title: m_9522_S7_3

description: Wild type 9522, anther development stage 7 (S7), rep 3.


title: Control (untreated) D. suzukii field population rep2

status: Public on Sep 23 2016

type: SRA

city: Athens

first: Ruchir

last: Mishra

state: GA

address: 120 Cedar St

department: Entomology

country: USA

institute: University of Georgia

description: Control_Zeta-cypermethrin_Field_gene_exp.diff.txt, Control_Spinosad_Field_gene_exp.diff.txt, Control_Malathion_Field_gene_exp.diff.txt

library_source: transcriptomic

data_processing:
Base calling, de-multiplexing and adapter removal were performed using Illumina BaseSpace. The encoding version is Illumina 1.9
Due to high sequencing base quality at both 3’ and 5’ ends according to the FastQC output  and availability of reference genome, preprocessing steps were not performed
The 24 samples (paired-end reads, including  replicates) were independently mapped onto the D. suzukii genome (SpottedWingFlybase v.1) by using Tophat v2.0.13 with parameters -p 4 -r 105 (or -r 113 (for F10, F11 and F12 samples)) --no-novel-juncs
After the alignment, Cufflinks v2.2.1 was used to estimate the expression values of the transcripts in FPKM (Fragments Per Kilobase per Million mapped reads) with the Cuffdiff 2 default geometric normalization
Genome_build: SpottedWingFlybase v.1 downloaded from (http://spottedwingflybase.oregonstate.edu/)
Supplementary_files_format_and_content: tab-delimited text files gene_exp.diff from Cuffdiff output  containing FPKM values and differentially expressed genes

molecule: total RNA

organism: Drosophila suzukii

source_name: Whole organism

extract_protocol:
Total RNA was extracted from the whole organism (D. suzukii) using TRIzol reagent (Ambion) and quantified with NanoDrop Spectrophotometer (N-  1000). KAPA Stranded mRNA-Seq Kit (KK8420) was used to create paired-end sequencing   libraries
RNA libraries were prepared for sequencing using KAPA Stranded mRNA-Seq Kit (KK8420) protocol
RNA-Seq (NGS Stranded RNA)

tag: strain

value: Field

tag: tissue

value: Whole organism

tag: age

value: 5-7 days old Adults

tag: genotype

value: Wild type


title: m_9522_S7_1

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: Wild type 9522, anther development stage 7 (S7), rep 1.

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: Rice Genome Annotation Project 7.0
Supplementary_files_format_and_content: tag count file

molecule: polyA RNA

organism: Oryza sativa

source_name: Rice spikelets

extract_protocol:
Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by TRIzol (Invitrogen) according to manufacturer's protocol.
Small RNA libraries were constructed from 1 microgram of  total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001).

value: Wild type 9522

tag: developmental stage

value: anther development stage 7 (S7)


title: Control (untreated) D. suzukii field population rep1


title: KC_cgRNAi_EC_3_3

city: Rehovot

first: Lilach

last: Gilboa

address: 234 Herzl Street,

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

library_source: genomic

data_processing:
The data was processed using UMI-4C pipeline (https://bitbucket.org/tanaylab/umi4cpackage). With default parameters.
Processed reads were mapped with bowtie2 with the parameters:  --reorder --end-to-end.
Genome_build: dm6
Supplementary_files_format_and_content: The processed adj files are a 4 columns tab delimited table with headers: viewpoint (bait), fragment end id1 (fend1), fragment end id2 (fend2), UMI count (count)

molecule: genomic DNA

organism: Drosophila melanogaster

extract_protocol:
5X10^6 cells used to generate the primary 3C template. Cells were collected, centrifuged at 1200rpm, the supernatant was removed and are resuspended in PBS/10% FBS. Then the cells are cross-linked with formaldehyde to final concentration of 2% for 10min. The reaction was quenched by addition of glycine to final concentration of 0.125M. The cells were centrifuged and resuspended in cold lysis buffer (50 mM Tris–HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TX-100, 1 tbl Protease inhibitor). The nuclei are extracted and resuspended in 450µl UPW. For digestion, we add 60µl DpnII buffer, 15µl 10% SDS and incubate on a Thermomixer (Eppendorf) 37c, 60 minutes. 75µl of 20% TX-100 are added and the tube is incubated again 37c, 60 minutes. The chromatin is then digested with HC DpnII (NEB R0543M) in three rounds as following: 200U for 2 hours, 200U overnight and 200U for 2 hours. An aliquot is taken from the tube and run on gel to inspect digestion efficiency. The enzyme is then inactivated by incubating 65c, 20min. Next, the chromatin is ligated with 15µl of HC T4 ligase (NEB M0202M), with 10x ligase buffer to final volume of 7mL and incubated overnight at 16c. Aliquot is taken from the sample and ran on gel to inspect ligation efficiency. The chromatin is then reverse cross-linked overnight at 65c with 30ul proteinase K (Sigma-Aldrich), and then 30ul  of RNase A are added and incubated for 45 minutes, 37c. The 3C DNA is then extracted by Ampure beads. Inverted head segments of  400 OR (wild type) or 200 cgKG000882/cg1 (mutant)  animals were fixed in 2% formaldehyde in PBS (20 min., Room Temperature). Fixed tissue was then washed twice with PBS/125mM Glycine/0.01% Triton]X]100, and a third time with PBS. Samples were  washed again with PBS/1% protease inhibitor cocktail (P8340,Sigma).Wing Imaginal discs were then dissected out and placed in an eppendorf tube. Excess fluid was removed and tissues were snap freezed in Liquid Nitrogen and stored at 80 C. To prepare DNA, discs were thawed on ice   and centrifuged at 13,000 rpm for 20 sec. Excess fluid was discarded. Discs were resuspended  in  50  ul  lysis  buffer (10  mM  Tris]HCl  pH  8.0,  10  mM  NaCl,  0.2%   Igepal CA360 (Sigma I8896)), and 10 ul/ml of protease Inhibitors (Sigma"P8340).Discs were  homogenized  with  a  plastic motorized  pestle  (3X2min) and continuation of the 4C protocol was as performed for KC cells.
5-10ug DNA in 200µl Elution Buffter (EB, 10mM Tris-HCl, pH 8) of 3C template is sonicated at 4°c using Bioruptor program: 5 cycles of 30s on, 60s off. The sonicated material is inspected by running 10µl on agarose gel to assure size distribution of 500-550 bps. The sonicated DNA is subjected to end-repair reaction - 20µl 10X end-repair buffer and 10µl end-repair mix (NEB E6050L) are added to the mix and incubated at 20°c for 30 minutes. The DNA is cleaned by x2.2 AmpureXP beads (Beckman Coulter) and eluted in 76µl EB. Two nested PCR reactions are used for UMI-4C library construction. The PCR reactions are performed in 50ul volume with the following reagents: 10ul GoTaq Flexi buffer (promga M792A), 3ul MgCl 25mM (promega A3511), 0.2mM dNTPs, 2µl 10mM bait primer (0.4mM final concentration), 2µl 10mM Illumina enrichment primer 2 (0.4mM final concentration), 1ul GoTaq (promga M3008) and 200ng UMI-4C DNA template. PCR program is 2 minutes 95°c, 20 cycles of 30s 95°c, 30s 56°c, 60s 72°c, final extension of 5min 72°c. Following the PCR reaction we clean the amplified DNA with x1 SPRI beads and use 75% of the eluate to a second PCR reaction. The second PCR reaction is identical to the first. The only difference is the use of the bait primer with the Illumina dangling adapter (As shown in figure 1B). In the second PCR reaction 15-18 cycles are used instead of 20. Then, A-tailing reaction is performed with 10µl NEBbuffer2, 4µl Klenow (NEB M0212M), and 10µl 10nM dATP. Following A-tailing, the 5’ ends of the DNA are dephosphorylated with 2µl of Alkaline Phosphatase (NEB M0290S) 50°c for 60 minutes, and the DNA is cleaned with AmpureXP beads (x2) and eluted in 67µl EB. The DNA template is ligated with 5µl 15µM Illumina indexed adapters (final concentration 0.4µM), 10µl ligase mix and 80µl 10X buffer (NEB M2200). To release the non-ligated strand of the adapter, the DNA is denatured at 95°c for 2 minutes and cleaned with SPRI beads x1.

tag: cell line

tag: cell type

value: Embryonic cells

tag: lineage

tag: conditions

value: cgRNAi EC

tag: viewpoint


title: KC_LacZ_E_12_2

value: LacZ EC


title: KC_LacZ_12_2

value: LacZ


title: m_9522_S5_3

description: Wild type 9522, anther development stage 5 (S5), rep 3.

value: anther development stage 5 (S5)


title: KC_cgRNAi_3_3

value: cgRNAi


title: m_9522_S5_2

description: Wild type 9522, anther development stage 5 (S5), rep 2.


title: Spinosad treated D. suzukii field population rep 2

description: Control_Spinosad_Field_gene_exp.diff.txt


title: KC_LacZ_E_3_3


title: m_msp1_S3_1

description: msp1 mutant, anther development stage 3 (S3), rep 1.

value: msp1 mutant

value: anther development stage 3 (S3)


title: m_9522_S5_1

description: Wild type 9522, anther development stage 5 (S5), rep 1.


title: KC_LacZ_3_3


title: KC_cgRNAi_13_1


title: KC_cgRNAi_EC_5_2


title: KC_cgRNAi_5_2


title: KC_LacZ_E_5_2


title: m_9522_S3_2

description: Wild type 9522, anther development stage 3 (S3), rep 2.


title: KC_LacZ_5_2


title: m_9522_S3_1

description: Wild type 9522, anther development stage 3 (S3), rep 1.


title: KC_cgRNAi_EC_5_1


title: KC_LacZ_E_5_1


title: KC_cgRNAi_5_1


title: KC_LacZ_5_1


title: KC_LacZ_E_3_1


title: m_9522_S3_3

description: Wild type 9522, anther development stage 3 (S3), rep 3.


title: KC_LacZ_3_1


title: KC_cgRNAi_EC_12_1


title: KC_cgRNAi_3_1


title: KC_cgRNAi_5_3


title: KC_cgRNAi_EC_5_3


title: KC_cgRNAi_EC_3_1


title: KC_LacZ_E_5_3


title: KC_LacZ_5_3


title: KC_cgRNAi_EC_3_2


title: KC_LacZ_12_1


title: KC_LacZ_E_3_2


title: KC_LacZ_3_2


title: WT-1

city: Kansas City

first: Robert

middle: C

last: De Lisle

state: KS

address: 3901 Rainbow Blvd

department: Anatomy & Cell Biology

institute: Univ Kansas Med Ctr

description: stranded mRNA

data_processing:
bcl2fastq Conversion Software v1.8.4 from illumina was used to generate fastq files
reads were trimmed with cutadapt and mapped to the Rat Rnor_6.0 genome with STAR_2.3.1z --genomeDir   Rnor_6.0 --readFilesIn R1.fastq R2.fastq --runThreadN 24 --outSAMstrandField intronMotif
differential gene expression was deterimined using stringtie -p 24  -G  cuffmerge -g  -p 24 and cuffdiff -p 24 -u -v --emit-count-tables --max-bundle-frags 100000000 --max-mle-iterations 500000
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab delimited files containing fpkm counts by group or sample, differential gene expression by gene.

organism: Rattus norvegicus

source_name: small intestine

extract_protocol:
The entire length of the small intestine was removed to ice cold PBS and trimmed free of fat and mesentery. The tissue was then flushed with PBS containing 10 mM dithiothreitol to remove the majority of digesta and mucus from the lumen. The tissue was then opened along the mesenteric border and cut lengthwise. Total RNA was isolated from the entire length of the small intestine by homogenization in Trizol followed by processing with a Phase Lock Gel Heavy according to the manufacturer's instructions. Stranded mRNA-Seq was performed using the Illumina HiSeq2500 Sequencing System. Total RNA (0.5 g) was used to initiate the Stranded mRNA-Seq library preparation protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: wild type

value: Sprague Dawley

value: small intestine

value: post natal day 21


title: dut/ung/sml1-S

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

data_processing:
Library strategy: Excision-Seq
Aligned to sacCer1 using Bowtie -m 1
Created bedfile
Normalized bedfile to # reads aligned (Reads per million, RPM)
Created bigWig file
Genome_build: sacCer1
Supplementary_files_format_and_content: Normalized bigWig containing genome position and # reads for post-digest Excision-seq signal (measures uracil depletion)

organism: Saccharomyces cerevisiae

source_name: Budding yeast_dut/ung/sml1

growth_protocol: S. cerevisiae grown at 30C

extract_protocol:
Yeast were spheroplasted to obtain high molecular weight DNA treated with RNAse
DNA libraries were created, treated with UDG/Endonuclease IV, and single read sequencing was performed on the Illumina HiSeq 2000 platform using 50bp reads


title: dut/ung/dcd1

source_name: Budding yeast_dut/ung/dcd1


title: WT-3

description: stranded mRNA


title: dut/ung/sml1-W


title: CF-4

description: stranded mRNA

value: cystic fibrosis


title: MEF2C_cKO_1

city: Charleston

first: Christopher

middle: W

last: Cowan

state: SC

address: 173 Ashley Ave, BSB 403

department: Neurosiences; Psychiatry

institute: Medical University of South Carolina

description: Protocol 1

data_processing:
Single-end reads were aligned in a staged manner. Reads were aligned with Tophat with Bowtie using default options to a reference sequence comprised of mitochondrial DNA (mm9 from UCSC).
RNA-seq Counts values were quantified using HTSeq python suite, providing gene definitions (mm9 GTF from UCSC).
RNA-seq RPKM values were then quantified using R based on the mm9 GTF annotation from UCSC.
Gene-level RPKMs and Counts quantifications were used for all downstream processing.
Genome_build: Mouse mm9
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample.

