw methylation data was normalized with lumi (Bioconductor R) to account for differences between the type I and type II intensities. The data quality was examined using the Methylaid package and all samples passed the five quality controls using the default Methylaid thresholds. Probes with a detection p-value below 0.01 were removed from the dataset. Also probed on sex chromosomes were removed since our patient group was a mixture of male and female.

label: Cy5 and Cy3

source_name: T cells

label_protocol: Standard Infinium Methylation array protocol.

extract_protocol: Genomic DNA was extracted using a Qiagen QIAamp Micro kit according to the manufacturer's protocol.

treatment_protocol: Flow cytometry assisted cell sorting of the T cells from peripheral blood mononuclear cells.

tag: patient

value: T cells

tag: timepoint

value: Post-transplantation

tag: future cscc

value: No

tag: current cscc


title: WT5_L002

tag: Sex


title: WT4_L004


title: N2-2027

tag: l1 arrest density

value: 20 egg/ul


title: colon_Se-def_replicate 09

tag: strain/background

tag: tissue

value: selenium-deficient diet


title: WT4_L003


title: WT4_L002


title: patient 435

tag: cell type


title: patient 432

tag: age


title: N2-2025


title: patient 433


title: colon_Se-adeq_replicate 12

description:
Se-adeq_repl12
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: selenium-adequate diet


title: patient 438

value: Male


title: patient 428


title: N2-2026


title: WT3_L004

value: Sprague-Dawley


title: colon_Se-def_replicate 08


title: WT3_L003

value: TBI


title: N2-2023


title: N2-2022


title: patient 425

value: Female


title: colon_Se-adeq_replicate 10

description:
Se-adeq_repl10
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: 9 or 10 weeks


title: patient 429


title: colon_Se-adeq_replicate 11

description:
Se-adeq_repl11
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: patient 426


title: colon_Se-def_replicate 07


title: patient 420


title: patient 421


title: N2-2021


title: WT2_L004


title: WT2_L003


title: N2-2018


title: WT2_L002


title: colon_Se-adeq_replicate 08

description:
Se-adeq_repl08
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: N2-2012


title: WT1_L004


title: patient 434


title: N2-2011


title: colon_Se-def_replicate 06

description:
Se-def_repl06
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: patient 416


title: WT1_L003


title: patient 419


title: N2-538

value: 5 egg/ul


title: colon_Se-adeq_replicate 09

description:
Se-adeq_repl09
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: colon


title: patient 412


title: patient 408


title: N2-537


title: WT1_L002


title: patient 418


title: N2-536


title: SW6_L004

value: Water


title: SW6_L003


title: colon_Se-adeq_replicate 05

description:
Se-adeq_repl05
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: mix of selenium-deficient and selenium-adequate diets

value: reference pool


title: N2-535

value: L1 larvae


title: colon_Se-adeq_replicate 06

description:
Se-adeq_repl06
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: male


title: SW6_L002


title: colon_Se-def_replicate 10

description:
Se-def_repl10
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: SW5_L004


title: N2-533


title: N2-534


title: colon_Se-def_replicate 05

description:
Se-def_repl05
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: colon_Se-adeq_replicate 04

description:
Se-adeq_repl04
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: colon_Se-adeq_replicate 03

description:
Se-adeq_repl03
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: N2-2017


title: SW5_L003


title: N2-531


title: colon_Se-def_replicate 04

description:
Se-def_repl04
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: SW5_L002


title: N2-528


title: SW3_L004


title: N2-526


title: colon_Se-def_replicate 03

description:
Se-def_repl03
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: colon_Se-adeq_replicate 02

description:
Se-adeq_repl02
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: N2-527


title: colon_Se-adeq_replicate 01

description:
Se-adeq_repl01
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: patient 338

value: T cells

value: Post-transplantation

value: Yes


title: SW3_L003


title: WT3_L002


title: colon_Se-def_replicate 02

description:
Se-def_repl02
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: selenium-deficient diet


title: SW3_L002


title: N2-525


title: patient 407

value: No


title: SW2_L004

value: Male


title: SW2_L003

value: Sprague-Dawley


title: N2-524


title: SW2_L002


title: patient 402


title: SW1_L004


title: colon_Se-def_replicate 01

description:
Se-def_repl01
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: N2-522


title: N2-521


title: patient 336


title: 5199 RNA-seq

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
For the ChIP-seq, paired-end reads were aligned to the human genome (hg19) using the Bowtie2 software. For the further analysis, the consistent pair reads were used. RNA-seq raw reads were aligned to the human genome hg19 and to gene annotations from RefSeq gene using TopHat v2.05.
The genome-wide read coverage was calculated by BEDTools and in-house Perl programs. For the RNA-seq datasets, Cufflinks v2.0.2 was used to quantify FPKM values of RNA-seq datasets.
The ChIP-seq peaks were identified by MACS2 using the default calling parameter; and the p value of cutoff was set to 0.001.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.bw: bigwig files were generated, scores represent the normalization reads density.

