title: siYap_rep4

city: Boston

first: Kenneth

middle: N

last: Ross

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Reads trimmed with Trimmomatic version 0.30 in single end mode and trimming steps set to ILLUMINACLIP:illuminaAdapters.fa:  2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35
Reads aligned to human genome with tophat version 2.0.8 using UCSC mm10 gene annotation and default settings.
Aligned reads processed to Fragments Per Kilobase of exon per Million fragments mapped (FPKM) using cuffdiff version 2.1.1 (http://cufflinks.cbcb.umd.edu/index.html) with the flag '--max-bundle-frags' set to 4 million to avoid HIDATA error for 43 very high expression genes, the flag '--frag-bias-correct' set to use the UCSC mm10 reference whole genome fasta, and the mm10 genes.gtf transcript file from UCSC.
Split apart the cuffdiff output file genes.read_group_tracking file into sample specific files.
Genome_build: mm10
Supplementary_files_format_and_content: genes.fpkm_tracking files are tab delimited text files output by cufflinks in a generic FPKM tracking format with estimated gene-level expression values in the form of FPKM values

source_name: Mst1-/-; Mst2Flox/Flox mouse HCC model

growth_protocol: Mice with liver-specific Mst1/Mst2 double-knockout (Adeno-Cre injected Mst1-/-; Mst2Flox/Flox mice) were monitored for the formation of HCC by ultrasound imaging.  The Mst1-/-; Mst2Flox/Flox mice were maintained in a mixed genetic background (C57BL/6; 129Sv). (See Zhou et al., Cancer Cell 2009 "Mst1 and Mst2 maintain hepatocyte quiescence and suppress hepatocellular carcinoma development through inactivation of the Yap1 oncogene.")

extract_protocol:
Tumor RNA was isolated.  RNA quality was measured using an Agilent Bioanalyzer and RNA was quantified using a Qubit Fluorometer (Life Technologies) before sequencing library generation.
RNAseq libraries were prepared using the ScriptSeq Complete Gold Kit (Epicentre). RNAseq libraries were uniquely indexed with custom primers (SriptSeq) and run on MiSeq (Illumina) to confirm quality of the library before sequencing to deeper coverage using a HiSeq2500 (Illumina). Approximately 50 million reads per sample were obtained.

treatment_protocol: Animals were then randomized to be treated by intravenous injection of siRNA-lipid nanoparticles (siRNA-LNPs) (either siYap-LNPs or siLuciferase-LNPs) for a period of 9 days.

value: Mst1-/-; Mst2Flox/Flox

tag: background strain

value: mixed (C57BL/6; 129Sv)

value: siYap-LNPs

tag: treatment time

value: 9 days


title: siYap_rep3

status: Public on Mar 07 2015

type: SRA

state: MA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype

tag: treatment


title: siYap_rep1


title: siLuc_rep8

value: siLuciferase-LNPs


title: siLuc_rep5


title: siLuc_rep6


title: siLuc_rep3


title: siLuc_rep2


title: siLuc_rep4


title: siLuc_rep1


title: X8_c

city: Leipzig

first: Mark

last: Stoneking

state: Saxony

address: Deutscher Platz 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

data_processing:
Base calling was performed with Ibis
Sequenced reads were trimmed for adaptor sequence, short and low-quality reads were filtered and remaining data was mapped to hg19 (GRCh37) using TopHat2 and annotated using Ensembl 70 genes
All raw count data was normalized using the variance stabilization procedure as described in DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: 2 tab-delimited text files include raw counts and variance stabilized normalized data. The file "filtered_normalized_library_counts.txt" contains data for 74 not 80 libraries as the libraries from 3 individuals (2 libraries (sample replicates) per individual) did not cluster together in clustering analyses thus presenting more variation within individual than among - an observation we attribute variation introduced during the sampling of the placenta. sample information: individual ID, sample ID, index number, ancestry and data on newborn and mother

molecule: polyA RNA

organism: Homo sapiens

source_name: placenta

extract_protocol:
Each placenta was collected and processed within an hour of delivery. Placentas were quartered, wrapped in aluminum envelopes, and immediately snap frozen in liquid nitrogen. From three of the four quarters of each placenta we dissected 100mg of centrally located villus parenchyma tissue (taking care to avoid decidua, chorion, or amnion tissue) from five nonadjacent locations, totaling 600 dissections. The five dissections from each quarter were pooled, resulting in three sample replicates from each placenta. All dissections were carried out on a sterilized steel plate situated on top of dry ice, thereby keeping the samples frozen at all times.  RNA was extracted and isolated from each of the three sample replicates from each placenta using TRIZOL reagent (Invitrogen) following manufacturer recommendations. Total RNA was purified using the Qiagen RNAeasy minElute Cleanup kits and RNA quality was determined using Agilent 6000 Nano kits and an Agilent Bioanalyzer.
Library construction followed a merging of Illumina’s RNA-Seq library preparation and an indexing protocol as described in Meyer M, Kircher M; Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc. 2010. Jun;2010(6). In brief: Library construction included the following steps: two rounds of mRNA capture with oligo dT magnetic beads, mRNA fragmentation, 1st strand synthesis, 2nd strand synthesis, end repair, index adapter ligation, adapter fill-in, size-selection, indexing/enrichment PCR, and finally quantification. All steps, including SPRI bead reaction clean-ups, were processed in parallel in a 96 well plate, where all samples were randomized across the plate, thereby eliminating any library processing batch effect.

tag: tissue

value: placental villus parenchyma


title: X7_b


title: X7_a


title: X5_a


title: X5_b


title: X3_b


title: X14_b


title: X3_a


title: siYap_rep5


title: X13_a


title: X15_b


title: X14_a


title: siYap_rep2


title: X13_c


title: X12_c


title: X10_c


title: X12_a


title: X1_c


title: X10_a


title: X1_a


title: S8_c


title: S6_c


title: S7_c


title: S7_b


title: S8_a


title: S5_a


title: S5_b


title: S4_b


title: S6_a


title: S4_a


title: siLuc_rep7


title: S3_c


title: S3_a


title: S2_b


title: S2_a


title: S11_b


title: S10_c


title: E9_b


title: S9_b


title: S9_c


title: S10_b


title: E9_c


title: E3_c.2


title: E3_b.3


title: E7_b.3


title: E7_a.2


title: E20_a.3


title: X15_a


title: E2_a


title: E16_a


title: E15_c


title: E15_a


title: S11_c


title: E12_c


title: E11_c


title: E12_a


title: E11_b


title: E10_c


title: A8_c


title: A7_b


title: E10_a


title: A8_a


title: A6_b2.3


title: A6_b.2


title: A2_a.4


title: A2_a.3


title: E2_c


title: E16_c


title: A14_c


title: A13_c


title: A17_a.4


title: A16_c


title: X8_a


title: A13_a


title: A14_a


title: CCSP/TGFalpha mice on Doxycycline 3 weeks_2

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of read counts was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CCSP/TGFalpha

value: lung


title: A12_c


title: CCSP/TGFalpha mice on Doxycycline 3 weeks_1


title: CCSP/TGFalpha mice on Doxycycline 3 weeks_3


title: CCSP/- mice on Doxycycline 3 weeks_3

value: CCSP/-


title: A12_a


title: CCSP/- mice on Doxycycline 3 weeks_2


title: LOS #4 Skeletal muscle

status: Public on Mar 06 2015

city: Columbia

first: Rocio

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri, Columbia

description: Raw read counts of imprinted genes in skeletal muscle

data_processing:
Base calling was perfomed using version 1.8 of the CASAVA package from Illumina
Adator sequences of the reads were removed with the use of FastqMcf program (version 1.04.636). Low quality reads were filtered out using DynamicTrim (version 1.13)
Reads were aligned using  TopHat2 (version 2.0.10) with Bowtie2 scoring option (--score-min L,0,-0.2 --mp 6,6). Known splice junction from RefSeq and Ensembl were supplied for alignment
Cufflinks (version 2.1.1) was used to assembl the transcripts and assembled transcripts of each sample were merged into a single set of genes and transcripts using Cuffmerge (version 2.1.1)
Htseq (version 0.5.4) was used to make read counts for each imprinted genes and edgeR was used for differential gene expression analysis.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab deliminated text file of raw read counts of the imprinted genes in each tissue of each fetus

organism: Bos indicus x Bos taurus

source_name: ~Day 105 fetal skeletal muscle

extract_protocol:
At tissue collection, liver, skeletal muscle, brain, and kidney were well diced, mixed, and snap frozen in liquid nitrogen and stored at -80°C. Total RNA from fetal tissues was isolated using Trizol Reagent (Invitrogen) according to the manufacturer's instructions. RNA quality was determined by both spectrometry and agarose gel electrophoresis.
For each sample, 5μg RNA was submitted to the DNA core at University of Missouri, Columbia for RNAseq library preparation using Illumina TruSeq RNA sample preparation kit. Briefly, poly-A containing RNA was purified using magnetic beads with oligo-dT attached. The purified RNA was fragmented and used as a template for cDNA synthesis using random primers. In the following end-repair procedure, an "A" was added to the 3' end of the cDNA. The cDNA fragments with A-tailing were then ligated with T-tailing adaptors. PCR amplifications of cDNA fragments were followed to generate the final RNAseq library.

tag: disease status

value: LOS

value: skeletal muscle

tag: developmental stage

value: Day 105 fetus


title: LOS #4 Liver

description: Raw read counts of imprinted genes in liver

source_name: ~Day 105 fetal liver

value: liver


title: LOS #4 Kidney

description: Raw read counts of imprinted genes in kidney

source_name: ~Day 105 fetal kidney

value: kidney


title: LOS #3 Kidney


title: LOS #4 Brain

description: Raw read counts of imprinted genes in brain

source_name: ~Day 105 fetal brain

value: brain


title: LOS #3 Brain


title: LOS #3 Skeletal muscle


title: LOS #2 Skeletal muscle


title: LOS #2 Brain


title: LOS #1 Liver


title: LOS #1 Skeletal muscle


title: LOS #1 Kidney


title: LOS #1 Brain


title: A1_a


title: Control #3 Liver

value: healthy


title: Control #4 Brain


title: Control #4 Liver


title: Control #3 Kidney


title: Control #3 Skeletal muscle


title: Control #3 Brain


title: A7_a


title: LOS #2 Liver


title: LOS #2 Kidney


title: Control #1 Skeletal muscle


title: Control #2 Brain


title: Control #2 Liver


title: Control #1 Liver


title: CCSP/- mice on Doxycycline 3 weeks_1


title: Control #2 Kidney


title: Control #1 Kidney


title: Control #1 Brain


title: Control #2 Skeletal muscle


title: Input_round_spermatid

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

description: Input in round spermatids

library_source: genomic

data_processing:
Bases called with CASAVA, most recent version, and demultiplexed with bcl2fastq 2.0
Alignment: bowtie v0.12.7 with parameters --best and -m 1 for all samples
PCR duplicate filtering: for any given genomic position (chromosome,start,stop,strand), multiple tags with identical parameters were collapsed to a single representative
Peak-calling: SICER was used to call peaks in all chIP-seq data using input as a control for local sonication bias. Window, fragment, and gap size parameters were fixed at 200bp; and the FDR was controlled at 0.1%.
Track creation: tracks were generated by using the BEDTools utility genomeCoverageBed (-bg) to convert BED files to coverage maps (bedGraphs). These were then normalized to a scalar coefficient to correct for sequencing bias in any sample. The normalized input map was then subtracted from each chIP-seq map. Resulting bedGraphs were used to generate bigWigs via the bedGraphToBigWig utility in the UCSC Genome Browser tool suite.
Genome_build: NCBI v37
Supplementary_files_format_and_content: Peak files (BED format) are SICER output files. BigWigs are provided for visual inspection of the data.