organism: Mus musculus

source_name: Somatosensory Cortex

growth_protocol: Mouse regional brain dissections were used and frozen at -80C

extract_protocol:
All RNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer.  Samples were randomized for RNA extraction and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA was extracted from frozen tissue using Qiagen's Rneasy Kit according to manufacturer's protocol.

value: mixed SVeV-129; C57BL/6J

tag: tissue type

value: Somatosensory Cortex

tag: Sex

value: M

value: 14 weeks old

tag: genotype/variation

value: Mef2c cKO (Mef2cfl/fl; Emx1-Cre)


title: WT-2

description: stranded mRNA


title: WT-4

description: stranded mRNA


title: KC_cgRNAi_3_2

value: Embryonic cells


title: MEF2C_cKO_2

description: Protocol 1

value: 12 weeks old


title: small RNA seq B6-Im830

city: Okayama

first: Jun

last: Wada

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Nephrology, Rheumatology, Endocrinology and Metabolism

country: Japan

institute: Okayama University

description:
processed data file:
NTR_2Fold_down.xlsx
NTR_2Fold_up.xlsx
Sample_Im830(smallRNA)

data_processing: Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.

source_name: Spleen CD4 plus T cells

extract_protocol:
CD4 plus T cells were negatibely depleted from spleenocyte using magnetic beads, and RNA was harvested using Qiazol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 16 week

tag: gender

value: female

value: Spleen

value: CD4+ T cell


title: small RNA seq MRL-Im831

description:
processed data file:
NTR_2Fold_down.xlsx
NTR_2Fold_up.xlsx
Sample_Im831(smallRNA)

value: MRL/lpr-Tnfrsf6lpr; MRL/lpr lupus model mice


title: MEF2C_WT_2

description: Protocol 1

value: control (Mef2cfl/fl)


title: KC_LacZ_E_12_1

value: LacZ EC


title: MEF2C_WT_1

description: Protocol 1


title: CF-3

description: stranded mRNA

value: Sprague Dawley

value: small intestine


title: KC_cgRNAi_12_1

value: cgRNAi


title: dut/ung

source_name: Budding yeast_dut/ung

value: dut/ung


title: MEF2C_WT_3

description: Protocol 1

value: mixed SVeV-129; C57BL/6J

value: Somatosensory Cortex


title: CF-2

description: stranded mRNA

value: cystic fibrosis

value: post natal day 21


title: mRNA seq MRL-Im831

description:
processed data file:
NTR_GE_down_miRNA_up.xlsx
NTR_GE_up_miRNA_down.xlsx
Sample_Im831(mRNA)


title: CF-1

description: stranded mRNA


title: mRNA seq B6-Im830

description:
processed data file:
NTR_GE_down_miRNA_up.xlsx
NTR_GE_up_miRNA_down.xlsx
Sample_Im830(mRNA)


title: MEF2C_cKO_3

description: Protocol 1

value: M

value: Mef2c cKO (Mef2cfl/fl; Emx1-Cre)


title: PAX8-KO FT194 rep2

city: Naples

first: Stella

last: Zannini

address: Via Pansini 5

country: Italy

institute: CNR IEOS

description: si-RNA Pax8 transfected

data_processing:
Illumina Configure BCL2FASTQ v1.8.4 software used for basecalling.
Sequenced reads were mapped to hg19/GRCh37 whole genome using Tophat 2.0.12
For each sample, Cufflinks was used to estimate the expression level, expressed as Fragment mapped per kilobase of exons per million mapped reads(FPKM)
Differential expression analyses were performed with Cuffdiff2 and expressed as Fragment mapped per kilobase of exons per million mapped reads(FPKM)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt files include FPKM values for each Sample derived from Cufflink analysis
Supplementary_files_format_and_content: xls files include FPKM values derived from CuffDiff analysis

organism: Homo sapiens

source_name: Fallopian tube epithelial cells

growth_protocol: The human ovarian carcinoma cell line SKOV-3 was grown in RPMI medium containing 10% fetal bovine serum. The immortalized Fallopian tube secretory epithelial cell line FT194 was maintained in DME-F12 medium containing 2% Ultroser G serum (PALL).

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (Qiagen). For RNA-seq 2μg of total RNA was  extracted 24h after transfection.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA interference experiments, SKOV-3 and FT194 cells were transfected in replicate with 5 nM of PAX8 siRNA or Non-Targeting siRNA (Ambion, Life Technologies).

value: Immortalized Fallopian tube secretory epithelial cell

tag: sirna

value: si-RNA Pax8 transfected


title: ChIP of dCas9-Dnmt3a + target gRNA (Dazl-Snrpn)

city: New York

first: Xuebing

last: Wu

state: NY

address: 630 West 168th Street

department: Medicine/Systems Biology

institute: Columbia University

description: Dazl-snrpn

data_processing:
reads were mapped to mm10 using STAR (v2.4.2a) with the following option: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --clip3pNbases 16
mapped reads were collapsed using the program samtools rmdup
collapsed reads were sampled from each sample to match sequencing depth
a bam file containing sampled reads were converted to a bigwig file containing normalized read density (rpm, read per million)
pairwise-peak calling was done as described in Wu et al 2014 Nature Biotechnology
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for normalized read density

source_name: V6.5 ES cells

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured on irradiated mouse embryonic fibroblasts (MEFs) with standard ESCs medium: (500 ml) DMEM supplemented with 10% FBS (Hyclone), 10 ug recombinant leukemia inhibitory factor (LIF), 0.1 mM ß-mercaptoethanol (Sigma-Aldrich), penicillin/streptomycin, 1 mM L-glutamine, and 1% nonessential amino acids (all from Invitrogen).

extract_protocol:
Collected cells were washed with PBS twice, and then re-suspended in 3.5 ml of sonication buffer. Sonication was performed for 10 cycles with 0.5 min pulse on and 1 min rest, and 24 watts in ice-water mixture. Then cell lysate was spun down with 14,000 x rpm for 10 min at 4 °C. 50 ul of supernatant was saved as input for gDNA. 10 ul of anti-CTCF antibody (EMD Millipore: 07729) was added and incubate overnight at 4 °C. 50 ul protein G dynabeads was added into antibody-cell lysate mixture and incubate overnight at 4 °C. Then beads were washed with sonication buffer, sonication buffer with high salt (500 mM NaCl), LiCl wash buffer, and TE buffer. Bound protein-DNA complex was eluted from beads by incubation in a 65 °C oven for 15 min, and then reverse cross-linked under 65 °C over-night. The bound DNA was purified with Qiagen QIAquick PCR Purification Kit
Illumina TruSeq DNA sample Preparation v2

treatment_protocol: Cells were cross-linked by 1% formaldehyde in the medium for 10 min in room temperature, and then quenched by adding 0.125 M Glycine for 5 min.

value: Mouse embryonic stem cells (mESCs)


title: WT FT-194 rep4

description: si-RNA Ctr transfected

value: si-RNA Ctr transfected


title: ChIP of dCas9-Dnmt3a + scrambled gRNA

description: scrambled


title: ChIP of dCas9-Dnmt3a + target gRNA (miR290)


title: WT FT-194 rep2

description: si-RNA Ctr transfected


title: input sample prior to IP

description: input


title: WT FT-194 rep3

description: si-RNA Ctr transfected


title: WT FT-194 rep1

description: si-RNA Ctr transfected


title: ChIP of dCas9-Dnmt3a alone


title: PAX8-KO FT194 rep1

description: si-RNA Pax8 transfected


title: ChIP of V6.5 mock cells (without dCas9-Dnmt3a)

description: mock


title: WT SKOV3 rep2

description: si-RNA Ctr transfected

source_name: ovarian cancer cells

value: Human ovarian adenocarcinoma


title: WT SKOV3 rep3

description: si-RNA Ctr transfected


title: PAX8-KO SKOV-3 rep3

description: si-RNA Pax8 transfected


title: RNA_H3.3 K36M_1

city: Madison

first: Peter

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

data_processing:
Reads were aligned using bowtie 1.0.0 with default parameters
Expression for annotated refseq genes was determined using RSEM 1.2.12 with default parameters
Differentially expressed genes were determined using EBSeq 1.1.4 with PPDE > 0.95 and >10-fold change
data matrix was transformed to log2 scale
Genome_build: mm9

source_name: C3H10T1/2 cells

growth_protocol: C3H10T1/2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, CellGro).

extract_protocol:
RNA was isolated using Trizol (Invitrogen).
libraries were prepared according to the Illumina TruSeq protocol

value: C3H embryo-derived mesenchymal multipotent cells

value: Stably expressing FLAG-HA-tagged K36M mutant H3.3

tag: passages

value: Passage 10-15


title: RNA_H3.3 WT_2

value: Stably expressing FLAG-HA-tagged wildtype H3.3


title: RNA_H3.3 K36M_2


title: RNA_H3.3 WT_1


title: PAX8-KO SKOV-3 rep2

description: si-RNA Pax8 transfected


title: H3K27me3_ChIPSeq_H3.3 K36M

description: ChIP-DNA using H3K27me3 antibody (Cell Signaling, 9733)

data_processing:
Reads that passed the quality score were aligned using bowtie 1.0.0 with default parameters
Peaks were called using mosaics (threshold = 20, FDR= 0.05, maxgap = 10000bp, minsize = 5000bp, binSize= 200bp, two component model, Input-Only analysis)
Genome_build: mm9
Supplementary_files_format_and_content: Bed file containing genomic coordinates for K27me3 and K36me3 peaks

extract_protocol:
~2x10^7 cells were lysed using digesting buffer (50 mM Tris-HCl pH 7.6, 1 mM CaCl2 and 0.2% Triton X-100) and digested with micrococcal nuclease to obtain mono-nucleosomes. The chromatin were then dialyzed into RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-Deoxycholate, 1% Triton X-100) for 2 h at 4°C. After centrifugation, soluble chromatin was incubated with 3-5 μg of antibody bound to 75 μl protein A or protein G Dynal magnetic beads (Invitrogen) and incubated overnight at 4°C, with 5% kept as input DNA. Magnetic beads were washed with RIPA buffer and LiCl buffer (0.25 M LiCl, 0.5% NP40, 0.5% Na-Deoxycholate) and chromatin was eluted. ChIP DNA was treated with Proteinase K (Roche) and recovered using Qiagen PCR purification kit.
libraries were prepared according to the Illumina TruSeq protocol


title: H3K36me3_ChIPSeq_H3.3 WT

description: ChIP-DNA using H3K36me3 antibody (active motif, 61101)


title: Input_DNA_H3.3 WT

description: 5% input DNA


title: H3K36me3_ChIPSeq_H3.3 K36M


title: Input_DNA_H3.3 K36M

description: 5% input DNA


title: HFDASBTi16w-Rep2_652

status: Public on Sep 22 2016

city: Atlanta

first: Astrid

last: Kosters

state: Georgia

address: 1760 Haygood Drive

institute: Emory University

data_processing:
RNA-seq data was mapped using Bowtie, version 0.12.7 ; parameters bowtie -v 3 -q -S
Genome_build: NCBI37/mm9, July 2007
Supplementary_files_format_and_content: RPKM values

source_name: Liver

extract_protocol:
Livers were flash frozen in liquid nitrogen, and RNA was isolated using Qiagen miRNA isolation kit.
Libraries were prepared using the Illumina TruSeq™ RNA kit as per manufacturer’s instructions.

treatment_protocol: Male C57/Bl6J mice were started on their respective diets at 4 weeks of age for a total duration of 16 weeks, after which livers were harvested and RNA was isolated and RNA-seq performed.

