title: ClutchA_polyA_7_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_14

source_name: Whole embryo, 7hpf, polyA+ RNA

value: A


title: ClutchA_polyA_8_hpf

status: Public on Jan 07 2016

type: SRA

city: Exeter

first: Nick

last: Owens

state: Exeter

address: Barrack Road

country: United Kingdom

institute: University of Exeter Medical School

description:
PolyA+ RNA
clutch_A_poly_A/Sample_16

library_source: transcriptomic

data_processing:
Read pairs were aligned to Xenopus tropicalis v7 genome along with known off-genome gene sequences and exogenouns ERCC and ArrayControl spike in sequences using tophat v2.010 and parameters "-r 13 --mate-std-dev 60 -g 200 --report-secondary-alignments".
Abundances were estimated using cufflinks v2.1.1 with parameters ""--compatible-hits-norm --max-bundle-frags 10000000 -b xt7.fa -u --max-mle-iterations 50000". This is with exception of mir427, in which reads aligning at least once to the locus and nowhere else in the genome were counted once to calculate the FPKM for the entire locus. Transcript FPKM were converted to TPM.
Relative gene abundances in TPM were absolute normalised against ERCC spiked RNA standards, resulting abundances are reported in transcripts per embryo.
Genome_build: Xtropicalis_v7
Supplementary_files_format_and_content: Tab-delimited text files containing relative and absolute normalised gene and isoform abundances.

molecule: total RNA

organism: Xenopus tropicalis

source_name: Whole embryo, 8hpf, polyA+ RNA

growth_protocol: We performed IVF and flooding of the eggs with 1/9xMMR after application of sperm to eggs was considered time zero. All fertilizations and subsequent culturing of embryos were performed in a temperature-controlled room maintained at ~24oC, with fluctuations +/- ~1oC over the entire timecourse. Unfertilized eggs and embryos were dejellied and embryos were cultured at low density, ~100 embryos per 150-mm dish containing ~120-150mls of 1/9thX MMR.

extract_protocol:
For most samples, 10 embryos/timepoint were thoroughly homogenized in 200 ml Trizol® and frozen at -80oC, with the exception of egg, 0.5, 1, 1.5, 2, 2.5 and 3hpf timepoints, which were sampled at 25, 30, 20, 20, 20, 15 and 15 embryos, respectively.
For the Clutch A timecourse, ERCC Spike In Mix 1 (10ul) (lot 1205006) was diluted in DEPC-treated water to a final volume of 1045ul. Diluted spike in mix was then pipetted directly into the Trizol homogenates such that 1ul was delivered per embryo, which in most cases required delivery of 10ul diluted spike in mix/sample, with the exception of the first several timepoints. Spike in mix was pipetted into samples in the order of their chronology. Total RNA was purified from the embryo homogenate according to the manufacturer’s recommendations. Following isopropanol precipitation, RNAs were resuspended in DEPC-treated water and any contaminating genomic DNA was removed by a subsequent overnight precipitation in 5M LiCl at 4oC. RNA was pelleted and washed twice with 70% ethanol made with DEPC-treated water. All RNAs were resuspended and quantitated by Bioanalyzer. RNA quality was assessed by Bioanalyzer and RNA Integrity Numbers were all in excess of 9.
For the Clutch B timecourse, ERCC spike in mix 1 (lot 1306008) was similarly diluted and delivered to all Trizol® homogenates, except the pipetting was done in reverse order to the chronology of the samples. Furthermore, we added an additional spike in mix that was pipetted independently and in order of sample chronology. Ambion ArrayControl™ spikes were used. Two microliters of spikes 1, 2 and 4 were diluted  to a final volume of 82ul in DEPC-treated water to create a solution of 2.439ng for each ArrayControl spike-in RNA per microliter. Approximately 5.125ul of this dilution was then further diluted into DEPC-treated water to a final volume of 1000ul as verified by weight to create a solution of ~12.5pg/ul. One microliter per embryo (~12.5pg) was added to Trizol® homogenates by pipetting of 10ul per tube except in the cases of the 0-3hpf samples. In both timecourses these early timepoint spike ins were pipetted by multiple rounds of 10ul (for 20 or 30ul delivery), or readjustment to 5ul (for 15ul delivery). RNAs were subsequently isolated as described above except we omitted the LiCl precipitation step. RNAs were similar quantitated and quality evaluated.
RNA quality and concentration were evaluated by running total RNA on an Agilent RNA Nano Bioanalyzer chip. All samples had an RNA integrity number (RIN) greater than 9. Ribosomal RNA was removed via polyA-selection or ribosomal RNA depletion. For polyA-extraction, polyadenylated RNA transcripts were selected from the total RNA using two rounds of enrichment with oligo(dT)25 beads (Invitrogen). Ribosomal-depletion was completed with the Ribo-Zero (Human/Mouse/Rat) Magnetic Ribosomal rRNA Removal kit (Epicenter) according to the manufacturer's recommendations. The supernatant from both approaches was purified and concentrated using RNAclean XP beads (Beckman Coulter). Following selection, the RNA was fragmented to approximately 140 base pairs and first-strand synthesis was completed with SuperScript III reverse transcriptase (Invitrogen) using random hexamers. Magnetic AMPure XP beads (Beckman Coulter) were used to purify the cDNA and remained with the sample throughout sequencing library construction. During preparation, DNA is selectively precipitated by weight and re-bound to the beads through the addition of a 20% polyethylene glycol, 2.5 M NaCl solution. We used T4 DNA polymerase and T4 polynucleotide kinase to blunt ends and phosphorylate the fragments. The large Klenow fragment then added a single adenine residue to the 3' end of each fragment, custom adapters (IDT) are ligated using T4 DNA ligase, and, for strand-specific libraries, UDG removes uracil residues. The product is then PCR amplified using custom-made primers (IDT) containing unique 6 bp indices.

tag: genotype/variation

value: wild type

tag: tissue

value: whole embryo

tag: clutch

tag: time (hpf)


title: MDA436_BRD4_JQ1

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

description: Chip-Seq for BRD4 in JQ1 treated cells

library_source: genomic

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie2 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences processed through MACS 1.4.2 and fragment pileup was outputted in .wig format

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Cells were growed with SUM medium

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: Cells were treated with 500 nM JQ1 or DMSO for the indicated time

tag: cell line

tag: chip antibody

value: BRD4 (Bethyl, catalog# A301-985A, lot# 4)

tag: drug treatment

tag: duration

value: 12 hour

tag: barcode (already removed)

value: CTTGTA


title: ClutchA_polyA_6.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_13

source_name: Whole embryo, 6.5hpf, polyA+ RNA


title: ClutchA_polyA_6_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_12

source_name: Whole embryo, 6hpf, polyA+ RNA


title: MDA436_BRD4_DMSO

description: ChIP-Seq for BRD4 in DMSO treated cells

value: DMSO

value: GGCTAC


title: ClutchA_polyA_5.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_11

source_name: Whole embryo, 5.5hpf, polyA+ RNA


title: ClutchA_polyA_5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_10

source_name: Whole embryo, 5hpf, polyA+ RNA


title: HCC1395_WCE_DMSO

description: ChIP-Seq whole cell extract input control from DMSO treated cells

value: TCCGTCTT


title: HCC1395_BRD4_JQ1

description: Chip-Seq for BRD4 in JQ1 treated cells

value: TAGCTT


title: rat1_37_rep2_OF_sample

city: New York

first: Iestyn

last: Whitehouse

state: New York

address: 1275 York Avenue

department: Molecular Biology

institute: Sloan-Kettering Institute

description: Okazaki fragment (OF).

data_processing:
Library strategy: Okazaki-fragment sequencing
Data were aligned to the sacCer3 (April 2011) build of the S. cerevisiae genome using BOWTIE2.
Position of 5' end of reads with Q30 or greater are reported in SGR files.
Genome_build: R64 (sacCer3)
Supplementary_files_format_and_content: SGR (tab-delimited text) files. Columns: Chromosome, Position (base-pair), Value.

organism: Saccharomyces cerevisiae

source_name: rat1, 37C, OF

growth_protocol: Cells were grown at 24°C or 37 °C in YEP medium supplemented with 2% glucose. At optical density (OD600) 0.3, doxycycline was added to final concentrations of 40 mg l-1, and the culture shaken at 30 °C for 2.5 h. Fifty-millilitre cultures were used for labeling experiments, and 200-ml cultures for purification and library generation.

extract_protocol:
Genomic DNA was purified and heat-denatured: DNA was bound to Source 15Q resin in batch at 50mM NaOH, pH12, and eluted in NaCl, using 50mM steps (at pH 12). Fractions from 600-750 mM NaCl were collected, concentrated by precipitation.
Double-stranded sequencing adaptors with N6 random overhangs ligated to each end; after second-strand synthesis using Taq, material from 200-1000bp was gel-purified and amplified by PCR. Products from 200-800 bp were gel-purified from two successive 2.5% agarose gels or using Ampure XP beads for size-selection.

tag: strain/background

tag: cell cycle stage

value: asynchronous culture

tag: growth temperature


title: ClutchA_polyA_4.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_09

source_name: Whole embryo, 4.5hpf, polyA+ RNA


title: HCC1395_BRD4_DMSO

description: ChIP-Seq for BRD4 in DMSO treated cells

value: GATCAG


title: rat1_37_rep1_OF_sample

description: Okazaki fragment (OF).


title: ClutchA_polyA_4_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_08

source_name: Whole embryo, 4hpf, polyA+ RNA


title: ClutchA_polyA_3_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_06

source_name: Whole embryo, 3hpf, polyA+ RNA


title: rat1_24_OF_sample

description: Okazaki fragment (OF).

source_name: rat1, 24C, OF


title: SUM1315_BRD4_DMSO

description: ChIP-Seq for BRD4 in DMSO treated cells

value: CAGATC


title: ClutchA_polyA_2_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_04

source_name: Whole embryo, 2hpf, polyA+ RNA


title: ClutchA_polyA_2.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_05

source_name: Whole embryo, 2.5hpf, polyA+ RNA


title: ClutchA_polyA_1.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_03

source_name: Whole embryo, 1.5hpf, polyA+ RNA


title: SUM149_BRD4_JQ1

description: Chip-Seq for BRD4 in JQ1 treated cells

value: CGATGTTT


title: ClutchA_polyA_1_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_02

source_name: Whole embryo, 1hpf, polyA+ RNA


title: WT_37_OF_sample

description: Okazaki fragment (OF).

source_name: WT, 37C, OF

value: WT [yIW347]


title: SUM149R_JQ1_12H_R1

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie2 with default parameters.
Genome_build: hg19
For all samples, transcriptome mapping was performed using tophat2 with default settings against the hg19 UCSC genes.gtf build. Quantification was performed using the cufflinks software suite by running the cuffquant command on all samples followed by the cuffnorm command. For all tophat2 and cufflinks data processing steps, default parameters were used.
Supplementary_files_format_and_content: TNBC_SUM149_RNASEQ.genes.fpkm_table.txt

molecule: polyA RNA

extract_protocol: total RNA was extracted using the standard QIAGEN RNeasy kit (74106). RNA concentrations were measured and quality controlled on a Bioanalyzer, RNA-Seq libraries were made using Illumina True-Seq RNA kits using the Sciclone NGSx workstation.