molecule: genomic DNA

source_name: Round spermatid

growth_protocol: Male 129S6/SvEvTac mice (Taconics, Germantown,NY) as well as Hrb-/- gene-disrupted mice (Kang-Decker 2001) were maintained according to the guidelines of the University of Pennsylvania Institutional Animal Care and Use Committee.

extract_protocol:
Spermatogenic cell fractionation was performed by sedimentation of cells prepared from adult mouse testes through a BSA gradient as previously described (Bryant et al. 2013).  Each fractionation experiment used approximately 22 testes.  Fractions were analyzed for purity based on cell and nuclear morphology (via DAPI staining) and pooled.  Mature spermatozoa were obtained from epididymides of adult mice, and contaminating cell types were eliminated by incubating in somatic cell lysis buffer (0.1% SDS, 0.5% Triton X-100 in DEPC H2O) on ice for 20 minutes.
Cells were cross-linked in 1% formaldehyde in PBS for 10 minutes at room temperature.  The reaction was quenched with 125mM glycine in PBS for five minutes at room temperature.  After cell lysis, lysates were sonicated for 20 minutes with a Covaris S220 sonicator (5% duty cycle, 140 watts peak incident power, 200 cycles per burst). For each IP, 500μg of protein (measured with BCA assay) from the cell lysate, 30uL protein G Dynabeads, and 5μg-10ug of antibody or IgG (Pierce 31235) were used.  ChIP libraries for sequencing were prepared using 5ng DNA and the NEBNext Ultra DNA library prep kit for Illumina.  Size selection was performed using AMPure XP beads (Beckman Coulter, Inc. #A63881).  Libraries were sequenced using a NextSeq 500 machine (Illumina) as per manufacturer's protocols.

tag: antibody

value: none (input)

tag: cell type

value: round spermatid


title: H4K5ac_round_spermatid

description: H4K5ac in round spermatids

value: Millipore 07-327


title: H4K16ac_round_spermatid

description: H4K16ac in round spermatids

value: Active Motif AM39167


title: H3K9me3_round_spermatid

description: H3K9me3 in round spermatids

value: Abcam ab8898


title: H4K12ac_round_spermatid

description: H4K12ac in round spermatids

value: Millipore 07-595


title: H3K9ac_round_spermatid

description: H3K9ac in round spermatids

value: Active Motif AM39137


title: Brd4-1_round_spermatid

description: Brd4 in round spermatids


title: LOS #3 Liver


title: RJ2.2.5 ATACseq (paired-end)

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description: ATAC-seq

data_processing:
Raw sequencing reads were mapped to the hg19 version of the mouse genome with Bowtie using the default options
For CIITA ChIPseq peak calling HOMER software (Heinz et al. Mol Cell, 2010. 38:576-589) was used with the options "-style factor"
For ATACseq paired-end and single end fastq files from the same cell type were merged into one bigWig file
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files are normalized to reads per million (rpm) using R/Bioconductor.  Bed files contain the genomic locations of significantly enriched peaks as determined by HOMER

source_name: RJ2.2.5 cells

growth_protocol: Raji and RJ2.2.5 cells were cultured in RPMI supplemented with 5% FCS, 5% FBS, and 100 U/ml Penecillin/Streptomycin

extract_protocol:
Briefly, 50,000 cells were FACS sorted into FACS sort buffer (1x PBS, 1 mM EDTA, 1% BSA, 0.25 μM filtered) and processed as described (Buenrostro et al. Nat Methods. 10(12):1213-8 2012).  Tagmentation was performed using the Illumina Nextera DNA Sample (FC-121-1030) and Indexing kits (FC-121-1011).  Following 10 cycles of PCR amplification, the adaptor ligated DNA was size selected to yield a 200-1,000 bp sequencing library.
See each sample for speicific extract protocols

value: RJ2.2.5 cells


title: H4K8ac_round_spermatid

description: H4K8ac in round spermatids

value: Millipore 07-328


title: Raji ATACseq (paired-end)

description: ATAC-seq

source_name: Raji cells

value: Raji cells


title: Raji ATACseq

description: ATAC-seq


title: Control #4 Kidney


title: Control #4 Skeletal muscle


title: A17_b.3

value: placental villus parenchyma


title: Raji H3K27ac rep1

extract_protocol:
1-0.1 ng of IP'ed DNA was processed into a sequencing library using the Kapa Hyper Prep kit (Cat# KK8500) according to the manufacturers instructions.
Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Scharer et al. Cancer Research, 69:709-717).  Briefly, the indicated cells were fixed in 1% formaldehyde for 10 minutes, nuclei isolated, and sonicated to an average chromatin fragment size of 200-600 bp.  30 mg chromatin was immunoprecipitated with 5 μg anti-CIITA, anti-H3K27ac or anti-H3K4me3 antibody over night at 4 degrees.  Antibody-chromatin complexes were captured with Protein A magnetic beads (Invitrogen), cross-links reversed, and DNA purified.  Input fraction was isolated after sonication and prior to the IP.
See each sample for speicific extract protocols

tag: chip antibody

value: H3K27ac (Millipore, 07-360)


title: RJ2.2.5 H3K27ac rep2


title: RJ2.2.5 ATACseq

description: ATAC-seq


title: Raji H3K27ac rep2


title: Raji CIITA Rockland rep2

value: CIITA (Rockland Immunochemicals, 100-401-249)


title: RJ2.2.5 H3K27ac rep1


title: H4Kac_round_spermatid

description: H4Kac in round spermatids

value: Millipore 06-866


title: Raji CIITA Diagenode rep2

value: CIITA (Diagenode, C15410062)


title: Raji CIITA Diagenode rep1


title: Raji CIITA Rockland rep1


title: Early Worker Destined 4

city: Norwich

first: Matthew

last: Beckers

state: Norfolk

address: Norwich Research Park

country: United Kingdom

institute: University of East Anglia

data_processing:
3' adapters were removed by matching the first 8nt of the adapter. Only sequences with trimmable matching adapters were kept for subsequent analysis.
Trimmed sequences were filtered for low nucleotide complexity, where sequences with less than three unique nucleotides were removed, and by size, where sequences of length 16nt-30nt were kept
The filtered sequences were mapped to the reference genome using PatMaN 1.2 with no mismatches or gaps
Mapped sequences were run through miRCat, with one miRCat run per library. The results were combined to include all unique predicted miRNAs from any library.
Mapped sequences were overlapped with results from a MapMi run on the reference genome. If a predicted miRNA from miRCat overlapped a MapMi miRNA, the miRNA was assigned the relevent miRBase ID. Otherwise, new miRNAs were assigned a new ID
The resulting miRNA list was subject to a final manual curation by inspection of secondary structure and sequence mapping patterns for obvious erroneous predictions.
Genome_build: Bter2011317
Supplementary_files_format_and_content: predicted_miRNAs.csv details identified miRNAs found using miRCat using count from all libraries and MapMi predictions based on known miRNA alignments to the reference genome. MiRNA.name: assigned name of miRNA, mirbaseID: ID in miRBase of matched known miRNA (if any), Mature.sequence: mature miRNA sequence, Precursor.sequence: Prevursor miRNA sequence, seqid:reference sequence ID, strand: strand of reference sequence, pre.start: precursor sequence start, pre.end: precursor sequence end, mature.start: mature sequence start, mature.end: mature sequence end, Prediction.method: method used to predict the miRNA, EW/LW 1/2/3/4: The mature sequence count for the named library.

organism: Bombus terrestris

source_name: whole body

growth_protocol: Worker-destined diploid larvae were harvested from four Bombus terrestris colonies. These were separated into early-instar worker-destined larvae (EW) from the first and second larval instars, and late-instar worker-destined larvae from the fourth larval instar.

extract_protocol:
Whole body larvae from the same colony and developmental stage were pooled into eight samples (four for each developmental stage). They were then flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols. However, instead of the Illumina 3' adaptor, a modified 3' HD adaptor with a 4bp degenerate nucleotide sequence (NNNN) on the 5' end was used during the adaptor ligation steps.

tag: development stage

value: Early


title: Late Worker Destined 1

value: Late


title: Late Worker Destined 2


title: Early Worker Destined 3


title: Early Worker Destined 2


title: Early Worker Destined 1


title: CRC1

city: Madrid

first: Ruggero

last: La Rosa

address: C/ Darwin 3, Campus de Cantoblanco

department: Department of Microbial Biotechnology

country: Spain

institute: National Centre for Biotechnology CNB-CSIC

description: Sample 3

data_processing:
Illumina Casava 1.8 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, unknown nucleotides larger than 10%, low quality (more than half of the bases' qualities are less than 5).
Clean reads were mapped to reference genome and genes sequences respectively using SOAP2 (Li, 2009). Mismatches no more than 5 bases were allowed in the alignment.
Gene expression was calculated using the RPKM method (Reads Per kb per Million reads) (Mortazavi, Williams et al. 2008).
Genome_build: NC_002947.3
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each gene

organism: Pseudomonas putida KT2440

source_name: KTCRC_bacterial cells

growth_protocol: Cells were cultivated at 30°C with vigorous shaking in M9 minimal salts medium (Sambrook and Russell, 2001) with trace elements (Bauchop and Elsden, 1960) supplemented with succinate (20 mM) and glucose (20 mM) as carbon sources.

extract_protocol:
Total RNAs were extracted during mid-exponential phase (A600 = 0.6) using the RNeasy kit (QIAGEN, Inc., Valencia, CA, USA) and RNase-Free DNase Set (QIAGEN, Inc., Valencia, CA, USA) was used for the complete elimination of residual DNA from the samples. The quality of the RNAs was evaluated in an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA).
RNA library construction was carried out by BGI (Shenzhen, China) using the Illumina mRNA sequencing sample preparation kit (cat. #RS-930–1001). Before fragmentation of mRNAs, rRNA were removed.