tag: strain

value: male

value: Liver

tag: diet

value: HFD/ASBTi 16 weeks


title: WT SKOV3 rep1

description: si-RNA Ctr transfected


title: HFDASBTi16w-Rep3_667

tag: tissue


title: HFDASBTi16w-Rep4_668


title: H3K27me3_ChIPSeq_H3.3 WT

tag: genotype


title: PAX8-KO SKOV-3 rep1

description: si-RNA Pax8 transfected


title: HFD-Rep4_664

value: HFD 16 weeks


title: HFD-Rep3_663


title: HFD-Rep1_661


title: HFD-Rep2_662


title: Chow-Rep1_C2

value: chow 16 weeks


title: HFDASBTi16w-Rep1_651


title: Chow-Rep1_C3


title: Chow-Rep1_C8


title: Chow-Rep1_C6


title: MG1655_anaero

city: La Jolla

first: Jonathan

last: Monk

state: California

address: 9226A Regents Rd

institute: UCSD

data_processing:
Gene expression data (3 biological replicates per strain) were analyzed in the statistical software program R (www.r-project.org ) using the EdgeR package (3). Data were normalized using the CQN package, which accounts for both gene length and GC content effects (4). Differentially expressed genes were determined by comparing expression values under anaerobic and aerobic conditions. Those genes with adjusted P values less than 0.01 (i.e., false discovery rate less than 1%) were identified as significantly differentially expressed genes. Finally, gene annotations were automatically made using the biomaRt package (5) together with the annotation files available at the Ensembl database (www.ensembl.org) and gene set enrichment analysis (GSEA) was performed using the piano package (6). All R packages used in this study are available in Bioconductor (www.bioconductor.org).
Supplementary_files_format_and_content: tab-delimited text files include gene expresion values for each Sample

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: Escherichia coli strains E.coli C (DSMZ 4860), E. coli Crooks (DSMZ 1576), E. coli DH5α (DSMZ 6897) E. coli W (DSMZ 1116), E. coli W3110 (DSMZ 5911) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures; E. coli BL21 (DE3) was purchased as competent cells from Agilent (Agilent Technologies Inc., USA), E. coli K-12 MG1655 (ATCC 700926). All strains were cultured in M9 minimal medium (1) containing Na2HPO4 x 7H2O (6.8 g), KH2PO4 (3 g), NaCl (0.5 g), NH4Cl (1 g), MgSO4 (2 mmol), CaCl2 (0.1 mmol), trace elements, Wolf’s vitamin solution (2) and glucose (2 g L-1). Anoxic M9 minimal media with glucose was obtained by flushing solution with oxygen free nitrogen (95%). Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density (OD600) of 0.01. Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml glucose-M9 minimal media in a shaking incubator at 37°C and 250 rpm.

extract_protocol:
Cells were harvested from aerobic and anaerobic cultures of seven E. coli strains grown to an OD600 of 0.6 (exponential phase). Cultures were divided into 10 ml aliquots and were immediately mixed with 0.2 volumes of ice-cold STOP solution (95% ethanol, 5% phenol (pH 4.7)). After 20 min incubation on ice, samples were spun down for 10 min at 4˚C and 7000 x g in a centrifuge. Pellets from one aliquot were gently resuspended in RNAProtect (QIAGEN, Germany) to further stabilize the RNA. Remaining samples were mixed with RNAlater (QIAGEN, Germany) and placed at -80˚C for archival storage. Total RNA was extracted using RNeasy Mini kit (QIAGEN, Germany) and on column DNase treatment following the manufacturers’ instructions. The 23S and 16S rRNAs were removed by subtractive hybridization using the MICROBExpress kit (Ambion, USA) with modifications. Compared with the standard protocol, 50% more capture oligonucleotides and magnetic beads were used. 5S rRNAs (120 nt in length) were removed during the total RNA extraction on column. Specifically, ribosomal depletion on total RNA isolated from the E. coli BL21 (DE3) was performed using RiboZero (Gram Negative Bacteria) kit (Epicenter, USA). RNA samples were stored at -80°C.
The sequencing libraries were constructed using the TruSeq RNA Sample Preparation kit (Illumina Inc., USA). Each library was prepared with RNA isolated from seven E. coli cultures grown in triplicate to an exponential phase under aerobic and anaerobic conditions. RT-PCR was performed with SuperScript® II One-step RT-PCR reagents (Invitrogen, USA). The libraries were sequenced using the Illumina HiSeq2000 platform with a paired-end protocol and read lengths of 50 nt.  The final concentration of DNA and RNA was measured using a Qubit 2.0 Fluorometer (Invitrogen, USA). The integrity of total RNA, DNA contamination, removal of rRNAs and cDNA library validation were assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, USA).


title: MG1655_aero


title: Sample_test_0_SuTpl_rep2

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

data_processing:
We performed single-end 50 bp sequencing on the HiSeq2000 Sequencing System (Illumina, San Diego CA) according to the manufacturer. De-multiplexed reads (Chastity > 0.6) FASTQ output was from Illumina CASAVA v.1.8.2. Reads were mapped to FlyBase release 6 version 4 of the Drosophila melanogaster genome appended with the ERCC sequences (Jiang et al., Genome Research, 2011, PMID 21816910; errors in the original beta-ERCC annotation were corrected: the ERCC-00009, ERCC-00014, ERCC-00057, ERCC-00059, ERCC-00099, ERCC-00108, ERCC-00116 were strand-corrected, and ERCC-00085 was identified as Subpool C). We used STAR (v2.4.2a) (Doblin et al., Bioinformatics, 2012, PMID 23104886) with pre-build annotation (--runMode genomeGenerate). We used HTSeq (v0.6.1p1) (--stranded=reverse) (Anders et al., 2015, Bioinformatics, PMID 25260700) to calculate gene-level read counts, and SAMtools (v0.1.19) (Li et al., Bioinformatics, 2009, PMID 19505943) to index chromosomes and sort alignments.
Genome_build: BDGP release 6 (obtained from FlyBase (http://www.flybase.org)
Supplementary_files_format_and_content: For this sample, there is a tab-delimited text file that contains HTSeq-generated read counts for each gene. There are also two supplementary files for the whole GSE77492 datasets: a tab-delimited file GSE77492_merged.star_htseq_read_count.txt that contains HTSeq-generated read counts for each gene and sample, and a GSE77492_dmel-all-r6.04.ERCC.gtf file that contains the annotation of Drosophila melanogaster (FlyBase release 6 version 4) plus the ERCC spike-ins.

source_name: Testes

growth_protocol: All Drosophila strains were maintained at The University of Geneva. We reared the flies on Drosophila food (per liter: 6.2 g agar, 59 g cornmeal, 59 g yeast, 5 mL propionic acid and 26 mL 99% methyl 4-hydroxybenzoate). Homozygous w*; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 virgin females were crossed to homozygous males carrying a UAS responsive transgene or homozygous males of control lines at 20 oC, and the progeny were reared at that temperature. Adult progeny were collected at 0-4 hours post-eclosion and were placed into fresh vials and shifted to 29 oC as indicated.

extract_protocol: Flies were removed from the indicated incubation temperatures and dissected immediately in Phosphate Buffered Saline solution at room temperature. Each sample was a pool from three flies. The testes were removed at the junction with the vas deferens. Ovaries were removed at the common oviduct, and any eggs in the ovipositor were also removed. Each dissected carcass or gonad was immediately crushed into 100 μL RNAlater solution (Life Technologies, Carlsbad CA) and sealed in a deep-well 96-well plate at room temperature after dissection and during transportation. After the samples arrived at NIH they were stored at -80 oC. For RNA extraction, 20-30 glass beads (1.0 mm dia, BioSpec Products, Bartlesville OK) were added to each well of samples with 100 μL frozen RNAlater. Then we added 600 μL RLT buffer from the RNeasy 96 kit (Qiagen, Valencia CA) to each well. After all samples were completed thawed, we homogenized the samples three times for 60 seconds each with a mini-beadbeater (Biospec Products, Bartlesville OK). Extraction of total RNA was performed using the RNeasy 96 kit according to manufacturer's guide (RNeasy 96 Protocol for Isolation of Total RNA from Animal Cells, III Using spin technology centrifuge), except that we used 700 μL of 70% ethanol (Warner-Graham, Cockeysville MD) in each well to dilute the RNAlater and RLT buffer. We mixed 400 ng of total RNA in 50 μl of nuclease-free water (Quality Biological, Gaithersburg MD). Then we prepared the polyA+ RNA with Dynabeads Oligo(dT)25 (Life Technologies, Carlsbad CA) and followed a strand-specific library preparation pipeline (Lee et al., Plos Genetics, 2016, PMID 27599372). We added to each sample 20 pg of External RNA Control Consortium (ERCC) spike-ins (Lee et al., Journal of Genomics, 2016, PMID 27512518) before the mRNA fragmentation step. In the first plate with all samples from the restrictive temperature experiment, ERCC pool 78A was added for all, except the sham control samples, for which we added ERCC pool 78B. In the second plate with all samples from the permissive temperature experiment, ERCC pool 78B was added for all, except sham control samples, for which we added ERCC pool 78A. Libraries were quantified with Quant-iT PicoGreen (Life Technologies, Carlsbad CA), and pooled for multiplexed sequencing.

value: w* / Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS00277}attP2


title: Sample_test_0_SuTpl_rep4


title: Sample_test_0_lilli_rep2

value: w* / Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS01066}attP2


title: Sample_test_0_SuTpl_rep1


title: Sample_test_0_lilli_rep3


title: Sample_test_0_lacZ_rep4

value: w* / Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{UASp-lacZ}


title: Sample_test_0_lacZ_rep3


title: Sample_test_0_gpp_rep2

value: w* / Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS00160}attP2


title: Sample_test_0_gpp_rep4


title: Sample_test_0_lacZ_rep1


title: Sample_test_0_gpp_rep3


title: Sample_ov_0_SuTpl_rep4

source_name: Ovaries

value: female

value: w* / y[1] sc[*] v[1]; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS00277}attP2


title: Sample_test_0_gpp_rep1


title: Sample_ov_0_SuTpl_rep3


title: Sample_ov_0_SuTpl_rep2


title: Sample_ov_0_lilli_rep3

value: w* / y[1] sc[*] v[1]; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS01066}attP2


title: Sample_ov_0_lilli_rep4


title: Sample_ov_0_lilli_rep1


title: Sample_ov_0_SuTpl_rep1


title: Sample_ov_0_lilli_rep2


title: Sample_ov_0_lacZ_rep4

value: w*; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{UASp-lacZ}


title: Sample_test_0_lacZ_rep2


title: wt_Ler_chipseq_rep3

city: NORWICH

last: Sablowski

state: Norfolk

address: The John Innes Centre

department: CDB

country: United Kingdom

institute: JIC

data_processing:
Reads aligned against the TAIR10 Col-0 reference sequence with Bowtie2 (v2-2.1.0)
Data were sorted and indexed with Samtools to generate .bam files
MACS 2.0.10 was used to call peaks and calculate fold enrichments and q-values, comparing the combined replicates with combined controls.
Filtering: to select peaks that were consistently detected across replicates, peak calling with MACS 2.0.10 was applied to individual replicates and overlapping peak regions were accepted if they had q-values of 10-3 or lower in each RPL:RPL-GFP replicate, were not detected in any of the negative controls and the overlapping region was at least 50 nucleotides long.
Association with gene models: filtered peaks were attributed to gene models within 3 kb upstream or 1.5 kb downstream of the corresponding coding sequence, without intervening coding sequences.
Genome_build: TAIR10
Supplementary_files_format_and_content: Summary table RPL-GFP_overlapping_peaks_and_genes.txt is a tab-delimited text file that lists:  AGI name, Gene start, Gene end, Number of overlapping MACS peaks, Fold enrichment, log10 q-value, Type, Short_description, Computational_description. narrowPeak files and peaks.xls files were generated using MACS 2.0.10; files list chromosome number, nucleotide start, nucleotide end, pileup, -log10 p-value, -log10 q value and peak name.

organism: Arabidopsis thaliana

source_name: inflorescence apices

growth_protocol: Plants were grown in a controlled environment room at 20-22 °C, 16 h light (100 µE) until they flowered and the inflorescences were around 12 cm tall.

extract_protocol:
ChIP was perfored as described in Schiessl et al. 2014, PNAS 111, 2830-2835.
Illumina TruSeq ChIP-Seq libraries were constructed as described in Kaufmann et al, 2009, PLoS Biology 7, e90.
ChIP-seq: 50 bp single-end reads sequenced with Illumina HiSeq 2500 (Rapid-Run mode) as described by the manufacturer.