treatment_protocol: Cells were treated with 500nM JQ1 or DMSO for the indicated time


title: SUM149_DMSO_12H_R2

value: GTGAAA


title: SUM149R_JQ1_12H_R2

value: GCCAAT


title: SUM149_JQ1_12H_R2

value: TGACCA


title: SUM149_JQ1_12H_R1

value: CGATGT


title: SUM149_DMSO_12H_R1

value: GTCCGC


title: ClutchA_polyA_0.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_01

source_name: Whole embryo, 0.5hpf, polyA+ RNA

value: wild type

value: whole embryo

value: A


title: FL39RUT1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
Color space reads were aligned using SHRiMP to a custom reference incorporating hg19 and subtelomere reference assemblies sequenced by the Riethman lab.  /cscb/cscbsoftware/centos5-x86_64/local/SHRiMP_2_2_3/bin/gmapper-cs --strata --sam-unaligned -o 102 -N 12 -L /cscb/genomes/Human/hgHyb/hgHybri.shrimp.color
Sequencing coverage maps were compiled using in house software which allow for partial mapping of multimapping reads uniformly across all possibly mapping locations as previously described (Deng et al., 2012a; Stong et al., 2014).  Read depth was average over a 20bp window.
Genome_build: hgHybrid (vader.wistar.upenn.edu/humansubtel)
Supplementary_files_format_and_content: bigWig and bedGraph files contain sequence pileups including multimapping reads whose weight is distributed uniformly to all possible mapping locations (up to 100)

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% FBS at standard conditions (37°C and 5% CO2)

extract_protocol:
Sonicated lystates were immuprecipitated with antibody then reversed crosslinked and resulting genomic DNA was isolated and purified.
ChIP-Seq was performed essentially as described previously (Lee et al., 2006).  HCT116 cells were treated with 5 μM Camptothecin (Sigma) for 8 hours, then crosslinked and harvested. Cells were sonciated using the Bioruptor sonicator (Diagenode) for 15 minutes, 30 seconds on, 30 seconds off at high power. Antibody incubation was performed overnight at 4°C with 15 μg FL393R (Santa Cruz), as described (Sykes et al., 2006).  ChIP-Seq analysis and mapping to human subtelomeres was described previously (Deng et al., 2012a; Stong et al., 2014).   Deep sequencing was performed using the Applied Biosystems-SOLiD 5500xl.   ChIP-Seq datasets were comprised of color space short reads that were mapped using SHRiMP 2.2.3 (Rumble et al., 2009), allowing for reads mapping up to 101 mapping positions (-o 102).  Once mapping positions were determined the pipeline followed was the same as Illumina-generated  ChIP-seq data sets.

treatment_protocol: Cells were treated with camptothecin or DMSO for 8 hours

tag: cell type

value: Colorectal cancer cells

tag: treated with

value: none (untreated control)

value: p53 Antibody (FL-393R)

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat.#


title: Input


title: SUM149R_DMSO_12H_R2

value: DMSO

value: ACAGTG


title: FL39RUT2


title: FL39RCPT2

value: 5 μM Camptothecin (Sigma) for 8 hrs


title: SUM159_H3K27AC_JQ1_R1

description:
ChIP-Seq for H3K27ac in JQ1 treated cells
Sample name: SUM159_H3K27AC_JQ1_R1

value: H3K27AC (Abcam, catalog# ab4729, lot# GR184557-1)

value: 3 hour


title: CAST primed

city: Cambridge

first: Jenny

last: Chen

address: 16 Divinity Ave

institute: Harvard

description: primed epiSCs from CAST mouse

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and aligned using TopHat v2.0.10 (-N 3 --read-edit-dist 3 --library-type fr-secondstrand --prefilter-multihits --max-multihits 15 --segment-length 20).  Optical duplicates were removed using Picard's MarkDuplicates utility
Transcripts were reconstructed from TopHat alignments using Scripturev3.1 (-coverage 0.2)
Fragments per Kilobase of exon per Megabase of library size (FPKM) was calculated using Cufflinks v2.1.1
Genome_build: mm9, rn5, hg19
Supplementary_files_format_and_content: tab-delimited text file of cufflinks estimation of coding gene FPKMs
Supplementary_files_format_and_content: tab-delimited text file of cufflinks estimation of lncRNA FPKMs
Supplementary_files_format_and_content: wig file representing RNA-Seq coverage of aligned reads

organism: Mus musculus castaneus

source_name: primed EpiSC

extract_protocol:
Briefly, 10ug of total RNA was polyA selected twice using Oligo(dT)25 beads (Life Technologies) and NEB oligo(dT) binding buffer.
PolyA-selected RNA was fragmented, repaired and cleaned using Zymo RNA concentrator-5 kit.  30ng of polyA-selected RNA per sample were used to make RNA-seq libraries. Adapter was ligated to RNA, RNA was reverse transcribed and second adapter was ligated on cDNA.

tag: strain

value: Castaneus

tag: cell state

value: epiblast


title: SUM149R_DMSO_12H_R1


title: ClutchA_polyA_0_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_00

source_name: Whole embryo, 0hpf, polyA+ RNA

tag: genotype/variation

tag: tissue


title: ClutchA_polyA_3.5_hpf

description:
PolyA+ RNA
clutch_A_poly_A/Sample_07

source_name: Whole embryo, 3.5hpf, polyA+ RNA

tag: clutch

tag: time (hpf)


title: FL39RCPT1

tag: cell line

tag: chip antibody


title: SUM159_H3K27AC_DMSO_R1

description:
ChIP-Seq for H3K27ac in DMSO treated cells
Sample name: SUM159_H3K27AC_DMSO_R1

tag: drug treatment

tag: duration

value: TTAGGC


title: rat1-1_MCM_ChIP_37C

data_processing:
Data were aligned to the May 2008 build of the S. cerevisiae genome: using BOWTIE2
Position of 5' end of reads with Q30 or greater are reported in SGR files.
Genome_build: R64 (sacCer3)
Supplementary_files_format_and_content: SGR (tab-delimited text) files. Columns: Chromosome, Position (base-pair), Value.

source_name: rat1-1 cells grown at 37C

growth_protocol: Cells were grown at 24°C in YEP medium supplemented with 2% glucose. At optical density (OD600) 1.0, were continued to grow for two additional hours at 24 °C or 37 °C.

extract_protocol:
Cells were croslinked with 1% formaldehyde, lysed and sonicated to obtain a DNA shear size of 100-800 bp. Immunoprecipitation was carried out with polyclonal antibodies against ORC or MCM (Gifts from Steve Bell, MIT *). Fragments were sequenced on an Illumina platform and reads were mapped using Bowtie and Bedtools.
* Antibodies raised by Steve Bell group: UM185 (polyclonal anti-Mcm2-7) and 1108 (polyclonal anti-Orc1-6)
Library was constructed by the sequencing core

value: Asynchronous culture

value: 37 °C

value: UM185 (polyclonal anti-Mcm2-7), gift from Steve Bell lab


title: SUM159_BRD4_JQ1_R1

description:
Chip-Seq for BRD4 in JQ1 treated cells
Sample name: SUM159_BRD4_JQ1_R1

value: BRD4 (Bethyl, catalog# A301-985A, lot# 2)

tag: barcode (already removed)

value: CGATGT


title: human

description: iPS cells from human

source_name: iPS

value: naïve


title: CAST naïve

description: naïve ESCs cells from CAST mouse

source_name: naïve ESC


title: M

city: SHANGHAI

first: GUOFENG

last: CHENG

address: #518,ZIYUE ROAD

country: China

institute: CAAS

description: Worms were isolated from BALB/C mice every day starting at 14 days post infection until 35 days post infection.

data_processing:
Run Solexa pipeline
Remove low qulity reads strictly
Trim 3' adaptor sequence
Remove 5' adaptor contaminants
Remove too small and polyA
Genome_build: sjr2_scaffold.fasta.zip from ftp://lifecenter.sgst.cn:2121/subjectData/schistosoma/ (http://lifecenter.sgst.cn/schistosoma/cn/schistosomaCnIndexPage.do)
Supplementary_files_format_and_content: text file containing sequence length, read count and sequence.

organism: Schistosoma japonicum

source_name: Schistosoma japonicum

growth_protocol: The life cycle of S. japonicum (Anhui isolate) was maintained in New Zealand rabbits and BALB/c mice using Oncomelania hupensis as the snail host. Unless indicated otherwise, New Zealand rabbits and BALB/c mice were infected with approximately 1,000 and 100 cercariae, respectively, by inoculating abdominal skin surface with a moist glass paste

extract_protocol:
Total RNA was extracted from each S. japonicum samples using TRIzol reagent (Invitrogen) according to the manufacturer's protocol.
Small RNA libraries were constructed according to Illumina's instructions. Briefly, RNAs between 15– and 30 nucleotides (nt) in length were excised from 15% TBE urea polyacrylamide gels (PAGE). The library was prepared using the Illumina Small RNA Library Kit

treatment_protocol: Homogenization

tag: isolate

value: Anhui

tag: Sex

value: Male

tag: source

value: Worms were isolated from BALB/C mice.


title: SUM159_DMSO_WCE_R1

description:
ChIP-Seq whole cell extract input control from DMSO treated cells
Sample name: SUM159_BRD4_DMSO_WCE_R1

value: DMSO

value: GGCTAC


title: 28M

description: Worms were isolated from New Zealand rabbits at 28 days of post infection.

value: Worms were isolated from New Zealand rabbits.


title: rat1-1_ORC_ChIP_37C

tag: cell cycle stage

tag: growth temperature

value: 37 °C

value: 1108 (polyclonal anti-Orc1-6), gift from Steve Bell lab


title: 22M

description: Worms were isolated from New Zealand rabbits at 22 days of post infection.


title: F

value: Female


title: rat1-1_ORC_ChIP_24C

source_name: rat1-1 cells grown at 24C

value: 24 °C


title: SUM159R_H3K27AC_DMSO_R1

description:
ChIP-Seq for H3K27ac in DMSO treated cells
Sample name: SUM159R_H3K27AC_DMSO_R1

value: H3K27AC (Abcam, catalog# ab4729, lot# GR184557-1)

value: 3 hour

value: ACAGTG


title: 28F


title: rat naïve

description: naïve iPS cells from rat

organism: Rattus norvegicus

source_name: naïve iPS


title: SUM159R_H3K27AC_JQ1_R1

description:
ChIP-Seq for H3K27ac in JQ1 treated cells
Sample name: SUM159R_H3K27AC_JQ1_R1

value: GCCAAT


title: 16M

description: Worms were isolated from New Zealand rabbits at 16 days of post infection.


title: SUM159R_DMSO_WCE_R1

description:
ChIP-Seq whole cell extract input control from DMSO treated cells
Sample name: SUM159R_BRD4_DMSO_WCE_R1

value: CTTGTA


title: rat1-1_MCM_ChIP_24C

value: Asynchronous culture

value: UM185 (polyclonal anti-Mcm2-7), gift from Steve Bell lab


title: TR

city: Chongqing

first: Yichao

last: Zhang

address: Tiansheng street

institute: Southwest University

description: biological replicate 1 raw file = SRR3056084; biological replicate 2 raw file = SRR3056085

data_processing:
Raw data were processed through Novogene Company’s Perl and Python scripts
The Bowtie  was used to map the sRNA tags to the T. urticae genome (http://bioinformatics.psb.ugent.be/orcae/overview/Tetur) and analyze the expression and distribution of the mapped sRNAs on the reference sequence
The mapped sRNAs were used to do a blastn search against the miRNA database (miRBasev. 20.0; released in June, 2013) to obtain the known miRNA, only perfectly matches were accepted and retained for the next analysis
The two available software miREvo and mirdeep2 were used to predict the new miRNA
The readcounts of miRNAs were normalized into TPM (transcript per million) through the Normalization formula: Normalized expression = (mapped readcount/Total reads) × 1000000. the package DESeq to analyze the differetially expressed miRNAs between susceptible and fenpropathrin-resistant strains of Tetranychus cinnabarinus , the P value were all adjusted by Benjamini–Hochberg false discovery rate (FDR) procedure
Genome_build: Tetranychus urticae genome (database web link: http://bioinformatics.psb.ugent.be/orcae/overview/Tetur)
Supplementary_files_format_and_content: Text files with non-normalized read count or normalized TPM values.