source_name: glioblastoma xenograft tissue

growth_protocol: GBM12-5199 and GBM12-3080 frozen xenograft tissues were generated in our lab a few years ago (Kitange et al. Clin Cancer Res. 2012).

extract_protocol:
Frozen tissues were cut, divided into 50 mg aliquots, and stored in tubes at -80°C. The frozen tissues were homogenized on ice for 15–30 seconds in 500 μL 1X PBS using a tissue grinder (ACTGene). Tissue homogenates or cultured cells were cross-linked with 1% formaldehyde (final concentration) for 10 min and quenched with 125 mM glycine for 5 min at room temperature and washed once with TBS. The pellets were resuspended in cell lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 min. Lysates were divided into two aliquots and washed with MNase digestion buffer (20 mM Tris-HCl, pH7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2). After re-suspending in 500 μL MNase digestion buffer containing a proteinase inhibitor cocktail (Sigma), the lysates were incubated in the presence of 1,000 units of MNase (NEB, Ipswich, MA, Cat.# M0247S) at 37 °C for 20 min with continuous mixing in thermal mixer (Fisher Scientific, Pittsburgh, PA). After adding the same volume of sonication buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate), the lysates were sonicated for 15 min (30 secs on / 30 secs off) using Bioruptor Twin (UCD-400) (Diagenode) and centrifuged at 21,130 x g for 10 min. The supernatants were collected and the chromatin content was estimated by the Qubit assay (Invitrogen). For the normalization of ChIP efficiency, S2 or Sf9 chromatin was added. The chromatin was then incubated with 5 µg of rabbit monoclonal anti-Ezh2 antibody (Cell Signaling, Cat.# 5246), 5 µg of rabbit monoclonal anti-H3K27me3 antibody (Cell Signaling, Cat.# 9733), 2 µg of rabbit polyclonal anti-H3K27M antibody (Millipore, Cat.# abe419), or 5 µg of mouse monoclonal anti-Jarid2 antibody (Novus, Cat.# NB100-2214) on a rocker overnight. Protein G-magnetic beads (30 μl, Life Technologies) were added for 3 hours incubation. The beads were extensively washed with ChIP buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 100 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), high salt buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl buffer (10 mM Tris-HCl, pH8.0, 0.25 M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and TE buffer. Bound chromatin was eluted and reverse-crosslinked at 65°C overnight. DNAs were purified using Min-Elute PCR purification kit (Qiagen) after the treatment of RNase A and proteinase K.
ChIP-seq libraries were prepared from 10 ng ChIP and input DNA using the Ovation ultralow DR Multiplex kit (NuGEN). The ChIP-seq libraries were sequenced to 51 base pairs from both ends on an Illumina HiSeq 2000 instrument in the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.
Briefly, for RNAseq, total RNA was extracted from cells. The RNA quality was further evaluated using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). The Illumina TruSeq RNA Sample preparation Kit v.4.1 (Illumina Inc., San Diego, CA) was used to prepare cDNA libraries from 2 µg of total RNA. Individual barcoded libraries were analyzed using Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was carried out on an Illumina HiSeq 2000 machine (Illumina) at Mayo Clinic Medical Genomic Facility.

tag: tissue type

value: frozen xenograft tissue

tag: cell cycle stage

value: asynchronization

tag: tmz sensitivity

value: sensitive


title: 3080 RNA-seq

value: resistant


title: patient 335

tag: gender


title: 3080 H3K36me3

tag: chip antibody

value: H3K36me3 (Active Motif, 61101)


title: SW1_L003

tag: treatment

value: Water


title: N2-518

tag: developmental stage

tag: strain

value: 5 egg/ul


title: N2-517


title: SW1_L002


title: N2-516


title: 3080 H3K27ac

value: H3K27ac (Abcam, Ab4729)


title: patient 318

tag: patient

tag: timepoint


title: Norm3 MeDIP seq

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

country: China

institute: Soochow University

data_processing:
After adaptor-trimming and low quality reads removing by cutadapt (v1.9.1) software, high quality reads were generated. Then these high quality reads were aligned to rat reference genome  (UCSC RN5) using bowtie2 software  (v2.2.4) with default parameters.
Peak calling was performed with MACS software (v1.4.3). Differentially methylated regions (DMRs) were identified by diffReps software (v1.55.4).The enriched methylated peaks were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation.
GO and KEGG Pathway analysis were performed on the peak-associated genes or differentially methylated region-associated genes.
Genome_build: RN5
Supplementary_files_format_and_content: excel format: enriched peaks

source_name: skin tissue from nonirradiated area

growth_protocol: SPF condition for the growth of SD rats.