tag: strain

value: KTCRC

tag: genotype/variation

value: crc::tet allele

tag: carbon source

value: succinate (20 mM) and glucose (20 mM)


title: WT2

description: Sample 2

source_name: WT_bacterial cells

value: wild type


title: CRC2

description: Sample 4


title: ZY1

description: Sample 5

source_name: KT2440-ZY_bacterial cells

value: crcZ::tet and crcY::acc3 alleles


title: ZY2

description: Sample 6


title: WT1

description: Sample 1


title: A1_c


title: Prefrontal_cortex_rep4

city: Jupiter

first: Sathyanarayanan

middle: V

last: Puthanveettil

state: Florida

address: 130 Scripps Way

department: Neuroscience

institute: Scripps Research

description: Total RNA isolation

data_processing:
Quality trimming performed by FastX-Toolkit v.0.0.13
Reads were aligned to Ensembl's NCBIM37 genome assembly using Tophat v.2.0.9
Cufflinks v.2.1.1 was used to obtain RPKM values.
Raw read counts were obtained HTSeq 0.6.0
Differential gene expression analysis was performed using DESeq
Genome_build: NCBIM37
Supplementary_files_format_and_content: Matrix xlsx file containing normalized read counts

source_name: Brain

extract_protocol:
Trizol RNA extraction
RNA libraries were prepared for sequencing using standard Illumina protocols. Hippocampus and prefrontal cortex were dissected from 7-9 weeks old C57Bl6 mice (Jackson Laboratories) and total RNA was isolated using Trizol (Invitrogen). There were 4 biological replicates and each replicates contain brain tissue from 2 adult mice.  Beginning with 200 ng total RNA sample, the sample is reverse transcribed with random hexamer and poly A primers after removing ribosomal RNAs using Ribo minus kit (Invitrogen). This product is converted into double stranded cDNA, followed by SPIA amplification. After purification the sample is end repaired and then has specific adapters ligated to the 5’ and 3’ ends. These products are then PCR amplified to enrich for the ligated products (Nugen San Diego, CA). The amplified samples are then purified and diluted down to a 10µM library. This library is then treated with NaOH to produce single stranded amplicons which are then add to the Illumina cBOT instrument to generate the double stranded clusters used for the massively parallel sequencing on the Illumina Genome Analyzer IIx according to manufacturer specifications.

tag: strain background

tag: age

value: 7-9 weeks

value: Prefrontal cortex


title: Late Worker Destined 4


title: Hippocampus_rep4

description: Total RNA isolation

value: Hippocampus


title: Prefrontal_cortex_rep3

description: Total RNA isolation


title: Prefrontal_cortex_rep2

description: Total RNA isolation


title: Fragilariopsis cylindrus

description: Fracy1 (JGI)

data_processing:
3' adapter removal using the first 8nt of the adapter sequence as a match (ATCTCGTA). Sequences that did not have a matching adapter were discarded
Filtered for sequences containing “N” or did not contain at least 3 unique bases
Mapped to available genomes PatMaN with no mismatches or gaps
Converted to BED format using a custom script
Filtered outlying rRNA sequences
Annotated mapped sequences using a custom script
Genome_build: See “genome build” information in the description field
Supplementary_files_format_and_content: Tab-delimited table of mapped reads, their raw counts, alignments, and best suggested annotation. Headers labelled “query.*” indicate alignment information of the read to the genome; “feature.*” indicates alignment information of suggested feature to the genome (if possible), and “alignment.*” indicates alignment information of read to the suggested feature (if possible).

organism: Fragilariopsis cylindrus CCMP1102

source_name: cell culture

growth_protocol: Ten litre cultures of T. pseudonana, and F. cylindrus were grown under optimum growth conditions for each of the species (T. pseudonana: 20°C, 100μmol photons m-2s-1 (24 hours light); F. cylindrus: 4°C, 50μmol photons m-2s-1 (24 hours light); nutrient replete F/2 medium; cells were harvested in the middle of exponential growth phase) to obtain RNA for either Illumina sequencing

extract_protocol:
Cells were washed from the filter using 1 ml lysis buffer from mirVana™ kit (Ambion) and bead beating for 60 sec using a Mini beadbeater (Biospec) to break the cells and release the nucleic acid from the samples. The samples were then centrifuged at 10,000×g for 1 min and the supernatants (750 µl) transferred to a fresh 1.5 ml-microtube. 200 µl additional lysis buffer were added to the filter, bead beating again and centrifuged. The protocol was finished according to the manufacturer´s recommendations. RNA integrity and purity were assessed in 1% (w/v) agarose gel stained with ethidium bromide and on a Nanodrop ND-1000 (Thermo Scientific, DE, USA), respectively
Total RNA from T. pseudonana and F. cylindrus was prepared using the small RNA v1.5 kit from Illumina according to manufacturer´s recommendations.  RNA was ligated to the adaptors, reverse transcribed, PCR amplified and purified from a polyacrylamide gel. cDNA libraries were sequenced (42 cycles) using an Illumina Genome Analyzer II at TGAC (Norwich, UK).


title: Prefrontal_cortex_rep1

description: Total RNA isolation


title: Hippocampus_rep3

description: Total RNA isolation


title: Raji CIITA Boss Lab

extract_protocol:
10 ng of CIITA ChIP DNA was End Repaired using 2U T4 DNA polymerase, 0.5U Klenow, and 5U T4 DNA Polynucleotide kinase for 30 min at 20° in NEB T4 DNA Ligase buffer supplemented with 0.4 mM DNTPs.  A-tailing was performed using 5U Klenow (3’->5’) exo- for 30 min at 37° in NEB buffer 2 supplemented with 0.2 mM dATP.  250 μM annealed adaptors were ligated onto A-tailed DNA using 2000U Quick Ligase for 20 min at room temperature in Quick Ligase buffer.  Adaptor ligated DNA was converted to double stranded DNA by 5 cycles of PCR using 2U of Phusion Polymerase in GC Buffer supplemented with 0.4 mM DNTPs and 0.5 mM Adaptor Primers. Double-stranded adaptor-ligated DNA was size selected on a 2% agarose gel by excising a 200-400 bp band.  Size selected DNA was PCR amplified for 8 additional cycles to generate sequencing libraries.
Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Scharer et al. Cancer Research, 69:709-717).  Briefly, the indicated cells were fixed in 1% formaldehyde for 10 minutes, nuclei isolated, and sonicated to an average chromatin fragment size of 200-600 bp.  30 mg chromatin was immunoprecipitated with 5 μg anti-CIITA, anti-H3K27ac or anti-H3K4me3 antibody over night at 4 degrees.  Antibody-chromatin complexes were captured with Protein A magnetic beads (Invitrogen), cross-links reversed, and DNA purified.  Input fraction was isolated after sonication and prior to the IP.
See each sample for speicific extract protocols

value: CIITA (Brown, JA et al. Nucleic acids research, 1998. 26:4128-36)


title: s2a

city: WuHan

first: XiaoLi

last: Shi

address: DongHU road

country: China

institute: WuHan University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were then trimmed for adaptor sequence, low-quality or low complexity sequence, then mapped  to mm9 whole genome using Tophat v2.0.13
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Genome_build: mm9
Supplementary_files_format_and_content: xls files include gene counts for each Sample

growth_protocol: MIN6 cells were maintained in DMEM medium containing 25 mM glucose supplemented with 15% (vol/vol) FCS

extract_protocol:
Total RNA from stable TLX overexpressing MIN6 cells and control cells were extracted with Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Insulinoma cells

value: wild type (control)


title: Hippocampus_rep2

description: Total RNA isolation


title: Hippocampus_rep1

description: Total RNA isolation


title: Late Worker Destined 3


title: Raji Input

extract_protocol:
10 ng of sonicated Raji genomic DNA was End Repaired using 2U T4 DNA polymerase, 0.5U Klenow, and 5U T4 DNA Polynucleotide kinase for 30 min at 20° in NEB T4 DNA Ligase buffer supplemented with 0.4 mM DNTPs.  A-tailing was performed using 5U Klenow (3’->5’) exo- for 30 min at 37° in NEB buffer 2 supplemented with 0.2 mM dATP.  250 μM annealed adaptors were ligated onto A-tailed DNA using 2000U Quick Ligase for 20 min at room temperature in Quick Ligase buffer.  Adaptor ligated DNA was converted to double stranded DNA by 5 cycles of PCR using 2U of Phusion Polymerase in GC Buffer supplemented with 0.4 mM DNTPs and 0.5 mM Adaptor Primers. Double-stranded adaptor-ligated DNA was size selected on a 2% agarose gel by excising a 200-400 bp band.  Size selected DNA was PCR amplified for 8 additional cycles to generate sequencing libraries.
Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Scharer et al. Cancer Research, 69:709-717 2009).  Briefly, the indicated cells were fixed in 1% formaldehyde for 10 minutes, nuclei isolated, and sonicated to an average chromatin fragment size of 200-600 bp.  30 mg chromatin was immunoprecipitated with 5 μg anti-CIITA, anti-H3K27ac or anti-H3K4me3 antibody over night at 4 degrees.  Antibody-chromatin complexes were captured with Protein A magnetic beads (Invitrogen), cross-links reversed, and DNA purified.  Input fraction was isolated after sonication and prior to the IP.
See each sample for speicific extract protocols

value: Raji cells


title: s1b

source_name: MIN6_TLX overexpression

value: TLX overexpression


title: Raji H3K4me3

extract_protocol:
10 ng of Raji H3K4me3 ChIP DNA was processed into a sequencing library using teh Bioo Scientific NEXTflex ChIP-seq kit (Cat# 5143-01) according to the manufacturers instructions.
Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Scharer et al. Cancer Research, 69:709-717).  Briefly, the indicated cells were fixed in 1% formaldehyde for 10 minutes, nuclei isolated, and sonicated to an average chromatin fragment size of 200-600 bp.  30 mg chromatin was immunoprecipitated with 5 μg anti-CIITA, anti-H3K27ac or anti-H3K4me3 antibody over night at 4 degrees.  Antibody-chromatin complexes were captured with Protein A magnetic beads (Invitrogen), cross-links reversed, and DNA purified.  Input fraction was isolated after sonication and prior to the IP.
See each sample for speicific extract protocols

value: H3K4me3 (Millipore, 07-473)


title: s1a


title: Replicate 2, Ribosomal footprinting, resting DCs

first: Catherine

middle: J

last: Wu

address: 450 Brookline Ave.