organism: Tetranychus cinnabarinus

source_name: adult tissue

growth_protocol: All strains feeding on fresh potted cowpea leaves were kept in artiﬁcial climate chamber under the conditions of 26 ± 1 °C, 55–70% relative humidity and a 14 h light /10 h dark cycle

extract_protocol:
RNA was extracted with Trizol reagent,the integrity and purity of the total RNA were confirmed by 1% agarose gel electrophoresis and NanoVue UV-Vis spectrophotometer,Moreover, the RNA integrity number (RIN) was measured by Novogene Company.
Qualified total RNA was used to construct the sRNA libraries with TruSeq small RNA Sample Pre Kit (Illumina). Briefly, total RNA was ligated to 5’ and 3’ adaptors, then synthesizing cDNA by reverse transcription. After PCR amplification of the cDNAs, the amplified PCR products within 130–160 bp were separated and purified by a 6% polyacrylamide gel. The Agilent Bioanalyzer 2100 system was used to assess the library quality using DNA High Sensitivity Chips.

treatment_protocol: Susceptible strain of Tetranychus cinnabarinus was originally obtained from the ﬁeld of Beibei District, Chongqing, China, which has been maintained without any acaricide treatments for 15 years. fenpropathrin resistant strain was generated from susceptible  strain and had been subsequently selected >70 generations (resistant level more than 100-fold) by fenpropathrin to maintain resistance

value: fenpropathrin resistant strain

tag: gender

value: female

tag: age

value: adults aged 3-5 days post emergence


title: 22F

value: Anhui


title: 16F


title: SUM159R_BRD4_JQ1_R1

description:
Chip-Seq for BRD4 in JQ1 treated cells
Sample name: SUM159R_BRD4_JQ1_R1

value: BRD4 (Bethyl, catalog# A301-985A, lot# 2)

value: TGACCA


title: TS

description: biological replicate 1 raw file = SRR3056080; biological replicate 2 raw file = SRR3056081

tag: strain

value: fenpropathrin susceptible strain


title: Infected sample, replicate 3b

status: Public on Jan 06 2016

city: Ciudad Real

first: Jose

last: De La Fuente

state: Ciudad Real

address: Ronda de Toledo s/n

country: Spain

institute: SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM

description:
I3b
Ixodes scapularis cells infected with Anaplasma phagocytophilum

data_processing:
Reads were mapped using Tophat 2.0.11
Transcripts assembly and abundance estimation performed using Cufflinks 2.0.11
Analysis of differentially expressed genes was performed using Cufflinks 2.0.11
Genome_build: JCVI_ISG_i3_1.0 (NZ_ABJB000000000)
Supplementary_files_format_and_content: GTF2 files generated with Cufflinks. The columns from the GTF2 format specification are: <seqname> <source> <feature> <start> <end> <score> <strand> <frame> [attributes]. FPKM values are included in the last column of the file.

organism: Ixodes scapularis

source_name: Ixodes scapularis embryo-derived cell line ISE6

growth_protocol: The I. scapularis embryo-derived tick cell line ISE6 was cultured in L-15B300 medium as described previously (Blouin et al. (2003) Vet. Parasitol 111, 247-260), except that the osmotic pressure was lowered by the addition of one-fourth sterile water by volume. Tick cells were inoculated with A. phagocytophilum (NY18 isolate)-infected HL-60 cells as described previously (Munderloh et al. (1999) J. Clin. Microbiol 37, 2518-2524; de la Fuente et al. (2005) Cell. Microbiol 7, 549–559). Uninfected and infected cultures with approximately 107 cells each were sampled at 7 days post-infection (dpi) (percent infected cells 71-77% (Ave±SD, 74±3). The percentage of cells infected with A. phagocytophilum was calculated by examining at least 200 cells using a 100x oil immersion objective.

extract_protocol:
Purified RNAs were used for library preparation using the TruSeq-based NEB-Next Ultra Directional RNA Library Prep kit (New England Biolabs, Ipswick, MA, USA). Briefly, 1 µg total RNA was used as starting material for library preparation. Messenger RNA was captured using oligo-dT magnetic beads (Poly(A) RNA Magnetic Isolation Module; New England Biolabs) and purified polyA+ RNA was chemically fragmented and reverse-transcribed.
A controlled fragmentation period was applied to obtain an insert size of approximately 320 nucleotides, best suited to generate non-overlapping reads after pair-end sequencing. The second strand was generated and dsDNA was purified using AMPure SPRI-based magnetic beads (Beckman Coulter, IZASA, Spain). Next, samples were end-repaired followed by adaptor ligation and removal of excess oligonucleotides by double AMPure selection, made according to NEB-Next recommendations as a function of library size. Adaptor oligonucleotides contained the signals for subsequent amplification and sequencing as well as sample-specific identifiers, which allowed multiplexing in the sequencing run. An enrichment procedure based on PCR was then performed to ensure that all molecules in the library conserved the adapters at both ends. The number of PCR cycles was adjusted to 13 for all four samples. The final amplified library was checked again on a BioAnalyzer 2100 (Agilent, Santa Clara, CA, USA), pooled, quantified by fluorimetric methods (PicoGreen®) and titrated by real-time PCR using a well-controlled library as standard. For RNAseq, libraries were denatured and seeded on the surface of a Pair-End Flowcell where clusters were generated and sequenced using a HiSeq2000 equipment (Illumina, San Diego, CA, USA), under a 2x100 recipe.

treatment_protocol: The cells were centrifuged at 10,000 g for 3 min, and cell pellets were frozen in liquid nitrogen until used for RNA extraction.

tag: infection

value: Anaplasma phagocytophilum human NY18 isolate


title: rat primed

description: primed iPS from rat

source_name: primed iPS

tag: cell state

value: epiblast


title: Infected sample, replicate 2b

description:
I2b
Ixodes scapularis cells infected with Anaplasma phagocytophilum

value: I. scapularis embryo-derived tick cell line ISE6


title: Uninfected sample, replicate 1b

description:
C1b
Ixodes scapularis cells uninfected

value: control


title: SUM159R_JQ1_CHEM_SEQ_R1

description: Chem-Seq for Biotin JQ1

data_processing:
library strategy: Chem-Seq
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie2 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences processed through MACS 1.4.2 and fragment pileup was outputted in .wig format

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were precipitated using streptavidin conjugated beads. Purified precipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: Sonicated nuclear lysates were incubated with Biotin-JQ1  for 6 hour

tag: sonicated nuclear lysates incubated with

tag: dna fragments precipitated using

value: Streptavidin

value: TAGCTT


title: SUM159_JQ1_CHEM_SEQ_R1

description: Chem-Seq for Biotin JQ1

tag: cell line

value: GATCAG


title: PWD Female3

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

description: processed data file: PWD_FPKM_RawCounts.xlsx

data_processing:
Sequences from Illumina adapters were trimmed using Trimmomatic (version 0.32) using the TruSeq3-SE.fa adapter sequence file provided with the program. A minimum length of 50 bases (MINLEN:50) was chosen as a cutoff for each read and 2 seed mismatches were allowed. All reads between 50 and 100 bases were included in further analyses.
The trimmed sequencing reads were aligned to the mouse genome (genome release GRCm38) using Tophat (2.0.13, --read-mismatches and --read-edit-dist set to 6). A General Transfer Format (GTF) file was used with Tophat (--GTF option) for the purpose of gene annotation (Mus_musculus.GRCm38.68.gtf).
Following mapping reads were futher processed (filtered, sorted and indexed) with Samtools and only reads that mapped to a single gene were used for further analysis.
The uniquely mapped reads were used to generate counts for each annotated gene using easyRNASeq (from Bioconductor version 3.0.2, geneModels summarization)
Differential expression analysis of count tables for male versus female comparisons of each strain was performed using the default settings of DESeq2 (1.8.1, Benjamini-Hochberg FDR correction).
Cufflinks (2.1.1, --no-effective-length-correction, --max-bundle-length 10000000 --GTF Mus_musculus.GRCm38.68.gtf) was used to generate FPKM (fragments per kilobase per million reads) normalized values.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Microsoft Excel Worksheet (.xlsx). Contains unnormalized counts generated by easyRNASeq and normalized FPKM values generated by Cufflinks. The raw counts were used by DESeq2 for differential expression analysis.

organism: Mus musculus

growth_protocol: Seven week old male and female mice were purchased from the Jackson Laboratory (Bar Harbor, ME). Animals were kept on a 12 hour light-dark cycle. Food and water were provided ad libitum. Animals of all strains, except PWD, were group housed. PWD mice were singly housed due to male aggression. After delivery, animals were acclimated for two weeks prior to euthanization by rapid decapitation at 63 +/- days old.

extract_protocol:
The hippocampus (from both sides of the brain) was dissected and rapidly frozen in liquid nitrogen and stored at -80 degrees. Total RNA was extracted from the entire hippocampus from each animal using TRI Reagent (Sigma-Aldrich) according to manufacturer’s directions.
RNA-Seq samples were prepared for each animal using the protocols of Mortazavi et al., 2008 and Chang et al., 2011.  The External RNA Controls Consortium (ERCC) RNA Mix 1 and Mix 2 Spike-in Controls (ERCC ExFold RNA Spike-In Mixes Ambion, catalog #4456739) were diluted 1:10 and spiked in to male and female libraries, respectively, just after mRNA isolation according to manufacturer’s suggestions. RNA-Seq sample quality was examined using Agilent High Sensitivity DNA Bioanalyzer Chips (Agilent Technologies 5067-4626) and quantified by KAPA Library Quantification Kits for Illumina sequencing platforms (KAPA Biosystems KK4824).Three libraries were generated for males and females from each strain. Barcodes were added to each library in order to combine multiple libraries in one sequencing lane. We multiplexed six libraries at a concentration of 12 pM and those were sequenced on an Illumina HiSeq 2500.

value: PWD/Ph

value: Female

value: 62 Days

tag: tissue

value: Hippocampus


title: PWD Female2


title: PWD Male2

value: Male


title: PWD Male3


title: PWD Male1


title: D2 Female3

description: processed data file: D2_FPKM_RawCounts.xlsx


title: mia2 d1/d5  batch3

city: La Jolla

first: Michael

last: Petrascheck

state: CA

address: 10550 N. Torrey Pines Rd

department: Chemical Physiology

institute: TSRI

description: Sample 35

data_processing:
We used Casava 1.8.2 (Illumina) to demultiplex and process the raw reads into fastq files.
RNA-seq reads in FASTQ files were aligned to the WormBase WS234 build of the C. elegans genome & annotated transcripts with Tophat version 2.0.0 (using Bowtie2 version 2.0.0.5 and Samtools version 0.1.18.0) with the "--prefilter-multihits" option. (TODO cite Tophat)
Reads were assigned to annotated genes and counted using the "summarizeOverlaps" function from the GenomicRanges Bioconductor package in "IntersectionNotEmpty" mode (TODO cite GenomicRanges: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118 ). Overlaps were computed to features of type "exon" with a Parent feature has type "mRNA" (excluding "ncRNA" in particular), grouped by gene ID (the Parent property of the mRNA feature to which each exon belongs).
Read counts were normalized across samples using the TMM method in the edgeR package with default options to produce counts-per-million (CPM) values normalized for compositional bias. (TODO cite http://genomebiology.com/2010/11/3/r25)
Gene CPM values were normalized for gene length by dividing by the length in kb of the longest transcript isoform for each gene to produce reads per kilobase per million reads (RPKM) values
Genome_build: c_elegans.WS234
Please note that the genome sequence and transcript annotations were obtained from the WS234 release of the C. elegans genome from WormBase, which was the most recent WormBase release as of the beginning of the analysis. The source URLs were:
Genome Sequence:
ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/sequence/genomic/c_elegans.WS234.genomic_softmasked.fa.gz
Transcripts:
ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/gff/c_elegans.WS234.annotations.gff2.gz
As shown in the following link, the WS234 release used the WBcel215 genome sequence (all releases from WS215 through WS234 used this same WBcel215 assembly but had possibly updated transcript annotations):
http://www.wormbase.org/species/c_elegans#28--10
Supplementary_files_format_and_content: tab-delimited text files (with column names in first line) with columns for Gene ID, raw read count, TMM-normalized CPM, and TMM-normalized RPKM