extract_protocol:
Genomic DNA was isolated using phenol–chloroform, precipitated with ethanol and sonicated to 100–500 bp using Bioruptor (Diagenode). Sonicated DNA was end repaired, A tailed, and ligated to adapters by using NEBNext® Ultra™ DNA Library Prep Kit (NEB). Then, MeDIP was performed with a monoclonal antibody against 5-methylcytosine by following the standard manufacturer’s protocol (Active Motif).
MeDIP DNA libraries were quantified using Quant-iT PicoGreen dsDNA Kits (Life Technologies), and subjected to high-throughput 150 base paired-end sequencing on Illumina Hiseq sequencer according to the manufacturer’s recommended protocol.

treatment_protocol: Male Sprague-Dawley (SD) rats (4 weeks old) were irradiated with a single 45-Gy dose of irradiation was administered to the treatment area at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA). The NC-group indicates non-irradiated skin areas.

value: skin

value: 4 weeks


title: N2-515

value: L1 larvae


title: N2-514


title: 5199 H3K27ac


title: 3080 H3K9ac

value: H3K9ac (Abcam, Ab4441)


title: Norm3 Input seq

value: male


title: Norm2 MeDIP seq


title: N2-513


title: patient 333

value: T cells

value: Post-transplantation

tag: future cscc

value: Yes

tag: current cscc


title: patient 326

value: Male

value: No


title: 5199 H3K36me3

value: frozen xenograft tissue

value: asynchronization


title: 3080 H3K9me3

value: resistant

value: H3K9me3 (Active Motif, 39161)


title: patient 321


title: colon_Se-adeq_replicate 07

description:
Se-adeq_repl07
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: 9 or 10 weeks

value: colon

value: selenium-adequate diet

value: mix of selenium-deficient and selenium-adequate diets

tag: sample type

value: reference pool


title: patient 316


title: patient 329


title: Norm1 Input seq

value: Sprague-Dawley

value: skin

tag: Sex

value: 4 weeks


title: patient 308

value: Female

value: T cells


title: patient 319

value: Post-transplantation

value: Yes


title: patient 332

value: Male

value: No


title: patient 325


title: NC3 MeDIP seq

source_name: skin tissue with 45 Gy radiation

tag: tissue

value: male


title: patient 307

tag: cell type


title: patient 328

tag: age


title: 3080 H3K4me3

tag: tissue type

value: frozen xenograft tissue

value: asynchronization

value: resistant

value: H3K4me3 (Abcam, Ab8580)


title: patient 320


title: N2-137

value: L1 larvae

tag: l1 arrest density

value: 1 egg/ul


title: 5199 H3K4me3

tag: cell cycle stage

tag: tmz sensitivity

value: sensitive


title: patient 312

tag: gender


title: 5199 H3K9me3

tag: chip antibody

value: H3K9me3 (Active Motif, 39161)


title: N2-511

tag: developmental stage

value: 5 egg/ul


title: 3080 H3K4me1

value: H3K4me1 (Abcam, Ab8895)


title: patient 334


title: N2-138

tag: strain


title: NC2 MeDIP seq

value: Sprague-Dawley

value: skin

value: 4 weeks


title: patient 302

tag: patient

value: Female

value: T cells

value: Post-transplantation

value: Yes


title: 5199 H3K9ac

value: frozen xenograft tissue

value: H3K9ac (Abcam, Ab4441)


title: N2-135


title: N2-136


title: N2-133


title: Norm2 Input seq

value: male


title: 5199 Input

value: asynchronization


title: 3080 Input

value: resistant


title: N2-134

value: L1 larvae

value: 1 egg/ul


title: 5199 H3K4me1

value: sensitive


title: N2-132


title: Norm  Input seq

data_processing:
After adaptor-trimming and low quality reads removing by cutadapt (v1.9.1) software, high quality reads were generated. Then these high quality reads were aligned to rat reference genome  (UCSC rn5) using bowtie2 software  (v2.2.4) with default parameters.
Peak calling was performed with MACS software (v1.4.3). Differentially enriched regions were identified by diffReps software (v1.55.4).The  enriched peaks were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation.
GO and KEGG Pathway analysis were performed on the peak-associated genes or differentially enriched peak-associated genes.
Genome_build: RN5
Supplementary_files_format_and_content: excel format: enriched peaks