institute: Dana Farber Cancer Institute

data_processing:
Sequencing reads were stripped of linker sequences using fastx_clipper from the FASTX-Toolkit with the following settings: -a CTGTAGGCACCATCAAT –n -Q 33. Reads mapping to miRNAs, rRNAs, snRNAs, snoRNAs, and tRNAs were filtered using bowtie2 in --local mode. Remaining reads were aligned using Tophat2 to the UCSC mm9 Known Gene transciptome. Tophat2 was run with the following settings --b2-very-sensitive --transcriptome-only --no-novel-juncs -max-multihits=64.
Footprints were filtered for read lengths 26-33 (inclusive). Footprints were mapped to their approximate P-site position by applying a 12 nucleotide offset from the 5' end. Footprint counts were averaged over the union of genomic positions corresponding to coding sequences of the genes in each “analysis group”, excluding positions within 3 nucleotides upstream or 15 nucleotides downstream of start codons or within 9 nucleotides upstream of stop codons.
The count of aligning nucleotides was divided by the length of the included region. This measure of ribosomal occupancy was renormalized to sum to 1 million across all genes.
Genome_build: mm9
Supplementary_files_format_and_content: ribosomalprofiling.csv

source_name: bone marrow-derived primary dendritic cells

growth_protocol: 6-8 week old female C57BL/6J mice were obtained from the Jackson Laboratories. RPMI medium (Invitrogen) supplemented with 10% heat inactivated FBS (Invitrogen), ß-mercaptoethanol (50uM, Invitrogen), L-glutamine (2mM, VWR), penicillin/streptomycin (100U/ml, VWR), MEM non-essential amino acids (1X, VWR), HEPES (10mM, VWR), sodium pyruvate (1mM, VWR), and GM-CSF (20 ng/ml; Peprotech) was used throughout the study. At day 0, bone marrow-derived dendritic cells (BMDCs) were collected from femora and tibiae and plated on twenty (per mouse), 100mm non tissue culture treated plastic dishes using 10ml medium per plate. At day 2, cells were fed with another 10ml medium per dish. At day 5, cells were harvested from 15ml of the supernatant by spinning at 1,400 rpm for 5 minutes; pellets were resuspended with 5ml medium and added back to the original dish. Cells were fed with another 5ml medium at day 7. At day 8, all non-adherent and loosely bound cells were collected and harvested by centrifugation. Cells were then resuspended with medium, plated at a concentration of 10x106 cells in 10ml medium per 100mm dish.

extract_protocol:
Unstimulated BMDCs were incubated with 100µg/mL cycloheximide for 1 minute at 37°C. Cells were collected by centrifugation at 300 ×g for 5 minutes at 4°C and either washed twice with cycloheximide (100µg/mL) in ice-cold PBS or flash frozen in liquid nitrogen after removing media.  Cell pellets were covered with 400µL of lysis buffer (4.75 mL polysome buffer + 250 µL 20% Triton X-100 (Sigma-Aldrich) + 60 units Turbo DNAse (Ambion)). Polysome buffer is 20mM Tris-HCl pH 7.56, 150mM NaCl, 5mM MgCl2, 100µg/mL CHX, 1mM DTT, and 8% glycerol.  Lysis was carried out by triturating 10 times. Whole-cell lysates were clarified by centrifuging at 20,000 ×g for 10 minutes at 4°C. Clarified lysate was collected and flash frozen in liquid nitrogen.
Ribosome-protected fragments were isolated and cloned from lysates via RNAse I (Ambion) treatment as described previously (Ingolia et al., 2012).  Samples were depleted of rRNA contamination with the Ribo-Zero rRNA Removal Kit (Epicentre) and sequenced on the Illumina HiSeq2500.

tag: gender

value: female

value: un-stimulated


title: s2b


title: Mm_e17O_INPUT_rep1

city: New Haven

first: Steven

middle: K

last: Reilly

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University

data_processing:
Bowtie (v0.12.9), cd /panfs/sequencers/sequencerP/runs/131130_SN356_0279_BC30AWACXX/Data/Intensities/BaseCalls/Unaligned-Skr2/Project_Skr2/Sample_SR_40_Index5; zcat *.gz > ~/Scratch/Steve/Hu_12Fpcw_INPUT_rep1.fastq.gz; source ~/.bashrc; cd ~/Scratch/Steve/; bowtie -q -n 2 -l 28 -m 1 -p 8 -5 1 -3 5 -t /home/jl56/GENOME/hg19/dna/hg19_nh ./Hu_12Fpcw_INPUT_rep1.fastq.gz ./Hu_12Fpcw_INPUT_rep1.bowtie
Custom perl script , Cotney et al, Cell 2013.
RSEQTools (0.6.0), cat Hu_12Fpcw_INPUT_rep1.bowtie | bowtie2mrf genomic > ../mrf/Hu_12Fpcw_INPUT_rep1.mrf
RSEQTools (0.6.0) and wigToBigWig, cat Hu_12Fpcw_INPUT_rep1.mrf | mrf2wig Hu_12Fpcw_INPUT_rep1; cat Hu_12Fpcw_INPUT_rep1_chr*.wig | grep -v track > Hu_12Fpcw_INPUT_rep1.wig;  wigToBigWig -clip Hu_12Fpcw_INPUT_rep1 /home/jl56/GENOME/hg19/dna/hg19_nh.chrom.sizes Hu_12Fpcw_INPUT_rep1.bw
Genome_build: hg19 for human samples, rheMac2 for rhesus samples, mm9 for mouse samples, Gencode V10 gene annotation
Supplementary_files_format_and_content: bigWig (signal tracks), bed (peak calls), bam (anonymized human reads), fastq (raw rhesus and mouse reads)

source_name: Mouse e17.5 Embryonic Occipital Cortex

growth_protocol: Human brain tissue and rhesus brain tissue were thawed and micro dissected. Mouse cortex tissue was directly prepared after harvesting.  Rhesus and mouse were harvested from timed pregnant mothers.

extract_protocol:
Nuclei were extracted in six pellet volumes of lysis buffer I (50 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x Roche Complete Protease inhibitor, 5 mM sodium butyrate) and incubating on ice for 15 minutes.  Tissue was homogenized with a dounce homogenizer and nuclei were harvested by centrifugation at 2000g for 10 minutes at 4°C.  Nuclei were resuspended in five pellet volumes of nuclear lysis buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 0.2% SDS, 1x Roche Complete Protease inhibitor, 5 mM sodium butyrate) and incubated on ice for 20 minutes.  300 mL nuclear lysates in 1.5 mL tubes were sonicated using a Misonix S4000 with 431A cup horn (10 second pulses, 10 second rest, 20 minutes total, 2°C maintained by circulating chiller).  Following sonication insoluble material was pelleted by centrifugation at 16000g for 10 minutes at 4°C.  A small sample of soluble crosslinked chromatin was purified, checked for correct sonication size range and DNA concentration was measured. For H3K27ac, 10-25 ug of chromatin was diluted to 450 mL with dilution buffer (16.7 mM Tris pH 8, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100, 1x Roche Complete Protease inhibitor, 5 mM sodium butyrate) and added to 50 uL of Protein G Dynabeads (Invitrogen) prebound with 2 mg of H3K27ac antibody.For H3K4me2, 10-25 ug of chromatin was diluted to 450 mL with dilution buffer (16.7 mM Tris pH 8, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100, 1x Roche Complete Protease inhibitor) and added to 50 uL of Protein G Dynabeads (Invitrogen) prebound with 10 mg of H3K4me2 antibody.  Samples were incubated overnight at 4°C with rotation.  Beads were precipitated on magnet stand and washed eight times with 1 mL of wash buffer (100 mM Tris pH8.0, 500 mM LiCl, 1% NP-40, 1% deoxycholic acid, 1x Roche Complete protease inhibitor) and once with TE.  Immunoprecipiated chromatin was eluted from beads with 50 mL of elution buffer (TE + 1% SDS) at 65°C for 10 minutes.  Crosslinks were reversed overnight at 65°C.  Chromatin was treated with RNAseA and proteinase K then purified with Qiagen PCR cleanup kit.  Concentration of eluted chromatin was measured with PicoGreen (Invitrogen).
Standard Illumina Multiplexed Paired-End Library Prep

treatment_protocol: All tissues  were briefly homogenized and crosslinked with 1% formaldehyde at room temperature with rotation for 15 minutes.  Crosslinking was quenched with 150 mM glycine. Tissue were harvested by centrifugation at 1500g for 5 min at 4C.   Pelleted tissue was washed twice with cold PBS, flash frozen and stored at -80°C.

value: Embryonic Day e17.5

value: Embryonic Occipital Cortex

tag: experiment type

value: ChIP-seq


title: Mm_e17O_INPUT_rep2


title: Mm_e17O_H3K27ac_rep2

value: H3K27ac (Abcam ab4729)


title: Mm_e17O_H3K4me2_rep2

value: H3K4me2 (Millipore 07-030)


title: Mm_e17O_H3K27ac_rep1


title: Mm_e17F_INPUT_rep1

source_name: Mouse e17.5 Embryonic Frontal Cortex

value: Embryonic Frontal Cortex


title: WT12

city: New York

first: Hyejin

last: Choi

state: NY

address: 1300 York Ave

institute: Weill Cornell Medical College

data_processing:
Illumina CASAVA v1.8.2 software was used for basescalling.
Fragment reads were mapped to the UCSC mouse genome (mm10/GRCm38) using Tophat2.
Raw counts for each gene were obtained by Cufflinks, then converted to FPKMs (Fragments Per Kilobase of transcript per Million mapped reads) and scaled via the median of the genomic means for each gene across all libraries as described (Anders and Huber, 2010 [PMID 20979621]).
Adjusted p values for each gene were obtained by cuffdiff 2.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each Sample.

source_name: WT lung

growth_protocol: HKP1 lung cancer cells line is cultured in DMEM supplemented with 10% FBS, penicillin/streptomycin, and L-glutamine.

extract_protocol:
Lungs were purfused, removed, and dissociated to make single suspension. After staining with proper antibody of surface markers, cells were sorted usign BD Aria II sorter. The RNA was harvested from the sorted cells using Arcturus PicoPure RNA isolation kit. Illumina TruSeq RNA Sample Prep Kit v2 (Cat#RS-122-2001) was used with 16-33ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols(Illumina TruSeq RNA Sample Prep Kit v2 (Cat#RS-122-2001)).

treatment_protocol: HKP1 lung cancer cells were injected via tail vein.