organism: Caenorhabditis elegans

source_name: mia2 d1/d5_whole animal

extract_protocol:
To extract RNA, frozen worms were re-suspended in ice-cold Trizol, zirconium beads, and glass beads (cat # 03961-1-103 and cat # 03961-1-104) in the ratio of 5:1:1 respectively, and disrupted in Precellys lysing system (6500 rpm, 3 x 10 s cycles) followed by chloroform extraction.The extracted RNA was precipitated and purified further using Qiagen RNAeasy Mini kit columns (cat # 74104). RNA was precipitated using isopropanol and washed once with 75% ethanol.
100 ng of total RNA per sample was processed using NuGEN Encore Complete DR RNA-Seq Prep Kit (NuGEN; San Carlos; CA, USA), as per manufacturer’s instructions
RNA-seq to determine changes in expression proflies

treatment_protocol: mianserin was dissolved in h2o

tag: treated with

value: mianserin (2uM)

tag: age when treatment starts

value: day 1

tag: age at rna harvest

tag: batch


title: mia50 d5/d10  batch3

description: Sample 34

source_name: mia50 d5/d10_whole animal

value: mianserin (50uM)

value: day 5


title: mia10d1/d5  batch3

description: Sample 36

source_name: mia10d1/d5_whole animal

value: mianserin (10uM)


title: D2 Female1

tag: Sex


title: D2 Male3


title: mia50 d1/d10  batch3

description: Sample 31

source_name: mia50 d1/d10_whole animal


title: mia50 d1/d5 batch3

description: Sample 30

source_name: mia50 d1/d5_whole animal


title: D2 Female2


title: h2o d1/d5  batch3

description: Sample 27

source_name: h2o d1/d5_whole animal

value: water (H2O)


title: h2o d1/d10  batch3

description: Sample 28

source_name: h2o d1/d10_whole animal


title: Uninfected sample, replicate 3b

description:
C3b
Ixodes scapularis cells uninfected


title: h2o d1/d3  batch3

description: Sample 26

source_name: h2o d1/d3_whole animal


title: D2 Male2


title: D1 Female3

description: processed data file: D1_FPKM_RawCounts.xlsx

value: 63 Days


title: D2 Male1


title: h2o d1/d1 batch3

description: Sample 25

source_name: h2o d1/d1_whole animal


title: mia50 d5/d10  batch2

description: Sample 22


title: D1 Female2


title: mia2 d1/d5  batch2

description: Sample 23


title: D1 Female1


title: mia10d1/d5  batch2

description: Sample 24


title: mia50 d3/d5  batch3

description: Sample 32

source_name: mia50 d3/d5_whole animal

value: day 3


title: mia50 d3/d5  batch2

description: Sample 20


title: D1 Male3


title: mia50 d3/d10  batch2

description: Sample 21

source_name: mia50 d3/d10_whole animal


title: mia50 d1/d5 batch2

description: Sample 18


title: mia50 d1/d3  batch2

description: Sample 17

source_name: mia50 d1/d3_whole animal


title: PWD Female1


title: mia50 d3/d10  batch3

description: Sample 33


title: mia50 d1/d3  batch3

description: Sample 29


title: h2o d1/d3  batch2

description: Sample 14


title: D1 Male1


title: h2o d1/d1 batch2

description: Sample 13


title: mia50 d1/d10  batch2

description: Sample 19


title: B6 Female3

description: processed data file: B6_FPKM_RawCounts.xlsx

value: 64 Days


title: mia2 d1/d5  batch1

description: Sample 11


title: A Female1

description: processed data file: A_FPKM_RawCounts.xlsx

value: A/J


title: B6 Female2


title: mia50 d3/d10  batch1

description: Sample 9


title: A Female2


title: B6 Female1


title: mia50 d3/d5  batch1

description: Sample 8


title: A Male2


title: h2o d1/d5  batch2

description: Sample 15


title: B6 Male3


title: h2o d1/d10  batch2

description: Sample 16


title: B6 Male2


title: A Male1


title: B6 Male1


title: by_neg2

city: Heidelberg

first: Wu

last: Wei

address: EMBL Heidelberg,Meyerhofstraße 1

department: Genome Biology Unit

country: Germany

institute: EMBL Heidelberg

data_processing:
Base-calling was done during processing of sequencing data with the Illumina HiSeq2000
Random barcode (8N) was extracted for each read
Reads were mapped to S. cerevisiae genome (SGD R64-1-1) using the Novoalign software with default settings
Reads with multiple alignments, or mapping quality <30, or carrying soft-clipped bases on the 5’ end were excluded from downstream analysis
5' end of reads passing quality filtering were extracted; total number of reads per genome location were calculated; total unique number of reads (or unique molecule, based on random barcode sequences) per genome location were calculated
Genome_build: Saccharomyces cerevisiae S288C reference genome R64-1-1 (sacCer3), downloaded from SGD(http://www.yeastgenome.org/).
Supplementary_files_format_and_content: Processed data contain the genomic location of 5' Cap RNA molecules and the number of identified unique identified molecules after controlling for presence of molecular barcodes for all samples.

growth_protocol: Strains were grown to mid-log phase (OD~1) at 30ºC in YPD (1% yeast extract, 2% peptone, 2% glucose)

extract_protocol:
All  samples were collected by centrifugation and frozen in liquid N2. Total RNA was isolated by a standard hot phenol method and treated with RNase-free DNaseI using Turbo DNA-free kit (Ambion)
Total RNA was isolated by a standard hot phenol method and treated with RNase-free DNaseI using Turbo DNA-free kit (Ambion). 60 µg of DNA-free total RNA was desphosphorylated by treatment with Calf Intestinal Alkaline Phosphatase, phenol purified and splited in 4 aliquots. Samples were treated with 5 units of Tobacco Acid Pyrophosphatase (Epicentre), Cap-Clip Acid Pyrophosphatase (CellScript, cat. no. C-CC15011H), Decapping Pyrophosphohydrolase  (Tebu-bio, cat. no. 436004-35UL) or omitting any decapping treatment.  After that each sample phenol purified and ligated overnight using T4 RNA ligase 1 (NEB) to a DNA/RNA oligo containing a random 8N molecular barcode (CTTTCCCTACACGACGCTCTTCCGATrCrUrNrNrNrNrNrNrNrN). Ligated total RNA was poly(A) purified, and reverse transcribed using random hexamers. Second strand was generated by 1 cycle PCR using oligo Biotin-TATAGCGGCCGCAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. Double stranded cDNA was bound to Streptavidin beads, washed, end repaired, dA added and ligated to P7. The PCR product were barcoded for multiplexing, size-selected using double Ampure XP size and libraries with an average size of 400-500bp .were submitted for Illumina 50bp single-end sequencing.

tag: genotype

value: Mat a; his3delta1 leu2delta0 ura3delta0 met15delta0

tag: treatment


title: A Female3


title: 129 Female2

description: processed data file: 129_FPKM_RawCounts.xlsx


title: mia10d1/d5  batch1

description: Sample 12


title: by_dpm2

value: Decapping Pyrophosphohydrolase


title: mia50 d5/d10  batch1

description: Sample 10


title: D1 Male2


title: h2o d1/d10  batch1

description: Sample 4


title: mia50 d1/d10  batch1

description: Sample 7


title: 129 Female1


title: by_capclip2

value: Cap-Clip


title: by_capclip1


title: 129 Female3

value: Female


title: mia50 d1/d5 batch1

description: Sample 6


title: mia50 d1/d3  batch1

description: Sample 5


title: by_tap2

value: TAP


title: dgv_2

status: Public on Jan 05 2016

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

data_processing:
Reads for each library were mapped using TopHat v2.0.6 9.  The following options were used: “--num-threads 8 --GTF mouseGtf.gtf” , where mouseGtf.gtf reflects the concatenated Ensembl NCBIM37 transcript annotation file and the annotated ERCC spike-in controls
For FPKM-based quantification and differential expression, the annotated mouseGtf.gtf was used in Cuffdiff v2.1.1 using the accepted_hits.bam files for all replicates.  The following options were used: “--frag-bias-correct mouseFa.fa --mask-file mouseMask.gtf --max-bundle-frags 10000000 --num-threads 8 --multi-read-correct --no-effective-length-correction”, where mouseFa.fa is the Ensembl NCBIM37 reference FASTA and mouseMask.gtf is a mask file that ignores all alignments corresponding to genes annotated in mouseGtf.gtf annotated as tRNA, rRNA, or snRNA; in addition, Nat8l, Psd2, Xist, Gm15459, and Gm10335 were masked.
For count-based quantification and differential expression, aligned reads were processed by HTSeq using the mouseGtf.gtf and the following options: "--format=bam --stranded=no".
Processed data were analyzed in the R environment using a combination of cummeRbund v3.0 (http://compbio.mit.edu/cummeRbund/), DESeq2, and custom scripts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited files containing FPKM values and pairwise DE calls, as well as count values

source_name: Ventral DG granule cells

extract_protocol:
Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007).
Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNAseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).

tag: cell population

value: Ventral DG granule cells

tag: location

value: DG


title: by_neg1


title: by_tap1


title: by_dpm1


title: dgv_1


title: A Male3

value: Male

tag: age

value: 62 Days

value: Hippocampus


title: 129 Male3

tag: strain


title: dgd_0

source_name: Dorsal DG granule cells

value: Dorsal DG granule cells


title: h2o d1/d5  batch1

description: Sample 3


title: 129 Male1


title: nac_2

source_name: Ventral CA1 nucleus accumbens-projecting pyramidal cells


title: h2o d1/d1 batch1

description: Sample 1


title: dgd_1


title: amyg_2

source_name: Ventral CA1 amygdala-projecting pyramidal cells


title: 129 Male2


title: post_2

source_name: Dorsal CA1 postsubiculum-projecting pyramidal cells


title: post_1

value: Dorsal CA1 postsubiculum-projecting pyramidal cells


title: post_0


title: nac_1

value: Ventral CA1 nucleus accumbens-projecting pyramidal cells


title: h2o d1/d3  batch1

description: Sample 2

value: water (H2O)


title: sst_2

source_name: SST interneurons

value: SST interneuron


title: dgd_2


title: ca3d_2

source_name: Dorsal CA3 pyramidal cells

value: Dorsal CA3 pyramidal cells


title: ca3v_0

source_name: Ventral CA3 pyramidal cells

value: Ventral CA3 pyramidal cells


title: ca3v_2


title: pv_2

source_name: PV interneurons

value: PV interneuron


title: ca3d_1


title: sst_0


title: pv_0


title: dgv_0


title: ca3v_1


title: ca3d_0


title: deep_1

source_name: Deep CA1 pyramidal cells

value: Deep CA1 pyramidal cells


title: superficial_1

source_name: Superficial CA1 pyramidal cells

value: Superficial CA1 pyramidal cells


title: nac_0


title: distal_2

source_name: Distal CA1 pyramidal cells

value: Distal CA1 pyramidal cells


title: deep_0


title: distal_1


title: superficial_2


title: amyg_1

value: Ventral CA1 amygdala-projecting pyramidal cells


title: distal_0


title: proximal_2

source_name: Proximal CA1 pyramidal cells

value: Proximal CA1 pyramidal cells


title: sst_1


title: amyg_0


title: pv_1


title: ventral_2

source_name: Ventral CA1 pyramidal cells

value: Ventral CA1 pyramidal cells


title: proximal_0


title: proximal_1


title: ventral_1


title: ventral_0


title: dorsal_1

source_name: Dorsal CA1 pyramidal cells

value: Dorsal CA1 pyramidal cells


title: intermediate_0

source_name: Intermediate CA1 pyramidal cells

value: Intermediate CA1 pyramidal cells


title: intermediate_2


title: dorsal_2


title: dorsal_0


title: HPC7_No_Treatment

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

description: Chromatin Immunoprecipitated DNA

data_processing:
Reads aligned to mm10 using Bowtie
bedGraphs created using bedtools
bigWigs created using UCSC utilities
Peaks called using MACS
Genome_build: mm10
Supplementary_files_format_and_content: bigWig (density profile of mapped reads) and bed (peaks)