extract_protocol:
Genomic DNA was isolated using phenol–chloroform, precipitated with ethanol. YY1-interacting DNA was isolated with ChIP grade YY1 antibody (ab38422)  .
Chromatin Immunoprecipitation was performed according to Wamstad et al. (2012) (See Supplementary Method below for detail). YY1-interacting DNA was isolated with ChIP grade YY1 antibody (ab38422). The yield of ChIPed DNA was determined via Quant IT fluorescence assay (Life Technologies) and enrichment efficiencies of ChIP reactions were evaluated by qPCR. Illumina sequencing libraries were generated with NEBNext® Ultra™ DNA Library Prep Kit (New England Biolabs) by following the manufacturer’s manual. The library quality was determined by using Agilent 2100 Bioanalyzer (Agilent), and then, subjected to high-throughput 150 base paired-end sequencing on Illumina Hiseq sequencer according to the manufacturer’s recommended protocol.

treatment_protocol: Male Sprague-Dawley (SD) rats (4 weeks old) were irradiated with a single 45-Gy dose of irradiation was administered to the treatment area at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA)


title: PANC-1 NC3

city: Hangzhou City, Zhejiang Province

first: Liangjing

last: Zhou

address: no. 3,QingChun east road,Jianggan District, Hangzhou City, Zhejiang Province

department: Department of General Surgery

institute: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China

data_processing:
bcl2fastq software were used for basecalling.
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).The steps are: 1) trim Smart-seq2 public primer sequence from the Reads; 2) remove the contaminated reads for adapters; 3) remove the low quality reads; and 4) remove the reads whose N base more than 5% for total bases.
Sequenced reads were mapped to hg38 using Bowtie2 v2.2.3 software.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0. and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from  Trapnell, C. et al., Nat. Biotechnol, 2010.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: pancreatic cancer

growth_protocol: PANC-1 was cultured in DMEM medium with 10% fetal bovine serum

extract_protocol:
Total RNA of cells was isolated and purified by miRNeasy Mini Kit (Qiagen, Maryland, USA), following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were seeded onto 6-well culture plates. PANC-1 cell lines were transfected with CD73 siRNA or negative control in serum-free medium, transfection was performed using Lipofectamine 3000 following the manufacturer’s protocol.

tag: cell line

value: pancreatic cancer cell line

tag: treatment

value: negative control


title: PANC-1 NC2


title: N2-131

extract_protocol:
Single L1 animals were placed in 5 ul of a typical worm lysis buffer (40mM Tris pH7.5, 10mM EDTA, 200mM NaCl, 0.5% SDS, and 0.4ug/ul Proteinase K), incubated at 55° for 10 minutes, and then frozen at -20°C until use for RNA-sequencing.
single-L1 RNA-seq/Nextera kit


title: N2-128


title: NC1 Input seq

value: Sprague-Dawley


title: N2-512

value: 5 egg/ul


title: Norm  ChIP seq

value: skin

value: 4 weeks


title: NC1 MeDIP seq


title: PANC-1 NC1


title: NC  Input seq


title: PANC-1 CD73si3

value: CD73 siRNA


title: NC2 Input seq


title: Norm1 MeDIP seq


title: NC ChIP seq


title: PANC-1 CD73si2


title: Normal mRNAseq

data_processing:
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC RN5) with hisat2 software (v2.0.4
cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs
Genome_build: RN5
Supplementary_files_format_and_content: excel format with FPKM

extract_protocol:
Total RNA was isolated using trizol.Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). 10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

treatment_protocol: Male Sprague-Dawley (SD) rats (4 weeks old) were irradiated with a single 45-Gy dose of irradiation was administered to the treatment area at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA). Skin tissues were then collected.


title: NC mRNAseq


title: NC3 Input seq


title: N2-117


title: PANC-1 CD73si1


title: N2-126


title: N2-121


title: N2-122


title: FPX-8d-r2

status: Public on Jul 12 2018

city: Ikoma

first: Misato

last: Ohtani

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

country: Japan

institute: NAIST

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. All signals were divided by median value of all probe sets.
Data processing was performed by two independent sets; 1) o1~9.CEL for auxin/cytokinin medium, and 2) o1~3.CEL and o10~15.CEL for FPX medium.

organism: Arabidopsis thaliana

source_name: Four-day-old seedlings treated with FPX for 8 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Four-day-old seedlings grown on the MS medium were transferred to the MS medium containing 45 µM FPX (FPX plate), or 0.5 mg/l 2,4-D and 0.1 mg/l kinetin (auxin/cytokinin plate).