value: Total lung cells

tag: time point of tumor growth

value: no tumor


title: Tum13

source_name: Tumor lung


title: WT13


title: WT11


title: Mm_e17F_H3K4me2_rep2


title: Mm_e17F_H3K27ac_rep2


title: Tum14


title: Tum12


title: Mm_e17F_INPUT_rep2


title: Replicate 1, Ribosomal footprinting, resting DCs

tag: treatment


title: WT8

value: Epcam+CD11b-CD11c- epithelial cells


title: Mm_e17F_H3K4me2_rep1

tag: tissue


title: Mm_e17F_H3K27ac_rep1


title: Mm_e14_INPUT_rep2

source_name: Mouse e14.5 Embryonic Cortex

value: Embryonic Day e14.6

value: Embryonic Cortex


title: WT9


title: Mm_e14_H3K4me2_rep2

value: Embryonic Day e14.5


title: Mm_e14_INPUT_rep1


title: A16_a

source_name: placenta

extract_protocol:
Each placenta was collected and processed within an hour of delivery. Placentas were quartered, wrapped in aluminum envelopes, and immediately snap frozen in liquid nitrogen. From three of the four quarters of each placenta we dissected 100mg of centrally located villus parenchyma tissue (taking care to avoid decidua, chorion, or amnion tissue) from five nonadjacent locations, totaling 600 dissections. The five dissections from each quarter were pooled, resulting in three sample replicates from each placenta. All dissections were carried out on a sterilized steel plate situated on top of dry ice, thereby keeping the samples frozen at all times.  RNA was extracted and isolated from each of the three sample replicates from each placenta using TRIZOL reagent (Invitrogen) following manufacturer recommendations. Total RNA was purified using the Qiagen RNAeasy minElute Cleanup kits and RNA quality was determined using Agilent 6000 Nano kits and an Agilent Bioanalyzer.
Library construction followed a merging of Illumina’s RNA-Seq library preparation and an indexing protocol as described in Meyer M, Kircher M; Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc. 2010. Jun;2010(6). In brief: Library construction included the following steps: two rounds of mRNA capture with oligo dT magnetic beads, mRNA fragmentation, 1st strand synthesis, 2nd strand synthesis, end repair, index adapter ligation, adapter fill-in, size-selection, indexing/enrichment PCR, and finally quantification. All steps, including SPRI bead reaction clean-ups, were processed in parallel in a 96 well plate, where all samples were randomized across the plate, thereby eliminating any library processing batch effect.

value: placental villus parenchyma


title: Tum10


title: Mm_e14_H3K4me2_rep1


title: Tum9


title: Mm_e17O_H3K4me2_rep1


title: Tum11


title: WT7

value: CD11b+Ly6G+ neutrophils


title: WT6


title: Mm_e14_H3K27ac_rep1


title: WT10


title: Mm_e14_H3K27ac_rep2


title: WT5


title: Tum8


title: WT4

value: CD11b+Ly6C+ monocytes


title: Mm_e11_H3K4me2_rep2

source_name: Mouse  e11.5 Embryonic Cortex

value: Embryonic Day e11.5


title: Tum6


title: E20_b.4


title: Tum5


title: WT3


title: Mm_e11_H3K4me2_rep1


title: Mm_e11_INPUT_rep1


title: Tum4


title: Replicate 2, RNA-Seq, LPS-stimulus, time 9h

description: processed data column name: RNA.R2.LPS.09

data_processing:
We constructed “analysis groups” using the following rules:   1. All transcripts in the same transcript group are in the same analysis group, where transcript groups are defined by the UCSC Table Browser (query settings: assembly=”July 2007 (NCBI37/mm9)”, group=”Gene and Gene Predictions”, track=”UCSC Genes”, table=”knownIsoforms”; see the fields “clusterID” and “transcript”) and represent groups of transcripts (isoforms) that are derived from the same genic locus and cannot easily be resolved.   2. All proteins in the same MaxQuant protein group are in the same analysis group, where MaxQuant determines protein groups on the basis of the peptide library supplied. The groups represent the level of ambiguity MaxQuant can confidently resolve.   3. If a protein and a transcript are associated with one another, then they are in the same analysis group, where we associate (one or more) Uniprot protein ID with (one or more) UCSC transcript ID based on ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_ organism/MOUSE_10090_idmapping.dat
We created a Bowtie15 index based on annotated transcripts from UCSC mm9 and aligned paired-end reads directly to this index using Bowtie v 0.12.7 with command line options: -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 -a –m 200. Next, we ran RSEM v1.1117 (with default parameters) and used the analysis groups (described above) to define which isoforms belong to the same gene. Analysis groups with no associated proteins (i.e. noncoding RNAs) were still used as input to avoid incorrect mappings. Expression quantifications were made for each analysis group, replicate, and condition.
Analysis groups (henceforth referred to as "genes" for simplicity) were excluded if they were not MS2-identified in at least 6 of the 10 time points in all conditions (time courses for LPS and MOCK stimulation), channels, and replicates. After applying this filter, we also excluded genes that did not have positive RNA-Seq values for at least 6 out of the 10 time points in all conditions and channels. We renormalized such that at each condition/time point the RNA-Seq expression values added up to exactly 1,000,000. Meanwhile, we normalized the protein data such that at each condition/time point protein (M+H) IBAQ values added up to exactly 1,000,000 (missing values were treated as zeroes).
For the shRNA RNA-Seq data: We created a Bowtie index based on the UCSC knownGene transcriptome, and aligned paired-end reads directly to this index using Bowtie v0.12.7 with command line options —-norc q --phred33-quals -n 2 -e99999999 -l 25 -I 1 -X 1000 -a -m 200, reflecting our strand-specific data. The output of this reflects the transcriptome alignment percentage for each library, which ranged between 57-65%. To calculate expression levels, we used this alignment as input for RSEM (v. 1.2.3) with default parameters as well as the -- forward-prob 1 and estimate-rspd options. We used the TPM output of RSEM as a normalized estimate of gene expression for each sample.
Genome_build: mm9
Supplementary_files_format_and_content: protein.norm.csv: normalized M-channel and H-channel protein expression values for each replicate, time point, and experimental condition
Supplementary_files_format_and_content: rna.norm.csv: normalized RNA expression values for each replicate, time point, and experimental condition
Supplementary_files_format_and_content: shRNA_RNAseq.xlsx: RNA-Seq expression (TPM) of genes according to respective knock down

extract_protocol:
RNA was extracted from cells using RNeasy Mini Kit (Quiagen), according to the manufacturer’s protocol.
Enrichment of polyadenylated RNA (polyA+ RNA) from total RNA was performed using Oligo(dT) dynabeads (Invitrogen) according to the manufacturer’s protocol. The mRNA was chemically fragmented into ~80-nt-long fragments using RNA fragmentation reagent (Ambion), followed by Turbo DNAse treatment (Ambion). Strand-specific RNA-seq libraries were generated as previously described (Engreitz et al., Science, 2013). Briefly, RNA was first subjected to FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific), followed by a 3’ ligation of an RNA adapter using T4 ligase (New England Biolabs). Ligated RNA was reverse transcribed using AffinityScript Multiple Temperature Reverse Transcriptase (Agilent), and the cDNA was subjected to a 3’ ligation with a second adapter using T4 ligase. The single-stranded cDNA product was then amplified for 9- to 14 cycles in a PCR reaction. Libraries were sequenced on an Illumina HiSeq 2500 generating 30bp paired-end reads.

treatment_protocol: At day 9, cells were stimulated for various time points with LPS (100ng/ml, rough, ultrapure E. coli K12 strain, Invitrogen) or MOCK (= no stimulation).

value: female

value: LPS-stimulated

tag: time point


title: Replicate 2, RNA-Seq, LPS-stimulus, time 6h

description: processed data column name: RNA.R2.LPS.06


title: Replicate 2, RNA-Seq, LPS-stimulus, time 12h

description: processed data column name: RNA.R2.LPS.12


title: Mm_e11_H3K27ac_rep1

tag: developmental stage


title: WT2

value: CD11c+CD11b- macrophages


title: WT1


title: Replicate 2, RNA-Seq, LPS-stimulus, time 2h

description: processed data column name: RNA.R2.LPS.02


title: Tum3

value: CD11c+CD11b+ macrophages


title: Replicate 2, RNA-Seq, LPS-stimulus, time 1h

description: processed data column name: RNA.R2.LPS.01


title: Tum2


title: Replicate 2, RNA-Seq, Mock-stimulus, time 12h

description: processed data column name: RNA.R2.MOCK.12

value: mock-stimulated


title: Mm_e11_INPUT_rep2

value: ChIP-seq


title: Tum7


title: Mm_e11_H3K27ac_rep2

value: H3K27ac (Abcam ab4729)


title: Replicate 2, RNA-Seq, Mock-stimulus, time 9h

description: processed data column name: RNA.R2.MOCK.09


title: hfd.ALAB.rep3

city: Worcester

first: Roger

last: Davis

address: 55 Lake Avenue North

department: Molecular Medicine

institute: University of Massachusetts Medical School

description:
Sample name: 24
AlbCre+ Jnk1flox/floxJnk2flox/flox high fat diet

data_processing:
We use Illumina RTA to do basecalling - which is created in Illumina 1.5 format
Sequenced reads were trimmed for adaptor sequence; reads that mapped to ribosome were removed; the rest was mapped to mm10 whole genome using Tophat with main parameters -g 15 -N 2 -G ucsc.gtf(from UCSC browser)
Cufflinks, Cuffmerge, Cuffdiff were used to create united transcripts and to calculate FPKM values
United transcripts were used further if as minimum one replica for one sample had FPKM>10
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimeted txt file includes FPKM values for each Sample for each transcript

source_name: Liver

extract_protocol:
RNA was isolated using the RNeasy kit (Qiagen).  RNA quality (RIN > 9) was verified using a Bioanalyzer 2100 System (Agilent Technologies
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice fed a control (chow) or a High fat diet for 16 weeks

value: Liver

value: knock down (AlbCre+ Jnk1flox/floxJnk2flox/flox)

tag: diet

value: high fat diet


title: hfd.ALAB.rep1

description:
Sample name: 22
AlbCre+ Jnk1flox/floxJnk2flox/flox high fat diet


title: Replicate 2, RNA-Seq, Mock-stimulus, time 2h

description: processed data column name: RNA.R2.MOCK.02


title: hfd.J2c.rep3

description:
Sample name: 21
AlbCre+ Jnk2flox/flox high fat diet

value: knock down (AlbCre+ Jnk2flox/flox)


title: hfd.J2c.rep2

description:
Sample name: 20
AlbCre+ Jnk2flox/flox high fat diet


title: Replicate 2, RNA-Seq, time 0

description: processed data column name: RNA.R2.MOCK.00 aka RNA.R2.LPS.00


title: Replicate 1, RNA-Seq, LPS-stimulus, time 12h

description: processed data column name: RNA.R1.LPS.12


title: Replicate 2, RNA-Seq, Mock-stimulus, time 1h

description: processed data column name: RNA.R2.MOCK.01


title: Replicate 2, RNA-Seq, Mock-stimulus, time 6h

description: processed data column name: RNA.R2.MOCK.06


title: Replicate 2, RNA-Seq, LPS-stimulus, time 4h

description: processed data column name: RNA.R2.LPS.05


title: hfd.J1c.rep3

description:
Sample name: 18
AlbCre+ Jnk1flox/flox high fat diet

value: knock down (AlbCre+ Jnk1flox/flox)