source_name: multipotent myeloid progenitor cell line_no_treatment

growth_protocol: Grown in IMDM plus 10% fetal calf serum and 10% SCF plus penicillin and streptomycin

extract_protocol:
As described in Wilson et al., Cell Stem Cell. 2010 Oct 8;7(4):532-44
According to Illumina TruSeq DNA Sample Prep Kit

treatment_protocol: TPO

tag: antibody

tag: vendor

value: Santa Cruz


title: HPC7_TPO

description: Chromatin Immunoprecipitated DNA

source_name: multipotent myeloid progenitor cell line_TPO


title: DM-342

city: Dallas

first: Ronak

last: Lakhia

state: Texas

address: 5323 Harry Hines

institute: UTSW

data_processing:
Base calling using Illumina bcl2fastq 1.8.4
Sequenced reads were trimmed for adaptor sequence and low quality bases by fastq-mcf 1.1.2-806. parameters:  -l 35
Filtered reads were mapped to mouse genome (mm10) using Tophat 2.0.12, guided by igenome annotations. Parameters: --b2-sensitive --no-coverage-search --max-multihits 10 --library-type fr-firststrand. Then duplicates were marked but not removed.
Aligned reads were assemblied into transcripts by cufflinks. Transcripts of all samples in this experiment were merged to generated a comprehensive set of transcripts.
The resulting gtf file of assembled transcripts was used for read counting by featureCounts from subread software 1.4.6. parameters: --primary -O.
Read counts were used by edgeR 3.2.4 and cutdiff for normalization and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files for each comparison. edgeR results including log CPM values, log fold change, and test statistics.

source_name: Kidney

extract_protocol:
Kidneys were removed, flash frozen on dry ice, and RNA was harvested using Qiazol miRNeasy RNA extraction kit. Illumina TruSeq Stranded Total RNA LT Sample Prep Kit was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina.

value: Pkhd1Cre; Pkd2 F/F; miR-21null

value: Post-natal day 21

value: kidney


title: DM-243


title: SM-122

value: Pkhd1Cre; Pkd2 F/F


title: DM-50


title: WT-327

value: wild-type


title: WT-326


title: WT-66


title: EBNA3B_ChIP-Seq

city: Madison

first: Eric

last: Johannsen

state: Wisconsin

address: 1111 Highland Ave

department: Department of Medicine

institute: UW-Madison

data_processing:
Basecalls performed by the Harvard Medical School Biopolymer facility as per Illumina recommendations
ChIP-seq reads were aligned to the human hg19 genome assembly using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml)
peaks were called using  MOSAiCS (MOdel-based one and two Sample Analysis and inference for ChIP-Seq Data) controlling the false discovery rate (FDR) at 0.05.
Genome_build: hg19 and V01555.2
Supplementary_files_format_and_content: wig files were generated using MOSAiCS; Scores represent read counts

source_name: Lymphoblast Cell Lines

growth_protocol: Cells were grown in RPMI media supplemented witth 10%fetal bovine serum, penicillin and streptomycin.

extract_protocol:
Protein A/G magnetic beads was used to capture the protein DNA complexed. The eluted protein-DNA complexes were reverse crosslinked and DNA was purified by a QIAquick PCR purification kit (28706; Qiagen).
Libraries were prepared using PrepX BeadX kit from IntegenX. Briefly, DNA was end-repaired. 3' A base was added and ligated to adaptors. After PCR amplification, DNA was purified and analyzed with Illumina HiSeq.

treatment_protocol: Cells were fixed with 1% formaldehyde. After wash with twice PBS, the cells were lyzed in ChIP lysis buffer. Lysates were sonicated and cleared by centrifugation. HA antibody F-7 (sc-7392; Santa Cruz) was incubated with the lysate overnight at 4ºC.

value: Epstein Barr Virus transformed  Lymphoblast Cell Line

tag: genotype/variation

value: expressing HA tagged EBNA3B protein

tag: chip antibody

value: HA-probe Antibody F-7 (sc-7392; Santa Cruz)


title: EBNA3C_ChIP-Seq

tag: cell line

value: expressing HA tagged EBNA3C protein


title: LP1_SGC-CBP30_BRD4

first: Barbara

middle: M

last: Bryant

address: 215 First Street

institute: Constellation Pharmaceuticals

data_processing:
50-nucleotide sequence reads were aligned to the hg19 genome using the BWA algorithm with default settings. Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches and mapped uniquely to the genome, were used in subsequent analyses.
The aligned read files were sorted and duplicates removed using sort and rmdup functions from samtools version 0.1.18 (Li et al., 2009).
WIG files were generated using IGVTools (version 2.2.2) count function with a window size of 25 nucleotides, an extension of 100 beyond the 50-nucleotide read length, and genome hg19 (Robinson et al., 2011; Thorvaldsdottir et al., 2013). The WIG files were scaled assuming an effective genome length of 2.79B base pairs, so that the mean signal would be 1.0.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files (gzipped) and corresponding TDF files suitable for visualization using the Integrative Genomics Viewer (IGV) available from the Broad Institute.

source_name: LP-1 cultured cells

growth_protocol: LP-1 cells (DSMZ) were grown in IMDM + 10% FBS according to manufacturer's recommendations.

extract_protocol:
Cells were fixed with a final concentration of 1% formaldehyde for 10 minutes at room temperature. Glycine was added to a final concentration of 0.125 M to stop crosslinking. Cells were washed twice in cold PBS followed by lysis at 4°C for 1 hour in buffer containing 10mM Tris-HCl pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.2% NP-40, + protease inhibitor cocktail (Sigma). Following lysis, nuclei were recovered by centrifugation, and resuspended in buffer containing 10 mM Tris-HCl, 0.1 mM EDTA, 5 mM MgAc2, 25% glycerol. An equal part 2X MNase buffer was added, containing 50 mM KCl, 8 mM MgCl2, 2 mM CaCl2, 100 mM Tris-HCl. Micrococcal nuclease (Roche) was added to 300 U/mL and chromatin was digested at room temperature for 20 minutes. Dilution buffer (0.1% SDS, 1.1% Triton-X 100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl) was added and nuclei were broken down by sonication. Chromatin was cleared by centrifugation and pre-cleared with protein A-conjugated magnetic beads (Life Technologies). 10-20 µg precleared chromatin was combined with 10 µg anti-EP300 antibody (Santa Cruz sc-585X) or 2.5 ug of anti-H3K18ac (Cell Signaling, 9675) or anti-H3K27ac (Abcam, ab4729) conjugated to protein A magnetic beads.
DNA was purified with the MinElute kit (QIAGEN), and libraries were prepared using the Ovation Ultralow DR Multiplex System (NuGEN) according to the manufacturer’s recommendations.

treatment_protocol: 5 x 10^7 LP-1 cells were treated for 6 hours with DMSO, 0.25 μM CPI-267203 or 2.5 μM SGC-CBP30 at a density of 5 x 10^5/mL.

tag: chip antibody vendor

value: Bethyl

tag: chip antibody vendor id

tag: chip antibody lot


title: LP1_CPI203_input


title: LP1_CPI203_BRD4


title: EBNA3A_ChIP-Seq

value: expressing HA tagged EBNA3A protein


title: LP1_CPI203_P300


title: islet_500_cells_1

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Trimming of adapter sequences was performed with trimmomatic (v 0.32) minimum read length after trimming: 25
Alignment of the trimmed reads to the human transcriptome (hg19 GRCh37 ftp://ftp.ensembl.org/pub/release-74/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.74.cdna.all.fa.gz) was performed with bowtie1 (v 1.1)
Calculation of normalized transcript-wise expression estimates (RPKM values) was performed based on the transcriptome alignments using the R (v 3.1.2) package BitSeq (v 1.10.0). Function: getExpression() with uniform=FALSE
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include transcript-wise RPKM values or read counts for each sample

source_name: pancreatic islet

extract_protocol:
To disassociate islets into single cells, islets were incubated in Accutase (Life technology) in 37 °C for 20 min, neutralized by CMRL medium. Purification of single cells was performed by flow cytometry cell sorting on a Moflo AstriosEQ (Beckman Coulter, Miami)
cDNA synthesis and enrichment was performed following the Smart-seq2 protocol as described (Picelli et al., 2014).

treatment_protocol: Islets were cultured in CMRL medium (Life technology) supplemented with 10% FBS, 2 mM glutamine, 100 U/mL penicillin, and 100 µg/mL streptomycin.

tag: assigned cell type

value: islet

tag: qc pass

value: TRUE

tag: cell count


title: islet_single_cell_70

value: alpha


title: islet_single_cell_68


title: islet_single_cell_69

value: beta


title: LP1_DMSO_BRD4

value: DMSO


title: SM-98

tag: genotype

tag: tissue


title: SM-27


title: islet_single_cell_67

value: acinar


title: islet_single_cell_64


title: islet_single_cell_65


title: islet_500_cells_2


title: islet_single_cell_61


title: islet_single_cell_60

value: FALSE


title: islet_single_cell_62


title: WT-81

value: Post-natal day 21


title: islet_single_cell_59


title: deep_2

tag: cell population

value: Deep CA1 pyramidal cells


title: islet_single_cell_58


title: islet_single_cell_56


title: islet_single_cell_55


title: islet_single_cell_57


title: islet_single_cell_54

value: duct


title: islet_single_cell_66


title: islet_single_cell_53


title: islet_single_cell_51

value: undefined


title: islet_single_cell_52


title: islet_single_cell_50

value: pp


title: islet_single_cell_44


title: islet_single_cell_49


title: islet_single_cell_43


title: islet_single_cell_46


title: islet_single_cell_45


title: islet_single_cell_42


title: islet_single_cell_41


title: islet_single_cell_39


title: islet_single_cell_40


title: islet_single_cell_38


title: islet_single_cell_36


title: islet_single_cell_34


title: islet_single_cell_63


title: islet_single_cell_48


title: islet_single_cell_35


title: islet_single_cell_33


title: islet_single_cell_47


title: superficial_0

value: Superficial CA1 pyramidal cells

tag: location


title: islet_single_cell_31


title: islet_single_cell_28


title: islet_single_cell_26


title: islet_single_cell_25


title: islet_single_cell_32


title: islet_single_cell_27


title: islet_single_cell_30


title: islet_single_cell_24


title: islet_single_cell_23


title: islet_single_cell_18


title: islet_single_cell_21


title: islet_single_cell_19


title: islet_single_cell_29


title: islet_single_cell_22


title: islet_single_cell_37


title: islet_single_cell_16


title: islet_single_cell_17


title: islet_single_cell_11


title: islet_single_cell_14


title: islet_single_cell_10


title: islet_single_cell_9


title: islet_single_cell_7


title: islet_single_cell_8

value: delta


title: islet_single_cell_6


title: islet_single_cell_1


title: islet_single_cell_5


title: LP1_SGC-CBP30_H3K27ac

treatment_protocol: 5 x 10^7 LP-1 cells were treated for 6 hours with DMSO or 2.5 μM SGC-CBP30 at a density of 5 x 10^5/mL.