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen) following instruction.

value: Whole seedlings

value: Four-day-old


title: FPX-8d-r3


title: FPX-2d-r2

source_name: Four-day-old seedlings treated with FPX for 2 days


title: FPX-8d-r1


title: FPX-2d-r3


title: FPX-2d-r1


title: 6Control-2

city: Charleston

first: Yordan

middle: S

last: Yordanov

state: IL

address: 600 Lincoln ave

department: Department of Biological Sciences

institute: Eastern Illinois University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the  Affymetrix GeneChip® Fluidics Station 450

scan_protocol: Arrays were scanned with an Affymetrix GeneChip® Scanner 3000 at 570nm. The Affymetrix eukaryotic hybridization control kit and Poly-A RNA control kit were used to ensure efficiency of hybridization and cRNA amplification. All cRNA was synthesized at the same time. Hybridizations were conducted with one replicate of all times and treatments concurrently. Each array image was visually screened to discount for signal artifacts, scratches or debris.

data_processing: The data were processed with RMAExpress (http://rmaexpress.bmbolstad.com/) using default analysis settings, quantile normalization and median polish.

organism: Populus tremula x Populus alba

source_name: plants grown in MS medium at 6h

label_protocol: Biotinylated cRNA were prepared according to the standard one_cycle Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: in vitro conditions

extract_protocol: We isolated RNA from about 0.3g tissue. RNA was extracted as previously described (Busov VB,at al, 2003, Plant Physiol 132: 1283-1291) using QIAGEN kits.

treatment_protocol: Tissues from PEG treated and and control roots were fixed in liquid Nitrogen and stored  at -80oC until RNA extraction.

value: MS medium at 6h

tag: ecotype

value: Populus tremula x Populus alba INRA 717-IB4

value: roots

tag: genotype

value: wild type


title: 0Control-2

source_name: plants grown in MS medium at 0h

value: MS medium at 0h


title: 96Control-2

source_name: plants grown in MS medium at 96h

value: MS medium at 96h


title: 6Control-1


title: 504PEG-2

source_name: plants grown in 5% PEG MS medium at 504h

value: 5% PEG MS medium at 504h


title: 504Control-1

source_name: plants grown in MS medium at 504h

value: MS medium at 504h


title: 24Control-2

source_name: plants grown in MS medium at 24h

value: MS medium at 24h


title: 48Control-2

source_name: plants grown in MS medium at 48h

value: MS medium at 48h


title: 24PEG-2

source_name: plants grown in 5% PEG MS medium at 24h

value: 5% PEG MS medium at 24h


title: 24Control-1


title: 504Control-2


title: 96Control-1


title: 48PEG-1

source_name: plants grown in 5% PEG MS medium at 48h

value: 5% PEG MS medium at 48h


title: 96PEG-1

source_name: plants grown in 5% PEG MS medium at 96h

value: 5% PEG MS medium at 96h


title: 48PEG-2


title: 504PEG-1


title: 96PEG-2


title: 6PEG-2

source_name: plants grown in 5% PEG MS medium at 6h

value: 5% PEG MS medium at 6h


title: 24PEG-1


title: 48Control-1


title: 0d-r2_re-analyzed

source_name: Four-day-old seedlings


title: 2,4-D+Kinetin-2d-r3

source_name: Four-day-old seedlings treated with 2,4-D+Kinetin for 2 days


title: 2,4-D+Kinetin-8d-r1

source_name: Four-day-old seedlings treated with 2,4-D+Kinetin for 8 days


title: 2,4-D+Kinetin-8d-r3


title: 2,4-D+Kinetin-8d-r2


title: 0d-r2


title: 2,4-D+Kinetin-2d-r2


title: 2,4-D+Kinetin-2d-r1


title: 0d-r1_re-analyzed


title: 0d-r1


title: 0d-r3


title: Low content in Intramuscular Fat, Individual 5

city: Zafra

first: María

middle: Muñoz

last: Muñoz

state: Badajoz

address: Centro I+D en Cerdo Ibérico, carretera Ex-101, km 4.7

country: Spain

institute: INIA

description: Gene expression data from Longissimus dorsi tissue

data_processing:
FastQC was used to evaluate the quality of the raw sequencing data
The sequences were trimmed to remove the sequencing adaptor and poly A and T tails with Trim Galore setting default values (stringency of 6bp) and paired-end reads where kept when both pairs were longer than 40 bp.
Filtered reads were mapped against the pig reference genome (Sscrofa11.1) using TopHat v2.1.0 applying default settings, except the reads were aligned first to the ENSEMBLE (Sscrofa11.1) transcriptome annotation (-G option) and the distance between pairs was set to 50 bp. (inner-mean distance) and the standard deviation at 150 bp.
Transcripts were assembled and quantified in FPKM using Cufflinks v2.2.1
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Sus scrofa