title: hfd.J2c.rep1

description:
Sample name: 19
AlbCre+ Jnk2flox/flox high fat diet


title: hfd.J1c.rep2

description:
Sample name: 17
AlbCre+ Jnk1flox/flox high fat diet


title: Replicate 1, RNA-Seq, LPS-stimulus, time 6h

description: processed data column name: RNA.R1.LPS.06


title: Replicate 1, RNA-Seq, LPS-stimulus, time 9h

description: processed data column name: RNA.R1.LPS.09


title: hfd.J1c.rep1

description:
Sample name: 16
AlbCre+ Jnk1flox/flox high fat diet


title: hfd.wt.rep3

description:
Sample name: 15
AlbCre+ high fat diet

value: wild type (AlbCre+)


title: Replicate 1, RNA-Seq, LPS-stimulus, time 1h

description: processed data column name: RNA.R1.LPS.01


title: hfd.wt.rep2

description:
Sample name: 14
AlbCre+ high fat diet


title: Replicate 1, RNA-Seq, LPS-stimulus, time 2h

description: processed data column name: RNA.R1.LPS.02


title: Tum1

tag: cell type


title: hfd.wt.rep1

description:
Sample name: 13
AlbCre+ high fat diet


title: Replicate 1, RNA-Seq, Mock-stimulus, time 12h

description: processed data column name: RNA.R1.MOCK.12


title: hfd.ALAB.rep2

description:
Sample name: 23
AlbCre+ Jnk1flox/floxJnk2flox/flox high fat diet


title: chow.ALAB.rep3

description:
Sample name: 12
AlbCre+ Jnk1flox/floxJnk2flox/flox Chow diet

value: chow diet


title: Replicate 1, RNA-Seq, Mock-stimulus, time 9h

description: processed data column name: RNA.R1.MOCK.09


title: Replicate 2, RNA-Seq, Mock-stimulus, time 4h

description: processed data column name: RNA.R2.MOCK.05


title: chow.ALAB.rep2

description:
Sample name: 11
AlbCre+ Jnk1flox/floxJnk2flox/flox Chow diet


title: Replicate 1, RNA-Seq, Mock-stimulus, time 6h

description: processed data column name: RNA.R1.MOCK.06


title: Replicate 1, RNA-Seq, Mock-stimulus, time 1h

description: processed data column name: RNA.R1.MOCK.01


title: Replicate 1, RNA-Seq, time 0

description: processed data column name: RNA.R1.MOCK.00 aka RNA.R1.LPS.00


title: chow.J1c.rep3

description:
Sample name: 6
AlbCre+ Jnk1flox/flox Chow diet


title: chow.J2c.rep2

description:
Sample name: 8
AlbCre+ Jnk2flox/flox Chow diet


title: chow.ALAB.rep1

description:
Sample name: 10
AlbCre+ Jnk1flox/floxJnk2flox/flox Chow diet


title: chow.J2c.rep3

description:
Sample name: 9
AlbCre+ Jnk2flox/flox Chow diet


title: Replicate 1, RNA-Seq, Mock-stimulus, time 2h

description: processed data column name: RNA.R1.MOCK.02


title: chow.J1c.rep1

description:
Sample name: 4
AlbCre+ Jnk1flox/flox Chow diet


title: chow.J1c.rep2

description:
Sample name: 5
AlbCre+ Jnk1flox/flox Chow diet


title: Replicate 1, RNA-Seq, Mock-stimulus, time 4h

description: processed data column name: RNA.R1.MOCK.05


title: chow.J2c.rep1

description:
Sample name: 7
AlbCre+ Jnk2flox/flox Chow diet


title: chow.wt.rep2

description:
Sample name: 2
AlbCre+ Chow diet


title: Replicate 1, RNA-Seq, LPS-stimulus, time 4h

description: processed data column name: RNA.R1.LPS.05


title: chow.wt.rep1

description:
Sample name: 1
AlbCre+ Chow diet


title: Rh_12Opcw_H3K4me2_rep2

organism: Macaca mulatta

source_name: Rhesus 12 p.c.w. Embryonic Occipital Cortex

value: 12 post conception weeks

value: Embryonic Occipital Cortex

tag: chip antibody

value: H3K4me2 (Millipore 07-030)


title: Rh_12Opcw_INPUT_rep1


title: Rh_12Opcw_H3K27ac_rep1


title: Rh_12Opcw_H3K4me2_rep1


title: Rh_12Fpcw_INPUT_rep2

source_name: Rhesus 12 p.c.w. Embryonic Frontal Cortex

value: Embryonic Frontal Cortex


title: Rh_12Opcw_H3K27ac_rep2


title: Rh_12Opcw_INPUT_rep2


title: Rh_12Fpcw_H3K4me2_rep2


title: Rh_12Fpcw_INPUT_rep1


title: IgG_ChIPSeq

city: Beijing

first: Chaobin

last: Li

state: Beijing

address: 2 Yuanmingyuan West Road, NMICC Building

institute: China Agricultural University

data_processing:
CASAVA1.8.2 (Illumina) were used for image analysis and base calling.
Raw fastq data were trimmed using SolexaQA v2.5 program with Q20 (Phred score) and L40 (Length).
Cleaned data were then mapped to the maize reference genome using Bowtie2 with default parameters and allowing unique reads only.
[Ensembl plants release-15 zea_mays] Peak detection was done using MACS v2.0.10 using the indicated criteria.
[Ensembl plants release-26 zea_mays] Peak calling was performed s using MACS2 (v2.1.0) (band width = 300?model fold = [5, 50]; qvalue cutoff =  5.00e-02)
UCSC bedGraph files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Genome_build: Ensembl plants release-15 zea_mays
Genome_build: Ensembl plants release-26 zea_mays
Supplementary_files_format_and_content: tab-delimited text file includes contains information about called peaks.
Supplementary_files_format_and_content: bed file includes the peak summits locations for every peaks.

organism: Zea mays

source_name: kernal

extract_protocol:
Endosperm Lysates were clarified from sonicated nuclei. O2-DNA complexes were isolated with antibody and IgG serves as antibody control
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit (Catalog# IP-202-1012). ChIP DNA samples were subjected to end repair and A-base addition, followed by ligation with adapters. Barcode sequences of adapters correspond to the following: AGTCAA, ChIP of O2; AGTTCC, ChIP of IgG. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Illumina Genome Analyzer (GA) sequencing was performed by the OSUCCC Nucleic Acid Shared Resource-Illumina GA II Core.

value: 15 days after pollination

value: Endosperm

tag: genotype

value: wildtype

value: rabbit IgG (Sigma, catalog# I5006, lot# SLBJ3775V, pack size 50MG)


title: Rh_8pcw_INPUT_rep1

source_name: Rhesus 8 p.c.w. Embryonic Cortex

value: 8 post conception weeks

value: Embryonic Cortex

value: ChIP-seq


title: Rh_12Fpcw_H3K27ac_rep2

value: H3K27ac (Abcam ab4729)


title: Rh_12Fpcw_H3K4me2_rep1


title: O2_ChIPSeq

description: The anti-O2 antibody recognizes the full length O2 protein and was used in a previous study (Zhang, N., Qiao, Z., Liang, Z., Mei, B., Xu, Z., and Song, R. (2012) Zea mays Taxilin protein negatively regulates opaque-2 transcriptional activity by causing a change in its sub-cellular distribution. PLoS One 7:e43822). This antibody was produced by our own. For O2 antibody production, a full length O2 cDNA was cloned into the BglII and HindIII sites of the pET-32a+ vector (Novagen), and the construct transformed into Rosetta (DE3). Cells were grown at 37°C and induced by the addition of isopropylthio-b-galactoside to a final concentration of 1 mM when the optical density at 600 nm was 0.6. The 6xHis fusion recombinant O2 protein was purified with the ÄKTA purification system using a 1 ml HisTrapTM FF crude column (GE Healthcare). Protein analysis and purification followed established procedures. Antibodies were produced in rabbits according to standard protocols of Shanghai ImmunoGen Biological Technology.

value: anti-O2 (made in-house)


title: Rh_12Fpcw_H3K27ac_rep1


title: chow.wt.rep3

description:
Sample name: 3
AlbCre+ Chow diet

tag: strain

value: Liver


title: Rh_8pcw_H3K4me2_rep1


title: Ectoderm control 1 (ET)

status: Public on Mar 05 2015

first: Valerie

last: Horsley

address: 260 Whitney

data_processing:
Raw reads were mapped to the human reference genome (hg19) with TopHat (version 2.0.6) algorithm
RNA abundance and differential expression was calculated by Cuffinks (version 2.0.2)
Genome_build: hg19

source_name: H1 human embryonic stem cells

growth_protocol: on matrigel (BD Biosciences) in mTESR1 medium (Stem Cell Technologies) at 37ºC, 5% O2 and 5% CO2 and passaged every 5-6 days using dispase (Stem Cell Technologies). Ectoderm specification of hESCs was performed according to previously described protocols [7]. Briefly, hESC colonies were incubated for 3 days with 0.5 nM of human recombinant bone morphogenic protein (BMP-4) (R&D Systems). From day 4 to day 10, BMP-4 was removed and cells were incubated in medium supplemented with 10% fetal calf serum (FCS; FCII Hyclone).

extract_protocol:
Trizol and Rneasy kit
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Cells were treated with ETOH or DAPT (5uM) in ETOH

value: ETOH


title: Patski_control_rep2

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

description: The Patski fibroblast line was originally derived from BL6/spretus hybrid embryonic kidney and has the inactive X from BL6. Two individual RNA samples prepared from Patski cells with the control treatment were used for indexed library preparation. Index adators 6 and 12 were used for Patski_control rep1 and 2 respectively.