value: Abcam


title: islet_single_cell_2


title: islet_single_cell_20


title: LP1_SGC-CBP30_H3K18ac

value: Cell Signaling


title: LP1_SGC-CBP30_input


title: LP1_DMSO_H3K18ac


title: LP1_SGC-CBP30_P300

value: Santa Cruz


title: islet_single_cell_3


title: LP1_DMSO_P300


title: LP1_DMSO_input


title: LP1_DMSO_H3K27ac


title: islet_single_cell_15


title: islet_single_cell_13


title: islet_single_cell_12


title: D2-2_pa_50ns

first: Aleksandra E

last: Kornienko

address: Lazarettgasse 14, AKH BT 25.3, 3rd floor

institute: CeMM  Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: Supplemental_table_2_granulocyte_de_novo_lncRNA_loci_annotation.bed, Supplemental_table_3_granulocyte_de_novo_lncRNA_transcript_annotation.bed, Supplemental_table_4_granulocyte_de_novo_mRNA_loci_annotation.bed, Supplemental_table_5_granulocyte_de_novo_mRNA_transcript_annotation.bed, granulocyte_denovo_lncRNA_loci_novelty_and_position_class.xls, granulocyte_denovo_lncRNA_novelty_and_position_class.xls

data_processing:
RNA sequencing data was aligned to the hg19 human genome using STAR (version 2.3) (See Kornienko, et al , Methods for details)
de novo lncRNA and mRNA annotations were obtained using Cufflinks, Cuffmerge and a series of filtering steps (described in Kornienko et al) for granulocytes (using granulocytes PolyA+ RNA-seq deposited here)
RPKMs were calculated using RSeQC package
Genome_build: hg19
Supplementary_files_format_and_content: deposited are expression levels (RPKM) of granulocyte lncRNA and mRNA transcripts and loci in 21 total granulocyte samples (used for variation analyses), excel table with first 6 column indication transcript/locus coordinate, name and strand, and next columns - RPKM values. Name of the column corresponds to the name of the sample.
Supplementary_files_format_and_content: "_variation analysis.xls" excel tables contain the position, name and the strand of the transcript / locus and data used to plot
Supplementary_files_format_and_content: "_novelty_and_position_class" are tables with the names of granulocyte de novo lncRNA loci/transcripts and their classification according to novelty (as shown in Fig 3A, Kornienko et al), or position relative to protein coding genes (as shown in Fig1C).
Supplementary_files_format_and_content: "_annotation" files are in BED12 format and contain de novo lncRNA and mRNA annotations obtained in the study for granulocytes and LCL

source_name: human primary granulocytes

extract_protocol:
Primary Granulocytes were isolated from fresh blood collected in the morning using Ficoll density centrifugation method. After erythrocyte depletion and washing in ice cold PBS (supplemented by 2mM EDTA) granulocytes were pelleted and immediately lyzed using TRI-reagent (Sigma-Aldrich T9424) and RNA was then isolated using the manufacturers protocol. Total RNA was DNaseI treated using the DNA-FreeTM kit (Ambion).
RNA for total RNA-seq was depleted for Ribosomal RNA using the RiboZero rRNA removal kit (Human/Mouse/Rat) (Epicentre) according to manufacturer's protocol. RNA for PolyA+ RNA-seq was enriched for polyadenylated RNA using TruSeq RNA Sample Prep Kit v2 (Illumina). Pretreeated RNA was then subject to library preparation. Strand-specific RNA-seq libraries were prepared employing the TruSeq RNA Sample Prep Kit v2 (Illumina) modified to obtain strand-specificity using dUTP incorporation and UDGase treatment. RNA-seq was performed by the Biomedical Sequencing Facility (BSF) in Vienna using the Illumina HiSeq 2000 platform.

tag: cell type

value: granulocyte

value: blood

tag: passages

value: primary


title: D7-3_pa_50ns


title: D3-3_pa_50ns


title: D10_pa_50ns


title: D9_pa_50ns


title: D8_pa_100ns


title: D1-2_pa_50ns


title: D6-2_pa_100ns


title: islet_single_cell_4

value: TRUE


title: D1-2_pa_100ns


title: D5-2_pa_100ns


title: D2-2_pa_100ss


title: D6-1_pa_100ss


title: D3-1_pa_100ss


title: D3-2_pa_100ns


title: D7-3_tot_100ss

description: granulocyte_denovo_lncRNA_loci_RPKM_total_gra_7donorsx3replicates.xls, granulocyte_denovo_lncRNA_loci_variation_analysis.xls, granulocyte_denovo_lncRNA_RPKM_total_gra_7donorsx3replicates.xls, granulocyte_denovo_lncRNAs_variation_analysis.xls, granulocyte_denovo_mRNA_loci_RPKM_total_gra_7donorsx3replicates.xls, granulocyte_denovo_mRNA_loci_variation_analysis.xls, granulocyte_denovo_mRNA_RPKM_total_gra_7donorsx3replicates.xls, granulocyte_denovo_mRNAs_variation_analysis.xls,


title: D1-2_pa_100ss


title: D7-2_tot_100ss


title: D6-3_tot_100ss


title: D6-2_tot_100ss


title: D5-3_tot_100ss


title: D6-1_tot_100ss


title: D5-1_tot_100ss


title: D5-2_tot_100ss


title: D7-1_tot_100ss


title: D2-1_pa_100ns


title: D4-3_pa_100ns


title: D2-2_tot_100ss


title: D4-3_tot_100ss


title: D1-3_tot_100ss


title: D4-2_tot_100ss


title: D4-1_tot_100ss


title: D3-3_tot_100ss


title: D1-1_tot_100ss


title: D3-2_tot_100ss


title: D2-3_tot_100ss


title: AZF_rep2, input

city: UNSW Sydney

first: WOOI FANG

last: LIM

state: NSW

address: School of Biotechnology and Biomolecular Sciences

department: BABS

country: Australia

institute: University of New South Wales

description: Input control

data_processing:
Reads were quality filtered, trimmed and adapter sequences were removed using Trimmomatic v0.3.2.
Alignment with Bowtie v2.2.1 to the hg19/GRCh37 Homo Sapiens genome.
Resulting alignments were sorted and indexed using Samtools v0.1.18.
Peak calling with HOMER v.4.7.2. using permissive settings (-P .1 -LP .1 -poisson .1).
Peaks lists were supplied to homer-IDR to determine the IDR (irreproducible discovery rate) statistic generating a final peak list satisfying the thresholds set by homer-IDR.
Peak calling with HOMER v.4.7.2. using default settings except with (-style factor -F 10).
Peak lists were supplied to DIFFBIND v1.10.2 for differential binding analysis.
Peak lists were annotated using annotatePeaks.pl using HOMER annotation set for hg19/GRCh37.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with peak scores and normalized tag counts.

growth_protocol: Stable human embryonic kidney (HEK293) cells expressing either AZF or KLF3FD-AZF were cultured in Dulbecco’s modifieid Eagle’s medium (DMEM) (Cat# 11320-082, Life Technologies) supplemented with 10% fetal bovine serum (Cat# 16000044, Life Technologies), 1% Penicillin-Streptomycin-Glutamate (Life Technologies #10378016) and 2.5ug/ml puromycin (to maintain selection)

extract_protocol:
Refer to Schmidt D 2009 et al. Methods and Burdach J 2014 et al. NAR.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP sample prep kit from Illumina, San Diego, CA (Cat #:  IP-202-1012).

tag: construct

value: AZF

tag: chip-antibody


title: D1-2_tot_100ss


title: D3-1_tot_100ss


title: KLF3FD-AZF_rep1, input

description: Input control


title: AZF_rep1, immunoprecipitation

description: IP

value: anti-V5 antibody (Cat# R960CUS, Life Technologies)


title: KLF3FD-AZF_rep2, input

description: Input control


title: LP1_DMSO_6h_R1 (SL62425)

data_processing:
Sequencing was performed on an Illumina HiSeq 2000.
Tophat 1.4.1 was used to perform sequence alignment, with UCSC human (hg19) as the reference genome.
The Normalized counts of sequence reads (FPKM) mapped to annotated UCSC genes were determined using Cufflinks software.
The data was filtered to keep genes with at least one sample above a 50-read threshold. Samples with fewer than 10 reads FPKM are replaced with the average across samples of 10 reads FPKM, to generate the final gene counts for each sample and gene.
Data processing was performed by Ocean Ridge Biosystems.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files describing Ensembl genes used as reference (probes.txt) and RPKM-based gene-level expression data for each sample (data.txt).

growth_protocol: 2.5 million LP-1 cells were grown in 5 mL of IMDM media + 10% FBS + 1% pen-strep. NOMO-1 parental or resistant cells were maintained in RPMI + 20% FBS + 1% pen-strep (+0.18 uM CPI203 for resistant cells).

extract_protocol: LP-1 RNA was prepared with Qiagen RNEasy kit with on column DNAse digestion according to the manufacturer’s protocol.  Purified NOMO-1 RNA was treated in solution with RNase-free DNase (QIAGEN), and subsequently purified on RNeasy columns (QIAGEN). 2ug (LP-1) or 5ug (NOMO-1) RNA was sent to Ocean Ridge Biosciences LLC (FL, USA) for QC, library prep and RNA-seq.

treatment_protocol: LP-1 cells were treated with DMSO, SGC-CBP30 (2.5 uM), or CPI203 (250 nM) for 6 h, and cells were pelleted. NOMO-1 cells were washed once in compound-free media and 2.5E6 cells were seeded at a density of 2.5E5/mL, and treated for 24 hours with 0.2% DMSO, 0.18 uM CPI203, or 2.0 uM CPI203 (parental), or 0.18 uM CPI203 or 2.0 uM CPI203 (resistant).  After 24 hours, cells were harvested and resuspended in 1 mL Trizol reagent (Life Technologies) and RNA was purified according to the manufacturer’s recommendations.

tag: treatment

value: DMSO 6h


title: AZF_rep1, input

description: Input control


title: AZF_rep2, immunoprecipitation

description: IP


title: LP1_DMSO_6h_R2 (SL62426)


title: LP1_CPI203_250_6h_R2 (CM38049004)


title: LP1_2.5uM_SGCCBP30_6h_R1 (SL62437)

value: 2.5uM SGCCBP30 6h


title: LP1_CPI203_250_6h_R1 (CM38049003)


title: LP1_DMSO_6h_R2 (CM38049002)


title: KLF3FD-AZF_rep1, immunoprecipitation

description: IP


title: LP1_2.5uM_SGCCBP30_6h_R2 (SL62438)


title: LP1_DMSO_6h_R1 (CM38049001)


title: D2-1_tot_100ss


title: Transgenic Flag-FTO mice/Flag-IP 1

city: Taoyuan

first: Chao-Yung

last: Wang

address: 5 Fu-Hsing street

department: Cardiology

country: Taiwan

institute: Chang Gung Memorial Hospital

description:
RNA-IP
Sample 1
Processed data file: IPcounts.txt

data_processing:
Illumina Casava 1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata .
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Immunoprecipitated reads were then compared between Samples 1/2 and Sample 3 (IgG) control. The total reads are in file IPcounts.txt.
Sample 2 presented with better gene reads compared to Sample 1 (Density.png). Sample 2 was chosen for further analysis.
Selection of all genes related to lipid metabolism, which has higher 'Sample 2 (Flag-IP)/Sample 3 (IgG)' (rnaSequencelipidlist.txt).
Genome_build: MGSCv36 (mm8)
Supplementary_files_format_and_content: IPcounts.txt: Tab-delimited text file includes the RPKMs for each Sample.
Supplementary_files_format_and_content: Density.png: Density of gene reads in Sample 2 compared to Sample 3 (IgG control).
Supplementary_files_format_and_content: rnaSequencelipidlist.txt: Genes related to lipid metabolism, which has higher 'Sample 2 (Flag-IP)/Sample 3 (IgG)'. L: Lipid homeostasis-related genes, F: Fatty acid homeostasis-related genes.