treatment_protocol: Three biological replicates were used for each treatment. Each replicate was prepared from 1-2 g of fresh tissue, fixed immediately after harvesting.

value: wild-type control (Landsberg-erecta)

tag: chip antibody

value: anti-GFP µMACS Microbeads (Milteyi Biotec)


title: Sample_test_0_SuTpl_rep3


title: Sample_ov_0_lacZ_rep2


title: Sample_ov_0_lacZ_rep3


title: Sample_test_0_lilli_rep4


title: wt_Ler_chipseq_rep1


title: RPL-GFP_chipseq_rep3

value: rpl-1 mutant transformed with genomic contruct expressing a fusion between RPL and GFP (pRPL:RPL-GFP)


title: Sample_ov_0_gpp_rep1

value: w* / y[1] sc[*] v[1]; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS00160}attP2


title: Sample_ov_0_gpp_rep4


title: Sample_ov_0_lacZ_rep1


title: Sample_ov_0_gpp_rep3


title: Sample_m_24_stil_rep3

source_name: Adult whole organisms without gonad

value: male

value: w*/ Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{UASp-stil+}Amm


title: Sample_m_48_stil_rep1


title: Sample_m_48_stil_rep3


title: RPL-GFP_chipseq_rep1


title: wt_Ler_chipseq_rep2


title: Sample_m_24_stil_rep1


title: RPL-GFP_chipseq_rep2


title: 5hmC C57BL6/j liver (W8) rep2

city: Tokyo

first: Mayumi

last: Oda

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

institute: Keio University

description: single end, 50bp

data_processing:
For paired-end reads, BAM files were generated from PE75 reads mapped by Bowtie2. For single-end reads, BAM files were generated from SE50 reads mapped as pretended paired-end reads with 250 bp length.
From generated BAM files, frequency per kilobase per million reads (FPKM) were calculated for promoter (from TSS-2000 to TSS+2000) and gene body (From TSS+2000 to TES) regions for each Ensemble gene record. To remove the replicates for gene symbols, a gene record with the longest genomic length was chosen for a gene symbol and subjected for the calculation.
Genome_build: mm9
Supplementary_files_format_and_content: frequency per kilobase per million reads (FPKM) were calculated for promoter (from TSS-2000 to TSS+2000) and gene body (From TSS+2000 to TES) regions for each Ensemble gene record

source_name: C57BL6/j liver, whole tissue

growth_protocol: Embryonic stem cells are cultured in LIF supplemented ES medium (Dulbecco’s modified medium+15%FBS+GlutaMax+nonessential amino acid+0.5nM 2-mercaptoethanol+penicilin/streptmicin ). Cells were passed every 3 days.

extract_protocol:
Genomic DNA was extracted from cell pellets or frozen tissues. cell pellets were lysed in [lysis buf+ SDS+proK]. Tissues were ground and lysed in lysis buffer. After the overnight digestion and 1hr RNAse treatment, DNA was extracted by PCI and ethanol precipitation. DNA pellet was dissolved in TE and stay in 4C for 2 days to completely dissolve.
Genomic DNA was fragmented around 300 bp length by Covaris. Fragmented DNA and UDP-azide-glucose was incubated with T4 BGT (NEB) with at 37°C overnight and perform biotin conjugation. Biotinylated DNA was purified, captured by streptavidin beads, washed and eluted. Eluted DNA was purified and subjected to construct DNA library using ChIP-seq Library Prep Master Mix Set with Q5 (NEB). The size of library was checked by BioAnalyzer2000 DNA high sensitivity (Agilent Technology) and the quantity was measured using  KAPA Library Quantification Kits (Illumina).
OTHER (hMe-Seal)

treatment_protocol: Heart and liver tissues were dissected from embryonic day 14, neonatal day 1 and 8-week adult mice and snap frozen by liquid N2.

value: liver, whole tissue

tag: age

value: 8 weeks

tag: strain background

value: C57BL6/j mouse strain


title: 5hmC C57BL6/j heart (W8) rep2

description: single end, 50bp

source_name: C57BL6/j heart, whole tissue

value: heart, whole tissue


title: Sample_m_0_stil_rep2


title: Sample_test_0_lilli_rep1

value: w* / Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS01066}attP2


title: Sample_m_48_stil_rep2


title: 5hmC C57BL6/j heart (E14) rep1

description: single end, 50bp

value: embryonic day 14


title: Sample_ov_0_gpp_rep2


title: Sample_m_0_stil_rep4


title: Sample_m_24_stil_rep2


title: Sample_f_48_stil_rep2

value: w*/ w1118; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{UASp-stil+}Amm


title: 5hmC C57BL6/j liver (E14) rep1

description: single end, 50bp


title: 5hmC C57BL6/j liver (W8) rep1

description: single end, 50bp


title: 5hmC C57BL6/j heart (W8) rep1

description: single end, 50bp


title: Sample_m_0_stil_rep3


title: Sample_m_0_stil_rep1


title: clone19_3

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

data_processing:
Single-end 50 bp reads generated on Illumina HiSeq were aligned to the human genome version GRCm38.74 using TopHat v2.0.4 (Trapnell et al., 2009). Read counts were obtained using HTSeq-count v0.5.3p9 (Anders et al., 2014), normalised and tested for differential gene expression using the Bioconductor package DESeq v1.10.1 (Anders and Huber, 2010).
Multiple testing corrections were applied using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). Genes were selected as differentially expressed such that FDR < 0.01.
Genome_build: GRCm38.74
Supplementary_files_format_and_content: HTSeq-count gene counts

source_name: Kidney cells

growth_protocol: cells grown in DMEM+10%FBS supplemented with 0.05mg/mL uridine

extract_protocol:
Qiagen Rneasy Plus Mini kit (74136)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Immortalised mouse epithelial cells

value: Fh1 deletion


title: Sample_f_48_stil_rep1

value: female


title: clone19_2


title: clone19_4


title: clone19_5


title: Sample_f_24_stil_rep2


title: clone1_2


title: Sample_f_24_stil_rep1


title: Sample_f_0_stil_rep3


title: Sample_f_48_stil_rep3


title: clone1_3


title: clone1_1


title: clone1_5


title: Sample_f_0_stil_rep4


title: clone1_4


title: Sample_m_48_w_rep3

value: w*/ Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / +


title: Sample_f_0_stil_rep1


title: Sample_f_0_stil_rep2


title: Sample_m_48_w_rep2


title: Rec_5

value: Fh1 wt re-expressed


title: Rec_4


title: Sample_m_48_w_rep1


title: Rec_2


title: Sample_m_48_SuTpl_rep1

value: w* / Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS00277}attP2


title: Sample_m_48_SuTpl_rep3


title: Sample_m_48_lilli_rep3


title: clone19_1


title: Rec_3


title: Sample_m_48_lilli_rep2


title: Sample_m_48_lacZ_rep3

value: w* / Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{UASp-lacZ}


title: Fh1_fl_fl_4

value: Fh1 wt


title: Sample_m_48_SuTpl_rep2

value: male


title: Sample_m_48_gpp_rep2

value: w* / Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS00160}attP2


title: Fh1_fl_fl_1


title: Sample_m_48_lacZ_rep2


title: Sample_m_48_gpp_rep3


title: Rec_1


title: Sample_m_48_gpp_rep1


title: Fh1_fl_fl_5


title: 5hmC C57BL6/j liver (P1) rep2

description: paired end, 75bp

value: liver, whole tissue

value: neonatal day 1-2


title: Fh1_fl_fl_3


title: 5hmC C57BL6/j heart (P1) rep1

description: paired end, 75bp

value: C57BL6/j mouse strain


title: 5hmC EB5 rep2

description: paired end, 75bp

source_name: EB5 embryonic stem cell line

value: embryonic stem cell line

value: day3, culture with LIF

value: 129/Ola mouse strain


title: Sample_m_48_lacZ_rep1


title: 5hmC EB5 rep1

description: paired end, 75bp


title: 5hmC C57BL6/j liver (P1) rep1

description: paired end, 75bp


title: Sample_m_48_lilli_rep1

value: w* / Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS01066}attP2


title: 5hmC C57BL6/j heart (P1) rep2

description: paired end, 75bp

value: heart, whole tissue


title: Fh1_fl_fl_2

value: Immortalised mouse epithelial cells


title: Sample_m_48_DNifm_rep3

value: w* / Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{UASp-Cdk9DN}Ifm1


title: Sample_m_48_DNifm_rep2


title: Sample_m_24_w_rep2

value: w*/ Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / +


title: Sample_m_48_DNifm_rep1


title: Sample_m_48_DNifmDNcff_rep3

value: w* / Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{UASp-Cdk9DN}Ifm1, P{UASp-Cdk9DN}Cff1


title: Sample_m_48_DNifmDNcff_rep2


title: Sample_m_48_DNifmDNcff_rep1


title: Crooks_aero

organism: Escherichia coli

value: Crooks


title: Sample_m_24_w_rep1


title: Crooks_anaero


title: Sample_m_24_SuTpl_rep3

value: w* / Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS00277}attP2


title: Sample_m_24_SuTpl_rep1


title: Sample_m_24_lacZ_rep3

value: w* / Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{UASp-lacZ}


title: Sample_m_24_w_rep3

value: male


title: Sample_m_24_SuTpl_rep2


title: Sample_m_24_lilli_rep1


title: Sample_m_24_lilli_rep2


title: Sample_m_24_lacZ_rep1


title: Sample_m_24_gpp_rep2

value: w* / Y; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS00160}attP2


title: Sample_m_24_gpp_rep3


title: Sample_m_24_DNifm_rep3


title: Sample_m_24_gpp_rep1


title: A422_113_07724_Day28_F_L7.D707

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

institute: Regeneron

data_processing:
Alignment STAR version 2.3.1d
Sequenced reads were filtered for low-quality sequence and the presence of 'N's, then mapped to hg19 whole genome using STAR 2.3.1d
HTSEQ was used to map the reads to the genes
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file includes gene counts for all samples as mapped by HTSEQ

source_name: PBMC

extract_protocol:
Paxgene RNA
TruSeq Stranded Total RNA Sample Prep Kit
50bp PE

treatment_protocol: PBMC collected on days 0, 14, 28, 56, 84 and 182 were suspended in TRIzol (Life Technologies, Inc.), and frozen

value: PBMC

tag: group

tag: day

tag: subjectid


title: A422_112_07724_Day14_F_L7.D706


title: A422_115_07724_Day84_F_L7.D709


title: Sample_m_24_DNifm_rep1


title: A422_114_07724_Day56_F_L7.D703


title: A422_111_07724_Day00_F_L7.D705


title: Sample_m_24_DNifmDNcff_rep3


title: Sample_m_24_DNifmDNcff_rep1


title: Sample_m_24_lacZ_rep2


title: Sample_m_0_w_rep4


title: Sample_m_0_w_rep3


title: Sample_m_24_lilli_rep3


title: Sample_m_0_w_rep2


title: A422_27_06923_Day14_B_L6.D706


title: Sample_m_0_SuTpl_rep3


title: A422_28_06923_Day28_B_L6.D707


title: Sample_m_24_DNifm_rep2


title: A422_26_06923_Day00_B_L6.D705


title: A422_120_06620_Day84_F_L8.D702


title: Sample_m_0_SuTpl_rep1


title: Sample_m_0_w_rep1


title: A422_118_06620_Day28_F_L8.D712


title: Sample_m_0_SuTpl_rep2


title: Sample_m_0_lilli_rep4


title: A422_119_06620_Day56_F_L8.D701


title: A422_117_06620_Day14_F_L8.D711


title: Sample_m_0_lilli_rep3


title: A422_116_06620_Day00_F_L8.D710


title: A422_29_06923_Day56_B_L6.D708


title: A422_79_06119_Day56_D_L8.D709


title: Sample_m_0_lilli_rep2


title: Sample_m_0_lilli_rep1


title: Sample_m_0_lacZ_rep4


title: A422_80_06119_Day84_D_L8.D710


title: A422_30_06923_Day84_B_L6.D709


title: Sample_m_0_lacZ_rep3


title: A422_76_06119_Day00_D_L7.D706


title: A422_77_06119_Day14_D_L8.D707


title: A422_78_06119_Day28_D_L8.D708


title: Sample_m_0_lacZ_rep2


title: Sample_m_0_SuTpl_rep4


title: Sample_m_0_gpp_rep4


title: A422_48_05916_Day28_C_L2.D703


title: Sample_m_0_gpp_rep3


title: A422_47_05916_Day14_C_L2.D702


title: Sample_m_24_DNifmDNcff_rep2


title: Sample_m_0_gpp_rep2


title: A422_5_05818_Day84_A_L1.D708


title: Sample_m_0_DNifm_rep4


title: A422_3_05818_Day28_A_L1.D706


title: Sample_m_0_DNifm_rep2


title: Sample_m_0_DNifm_rep3


title: A422_4_05818_Day56_A_L1.D707


title: Sample_m_0_gpp_rep1


title: A422_2_05818_Day14_A_L1.D705


title: A422_46_05916_Day00_C_L2.D701


title: Sample_m_0_DNifm_rep1


title: Sample_m_0_DNifmDNcff_rep4


title: Sample_m_0_DNifmDNcff_rep3


title: A422_84_05515_Day56_E_L1.D702


title: A422_1_05818_Day00_A_L1.D704


title: A422_49_05916_Day56_C_L2.D704


title: Sample_f_48_w_rep3

value: female


title: Sample_m_0_DNifmDNcff_rep1


title: Sample_m_0_DNifmDNcff_rep2


title: A422_83_05515_Day28_E_L1.D701


title: Sample_f_48_SuTpl_rep3

value: w* / y[1] sc[*] v[1]; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS00277}attP2