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were first sorted by their index sequencing for each replicate. A pseudo-spretus genome was assembled by replacing available SNPs between C57BL/6J and M. spretus (Sanger Center) into the BL6 reference genome. 36bp reads were aligned to the C57BL/6J reference sequence (mm9, UCSC) and to the pseudo-spretus genome separately using TopHat with default parameters, except that the “min-isoform-fraction” flag was set to zero, "--no-novel-juncs" was specified to constrain the search to annotated exon:exon boundaries, and the RefSeq mouse gene annotation was used.
RPKM values were obtained using Cufflinks with default parameters and “min-isoform-fraction” set to zero.
Only high-quality uniquely-mapped reads were used for assignment to each haploid genome based on available SNPs.
The SNP-associated read counts were used to assess allelic expression.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include 5 columns: gene_id, locus, regular RPKM values, BL6-exon-SNP-read count, spretus-exon-SNP-read count.

organism: Mus musculus x Mus spretus

source_name: Patski cells

growth_protocol: Standard cell culturing protocol using 10% FBS in DMEM.

extract_protocol:
RNA were extracted from Patski cells by the Qiagen RNeasy kit with on-column DNaseI digestion.
RNA-seq indexed libraries were prepared using Illumina TruSeq RNA sample preparation kit with standard Illumina protocols. Index adators 6 and 12 were used for Patski_control rep1 and 2 resepecitvely, as well as for Patski_Firre KD rep1 and 2 resepecitvely.

treatment_protocol: Two biological replicates from control or stable Firre knockdown (si&shRNA) Patski cells were used for RNA-seq.

tag: genotype/variation

value: control

value: Fibroblasts derived from hybrid embryonic kidney


title: Ectoderm DAPT 3 (DT)

value: DAPT


title: Ectoderm DAPT 2 (DT)


title: Patski_control_rep1


title: Thalassiosira pseudonana

description: Thaps3 (JGI)

organism: Thalassiosira pseudonana CCMP1335

source_name: cell culture


title: Patski_FirreKD_rep1

description: The Patski fibroblast line was originally derived from BL6/spretus hybrid embryonic kidney and has the inactive X from BL6. Two individual RNA samples prepared from Patski cells with the Firre knockdown were used for indexed library preparation. Index adators 6 and 12 were used for Patski_Firre KD rep1 and 2 respectively.

value: stable Firre knockdown


title: Ectoderm control 2 (ET)


title: Rh_8pcw_H3K27ac_rep1


title: Ectoderm DAPT 1 (DT)


title: MM047_TEAD-KD2

city: Leuven

first: Zeynep

last: Kalender Atak

address: Herestraat 49

country: Belgium

institute: KULeuven

description: biological replicate

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence and for the first the basepair.
The reads are then mapped to hg19 whole genome usingTopHat2 v2.0.9 and Bowtie2 v2.1.0 with --read-realign-edit-dist 0 and sensitive-local  setting
Read counts per gene were obtained from the aligned reads using htseq-count package (HTSeq 0.5.4p5)
Genome_build: hg19 - GENCODE v18
Supplementary_files_format_and_content: tab-delimited text files include gene based read counts per sample

source_name: low passage primary melanoma cultures

growth_protocol: cells were grown at 37°C to 85% confluency before harvest. Medium used was Ham's F-10 nutrient mix supplemented with FBS and l-alanyl-glutamine.

extract_protocol:
RNA was extracted using the Rneasy protocol from Qiagen
illumina TruSeq library prep

value: low passage primary melanoma cultures

tag: growth protocol

value: cells were treated with 10nM pool of siRNAs against all 4 TEADs. Cells were harvested 72h after transfection.


title: MM074_FAIRE

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to the genome using Bowtie2 2.1.0.
The sensitive-local setting for Bowtie2 was used to correct for a high percentage of mismatches at the start of a read, resulting in the removal of the first five base pair for each read
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bam files using BEDTools 2.17.0 and the scores represent the coverage

extract_protocol:
Chromatin was extracted using the Magna ChIP kit; cells were sonicated for 12 cycles with 30sec pulses using the biorupter; phenol/chlorophorm extraction was performed using the Maxtract tubes (qiagen)
Illumina Truseq


title: MM057_FAIRE


title: MM047_scramble3

description: biological replicate

value: cells were treated with 10nM of scamble siRNA. Cells were harvested 72h after transfection.


title: MM099_FAIRE


title: MM001_FAIRE


title: MM047_TEAD-KD1

description: biological replicate


title: MM031_FAIRE


title: MM118_FAIRE


title: MM034_FAIRE


title: Ectoderm control 3 (ET)


title: MM087_FAIRE


title: MM011_FAIRE


title: MM047_TEAD-KD3

description: biological replicate


title: MM047_scramble1

description: biological replicate


title: MM047_scramble2

description: biological replicate


title: SKMEL5_RNA

source_name: melanoma cell line

value: melanoma cell line


title: Patski_FirreKD_rep2


title: SK-MEL-5_FAIRE


title: MM047_FAIRE


title: MM099_RNA


title: Mre11-KD sample B

city: West Hollywood

first: Hisashi

last: Tanaka

state: CA

address: 8700 Beverly Blvd

department: Surgery

institute: Cedars-Sinai Medical Center

data_processing:
tophat -G ref_CriGri_1.0_scaffolds.gff3 bowtie2Index/choAssembly [file]
grep "exon" ref_CriGri_1.0_scaffolds.gff3 | gawk -F"\t" 'BEGIN {OFS = "\t"} {print $1, $4-1, $5, $9}' > ref_CriGri_1.0_scaffolds.bed
counts per exon generated by custom perl scripts
The following steps were peformed in R using the edgeR package:
combinedCounts <- read.delim("combinedCounts.txt", header = F)
colnames(combinedCounts) <- c("sequence_4", "sequence_6", "sequence_5", "sequence_7")
keep <- rowSums(combinedCounts) > 40
combinedCounts <- combinedCounts[keep, ]
groups <- c(1, 1, 2, 2)
comparison <- DGEList(combinedCounts, group = groups)
comparison <- estimateCommonDisp(comparison)
comparison <- estimateTagwiseDisp(comparison)
comparisonET <- exactTest(comparison)
toptags <- topTags(comparisonET, n = 9999999)$table
choRNAseqResults <- merge(toptags, combinedCounts, by = "row.names", all = T)
write.table(choRNAseqResults, "edgeRoutput.txt", quote = F, sep = "\t", row.names = F, col.names = T)
Genome_build: July 2013 C_griseus_v1.0
Supplementary_files_format_and_content: Read counts for each sample included in edgeRoutput.txt

organism: Cricetulus griseus

source_name: CHO cells treated with shRNA against Mre11

extract_protocol:
Total RNA was isolated from Mre11-KD and control cells (infected with LV-GFP) using RNeasy plus mini kit (QIAGEN)
Illumina TrueSeq RNA Sample Preparation Kit

tag: tag

value: Chinese hamster ovary (CHO) cells

tag: phenotype

value: Mre11 knockdown


title: MM074_RNA


title: MM118_RNA


title: Control sample B

source_name: Control CHO cells

value: GFP-expressing


title: MM087_RNA


title: MM047_RNA


title: MM074_Me3

description: 4 µg of antibody was used on 2 million cells

extract_protocol:
Chromatin was extracted using the MagnaChIP-seq kit (millipore). Sonication was performed for 12 cycles, 30 sec pulses using the biorupter
Illumina Truseq

tag: antibody

value: H3K27me3 (07-499, Millipore)


title: MM087_Me3


title: MM011_RNA


title: MM031_RNA


title: MM034_RNA


title: SKMEL5_Me3

tag: cell line


title: MM011_MITF

value: anti-MITF (ab12039, abcam)


title: MM057_Me3


title: MM001_RNA


title: Mre11-KD sample A


title: MM031_MITF


title: MM118_Me3


title: Pollinated Seed Flower

city: Rochester

first: Ellen

middle: O'Hara

last: Martinson

department: Biology

institute: University of Rochester

data_processing:
read quality assessed in FastQC Version 0.10.0  the first 10 base pairs were removed from of every read because they contained a skewed GC content
Further trimming was performed using Trimmomatic Version 0.22, low quality reads (phred scores <15) were identified from both ends and across the entire read by a 15 bp sliding window. After trimming, reads shorter than 75 bp were removed
De novo assembly was performed using Oases version 0.2.08 Six different builds were created per sample using a range of hash lengths from 31 to 51 kmers with the minimum contig length set to twice the kmer length.  The final build was constructed using the largest hash length (51 kmer) and included the five additional builds as long sequences enabling the Oases “conserve long” option
Oases clusters highly similar sequences into groups likely derived from the same loci. If multiple transcripts were listed in one of these groups, the longest read in the group was used for subsequent analyses
Sequence reads from each sample were mapped to the non-redundant reference metatranscriptome to quantify the abundance of each assembled transcript using the default parameters in CLC Genomics Workbench software
Supplementary_files_format_and_content: tab delimited files with the length, annoataion, and RPKM values for all samples

organism: Ficus obtusifolia

source_name: Ficus flowers

extract_protocol:
Before extraction, each sample was soaked in RNase-free water for 1 minute to remove residual RNAlater and then ground in liquid nitrogen. Total RNA was extracted from the four collected samples (receptive gall flowers, receptive seed flowers, pollinated gall flowers, and pollinated seed flowers) using the Spectrum Plant Total RNA Kit (following manufacturer's instructions; Sigma-Aldrich, St. Louis, MO) and visualized on an Agilent 2100 Bioanalyzer (Santa Clara, CA) to assess quality
mRNA was purified using a poly(T) oligo, selecting for all eukaryotic sequences in the sample. cDNA library creation was performed at the University of Arizona Genetics Core (UAGC)

treatment_protocol: Syconia of the recipient tree were covered individually with fine mesh bags to exclude pollinating and non-pollinating fig wasps. When syconia on the recipient tree became receptive, a single foundress (Pegoscapus hoffmeyerii), obtained from syconia on the source tree, was introduced to each fig. Each recipient syconium was then re-bagged for the subsequent 24 hours to ensure pollination and galling by a single individual with a known entrance time. A ‘receptive’ sample of fig syconia was collected from the recipient tree prior to the introduction of foundresses, and a ‘pollinated’ sample of fig syconia was collected 24 hours after foundress introduction. Syconia were submerged immediately in RNAlater (Qiagen) and held at -20°C until putative gall- and seed flowers were collected based solely on their location within the syconium (Figure 1). Flowers were removed with sterile microforceps, pooled with flowers of the same position and pollination status from 2-3 additional syconia from the same recipient tree, and stored separately in 0.2ml tubes in RNAlater at -80°C

tag: flower type

value: Seed flower

tag: pollination status

value: Pollinated


title: MM047_Me3


title: zld_NC13-input

city: Evanston

first: Shelby

middle: A

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

data_processing:
Multiplex libraries were split using the ‘split barcodes’ function in Galaxy.
Reads were mapped to the Drosophila genome (R5/dm3) using default parameters on Bowtie
SAM-formatted mapped reads were converted to BAM using samtools
Coverage of mapped reads in 25 bp windows was calculated in R, using the GenomicRanges package. Reads were CPM normalized and reflect mean coverage within a 25 bp window.
Genome_build: dm3
Supplementary_files_format_and_content: .bed files were generated from the coverage calculations described above using the rtracklayer package in R.

organism: Drosophila melanogaster

source_name: embryo

extract_protocol:
150 embryos (NC12 and NC13) or 100 embryos (NC14 E, M, or L) were hand selected on the basis of nuclear morphology and density following 15’ cross linking in 1% formaldehyde/Heptane/PBS/0.5% Triton X-100. Samples were homogenized in 1% RIPA buffer plus protease and phosphatase inhibitors and 1mM DTT. Cleared nuclear pellets were sonicated for 7x 20 seconds to shear chromatin to ~300 bp average size followed by overnight immunoprecipitation and 1h complex capture on Protein G dynabeads. Following two low and high salt washes, purified complexes were eluted, RNase treated, and cross links were reversed in the presence of Proteinase K. DNA was purified via Qiagen spin column.
NEBNext ChIP Seq library master mix kit for Illumina was used according to the manufacturer’s specifications, using 1 ng input chromatin or the entire ChIP sample for library preparation. Ampure beads were used for size-selection prior to PCR amplification with barcoding primers. Mean library fragment size was ~270 bp. Libraries were sequenced on an Illumina HiSeq 2500 with read length of 67 bp except for mei-41 samples which were sequenced at 141 bp.