source_name: Longissimus dorsi, male

growth_protocol: Pigs fattened in a free-range system based on the ad libitum intake of acorns and grass.

extract_protocol:
RiboPure RNA isolation kit
Paired-end libraries were prepared using TruSeq SBS Kit v3-(Illumina, San Diego CA) for each sample. Multiplex sequencing of the libraries was carried out on a HiSeq2000 sequence analyzer (Illumina, Inc) with four samples per lane, according to the manufacturer’s instruction at Centro Nacional de Análisis Genómico. Paired-end reads of 76 bp were generated.

treatment_protocol: Longissimus dorsii muscle were manteined at -80 ºC

tag: intramuscular fat (imf) group

value: Low content in IMF group

tag: intramuscular fat %

tag: ebv intramuscular fat


title: Low content in Intramuscular Fat, Individual 6


title: V6.5 EpiC subclone 1

first: Amy

last: Chen

state: CA

address: 279 Campus Drive West

hyb_protocol: standard Illumina hybridization protocol

scan_protocol: standard Illumina scanning protocol

data_processing: Data was quantile normalized using Beadarray. Differential gene expression was performed using limma.

source_name: epiblast cells

label_protocol: not provided

growth_protocol: All cells were grown in Knockout DMEM with 15%FBS, Pen/Strep, L-glutamine and Non-essential amino acids. ESCs were also grown in Lif and 2i (GSKi and MEKi). EpiCs were generated by removal of LIF and 2i from ESCs for 3 days.

extract_protocol: Total RNA was extracted using Trizol

value: GRHL2 wildtype

value: -LIF -2i 3 days

tag: tissue

value: epiblast cells


title: GRHL2 knockout EpiC clone 1

value: GRHL2 knockout


title: V6.5 EpiC subclone 3


title: GRHL2 knockout EpiC clone 3


title: V6.5 EpiC subclone 4


title: GRHL2 knockout EpiC clone 4


title: V6.5 EpiC subclone 2


title: 0d-r3_re-analyzed

value: Whole seedlings

tag: age

value: Four-day-old


title: GRHL2 knockout EpiC clone 2


title: 0Control-1

value: MS medium at 0h

value: Populus tremula x Populus alba INRA 717-IB4

value: roots

value: wild type


title: Low content in Intramuscular Fat, Individual 4


title: Low content in Intramuscular Fat, Individual 3


title: Low content in Intramuscular Fat, Individual 2


title: Low content in Intramuscular Fat, Individual 1


title: High content in Intramuscular Fat, Individual 4

value: High content in IMF group


title: High content in Intramuscular Fat, Individual 3


title: High content in Intramuscular Fat, Individual 2


title: High content in Intramuscular Fat, Individual 1


title: 6PEG-1


title: High content in Intramuscular Fat, Individual 6


title: High content in Intramuscular Fat, Individual 5


title: Episomal-iPS-Edom-iPS-08_P20

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

description:
9431213090_R05C01
Edom18-derived iPS cslls

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio V2011.1

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

value: Female

tag: cell type

value: inducible pluripotent stem cells (iPSCs)