title: A422_82_05515_Day14_E_L1.D712


title: Sample_f_48_w_rep2


title: A422_90_04114_Day84_E_L2.D708


title: A422_87_04114_Day14_E_L2.D702


title: Sample_f_48_w_rep1


title: A422_88_04114_Day28_E_L2.D706


title: A422_85_05515_Day84_E_L1.D703


title: A422_89_04114_Day56_E_L2.D707


title: A422_81_05515_Day00_E_L1.D711


title: A422_99_03310_Day56_E_L4.D705


title: Sample_m_0_lacZ_rep1


title: Sample_f_48_SuTpl_rep2


title: A422_86_04114_Day00_E_L2.D704


title: Sample_f_48_lilli_rep2

value: w* / y[1] sc[*] v[1]; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS01066}attP2


title: Sample_f_48_lilli_rep3


title: Sample_f_48_lacZ_rep3

value: w*; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{UASp-lacZ}


title: A422_100_03310_Day84_E_L4.D706


title: Sample_f_48_lilli_rep1


title: A422_55_03211_Day84_C_L3.D709


title: Sample_f_48_lacZ_rep1


title: Sample_f_48_lacZ_rep2


title: Liver_tissue_from_24h_fasting_mice_rep4

first: Haiming

last: Cao

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description:
Sample 8
Liver tissue from 24h fasting mice, biological replicate 4

data_processing:
Illumina bcl2fastq v2.17 software was used for basecalling.
The raw reads were mapped to the NONCODE 2016 mouse database using BWA (bwa aln; bwa sampe with the default parameters).
Proper-paired reads were then counted on each noncoding transcript to calculate the RPKM by normalizing the read count on each transcript with transcript length and total library size. Transcripts with RPKM >= 0 in at least one sample were retained.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file include NONCODE transcript IDs, annotations, raw reads, and RPKM values for all 8 Samples.

source_name: Liver tissue from 24h fasting mice

extract_protocol:
Total RNAs were extracted by Trizol reagent (Invitrogen) according to the manufacturer's instructions. Total RNA Cleanup with Dnase Digestion was performed using the Qiagen Rneasy Protocol.
The libraries were prepared from 1 ug of total RNA using the TruSeq® Stranded Total RNA Sample Preparation kit following manufacturer’s protocol (Illumina). Libraries were validated by Illumina miseq as recommended by the manufacturer.

treatment_protocol: Male C57BL/6 mice from the Jackson Laboratory were used for all experiments. Groups of co-housed mice were randomly assigned to experimental groups with age and weight matched between groups. Mice of around 20 weeks of age were either allowed free access to food or were subjected to a 24-hour fast before being euthanized for tissue harvest (sacrificed at 10am).

value: Liver

tag: condition

value: 24h fasting


title: Liver_tissue_from_24h_fasting_mice_rep3

description:
Sample 7
Liver tissue from 24h fasting mice, biological replicate 3


title: A422_97_03310_Day14_E_L4.D703


title: Liver_tissue_from_24h_fasting_mice_rep2

description:
Sample 6
Liver tissue from 24h fasting mice, biological replicate 2


title: Sample_f_48_SuTpl_rep1

tag: Sex


title: Sample_f_48_gpp_rep3

value: w* / y[1] sc[*] v[1]; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS00160}attP2


title: A422_54_03211_Day56_C_L3.D701


title: Sample_f_48_gpp_rep2


title: Sample_f_48_gpp_rep1


title: A422_52_03211_Day14_C_L3.D706


title: Liver_tissue_from_ad_libitum_mice_rep2

description:
Sample 2
Liver tissue from ad libitum mice, biological replicate 2

source_name: Liver tissue from ad libitum mice

value: Ad libitum


title: A422_53_03211_Day28_C_L3.D707


title: Liver_tissue_from_ad_libitum_mice_rep4

description:
Sample 4
Liver tissue from ad libitum mice, biological replicate 4


title: A422_96_03310_Day00_E_L4.D702


title: Sample_f_48_DNifm_rep2

value: w* / w1118; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{UASp-Cdk9DN}Ifm1


title: Liver_tissue_from_ad_libitum_mice_rep3

description:
Sample 3
Liver tissue from ad libitum mice, biological replicate 3


title: Liver_tissue_from_ad_libitum_mice_rep1

description:
Sample 1
Liver tissue from ad libitum mice, biological replicate 1


title: A422_98_03310_Day28_E_L4.D704


title: Sample_f_48_DNifm_rep3


title: A422_51_03211_Day00_C_L2.D705


title: A422_35_02809_Day84_B_L7.D702


title: A422_34_02809_Day56_B_L5.D705


title: Sample_f_48_DNifm_rep1


title: DhepA-C

city: jinan

first: Zhang

last: Xiujun

state: shandong province

address: south road of shanda

country: China

institute: shandong university

data_processing:
Base-calling using Illumina Casava 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence.
Reads were mapped to Penicillium oxalicum 114-2 coding sequences using SOAPaligner/SOAP2 v2.21 with parameters -m 0 -x 10000 -s 28 -l 32 -v 3 -p 3
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Penicillium oxalicum 114-2 sequences (NCBI accession: PRJNA60877)
Supplementary_files_format_and_content: One matrix table in Excel .xlsx format includes unique reads numbers, coverage and RPKM values for each genes. Samples were named according to the names of raw files.

organism: Penicillium oxalicum

source_name: Fungal mycelia

growth_protocol: The conidia of Penicillium oxalicum were inoculated in modifeid Czapek culture medium with 2% glucose as carbon resource for 20 h at 30 °C as the pre-culture, and then mycelia were transferred and grown in the new medium for 48 h.

extract_protocol:
Total RNA was prepared from the mycelia by grinding under liquid nitrogen with a mortar and pestle, followed by extraction using the RNAisoTM reagent (TaKaRa, Japan) according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mycelia were filtered by filter paper.

value: hepA deletion

tag: medium

value: Modifeid Czapek culture medium with 1% wheat bran and 1% cellulose as carbon resource

tag: culture time

value: 48 h after transferring washed mycelia to the new medium


title: A422_33_02809_Day28_B_L7.D712


title: Sample_f_48_DNifmDNcff_rep3

value: w* / w1118; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{UASp-Cdk9DN}Ifm1, P{UASp-Cdk9DN}Cff1


title: WT-C

value: wild type


title: A422_31_02809_Day00_B_L7.D710


title: WT-G

value: Modifeid Czapek culture medium with 2% glucose as carbon resource


title: Sample_f_48_DNifmDNcff_rep1


title: A422_32_02809_Day14_B_L7.D711


title: Liver_tissue_from_24h_fasting_mice_rep1

description:
Sample 5
Liver tissue from 24h fasting mice, biological replicate 1


title: Sample_f_48_DNifmDNcff_rep2


title: A422_105_02730_Day84_F_L5.D711


title: A422_104_02730_Day56_F_L5.D710


title: A422_103_02730_Day28_F_L5.D709


title: Sample_f_24_SuTpl_rep3


title: Sample_f_24_w_rep3


title: A422_9_02408_Day56_A_L2.D712


title: A422_102_02730_Day14_F_L5.D708


title: Sample_f_24_SuTpl_rep1


title: A422_101_02730_Day00_F_L5.D707


title: DhepA-G


title: Sample_f_24_lilli_rep3


title: Sample_f_24_lilli_rep2


title: A422_7_02408_Day14_A_L2.D710


title: A422_8_02408_Day28_A_L2.D711


title: Sample_f_24_lacZ_rep2


title: Sample_f_24_gpp_rep3


title: A422_6_02408_Day00_A_L2.D709


title: Sample_f_24_gpp_rep2


title: A422_10_02408_Day84_A_L2.D701


title: A422_72_01803_Day14_D_L7.D702


title: Sample_f_24_lilli_rep1


title: Sample_f_24_gpp_rep1


title: A422_75_01803_Day84_D_L7.D705


title: A422_74_01803_Day56_D_L7.D704


title: Sample_f_24_SuTpl_rep2


title: A422_73_01803_Day28_D_L7.D703


title: A422_20_01704_Day84_A_L4.D711


title: Sample_f_24_w_rep2


title: Sample_f_24_w_rep1


title: A422_71_01803_Day00_D_L6.D701


title: Sample_f_24_lacZ_rep3


title: Sample_f_24_DNifm_rep3


title: Sample_f_24_DNifm_rep2


title: A422_19_01704_Day56_A_L4.D710


title: Sample_f_0_w_rep4


title: A422_18_01704_Day28_A_L4.D709


title: Sample_f_0_w_rep3


title: A422_44_00301_Day56_C_L1.D711


title: Sample_f_0_w_rep2


title: A422_43_00301_Day28_C_L1.D710


title: Sample_f_24_DNifm_rep1


title: Sample_f_24_DNifmDNcff_rep2


title: Sample_f_24_lacZ_rep1


title: A422_17_01704_Day14_A_L4.D708


title: Sample_f_0_SuTpl_rep2


title: Sample_f_24_DNifmDNcff_rep1


title: A422_16_01704_Day00_A_L4.D707


title: Sample_f_0_SuTpl_rep4


title: A422_42_00301_Day14_C_L1.D709


title: A422_93_07221_Day28_E_L3.D711

value: BCG


title: Sample_f_0_lilli_rep3


title: A422_92_07221_Day14_E_L3.D710

value: PBMC


title: A422_41_00301_Day00_C_L1.D708


title: Sample_f_0_lilli_rep2

value: female


title: Sample_f_0_SuTpl_rep1

value: w* / y[1] sc[*] v[1]; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS00277}attP2


title: Sample_f_0_SuTpl_rep3


title: A422_94_07221_Day56_E_L3.D712


title: Sample_f_0_lilli_rep1

value: w* / y[1] sc[*] v[1]; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS01066}attP2


title: A422_45_00301_Day84_C_L1.D712


title: Sample_f_0_lilli_rep4


title: A422_91_07221_Day00_E_L3.D709


title: A422_40_06822_Day84_B_L8.D707


title: A422_95_07221_Day84_E_L3.D701


title: A422_39_06822_Day56_B_L8.D706


title: A422_38_06822_Day28_B_L8.D705


title: A422_37_06822_Day14_B_L8.D704


title: Sample_f_0_lacZ_rep3

value: w*; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{UASp-lacZ}


title: Sample_f_0_lacZ_rep1


title: A422_36_06822_Day00_B_L8.D703


title: Sample_f_0_lacZ_rep4


title: A422_110_06017_Day84_F_L6.D704


title: Sample_f_0_gpp_rep4


title: Sample_f_0_gpp_rep3


title: A422_109_06017_Day56_F_L6.D703


title: epithelial cells tg rep3

city: Zurich

first: Isabelle

last: Frey-Wagner

address: Raemistr. 100

department: Division of Gastroenterology

country: Switzerland

institute: University hospital Zurich

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality ends
Quality assessment based on the remaining reads using the FASTQC quality control tool version 0.10.
RSEM v1.2.11 was used for mapping and quantification against the mouse transcriptome
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include Identifier and quantification measures (TMP, FPKM) from RSEM

source_name: epithelial cells

extract_protocol:
Whole colon wall samples (10 mm in length, approximately 10 – 20 mm proximal to the rectum) or epithelial cells were homogenized mechanically in RLT buffer and mRNA was isolated using RNeasy Mini Kit in a QIACUBE operating facility (Qiagen, Venlo, Netherlands) according to the manufacturer`s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: epithelial cells