source_name: White fat, Flag-FTO transgenic, Flag-IP

extract_protocol:
Transgenic FTO mice were fasted overnight and adipose tissues were lysed in passive lysis buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP-40) containing 1 mM DTT, SUPERase In (100 U/mL, Ambion), and protease inhibitor cocktail (Roche).
Homogenates were then gently lysed with repeated freezing at -80 °C and subsequent thawing. Passive lysis buffer lysates were diluted 10-fold in NET-2 buffer (50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1 mM MgCl2, 0.05% NP-40, 20 mM EDTA, pH 8.0, 1 mM DTT, 100 U/mL SUPERase In), precleared with protein-G beads, and immunoprecipitated with antibody specific to FLAG M2 agarose (Sigma-Aldrich, cat# F1804) or IgG for 90 min.
Agaroses were washed 6 times with cold NT-2 buffer (50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1 mM MgCl2, 1% NP-40). The input and beads were resuspended in 150 μL proteinase K buffer (NT-2 buffer supplemented with 1% SDS and 1.2 mg/mL proteinase K) for 30 min at 55 °C. Immunoprecipitated RNA was extracted by acid-phenol/chloroform for further analysis.
Illumina HiSeq 2000 system.

tag: strain/background

tag: transgenic

value: Flag-FTO

value: white fat

tag: age

value: 16 weeks

tag: antibody

value: anti-Flag M2 monoclonal


title: B6-RNASeq

first: Gloria

last: Sheynkman

state: WI

address: 1101 University Ave.

department: Chemistry

description: B6 mouse islets

data_processing:
alignment: bowtie
quantification: RSEM
Genome_build: mm9
Supplementary_files_format_and_content: tsv file reports TPM and FPKM

source_name: islets

extract_protocol:
Total RNA was isolated from mouse islets using RNeasy spin columns according to the manufacturer’s directions (Qiagen). RNA quantity was determined using a Nanodrop (Thermo Scientific) and the quality assessed by a Bioanalyzer (Agilent). Total mouse RNA was used for RNA-sequencing on an Illumina HiSeq 2000.
TruSeq

tag: strain

value: whole pancreatic islets


title: Transgenic Flag-FTO mice/IgG-IP 1

description:
RNA-IP
Sample 3
Processed data file: IPcounts.txt
Processed data file: Density.png
Processed data file: rnaSequencelipidlist.txt

source_name: White fat, Flag-FTO transgenic, IgG IP

value: IgG


title: KLF3FD_rep2, input

description: Input control

data_processing:
Reads were quality filtered, trimmed and adapter sequences were removed using Trimmomatic v0.3.2.
Alignment with Bowtie v2.2.1 to the hg19/GRCh37 homo sapienss genome.
Resulting alignments were sorted and indexed using Samtools v0.1.18.
Peak calling with HOMER v.4.7.2. using permissive settings (-P .1 -LP .1 -poisson .1).
Peaks lists were supplied to homer-IDR to determine the IDR (irreproducible discovery rate) statistic generating a final peak list satisfying the thresholds set by homer-IDR.
Peak calling with HOMER v.4.7.2. using default settings except with (-style factor -F 10).
Peak lists were supplied to DIFFBIND v1.10.2 for differential binding analysis.
Peak lists were annotated using annotatePeaks.pl using HOMER annotation set for hg19/GRCh37.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with peak scores and normalized tag counts.

growth_protocol: Stable human embryonic kidney (HEK293) cells expressing either, KLF3FD, AZF or KLF3FD-AZF were cultured in Dulbecco’s modifieid Eagle’s medium (DMEM) (Cat# 11320-082, Life Technologies) supplemented with 10% fetal bovine serum (Cat# 16000044, Life Technologies), 1% Penicillin-Streptomycin-Glutamate (Life Technologies #10378016) and 2.5ug/ml puromycin (to maintain selection)

extract_protocol:
Refer to Schmidt D 2009 et al. Methods and Burdach J 2014 et al. NAR.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP sample prep kit from Illumina, San Diego, CA (Cat #: IP-202-1012).


title: KLF3FD-AZF_rep2, immunoprecipitation

description: IP


title: USA300_TSB

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

data_processing:
Raw data files (.sff) were imported into the CLC Genomics Workbench software platform for analysis
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Expression values were exported into excel files
Genome_build: The accession numbers for the Genbank genome files used as references were CP000255(for USA300 TSB and USA300 serum), NC_002952 (for UAMS-1 TSB), and NC_007795(for NCTC8325 TSB).
Supplementary_files_format_and_content: Expression values calculated for each gene are presented as RPKM values in excel format

organism: Staphylococcus aureus

source_name: Bacterial cells, pelleted

growth_protocol: Strains were grown in TSB medium at 37°C with shaking

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free
Library construction was performed using the Ion Total RNA-Seq v2 Kit from Life Technologies

treatment_protocol: Samples were stored at -80°C prior to RNA extraction

value: USA300 Houston

tag: genotype/variation

value: wild-type

tag: growth medium

value: TSB

tag: growth conditions (time/temp/shaking)

tag: molecule subtype

value: total RNA, rRNA-depleted


title: KLF3FD_rep1, input

description: Input control


title: USA300_serum

value: Human Serum


title: small RNA sequencing in ∆rrp6 dhp1-2 cells

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description:
sRNA ∆rrp6 dhp1-2
small RNA

data_processing:
Aligment of small RNAs; Novocraft 2.07.13
Adapters were trimmed and duplications were removed using Novoalign.
SGRs were generated from the aligned files and repeat nromalized to per million mapped reads.
Genome_build: ASM294v2 [asm294v2.28]
Supplementary_files_format_and_content: The data is uploaded as SGR file where first column denotes the chromosome, second column denotes the position on the chromosome counted from the 5' end on the + strand, and the 3rd column denotes the count (normalized to million mapped reads).

organism: Schizosaccharomyces pombe

source_name: ∆rrp6 dhp1-2 cells

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Cultures were first grown at 30˚C to OD600=~0.2 and then shifted to 37˚C for 5 hours.

extract_protocol:
RNA was extracted using the MasterPure™ Yeast RNA Purification Kit (epicentre)
21-25nt small RNAs were isolated by denaturing gel electrophoresis and after ethanol precipitation. Libraries were then constructed using the NEBNext Small RNA Library Prep Set for Illumina (NEB). Amplified DNA of 140-150bp was extracted from a 6% PAGE gel. Eluted DNA was ethanol precipitated overnight and resuspended in TE buffer.
Libraries were analyzed using an Agilent 2100 BioAnalyzer (Agilent) and sequenced on the Illumina MiSeq platform.

treatment_protocol: dhp1-2 mutation in ∆rrp6

value: {delta}rrp6 dhp1-2 mutant

tag: growth stage

value: log. growing cells


title: Transgenic Flag-FTO mice/Flag-IP 2

description:
RNA-IP
Sample 2
Processed data file: IPcounts.txt
Processed data file: Density.png
Processed data file: rnaSequencelipidlist.txt

tag: tissue


title: UAMS-1_TSB

value: TSB (dextrose depleted)


title: KLF3FD_rep2, immunoprecipitation

description: IP

value: anti-V5 antibody (Cat# R960CUS, Life Technologies)


title: SH1000_TSB


title: KLF3FD_rep1, immunoprecipitation

description: IP


title: small RNA sequencing in ∆rrp6 cells

description:
sRNA ∆rrp6
small RNA

source_name: ∆rrp6 cells

value: {delta}rrp6 mutant


title: IGFBP5-A375

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

description: Sample 1

data_processing:
Tophat v2.0.13 used for first-step mapping
Bowtie2 v2.2.4 used for secon-step mapping with the unmapped reads produced by Tophat
Combine two-step mapping using samtools v1.1, then calculated the RPKM for each gene using Cufflinks v2.2.0
Computation and visualization were achieved using the heatmap plus package in R.
DAVID v6.7 for functional analysis of specific genes
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized RPKM values for each Sample

growth_protocol: cells were cultured in an incubator at 37°C, 5% CO2

extract_protocol:
Total RNA was extracted from two samples by TRIzol, and poly(A) RNA was enriched by Dynabeads mRNA Purification Kit according to manufacturer's instruction.
The whole transcriptome libraries were prepared by ion total RNA-seq kit v2 according to its user guide.

treatment_protocol: IGFBP5-A375 (Sample 1) was stabely transfected with pcDNA-IGFBP5, which result in over expression of IGFBP5.  A375-control (Sample 2) was stably transfected with pcDNA empty plasmids as control.

tag: cell line

value: Melanoma cell line

tag: transfected with

value: IGFBP5 overexpression


title: Submergence (48h) Bd21 replicate 2

status: Public on Jan 04 2016

city: Tuxtepec, OAX

first: Julian

last: Pena-Castro

state: South America

address: Circuito Central 200

department: Biotechnology

country: Mexico

institute: Universidad del Papaloapan

description: Six leaves stage

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic (Bolger, 2014), then mapped to Brachypodium genome (Bdistachyon_283_v2.0) using TopHat2 with parameters  -p 4 --library-type fr-firststrand
Reads aligned to genic region were counted by using HTseq library (Anders et al. 2014)
Analysis of differentially expressed genes was performed in the R environment using the edgeR package with GLM (generalized linear model)
Genome_build: Bdistachyon_283_v2.0 (http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV10#)
Supplementary_files_format_and_content: Tables with counts for all gene models and results for the differential expression analysis

organism: Brachypodium distachyon

source_name: Submerged aerial whole tissue

growth_protocol: Seeds were disinfected in 10 ml of 1:1 household bleach (sodium hypoclorite 1.6%) and one volume of distilled, deionized and autoclaved water (ddH20), rinsed 5 times in 20 ml of ddH20, scarified in water for 4 d at 4ºC and sawn horizontally in autoclaved substrate (Sunshine Mix #3 plus 1:4 v/v perlite:substrate, autoclaved for 2 h) and mixed with 2% w/w slow liberation fertilizer NPK (15:15:17; Nitrofoska). Germination and growth was under long-day conditions (16 h light/8 h dark, 180 μE m−2 s−1, 50% humidity) in a growth room with irrigation every 2 d using filtered tap water.

extract_protocol:
Above ground tissue was collected immediately in liquid nitrogen and stored at -80ºC in an ultra freezer until further processing. Tissue was ground to powder with mortar, pestle and liquid nitrogen avoiding thawing. Control and submerged total RNA was extracted with TRIzol reagent (Invitrogen, 15596018), purified with Direct-zol RNA mini prep columns (Zymo Research, R2050) and digested in-column with DNAse I (ThermoScientific, #EN0521). RNA integrity and concentration was verified in denaturing 1.0% agarose gels, Nanodrop 2000 (ThermoScientific) and in a Bioanalyzer 2100 (Agilent) with the integrated software 2100 Expert, samples had a RNA Integrity Number (RIN) between 6.4-7.2 characteristic of aerial plant tissue (Babu and Gassman, 2011).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Brachypodium plants (14-day-old, 6 leaves stage) were submerged in a water column of 30 cm inside opaque-wall plastic tanks. Light still reached the plants at 40 μE m−2 s−1. Ecotypes were submerged side-by-side in a randomized manner; only plants submerged in the same tank were compared. Controls were grown in plastic tanks without a water column. Submergence stress started at ZT14 (2h before night) and plants were rescued by gentle subtraction from the water column and left to grow at normal conditions for the time indicated in each experiment.