tag: disease state

value: normal

tag: vector type

value: episomal vectors


title: Episomal-iPS-Edom-iPS-09_P20

description:
9431213090_R04C02
Edom21-derived iPS cslls

tag: gender


title: Episomal-iPS-Edom-iPS-09_P40

description:
9431213090_R06C02
Edom22-derived iPS cslls


title: Primary-Edom22_P7

description:
9513149031_R02C02
Menstrual blood-derived cells

value: Menstrual blood-derived cells


title: Episomal-iPS-Edom-iPS-09_P10

description:
9431213090_R03C02
Edom20-derived iPS cslls


title: Episomal-iPS-Edom-iPS-01_P40

description:
9431213090_R04C01
Edom16-derived iPS cslls


title: Sendai-iPS-Edom-iPS-39_P10

description:
7539308071_R04C01
Edom12-derived iPS cslls

value: Sendai virus


title: Sendai-iPS-Edom-iPS-39_P20

description:
7539308071_R05C01
Edom13-derived iPS cslls


title: Episomal-iPS-Edom-iPS-01_P20

description:
9431213090_R02C01
Edom15-derived iPS cslls


title: Episomal-iPS-Edom-iPS-01_P16

description:
9431213090_R01C01
Edom14-derived iPS cslls


title: Episomal-iPS-Edom-iPS-08_P40

description:
9431213090_R02C02
Edom19-derived iPS cslls


title: STOMP sample 6-0195-03

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array at 50C for 17 hours according to the manufacturer's instructions. DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array at 50C for 17 hours according to the manufacturer's instructions.

scan_protocol: The array was washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000. The array was washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
To achieve comprehensive CNV calling, we used three separate algorithms to detect CNVs; Birdsuite, iPattern, and Genotyping Console. CNVs were considered stringent calls if detected by two or more of the algorithms used. For all algorithms, we have used 8 probes and >1kb as a base line cutoff for CNV detection.
Genotype Call (SNP call): AA, AB, BB, and NoCall
To achieve comprehensive CNV calling, we used four separate algorithms to detect CNVs; Affymetrix Chromosome Analysis Suite (ChAS), iPattern, Nexus and Partek. Our primary analysis was performed based on ChAS CNV calls, which were then supported using the remaining three algorithms to construct a confidence set of CNVs14. For all algorithms, we have used 8 probes and >1kb as a base line cutoff for CNV detection.
Genotype Call (SNP call): AA, AB, BB, and NoCall

source_name: whole blood

label_protocol:
As per manufacturer (Affymetrix)
As per manufacturer (Affymetrix)

growth_protocol:
DNA was extracted from whole blood.
Cell lines were grown according to standard conditions.

extract_protocol: Lymphocyte isolation by the Ficoll separation procedure followed by cryopreservation and storage in liquid nitrogen and cell lines were established using EBV-transformation.

tag: ethnicity

value: whole blood

tag: diagnosis

value: pediatric obesity


title: STOMP sample 6-0210-03

value: Male


title: STOMP sample 6-0190-03


title: Sendai-iPS-Edom-iPS-35_P20

description:
7539308071_R02C01
Edom11-derived iPS cslls


title: STOMP sample 6-0234-03


title: STOMP sample 6-0194-03


title: STOMP sample 6-0203-03


title: STOMP sample 6-0211-03


title: STOMP sample 6-0209-03


title: STOMP sample 6-0198-03


title: STOMP sample 6-0236-03


title: STOMP sample 6-0235-03


title: STOMP sample 6-0206-03


title: STOMP sample 6-0233-03


title: PB1131Pop3

city: Atlanta

first: Greg

last: Gibson

state: GA

address: 950 Atlantic Dr. NW

department: Biological Sciences

institute: Georgia Institute of Technology

data_processing:
Paired end 100bp reads were mapped to hg38, using Tophat2 to generate bam files
HTseq (version) was then used to assess read counts at the gene level in each gene
The mapped libraries were then normalized accounting for differences in size and dispersion using the default parameters of EdgeR for gene abundance levels)
Read counts were converted to the log base 2 scale and principal component variance analysis (PCVA) in JMP-Genomics (version 8.0) was used to assess the contributions of Individual, Batch, Cell Population, and Tissue to the weighted average variance explained by the first 3 PCs
Since Batch explained 53% of the variance, in order to maximize the contrasts across the populations, we elected to use remove the batch effect using the SNM (supervised normalization of microarray) method 54 with Cell Population as the Biological variable and Batch as the adjustment variable with the Rm=True option
Genome_build: hg38
Supplementary_files_format_and_content: CSV file containing log2 of normalized read counts (expression values).

source_name: ASC, Pop3

growth_protocol: FACS-based purified ASCs

extract_protocol:
RNA was purified using QIAGEN Micro RNEasy columns, and RNA quality assessed using Agilent Bioanalyzer
2 ng of total RNA was used as input for mRNA amplification using 5’ template-switch PCR with the Clontech SMART-Seq v4 Ultra Low Input RNA kit, according to manufacturer’s instructions. Amplified mRNA was fragmented and appended with dual indexed bar codes using Illumina NexteraXT DNA Library Prep kits