title: epithelial cells tg rep4


title: Sample_f_0_gpp_rep2


title: epithelial cells wt rep4

value: VilCre


title: epithelial cells tg rep1


title: epithelial cells tg rep2


title: A422_108_06017_Day28_F_L6.D702


title: Sample_f_0_gpp_rep1

value: w* / y[1] sc[*] v[1]; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{TRiP.HMS00160}attP2


title: A422_107_06017_Day14_F_L6.D701


title: epithelial cells wt rep3


title: Sample_f_0_DNifm_rep4


title: Sample_f_0_lacZ_rep2


title: Sample_f_0_DNifm_rep3


title: A422_64_05113_Day56_D_L5.D706


title: A422_106_06017_Day00_F_L6.D712


title: colon tg DSS rep4

source_name: colon

value: Dextran Sulfate Sodium

value: colon


title: epithelial cells wt rep2


title: A422_65_05113_Day84_D_L5.D707


title: Sample_f_0_DNifm_rep2

value: w* / w1118; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{UASp-Cdk9DN}Ifm1


title: Sample_f_0_DNifm_rep1


title: A422_63_05113_Day28_D_L5.D705


title: colon tg DSS rep2


title: Sample_f_0_DNifmDNcff_rep4


title: Sample_f_0_DNifmDNcff_rep3


title: A422_62_05113_Day14_D_L5.D704


title: epithelial cells wt rep1


title: A422_61_05113_Day00_D_L4.D703


title: colon wt DSS rep4


title: A422_15_03612_Day84_A_L3.D706


title: Sample_f_0_DNifmDNcff_rep1


title: colon wt DSS rep3


title: A422_14_03612_Day56_A_L3.D705


title: A422_13_03612_Day28_A_L3.D704


title: control_RPE

city: Beijing

first: zi

last: ye

address: FuXing Road 28

institute: PLA General Hospital

data_processing:
Sequenced reads were aligned to the hg19 human genome using Bowtie with Tophat. Only reads that had at most 2 mismatches and 2 gaps to the hg19 genome were accepted.
To assess the transcript level in sample and control, reads per kilobase of transcript per million mapped reads (RPKM) value was calculated.
The numbers of mapped reads were calculated for each miRNA and the read count of each unique sequence was normalized using the reads per million (RPM) normalization according to the formula: RPM = (number of reads mapping to miRNA reference/total number of mapped reads) * 106. Differential expression analysis was performed by Cuffdiff .
Each sequence was annotated by simply aligning to known RNA sequences that downloaded from Rfam11.0 (rfam.janelia.org, rRNA, snRNA, snoRNA), miRBase (http://microrna.sanger.ac.uk/sequences/index.shtml, release version 21.0, miRNA), UCSC (http://genome.ucsc.edu, tRNA) and pirnabank (http://pirnabank.ibab.ac.in/, piRNA). Novel miRNAs were predicted by miREAP algorithm according to the manual. RNA secondary structures were predicted by RNAfold.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: all genes txt file includes gene, Pos Strand, control Count, CLU group Count, log2(Fold_change), p-value, q-value, Description, Web

source_name: Retinal Pigment Epithelial (RPE) cells_control

growth_protocol: Human adult RPE cells D407 were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 μg/ml streptomycin, 100 U/ml penicillin and 2.5 μg/ml amphotericin B at 37 °C/95% in 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated from D407 cells using Trizol reagent (Invitrogen) according to the manufacturer’s protocol. RNA sample was treated with DNase I (Invitrogen) to remove DNA. RNA quality was analyzed by Nanodrop and gel electrophoresis. RNA samples were then stored at -80 °C for sequencing libraries construction.
To sequence lncRNA associated with function of clusterin on RPE cell, mRNA library was constructed according to Illumina manufacturer’s instruction. Briefly, mRNA was enriched using oligo (dT) magnetic beads and then interrupted to ~ 200bp short fragments. First-strand cDNA was synthesized using random hexamer primer and then the second strand was synthesized.

treatment_protocol: For 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium (MTT) viability D407 cell were trypsinized and seeded into 96-well plate at a density of 104/well. After reaching 90% confluence, the medium was removed and treated with clusterin.

value: Human RPE cells

tag: cell line

tag: agent

value: control


title: Sample_f_0_DNifmDNcff_rep2

value: w* / w1118; +; P{tubP-GAL4}LL7, P{tubP-GAL80ts}7 / P{UASp-Cdk9DN}Ifm1, P{UASp-Cdk9DN}Cff1


title: CLU_RPE

source_name: Retinal Pigment Epithelial (RPE) cells_clusterin-treated

value: clusterin


title: A422_12_03612_Day14_A_L3.D703


title: colon wt DSS rep1

tag: strain


title: colon tg DSS rep3

tag: tissue


title: A422_11_03612_Day00_A_L3.D702


title: colon tg water rep3

tag: genotype


title: A422_60_02507_Day84_C_L4.D702


title: CATCH_MYC_experimental

city: Chicago

first: Hari

last: Singhal

state: IL

address: 929 E 57th St

department: Ben May Department for Cancer Research

institute: University of Chicago

description: Processed is the unfixed data subtracted from the experimental

data_processing:
Library strategy: CATCH-Seq
1.       Subtract the unfixed pulldown data from the experimental pulldown data (bigwig files; obtained from aligning the FASTQ files to HG19 genome using Bowtie; subtraction of datasets is processed using Galaxy DeepTools)
2.       The bigwig files are essentially raw output, minimally processed in galaxy ß these are not already-called peaks
3.       Output that subtraction as a bedgraph file (this can all be done in Galaxy DeepTools, http://deeptools.ie-freiburg.mpg.de/, bigwigcompare tool) ß also not already-called peaks
4.       Upload the bedgraph files into R code submitted along with the manuscript
5.       The bedgraph files get subsetted by chromosome of interest
6.       And then subsetted by signal threshold (in our code the threshold is auto-set based on the # of promoter interactions we want to discover)
7.       The identification of that threshold determines the signal strength at which you “call peaks” (anything above the threshold is a peak)
8.       Annotate the gene promoters that have “peaks” within 2k of their promoters
Genome_build: HG19
Supplementary_files_format_and_content: bedgraph

source_name: CATCH on chr8 at enhancer downstream of MYC (experimental)

growth_protocol: 37C, 50% confluency, RPMI media w/ 10% FBS

extract_protocol:
Capture of Associated Targets on Chromatin (CATCH)
Standard genomic DNA library preparation with Kappa library kit

treatment_protocol: 10 nM estradiol for all except SIAH2_VEH_CATCH, which was treated with ethanol


title: CATCH_SIAH2_unfixed

source_name: CATCH on chr3 downstream of SIAH2 (unfixed)


title: A422_59_02507_Day56_C_L4.D701


title: CATCH_MYC_unfixed

source_name: CATCH on chr8 at enhancer downstream of MYC (unfixed)


title: colon tg DSS rep1


title: colon tg water rep2


title: colon tg water rep1


title: CATCH_SIAH2_E2_experimental

source_name: CATCH on chr3 downstream of SIAH2 after 10nM E2 treatment, rep2 (experimental)


title: colon wt water rep4


title: A422_58_02507_Day28_C_L4.D712


title: CATCH_EIF4A1_rep2_unfixed

source_name: CATCH on chr17 at EIF4A1 promoter rep 2 (unfixed)


title: colon wt DSS rep2


title: colon wt water rep3


title: A422_25_02005_Day84_B_L5.D704


title: CATCH_EIF4A1_rep1_unfixed

source_name: CATCH on chr17 at EIF4A1 promoter rep 1 (unfixed)


title: CATCH_EIF4A1_rep2_experimental

source_name: CATCH on chr17 at EIF4A1 promoter rep 2 (experimental)


title: colon wt water rep1


title: A422_56_02507_Day00_C_L3.D710


title: colon tg water rep4


title: colon wt water rep2


title: CATCH_Chr17_rep2_unfixed

source_name: CATCH 'control' on chr17 rep 2 (unfixed)


title: A422_24_02005_Day56_B_L5.D703


title: A422_23_02005_Day28_B_L5.D702


title: CATCH_EIF4A1_rep1_experimental

source_name: CATCH on chr17 at EIF4A1 promoter rep 1 (experimental)


title: CATCH_Chr17_rep2_experimental

source_name: CATCH 'control' on chr17 rep 2 (experimental)


title: A422_22_02005_Day14_B_L7.D704

source_name: PBMC


title: A422_21_02005_Day00_B_L5.D712


title: CATCH_Chr17_rep1_experimental

source_name: CATCH 'control' on chr17 rep 1 (experimental)


title: A422_57_02507_Day14_C_L4.D711


title: CATCH_Chr17_rep1_unfixed

source_name: CATCH 'control' on chr17 rep 1 (unfixed)


title: CATCH_SIAH2_VEH_experimental

source_name: CATCH on chr3 downstream of SIAH2 after ethanol treatment, rep1 (experimental)


title: A422_68_00202_Day28_D_L6.D710


title: A422_70_00202_Day84_D_L6.D712


title: A422_67_00202_Day14_D_L6.D709


title: UOK262pFH_rep10

data_processing:
Single-end 50 bp reads generated on Illumina HiSeq were aligned to the human genome version GRCh37.64 using TopHat v2.0.4 (Trapnell et al., 2009). Read counts were obtained using HTSeq-count v0.5.3p9 (Anders et al., 2014), normalised and tested for differential gene expression using the Bioconductor package DESeq v1.10.1 (Anders and Huber, 2010).
Multiple testing corrections were applied using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). Genes were selected as differentially expressed such that FDR < 0.01.
Genome_build: GRCh37.64
Supplementary_files_format_and_content: HTSeq-count gene counts

source_name: mediastinum metastasis

growth_protocol: cells grown in DMEM+10%FBS

value: Immortalised human mediastinum metastastic cells

tag: disease

value: HLRCC patient

tag: genotype/variation

value: Fh1 wt re-expressed


title: A422_66_00202_Day00_D_L5.D708

value: PBMC

value: BCG


title: UOK262pFH_rep8


title: UOK262pFH_rep9


title: UOK262pFH_rep7


title: UOK262pFH_rep6


title: UOK262pFH_rep5


title: UOK262pFH_rep4


title: Tricuspid aortic valve_non-calcified_YBO063

city: Quebec

first: Sandra

last: Guauque-Olarte

address: 2725, chemin Sainte-Foy

country: Canada

institute: CRIUCPQ

description: duplicate of GSM1338138

data_processing:
Illumina CASAVA software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to Hg19 whole genome using tophat v2.0.9-1 (-r85 --mate-std-dev 75) and bowtie v1.0.0-1 (Trapnell, Nat Biotechnol. 2013;31:46-53)
The aligned reads were assembled by Cufflinks program to produce transcripts annotated to the same reference genome. The tool Cuffdiff of Cufflinks was utilized to quantify the transcriptomes and compare them across calcified and normal tricuspid valves  (Trapnell, Nat Biotechnol. 2013;31:46-53).
Genome_build: Hg19
Supplementary_files_format_and_content: Tab-delimited text files include genes FPKMs and isoforms FPKMs.

source_name: Human aortic valve leaflet

extract_protocol:
RNA was extracted from 30 mg and 100 mg of normal and calcified tissue, respectively, using a modified TRIzol protocol followed by RNA cleanup using QIAGEN RNeasy Mini Kit. Illumina TruSeq RNA Sample Prep Kit was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

tag: gender

value: Male

value: Non-calcified tricuspid aortic valve (TAV)


title: Tricuspid aortic valve_non-calcified_YBO048

description: duplicate of GSM1338141


title: Tricuspid aortic valve_non-calcified_YBO037

description: duplicate of GSM1338140


title: Tricuspid aortic valve_non-calcified_YBO043

description: duplicate of GSM1338135


title: Tricuspid aortic valve_non-calcified_YBO051

description: duplicate of GSM1338136


title: UOK262pFH_rep2

tag: cell type


title: UOK262pFH_rep1


title: Tricuspid aortic valve_non-calcified_YBO040

description: duplicate of GSM1338133


title: UOK262_rep14


title: Tricuspid aortic valve_calcified_YBO044

description: duplicate of GSM1338131

value: Calcified tricuspid aortic valve (TAV)


title: UOK262_rep15


title: Tricuspid aortic valve_calcified_YBO046

description: duplicate of GSM1338132


title: UOK262_rep17


title: Tricuspid aortic valve_calcified_YBO062

description: duplicate of GSM1338129


title: A422_69_00202_Day56_D_L6.D711

tag: group

tag: day


title: UOK262_rep16


title: UOK262_rep13


title: Tricuspid aortic valve_calcified_YBO054

description: duplicate of GSM1338130


title: UOK262_rep10


title: UOK262_rep11


title: Tricuspid aortic valve_calcified_YBO058

description: duplicate of GSM1338128


title: UOK262pFH_rep3


title: UOK262_rep9


title: Tricuspid aortic valve_calcified_YBO050

description: duplicate of GSM1338127


title: Tricuspid aortic valve_non-calcified_YBO060

description: duplicate of GSM1338137


title: Tricuspid aortic valve_calcified_YBO042

description: duplicate of GSM1338126


title: Tricuspid aortic valve_calcified_YBO057

description: duplicate of GSM1338125


title: Tricuspid aortic valve_non-calcified_YBO056

description: duplicate of GSM1338134


title: UOK262_rep7


title: UOK262_rep5


title: Tricuspid aortic valve_calcified_YBO034

description: duplicate of GSM1338124


title: Bicuspid aortic valve_calcified_YBO047

value: Calcified bicuspid aortic valve (BAV)


title: Bicuspid aortic valve_calcified_YBO036


title: Bicuspid aortic valve_calcified_YBO059


title: UOK262_rep12


title: UOK262_rep4


title: UOK262_rep6


title: UOK262_rep3


title: UOK262_rep2


title: Bicuspid aortic valve_calcified_YBO045


title: UOK262_rep1


title: day 21 sample stimulated with human interferon-alpha A - biological replicate #2

city: Los Angeles

first: Wolf

last: Wiedemeyer

address: 8700 Beverly Blvd.