value: Bd21 (ecotype)

value: Aerial whole tissue

value: 16-day-old after germination

tag: genotype

value: wild type


title: Control Bd21 replicate 3

description: Six leaves stage

source_name: Aerial control whole tissue


title: Submergence (48h) Bd21 replicate 1

description: Six leaves stage


title: Submergence (48h) Bd21 replicate 3

description: Six leaves stage


title: A375-control

description: Sample 2

tag: cell type

value: pcDNA empty plasmid

value: vector control


title: Control Bd21 replicate 1

description: Six leaves stage


title: Control Bd21 replicate 2

description: Six leaves stage


title: Submergence (48h) Bd2-3 replicate 3

description: Six leaves stage

value: Bd2-3 (ecotype)


title: Submergence (48h) Bd2-3 replicate 2

description: Six leaves stage


title: Submergence (48h) Bd2-3 replicate 1

description: Six leaves stage


title: Control Bd2-3 replicate 2

description: Six leaves stage


title: Control Bd2-3 replicate 1

description: Six leaves stage


title: Msbud

city: Seoul

first: Minseok

last: Seo

address: Kwan-ak ro 1

department: Interdisciplinary program of bioinformatics

country: South Korea

institute: Seoul National University

data_processing:
Adaptor sequences and low quality bases with PHRED scores (Q) ≤ 30 were removed. And we employed Trimmomatic for removal of adapter sequences.
The read mapping into assembled transcriptome was performed using bowtie2 implemented in tophat2;
For the abundance estimation, we employed the HTSeq tool.
Genome_build: We used watermelon reference genome (97103) version 1 in Curcurbit Genomics Database.
Supplementary_files_format_and_content: CSV file including all samples

organism: Citrullus lanatus

source_name: floral bud tissue in DAH3615-MS line

extract_protocol:
Total RNA was prepared from 2 tissues of 2 phenotypically different watermelons. Total RNA was extracted using TRIzol reagent (MRC).
Libraries were prepared using  illimina manual and platform.

tag: breed

value: Floral bud


title: MSflower

source_name: flower tissue in DAH3615-MS line

value: Flower


title: MFflower

source_name: flower tissue in DAH3615 line

value: DAH3615 line


title: A375-shMAGE-A1

data_processing:
Tophat v2.0.13 used for first-step mapping
Bowtie2 v2.2.4 used for secon-step mapping with the unmapped reads produced by Tophat
Combine two-step mapping using samtools v1.1, then calculated the RPKM for each gene using Cufflinks v2.2.0
Computation and visualization were achieved using the heatmap plus package in R.
DAVID v6.7 for functional analysis of specific genes
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

treatment_protocol: Sample 1 was stabely transfected with pcDNA3 vector, which resulted in as a negative control for OE. Sample 2 was stabely transfected with pcDNA3-MAGE-A1 plasmids as overexpression of MAGE-A1.Sample 3 was stabely transfected with pRNAT-scramble vector, which resulted in as a negative control for KD.Sample 4 was stabely transfected with pRNAT-shMAGE-A1 plasmids as knockdown of MAGE-A1.


title: S5p_MG

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
Basecalling and Demultiplexing was performed using BaseSpace from Illumina.
Reads were aligned to the human genome (hg19) with BOWTIE2 v2.1.0 using  standard-options
Bedgraph files were generated using Bedtools
All further analysis were performed in R or Bedtools
Genome_build: hg19
Supplementary_files_format_and_content: Files in bedgraph format are provided.

source_name: IMEC cell line

extract_protocol:
Where indicated, MYC K52o-HA was induced with doxycycline (pInducer samples) or treated with EtOH as solvent control. Where indicated MG-132 (10 µM) or EtOH as a control was added to the cells 4 hr prior to fixation. Cells were crosslinked with 1% formaldehyde for 10min. Cells were lysed and after centrifugation nuclei were re-suspended in RIPA buffer. DNA was sonicated with a Branson sonifier to obtain DNA fragments at nucleosomal size. Chromatin was precipitated by incubation with specific antibodies pre-adsorbed to Protein A dynabeads beads overnight. After several washings chromatin was eluted with 1 % SDS and  crosslinking was reverted overnight. DNA was purified by Phenol/Chloroform extraction and enrichments were checked by qPCR.
Libraries for ChIP-seq samples were contructed following manufactor's intructions using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (E6240). Briefly, ChIP DNA was end repaired,  A-tailed  and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of a agarose gel and extracted with a Qiagen PCR purification column. Size-selected DNA was amplified with 18 PCR cycles.

tag: generation of cells

value: primary breast epithelial cells

tag: mg treatment

value: MG


title: S2p_MG


title: S5p_EtOH

value: EtOH


title: A375-pRNAT-scramble


title: S5p_K52o_Dox

tag: dox treatment

value: DOX

tag: construct


title: A375-pcDNA-control


title: A375-MAGE-A1-OE


title: S5p_K52o_EtOH

tag: antibody


title: intermediate_1

data_processing:
Reads for each library were mapped using TopHat v2.0.6 9.  The following options were used: “--num-threads 8 --GTF mouseGtf.gtf” , where mouseGtf.gtf reflects the concatenated Ensembl NCBIM37 transcript annotation file and the annotated ERCC spike-in controls
For FPKM-based quantification and differential expression, the annotated mouseGtf.gtf was used in Cuffdiff v2.1.1 using the accepted_hits.bam files for all replicates.  The following options were used: “--frag-bias-correct mouseFa.fa --mask-file mouseMask.gtf --max-bundle-frags 10000000 --num-threads 8 --multi-read-correct --no-effective-length-correction”, where mouseFa.fa is the Ensembl NCBIM37 reference FASTA and mouseMask.gtf is a mask file that ignores all alignments corresponding to genes annotated in mouseGtf.gtf annotated as tRNA, rRNA, or snRNA; in addition, Nat8l, Psd2, Xist, Gm15459, and Gm10335 were masked.
For count-based quantification and differential expression, aligned reads were processed by HTSeq using the mouseGtf.gtf and the following options: "--format=bam --stranded=no".
Processed data were analyzed in the R environment using a combination of cummeRbund v3.0 (http://compbio.mit.edu/cummeRbund/), DESeq2, and custom scripts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited files containing FPKM values and pairwise DE calls, as well as count values

source_name: Intermediate CA1 pyramidal cells

extract_protocol:
Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007).
Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNAseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).

tag: cell population

value: Intermediate CA1 pyramidal cells

tag: location


title: S2p_K52o_EtOH


title: N20_K52o_Dox


title: S2p_EtOH


title: Input_K52o_Dox


title: S2p_K52o_Dox


title: Control Bd2-3 replicate 3

description: Six leaves stage

tag: strain

tag: age


title: rep2_siCDC73

description:
polyA RNA
norm_count_table_for_siMYC_siCDC73.csv

data_processing:
Basecalling and Demultiplexing was performed using BaseSpace from Illumina.
Reads were aligned to the human genome (hg19) with BOWTIE2 v2.1.0 using  standard-options
Bedgraph files were generated using Bedtools
Differential expression and statistical inference was done using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: The csv-files contain a table showing the edgeR normalized counts for each transcript. The bedgraph files were generated using Bedtools for each sample.

growth_protocol: IMEC cell lines were grown in DMEM/F-12 with appropriate supplements.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) including on-column DNase digestion. Poly-A RNA was isolated from total RNA using the NEBNext Poly(A)mRNA Magnetic Isolation Module (E7490). For 4-SU seq, nascent RNA transcripts were labelled for 10 min using 1 mM 4-thiouridine (4sU, Sigma T4509). After RNA isolation the 4SU-labelled RNAs were biotinylated and enriched using MyOne Streptavidin beads (Life Technologies). Eluted RNAs were subsequently used for library preparation using NEBNext RNA-Sequencing kits.
Libraries for the RNA-seq samples were constructed using the NEBNext Library Prep Kit (6100) following the instruction manual. Briefly, poly-A RNA was fragmented to generate 200 nucleotides long fragments. First and second strand cDNA synthesis was performed and the resulting cDNA was end-repaired, ligated to NEBNext adaptors. The cDNA was size selected using agarose gels and amplified by PCR. For the resulting RNA-seq libraries, amplicon sizes and quantities were determined using the Biorad Experion system. Libraries were sequenced on an Illumina NextSeq 500 following the manufacture’s instructions.

treatment_protocol: Cells were infected with the indicated doxycycline-inducible constructs and treated with Dox or EtOH as solvent control or transfected with the indicated siRNAs.

tag: sirna

tag: replicates


title: N20_K52o_EtOH


title: rep1_siMYC

value: siMYC


title: rep2_siCtrl

value: siCtrl


title: Input_K52o_EtOH


title: rep1_siCtrl_for_MYC


title: Mfbud

source_name: floral bud tissue in DAH3615 line

tag: tissue


title: WT_EtOH_2

description:
polyA RNA
norm_count_table_k52o.csv

tag: infected construct

tag: etoh/dox treatment

value: Dox


title: rep1_siCDC73


title: rep1_siCtrl_for_CDC73


title: K52o_EtOH_2

description:
polyA RNA
norm_count_table_k52o.csv


title: 4SU_rep2_WT_Dox

description: 4SU-labelled RNA


title: 4SU_rep2_Kless_EtOH

description: 4SU-labelled RNA


title: 4SU_rep2_Kless_Dox

description: 4SU-labelled RNA


title: 4SU_rep1_Kless_EtOH

description: 4SU-labelled RNA


title: 4SU_rep1_WT_EtOH

description: 4SU-labelled RNA


title: 4SU_rep1_WT_Dox

description: 4SU-labelled RNA


title: K52o_Dox_2

description:
polyA RNA
norm_count_table_k52o.csv


title: S5p_WT_EtOH.wig

data_processing:
Basecalling was performed with the real time analysis (RTA) package within the Genome Analyzer Sequencing Control Software (SCS2.10).
Demultiplexing and generation of Fastq files was done with the CASAVA software only considering high quality sequences (PF-cluster).
Reads were aligned to the human genome (hg19) with BOWTIE v0.12.8 using  standard-options
Peaks were called and wig-files were produced with MACS-1.4.2
All further analysis were performed in R or Bedtools
Genome_build: hg19
Supplementary_files_format_and_content: MACS-output files in wig-format are provided.

extract_protocol:
Where indicated, MYC was induced with doxycycline (pInducer samples) or treated with EtOH as solvent control. Cells were crosslinked with 1% formaldehyde at 37°C for 10min. Cells were lysed and after centrifugation nuclei were re-suspended in RIPA buffer. DNA was sonicated with a Branson sonifier to obtain DNA fragments at nucleosomal size. Chromatin bound to target proteins (HA-tag) was preciüitated by incubation with Protein A dynabeads beads overnight. After several washings chromatin was eluted with 1 % SDS and  crosslinking was reverted overnight. DNA was purified by Phenol/Chloroform extraction and enrichments were checked by qPCR.
Libraries for ChIP-seq samples were contructed following manufactor's intructions using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (E6240). Briefly, ChIP DNA was end repaired,  A-tailed  and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of a agarose gel and extracted with a Qiagen PCR purification column. Size-selected DNA was amplified with 18 PCR cycles.


title: S5p_Kless_EtOH.wig


title: 4SU_rep2_WT_EtOH

description: 4SU-labelled RNA


title: Kless_Dox_2

description:
polyA RNA
norm_count_table_k52o.csv


title: S5p_Kless_Dox.wig


title: S5p_WT_Dox.wig


title: S2p_Kless_EtOH.wig


title: S2p_Kless_Dox.wig


title: rep2_siMYC


title: S2p_WT_Dox.wig


title: 4SU_rep1_Kless_Dox

description: 4SU-labelled RNA


title: N20_Kless_EtOH.wig


title: N20_Kless_Dox.wig


title: WT_Dox_2

description:
polyA RNA
norm_count_table_k52o.csv


title: Kless_EtOH_2

description:
polyA RNA
norm_count_table_k52o.csv


title: Input_WT_EtOH.wig


title: Input_WT_Dox.wig