tag: samplenum

tag: samplename

tag: individual

tag: cellpopulation

value: Antibody Secreting Cell

value: Peripheral Blood

tag: batch


title: PB1201Pop5

source_name: ASC, Pop5


title: PB1438Pop2

source_name: ASC, Pop2


title: STOMP sample 6-0193-03


title: PB1201Pop2


title: PB1438Pop3


title: PB1201Pop3


title: Episomal-iPS-Edom-iPS-08_P10

description:
9431213090_R06C01
Edom17-derived iPS cslls


title: Sendai-iPS-Edom-iPS-05_P10

description:
5822986027_R04C01
Edom2-derived iPS cslls


title: PB51Pop5


title: STOMP sample 6-0229-03


title: PB103Pop5


title: Sendai-iPS-Edom-iPS-35_P10

description:
7539308071_R01C01
Edom10-derived iPS cslls


title: PB103Pop2


title: PB103Pop3


title: PB48Pop2


title: PB48Pop3


title: Sendai-iPS-Edom-iPS-31_P20

description:
7539308071_R01C02
Edom8-derived iPS cslls


title: PB51Pop3


title: Retro-iPS-Edom-iPS-02_P22

description:
5822986025_R03C02
Edom0-derived iPS cslls

value: retrovirus


title: Sendai-iPS-Edom-iPS-23_P20

description:
5822986027_R02C02
Edom5-derived iPS cslls


title: PB51Pop2


title: PB48Pop5


title: Sendai-iPS-Edom-iPS-05_P20

description:
5822986027_R05C01
Edom3-derived iPS cslls


title: Sendai-iPS-Edom-iPS-30_P10

description:
7539308057_R04C02
Edom6-derived iPS cslls


title: Retro-iPS-Edom-iPS-02_P42

description:
5822986025_R05C02
Edom1-derived iPS cslls


title: Sendai-iPS-Edom-iPS-30_P20

description:
7539308057_R05C02
Edom7-derived iPS cslls


title: Sendai-iPS-Edom-iPS-23_P10

description:
5822986027_R01C02
Edom4-derived iPS cslls


title: ChIPseq_H2B_WT_NKI6061_2

first: Tessy

last: Korthout

state: Noord-Holland

address: Plesmanlaan 121

department: Gene Regulation

institute: The Netherlands Cancer Institute

data_processing:
mapping of the reads to reference genome
filter for mapping quality < 37
merge BAM files of replicate samples
extend each read with 150 bp
normalize for sequencing depth
convert to bigwig
Genome_build: R64-2-1
Supplementary_files_format_and_content: bigwig

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown in YEPD.

extract_protocol:
Cells were cross-linked for 20 min with of the volume of freshly prepared Fix Solution containing 1% formaldehyde. Cells were washed once in cold TBS with 0.2 mM PMSF and lysed by bead beating in 200 μl breaking buffer with Zirconia/silica beads. The lysate was washed twice in FA buffer and sonicated using the Bioruptor PICO for 10 min.
Libraries were prepared using the KAPA HTP Library Preparation Kit (Illumina), using Illumina-provided adapters at 200nM. After eleven PCR cycles, cleanup and pooling was as described above. After 11 PCR cycles, a size selection cleanup was performed using 0.5X Agencourt AMPure XP PCR Purification beads to get rid of large fragments due to crosslinking DNA. The supernatant of the 0.5X cleanup was used to catch the smaller fragments; this supernatant was cleaned up 2 times with 1X beads to remove primers present in the libraries.

tag: genetic background strain

tag: strain

tag: genotype

value: WT

tag: chip antibody

value: H2B, Active Motif, Catalog# 39238, Lot# 03108001


title: ChIPseq_H2B_WT_NKI6061_1


title: ChIPseq_H2Bub_Dot1OE_NKI6151_1

value: H2Bub, developed by our lab from clone H2Bub1B3F12/A9


title: ChIPseq_H2Bub_Dot1OE_NKI6151_2


title: ChIPseq_H2Bub_ubp8KO_NKI4656_2


title: Small RNAs from ovaries of EY03383 transgenic strain, technical rep2

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

data_processing:
The reads with clipped 3'-adapter (5'-TGGAATTCTCGGGTGCCAAGG) were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie to dm3 genome assembly with requiring of perfect matching.
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited files include the raw counts of clipped read occurrences in each library.

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
Total RNA was isolated by Trizol (Invitrogen) and size-fractioned by PAGE (19-29 nt)
Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012)

tag: tissue

value: ovaries

tag: strain/background

tag: technical replicate


title: Small RNAs from ovaries of EY03383 transgenic strain, technical rep1


title: ChIPseq_H2Bub_ubp8KO_NKI4656_1


title: ChIPseq_H2Bub_WT_NKI6061_2