department: BMS

institute: Cedars-Sinai

data_processing:
Reads were  aligned to the UCSC human reference genome (hg19) using TOPHAT (Trapnell, Pachter et al.  2009).
Gene expression was calculated using reference-guided transcript assembly using a  gene transfer file (GTF) from UCSC genes and normalized quantification of reads as FPKM (#  of Fragments Per Kilobase of ORF per Million reads aligned) calculated with Cufflinks (Cufflinks  2014) and compiled into a gene counts table for all samples.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values for each sample

growth_protocol: The human embryonic stem cell (hESC) lines were cultured using serum free-chemically defined  media, mTeSR1, (STEMCELL Technologies, Canada) with every day media change regimen. For in vitro differentiation, single cell preparation of the hESCs was plated on matrigel-coated 6  well-plate, cultured at 37oC in 5% CO2. The cells were subjected to a 3 week hepatic  differentiation protocol that consisted of three phases, including endoderm induction (day 1-5),  hepatic specification (day 6-15) and hepatic maturation (day 16-21). The protocol could yield  endoderm cells (day 5), hepatoblast (day 15) and immature hepatocytes (day 21). The  cytokines were procured from Peprotech Inc., (Rocky Hill, NJ) unless otherwise mentioned. For  differentiation we used a serum free defined (SFD) media described by Cheng and colleagues  (Cheng, Ying et al. 2012). SFD base media comprised of IMDM (75%), Ham’s F12 (25%)  growth media supplemented with N2 and B27 (without vitamin A) supplements (Life  Technologies). For endoderm differentiation, Wnt 3A (40 ng/ml, R and D Systems) and Activin A  (100 ng/ml) supplement was used in RPMI media (Life Technologies) for the first one day and  the following four days the cells were treated with Activin A, VEGF (10 ng/ml), BMP4 (0.5 ng/ml)  and bFGF (10 ng/ml) in SFD media. From day 6 onwards, the SFD media supplemented with  BMP4 (50 ng/ml), VEGF (10 ng/ml), EGF (10 ng/ml), TGF-α (20 ng/ml), HGF (100 ng/ml),  dexamethasone (1x10-7M; Sigma-Aldrich, St. Louis, MO), DMSO (1%, Sigma-Aldrich), ascorbic  acid (50 μg/ml), and monothioglycerol (4.5x10-4 M) was used. From day 12 onwards, BMP4  and TGF-α were removed from the cocktail. For hepatocyte maturation phase, HGF,  dexamethasone and oncostatin M (20 ng/ml) were included in the SFD media from day 16  onwards. At indicated time points, endoderm and hepatic lineage specific markers were  assessed by immunocytochemistry (ICC), flow cytometry and reverse transcription-quantitative  PCR (RT-qPCR).

extract_protocol:
Total RNA from cells was isolated using RNeasy Mini Kit (QIAGEN, USA). RNase-Free DNase  treatment was performed on column to remove residual DNA.
cDNA libraries of poly-A selected RNA were constructed from one microgram of total RNA from each  sample using illumina (San Diego, CA) TruSeq RNA Sample Preparation Kit v2 per  manufacturer’s instructions. mRNA was purified from total RNA samples using oligo-dT attached magnetic, fragmented, and primed for cDNA synthesis according to manufactures’ recommendations. The RNA was then reverse transcribed and Illumina adapters were ligated to each cDNA library with a unique index to enable multiplexing of libraries during sequencing. Libraries were then sequenced on an Illumina HiSeq 2500.

treatment_protocol: At day 5, day 15 and day 21 post-differentiation, the cells were stimulated with human  interferon-alpha A (R and D Systems) at a concentration of 1000 IU or 5000 IU for 6 hours.  Untreated cells were included as negative control. The 5000 IU IFN-α treated (D5, D15 and  D21) and untreated (D5, D15 and D21) cell samples were collected for RNA sequencing  analysis and gene expression studies. Experiments for RNA sequencing were done in duplicate  with two independent biological repeats (n=2).

tag: developmental stage

value: immature hepatocytes

tag: control or ifn-treated

value: IFN-treated

tag: days of differentiation


title: Bicuspid aortic valve_calcified_YBO049


title: Bicuspid aortic valve_calcified_YBO061


title: day 21 sample stimulated with human interferon-alpha A - biological replicate #1


title: day 21 control sample - biological replicate #2


title: Bicuspid aortic valve_calcified_YBO053


title: day 21 control sample - biological replicate #1


title: Bicuspid aortic valve_calcified_YBO055


title: UOK262_rep8


title: day 15 sample stimulated with human interferon-alpha A - biological replicate #1

value: post differentiation hepatoblast


title: day 15 control sample - biological replicate #2


title: BR018

city: New Haven

first: Dejian

last: Zhao

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale School of Medicine

data_processing:
reads were aligned with TopHat (v 2.0.4) to the human genome (hg19)
htseq (v0.6.1) was used to count reads for each gene (mode=union)
DESeq2 (v1.6.3) was then used to determine differentially expressed genes
Relative expression was measured in transcripts per million (TPM) (Wagner, G., et al. (2012). "Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples." Theory in Biosciences 131(4): 281-285.)
Unless otherwise stated, only genes with a TPM>1 in non-silencing control samples and q<0.05 were considered differentially expressed.
Genome_build: Homo_sapiens/NCBI/build37.2
Supplementary_files_format_and_content: tab-delimited gene expression values (htseq counts)

source_name: Neural progenitor cells derived from induced pluripotent stem cells

extract_protocol:
Total RNA was isolated from cells using miRNAeasy Kit (Qiagen) according to the manufacturer’s protocol. An additional DNaseI digestion step was performed to ensure that samples were not contaminated with genomic DNA. RNA quality was assessed via an Agilent bioanalyzer. mRNAs were enriched from total RNA samples using a poly-A pull-down.
Libraries were prepared using an Illumina TrueSeq RNA prep kit.

value: NPCs derived from iPSCs

value: CYFIP1 knockdown


title: BR015

value: non-silencing control


title: day 5 sample stimulated with human interferon-alpha A - biological replicate #2

value: endodermal cells


title: BR013


title: Bicuspid aortic valve_calcified_YBO038


title: day 15 control sample - biological replicate #1

value: control


title: BR014


title: Bicuspid aortic valve_calcified_YBO041


title: day 5 sample stimulated with human interferon-alpha A - biological replicate #1


title: day 5 control sample - biological replicate #2


title: BR012


title: day 5 control sample - biological replicate #1


title: BR011


title: BR009


title: dIME4_3_single-end

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

institute: University of Nottingham

data_processing:
Pooled indexed libraries were sequenced on a Illumina HiSeq to yield 40-46 million single-end 125 bp read for controls (x3) and IME4 mutant (x3).
Basecalls performed using CASAVA version 1.8.2
After demultiplexing, sequence reads were aligned to the genome using Tophat2.0.6 against the Drosophila genome (dmel-r6.02).
Bedgraph files were created from BAM alignments using Bedtools genomecoverage
Genome_build: dmel-r6.02
Supplementary_files_format_and_content: Bedgraph; columns are: chromosome, start, end, coverage

source_name: head/thorax

extract_protocol:
Total RNA was extracted from 15 pulverized head/thoraces previously flash frozen in liquid nitrogen, using Trizol reagent, total RNA was treated with DNase I. Stranded libraries for Illumina sequencing were prepared after polyA selection from 1 µg of total RNA with the TruSeq stranded mRNA kit (Illumina).
Illumina TruSeq stranded mRNA libraries were prepared for sequencing using standard Illumina protocols; single-end sequencing protocol

value: w dIME4 delta_22-3 null strain outcrossed with deficiency strain Df(3R)Exel6197

value: head/thorax


title: BR008


title: day 15 sample stimulated with human interferon-alpha A - biological replicate #2


title: dIME4_2_single-end


title: dIME4_1_single-end

description:
HDQ10
Same RNA sample that was used in GSM2083236 (HDQ6) with paired-end sequencing.


title: BR017


title: WT_3_single-end

value: w control strain outcrossed with deficiency strain Df(3R)Exel6197


title: BR016


title: BR006


title: BR005


title: WT_2_single-end

description:
HDQ8
Same RNA sample that was used in GSM2083233 (HDQ3) with paired-end sequencing.


title: WT_1_single-end


title: BR004


title: dIME4_3_paired-end

description:
HDQ6
Same RNA sample that was used in GSM2083351 (HDQ10) with single-end sequencing.

data_processing:
Pooled indexed libraries were sequenced on a Illumina HiSeq to yield 40-46 million paired-end 100 bp read for controls (x2) and IME4 mutant (x3).
Basecalls performed using CASAVA version 1.8.2
After demultiplexing, sequence reads were aligned to the genome using Tophat2.0.6 against the Drosophila genome (dmel-r6.02).
Bedgraph files were created from BAM alignments using Bedtools genomecoverage
Genome_build: dmel-r6.02
Supplementary_files_format_and_content: bedGraph, columns are: chromosome, start, end, coverage

extract_protocol:
Total RNA was extracted from 15 pulverized head/thoraces previously flash frozen in liquid nitrogen, using Trizol reagent, total RNA was treated with DNase I. Stranded libraries for Illumina sequencing were prepared after polyA selection from 1 µg of total RNA with the TruSeq stranded mRNA kit (Illumina).
Illumina TruSeq stranded mRNA libraries were prepared for sequencing using standard Illumina protocols; paired-end sequencing protocol.

value: head and thorax


title: BR007


title: dIME4_1_paired-end


title: BR010


title: WT_2_paired-end

description:
HDQ3
Same RNA sample that was used in GSM2083349 (HDQ8) with single-end sequencing.


title: BR001


title: BR003


title: BR002


title: W3110_anaero

data_processing:
Gene expression data (3 biological replicates per strain) were analyzed in the statistical software program R (www.r-project.org ) using the EdgeR package (3). Data were normalized using the CQN package, which accounts for both gene length and GC content effects (4). Differentially expressed genes were determined by comparing expression values under anaerobic and aerobic conditions. Those genes with adjusted P values less than 0.01 (i.e., false discovery rate less than 1%) were identified as significantly differentially expressed genes. Finally, gene annotations were automatically made using the biomaRt package (5) together with the annotation files available at the Ensembl database (www.ensembl.org) and gene set enrichment analysis (GSEA) was performed using the piano package (6). All R packages used in this study are available in Bioconductor (www.bioconductor.org).
Supplementary_files_format_and_content: tab-delimited text files include gene expresion values for each Sample

organism: Escherichia coli str. K-12 substr. W3110


title: DH5a_anaero

organism: Escherichia coli DH5[alpha]


title: WT_1_paired-end


title: W3110_aero


title: DH5a_aero


title: BL21_anaero

organism: Escherichia coli BL21


title: C_anaero

organism: Escherichia coli C

value: C


title: BL21_aero


title: W_aero

organism: Escherichia coli W

value: W


title: W_anaero


title: Rorc KO thymic lymphoma cells-MIRG1-Rorc-GFP US-1487260_PID20985_RNA-Seq_21Apr2014

status: Public on Sep 21 2016

city: Boston

first: Kenzie

last: MacIsaac

state: MA

address: 33 Avenue Louis Pasteur

department: Genetics and Pharmacogenomics

institute: Merck Research Labs

description:
US-1487260_PID20985_RNA-Seq_21Apr2014
PID20985_21-04-2014.xlsx

data_processing:
Reads were aligned to the mouse genome (mm10) and mRNA transcript abundance was quantified using the Omicsoft ArrayStudio software
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is available in an Excel file containing five tabs; the first tab contains total read counts aligning to each gene; the second tab contains gene annotation information; the third tab contains FPKM values for each gene; the fourth tab contains an alignment report for each sample; the fifth tab contains a filtering report for each sample

source_name: Rorc KO thymic lymphoma cells

growth_protocol: 1. Thymus were removed from C57BL/6 mice, were prepared in single cell suspension and cultured in vitro with MRL-871 or DMSO for 2hr; 2.C57BL/6 mice were treated with 20mg/kg MRL-871 or vehicle control. Thymus were removed at 2hr post-treatment, and single cell suspension was prepared; 3. Rorc KO thymic lymphoma cell line was derived from Rorc KO mice and maintained in RPMI. MIGR1-GFP or MIGR1-Rorc-GFP was used to transfect the cell line. GFP+ cells were FACS sorted on Aria.

extract_protocol:
RNA was extracted using QIAGEN RNeasy mini kit
Library construction and sequencing were performed using standard Illumina protocols by the Beijing Genomics Institute (BGI)

treatment_protocol: MRL-871 or DMSO in vitro; MRL-871 or vehicle in vivo; MIGR1-GFP or MIGR1-Rorc-GFP.

tag: sample type

value: transfection


title: Nkx2-1KO_Input_1

city: Davis

first: Alex

last: Nord

state: CA

address: 1544 Newton Court

department: Neurobiology, Physiology, and Behavior

institute: University of California Davis

description: Nuclei isolated via sonication

data_processing:
Base-calls were performed with CASAVA (v1.8.2) and bcl2fastq (v1.8.4).
ChIP-seq reads were filtered and aligned to whole mouse genome mm9 using BWA (v0.6.2).
Peak-calling was performed with MACS2 (v2.1.0).
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing coverage and txt files containing MACS2 peak-calls.

source_name: Medial ganglionic eminence

extract_protocol:
Tissue was micro-dissected and prepared for TF or native ChIP, cross-linked, and sheared. Protein/antibody complexes were isolated with antibodies and collected using Dynabeads.
ChIP-seq libraries were generated using the Ovation Ultralow DR Multiplex System (NuGEN #0330).

tag: chip antibody

value: embryonic day 13.5

value: Medial ganglionic eminence


title: Nkx2-1KO_Input_2

description: Nuclei isolated via sonication


title: Nkx2-1KO_H3K4me3

description: Nuclei isolated via sonication


title: Sid1 embryo

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

institute: Imperial College London

description: 5' polyphosphatase treated

data_processing:
Adapter trimming using FastX toolkit fastx_trimmer module
fastq to fasta conversion, selection for small RNAs of 15-30nt in length using custom Perl scripts using Perl v5.12.4
fasta collapsed using FastX toolkit fastx_collapser module
Genome_build: seq_id + number of reads

organism: Caenorhabditis elegans

source_name: Total RNA whole animal

extract_protocol:
Total RNA extracted using Trisure (BioLine) according to manufacturer's instructions
Illumina Truseq small RNA according to manufacturer's instructions

value: Embryo

tag: generation


title: Rorc KO thymic lymphoma cells-MIRG1-Rorc-GFP US-1487258_PID20985_RNA-Seq_21Apr2014

description:
US-1487258_PID20985_RNA-Seq_21Apr2014
PID20985_21-04-2014.xlsx

tag: treatment


title: Rorc KO thymic lymphoma cells-MIRG1-Rorc-GFP US-1487256_PID20985_RNA-Seq_21Apr2014

description:
US-1487256_PID20985_RNA-Seq_21Apr2014
PID20985_21-04-2014.xlsx


title: Nkx2-1KO_H3K27ac

description: Nuclei isolated via sonication

tag: strain


title: Rorc KO thymic lymphoma cells-MIRG1-GFP US-1487257_PID20985_RNA-Seq_21Apr2014

description:
US-1487257_PID20985_RNA-Seq_21Apr2014
PID20985_21-04-2014.xlsx


title: Nkx2-1KO_H3K27me3

description: Nuclei isolated via sonication

value: H3K27me3 (Active Motif #39155 RRID:AB_2561020)

tag: tissue


title: Rorc KO thymic lymphoma cells-MIRG1-Rorc-GFP US-1487253_PID20985_RNA-Seq_21Apr2014

description:
US-1487253_PID20985_RNA-Seq_21Apr2014
PID20985_21-04-2014.xlsx


title: Rorc KO thymic lymphoma cells-MIRG1-Rorc-GFP US-1487252_PID20985_RNA-Seq_21Apr2014

description:
US-1487252_PID20985_RNA-Seq_21Apr2014
PID20985_21-04-2014.xlsx


title: MRL871-in vivo US-1417481_PID20985_RNA-Seq_23Apr2014

description:
US-1417481_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx

source_name: C57/BL6 thymocytes

value: in vivo


title: Rorc KO thymic lymphoma cells-MIRG1-Rorc-GFP US-1487251_PID20985_RNA-Seq_21Apr2014

description:
US-1487251_PID20985_RNA-Seq_21Apr2014
PID20985_21-04-2014.xlsx


title: Rorc KO thymic lymphoma cells-MIRG1-GFP US-1487259_PID20985_RNA-Seq_21Apr2014

description:
US-1487259_PID20985_RNA-Seq_21Apr2014
PID20985_21-04-2014.xlsx


title: Nkx2-1KO_H3K4me1

description: Nuclei isolated via sonication

tag: genotype


title: Rorc KO thymic lymphoma cells-MIRG1-GFP US-1487255_PID20985_RNA-Seq_21Apr2014

description:
US-1487255_PID20985_RNA-Seq_21Apr2014
PID20985_21-04-2014.xlsx


title: C_aero

city: La Jolla

first: Jonathan

last: Monk

address: 9226A Regents Rd

institute: UCSD

extract_protocol:
Cells were harvested from aerobic and anaerobic cultures of seven E. coli strains grown to an OD600 of 0.6 (exponential phase). Cultures were divided into 10 ml aliquots and were immediately mixed with 0.2 volumes of ice-cold STOP solution (95% ethanol, 5% phenol (pH 4.7)). After 20 min incubation on ice, samples were spun down for 10 min at 4˚C and 7000 x g in a centrifuge. Pellets from one aliquot were gently resuspended in RNAProtect (QIAGEN, Germany) to further stabilize the RNA. Remaining samples were mixed with RNAlater (QIAGEN, Germany) and placed at -80˚C for archival storage. Total RNA was extracted using RNeasy Mini kit (QIAGEN, Germany) and on column DNase treatment following the manufacturers’ instructions. The 23S and 16S rRNAs were removed by subtractive hybridization using the MICROBExpress kit (Ambion, USA) with modifications. Compared with the standard protocol, 50% more capture oligonucleotides and magnetic beads were used. 5S rRNAs (120 nt in length) were removed during the total RNA extraction on column. Specifically, ribosomal depletion on total RNA isolated from the E. coli BL21 (DE3) was performed using RiboZero (Gram Negative Bacteria) kit (Epicenter, USA). RNA samples were stored at -80°C.
The sequencing libraries were constructed using the TruSeq RNA Sample Preparation kit (Illumina Inc., USA). Each library was prepared with RNA isolated from seven E. coli cultures grown in triplicate to an exponential phase under aerobic and anaerobic conditions. RT-PCR was performed with SuperScript® II One-step RT-PCR reagents (Invitrogen, USA). The libraries were sequenced using the Illumina HiSeq2000 platform with a paired-end protocol and read lengths of 50 nt.  The final concentration of DNA and RNA was measured using a Qubit 2.0 Fluorometer (Invitrogen, USA). The integrity of total RNA, DNA contamination, removal of rRNAs and cDNA library validation were assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, USA).


title: Nkx2-1KO_IgG

description: Nuclei isolated via sonication

value: Rabbit IgG control (Santa Cruz Biotechnology #sc-2027 RRID:AB_737197)


title: WT_H3K4me3

description: Nuclei isolated via sonication

value: Wildtype


title: WT_H3K27ac

description: Nuclei isolated via sonication


title: MRL871-in vivo US-1417472_PID20985_RNA-Seq_23Apr2014

description:
US-1417472_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx


title: WT_Input_1

description: Nuclei isolated via sonication


title: WT_H3K27me3

description: Nuclei isolated via sonication


title: MRL871-in vivo US-1417466_PID20985_RNA-Seq_23Apr2014

description:
US-1417466_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx


title: WT_H3K4me1

description: Nuclei isolated via sonication


title: MRL871-in vivo US-1417375_PID20985_RNA-Seq_23Apr2014

description:
US-1417375_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx


title: Vehicle control-in vivo US-1417337_PID20985_RNA-Seq_23Apr2014

description:
US-1417337_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx

value: Vehicle


title: Vehicle control-in vivo US-1417342_PID20985_RNA-Seq_23Apr2014

description:
US-1417342_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx


title: MRL871-in vivo US-1417384_PID20985_RNA-Seq_23Apr2014

description:
US-1417384_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx


title: WT_Input_2

description: Nuclei isolated via sonication


title: WT_IgG

description: Nuclei isolated via sonication


title: Vehicle control-in vivo US-1417332_PID20985_RNA-Seq_23Apr2014

description:
US-1417332_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx


title: DMSO-in vitro US-1336690_PID20985_RNA-Seq_23Apr2014

description:
US-1336690_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx

value: in vitro

value: DMSO


title: MRL871-in vitro US-1336681_PID20985_RNA-Seq_23Apr2014

description:
US-1336681_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx


title: MRL871-in vitro US-1336746_PID20985_RNA-Seq_23Apr2014

description:
US-1336746_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx


title: DMSO-in vitro US-1332447_PID20985_RNA-Seq_23Apr2014

description:
US-1332447_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx


title: MRL871-in vitro US-1332355_PID20985_RNA-Seq_23Apr2014

description:
US-1332355_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx


title: MRL871-in vitro US-1336680_PID20985_RNA-Seq_23Apr2014

description:
US-1336680_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx


title: DMSO-in vitro US-1332333_PID20985_RNA-Seq_23Apr2014

description:
US-1332333_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx


title: MRL871-in vitro US-1332272_PID20985_RNA-Seq_23Apr2014

description:
US-1332272_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx


title: DMSO-in vitro US-1332275_PID20985_RNA-Seq_23Apr2014

description:
US-1332275_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx


title: Ad_378_CT22_rep2

city: ShangHai

first: Haifang

last: Wang

address: NO 320, Yueyang Road

department: functional genomics group

institute: PICB

data_processing:
Fastq files containing raw sequence reads were aligned to mouse genome (mm9) by Tophat (default parameters). Then bedtools (v2.16.2) were applied to calculate the number of reads of each transcript based on the gene annotations from UCSC genome browser. The transcripts with summed reads number<20 in the samples were removed. The reads numbers were normalized to reads per kilobase per million tags (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: The mice were housed under a 12-h light/12-h dark regimen with food and water available ad libitum for one week before being switched to complete darkness. The mice were switched to complete darkness two days before execution. ZT0 is defined as the time when the lights are turned on. All animal handing protocols have been approved by “Committee of Institute of Nutrition Science”.

extract_protocol:
Livers of all mice were quickly dissected and snap-frozen in liquid nitrogen and stored at −80 °C. Total RNA was extracted from each liver sample using Trizol.
The RNA samples of ad-378 and ad-null mice were converted into Illumina sequencing libraries by using Illumina TruSeq RNA Sample Prep Kit v2 as per manufacturer’s protocol.

treatment_protocol: DNA fragments encoding miR-378 were introduced into pENTR/U6 vector under the control of the human U6 promoter. 5 × 108 plaque-forming unit viruses were administered to four ad-378 mice through tail vein injection for miR-378 over-expression. Control viruses were injected to four ad-null mice. Two ad-378 and two ad-null mice were sacrificed at CT10 and CT22 respectively eight days after injection.

value: liver

value: 8 weeks


title: Ad_378_CT22_rep1


title: MRL871-in vitro US-1332278_PID20985_RNA-Seq_23Apr2014

description:
US-1332278_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx


title: Ad_378_CT10_rep1


title: Ad_null_CT10_rep2


title: Ad_null_CT22_rep1


title: Ad_null_CT10_rep1


title: Sid1 Adult progeny

description: 5' polyphosphatase treated

value: Young Adult


title: dIME4_2_paired-end

value: w dIME4 delta_22-3 null strain outcrossed with deficiency strain Df(3R)Exel6197

value: head and thorax


title: Ad_378_CT10_rep2