tag: maternal genotype


title: zld_NC13-pSer5

value: anti-RNA Pol II (CTD-pSer5), abcam ab5408


title: mei-41_NC13-IgG

value: Protein A purified control rabbit IgG


title: Pollinated Gall Flower

value: Gall flower


title: MM034_Me3


title: Control sample A


title: MM057_RNA


title: Receptive Seed Flower

value: Receptive


title: Receptive Gall Flower


title: MM099_Me3


title: MM011_Me3


title: WT_NC14L-input


title: MM031_Me3


title: zld_NC13-Rpa70

value: anti-Green Fluorescent Protein, millipore ab3080


title: WT_NC14M-input


title: WT_NC14L-pSer5


title: SKMEL5_Ac

value: H3K27ac (ab4729, abcam)


title: MM118_Ac

value: low passage primary melanoma cultures


title: MM099_Ac


title: WT_NC14E-input


title: WT_NC13-input


title: WT_NC14M-pSer5


title: WT_NC14E-pSer5


title: MM057_Ac


title: MM087_Ac


title: MM074_Ac


title: WT_NC13-pSer5


title: WT_NC13-Rpa70


title: MM047_Ac


title: mei-41_NC13-pSer5


title: WT_NC13-IgG


title: MM011_Ac

description: 5 µg of antibody was used on 2 million cells


title: MM034_Ac


title: WT_NC12-input


title: MM001_Ac


title: MM031_Ac


title: MEK_EGFR6

city: Salt Lake City

first: Andrea

last: Bild

state: Utah

address: 201 Presidents Circle

institute: University of Utah

data_processing:
Casava v1.8.2 software used for basecalling and demultiplexing
FastQC used for quality check
Sequenced reads were trimmed for adaptor sequence and low quality ends then mapped to hg19 reference genome using TopHat v2.0.6
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using Cufflinks v2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: MCF10A Cell Line

growth_protocol: MEBM + MEGM Bullet kit

extract_protocol:
Qiagen RNeasy mini kit
Illumina TrueSeq stranded mRNA ver2

treatment_protocol: Infected with adenovirus expressing gene of interest

tag: treatment

value: infection with adenovirus with MEK and EGFR

value: Non-tumorigenic immortalized breast epithelia line


title: EGFR6

value: infection with adenovirus with EGFR


title: WT_NC12-pSer5


title: 12h

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

description: fungal cell

data_processing:
Sequence reads were assigned to each sample by matching the decoded barcode used for each library and quality-filtered using a method developed for SOLiD reads (Sasson and Michael, 2010, Bioinformatics).
Reads were mapped to T. rurbum genome using bowtie v0.12.2 and TopHat v1.1.0.
Differential gene expression RPKM values were estimated using Cuffdiff v1.1.0.
Genome_build: Trichophyton rubrum genome available at Broad Institute's Dermatophyte Database Accession number: ACPH1000000.
All the comparisons were performed between each sample and the 0 h control.

organism: Trichophyton rubrum

source_name: 12h acriflavine

growth_protocol: Approximately 1 × 106 conidia were inoculated into 100 mL of Sabouraud media and incubated at 28oC for 96 h under agitation (0 h).

extract_protocol: RNA was fragmented using the SOLiD 4 Total RNA Seq Kit (Applied Biosystem ) and reverse transcribed using ArrayScript Reverse Transcriptase (Ambion). The cDNA synthesized was purified with the Qiagen MinElute PCR Purification Kit (Qiagen) and was run on a Novex 6% TBE-urea gel (Invitrogen) for size selection. cDNA was excised from the gel at a size range of 150–250 bp and in-gel PCR reactions were performed to obtain enough material for subsequent emulsion PCR (ePCR). During the PCR reaction, each library was barcoded using PCR primers with different barcodes to allow for multiplex sequencing. ePCR and emulsion break were performed according to the Applied Biosystems SOLiD 4 System Templated Bead Preparation Guide. The amplified beads were first run on a workflow analysis slide to determine the quality and quantity of beads, which was followed by a single sequencing run, performed according to the Applied Biosystems SOLiD 4 System Instrument Operation Guide.

treatment_protocol: The mycelia were exposed to sub-inhibitory concentration 1.75 µg/mL of acriflavine (Sigma). After 3, 12, and 24 h of incubation at 28°C under agitation, the resultant mycelia were collected and used for library preparation.

value: wild type


title: MM001_Me3


title: 24h

description: fungal cell

source_name: 24h acriflavine


title: ChIP-seq_ER_siFOXA1_E2+TNF_rep2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: siRNA targeted to FoxA1 transfected into MCF-7 cells 48 hrs prior to treatment with E2+TNF

data_processing:
Alignment: Short-reads were aligned to the human reference genome (hg19). Bowtie software package (Langmead et al., 2009) was used to align reads and the output was processed using custom Perl scripts, and imported into R for most the analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bed

growth_protocol: MCF-7 breast cancer cells were obtained from the ATCC and maintained in Minimum Essential Medium Eagle supplemented with 5% calf serum.

extract_protocol:
ChIP-seq libraries were generated from two biological replicates for each condition.  The immunoprecipitated DNA was purified using a MiniElute PCR Purification Kit from Qiagen.  After purification, 50 ng of ChIPed DNA for each condition was used to generate libraries for deep sequencing, as previously described (Quail et al., 2008), with some modifications.  Briefly, the DNA was end-repaired and a single “A”-base overhang was added using the Klenow fragment of E. coli DNA polymerase.  The A-modified DNA was ligated to Illumina sequencing adaptors using the Illumina TruSeq DNA Sample Prep Kit.  The ligated DNA (250-300 bp) was size-selected by agarose gel electrophoresis and purified using a Qiagen Gel Extraction Kit.
The size-selected fragments were amplified using Illumina TruSeq P5 and P7 PCR primers, and purified using AMPure beads (Beckman Coulter).  Quality control was performed to determine the size, purity, and concentration of the final libraries, which were sequenced using an Illumina HiSeq 2000 per the manufacturer’s instructions.

treatment_protocol: Prior to all treatments, the cells were grown for 3 days in phenol red-free MEM Eagle medium supplemented with 5% charcoal-dextran-treated calf serum.  All treatments were performed for 40 min with 100 nM 17β-estradiol, 25 ng/mL TNFα, or both.

value: ER Positive Breast Cancer Cells

value: ER alpha (rabbit polyclonal generated in the Kraus Lab)


title: ChIP-seq_ER_siFOXA1_E2+TNF_rep1


title: ChIP-seq_Input_siFOXA1_E2+TNF_rep2

description: A Nonspecific siRNA oligo transfected into MCF-7 cells 48 hrs prior to treatment with E2+TNF


title: MEK5

value: infection with adenovirus with MEK


title: Control5

value: infection with adenovirus with GFP


title: MEK6


title: 0h

description: fungal cell

source_name: 0h acriflavine


title: ChIP-seq_Input_siFOXA1_E2+TNF_rep1


title: MEK_EGFR5


title: ChIP-seq_ER_siCTRL_E2+TNF_rep2


title: Control6


title: DSBs-long

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

description: DNA fraction >400 bp

data_processing:
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control.
Single sequenced reads were trimmed for adaptor sequences and low quality sequences by cutadapt v. 1.3 using the following options: --minimum-length=30 --trimmed-only --quality-base=33 --quality-cutoff=3 -n 2 -g CTGGTGAGGGCATG  -g GAATTCCCTGCTTCCCATT
Paired-end sequenced reads were trimmed for adaptor sequences and low quality sequences by cutadapt v. 1.3 using the following options: --minimum-length=30 --trimmed-only --quality-base=33 --quality-cutoff=3 -n 2 -g CTGGTGAGGGCATG  -g GAATTCCCTGCTTCCCATT and new algorithm designed especially for pair-end readings.
Trimmed reads from Single-Long and PairEnded-Short experiments were mixed together and mapped to hg19p10 by bwa 0.7.5a using the mem algorithm and by samtools 0.1.19
Mapping and alignment results were converted to resulting table using ad hoc Perl scripts.
Postmapping 1: We removed all readings that don't contain SAU sequence (GATC) or contain it few times as erroneous and then calculated the coordinate of each Double Strand Break as the opposite side to SAU sequence.
Postmapping 2: We removed all readings that was mapped below 5% and above 95% of coverage (column 5 of DSB2013_total.txt). The result at this step is deposited as DSB2013_filtered.bed
Postmapping 3: We merged all readings that are 1kbp close to each other to groups, and replaced groups with the maximum coverage value for each group. The result in SGR file contains the DSB with one-nucleotide resolution and its coverage.
Genome_build: Homo Sapiens hg19/GRCh37.p10 genome, MFA sequences with High/low complexity regions marked as big/small letters
Supplementary_files_format_and_content: Tab-delimited text file DSB2013_total.txt includes all mapped readings and contains the following features of each mapping: begin, end, length, coverage, number of reads, sequence.
Supplementary_files_format_and_content: Tab-delimited SGR file DSB2013_filtered.sgr includes filtered by postmapping procedure entries – one-nucleotide resolution coordinate of each DSB and its coverage.

source_name: DSBs-long

growth_protocol: The cells were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemente+B29d with 10% FBS penicillin (100 U/ml), streptomycin (100 ug/ml) and L-glutamine (4 mM).

extract_protocol:
DNA-agarose plugs were prepared as described before [Tchurikov NA and Ponomarenko NA (1992) Detection of DNA domains in Drosophila, human and plant chromosomes possessing mainly 50- to 150-kilobase stretches of DNA. Proc Natl Acad Sci USA 89: 6751-6755]. About 6 millions of HEK293T cells in 2 ml of culture medium were pelleted by centrifugation at 2000 rpm, resuspended in 0.3 ml of the same medium, gently mixed at 42°C with an equal volume of a 1% agarose L (LKB) in PBS solution, and distributed on a mold containing 100-microliters wells. The mold was placed on ice for 2-5 min, covered with parafilm. The agarose plugs were then placed in Petri dishes with 5 ml of solution containing 0.5 M EDTA (pH 9.5), 1% sodium laurylsarcosine, and 1-2 mg of proteinase K solution per ml for 40-48 hr at 50°C, and stored at 4°C in the same solution. Each DNA-agarose plus usually contained about 15 microgramms of DNA corresponding to about 1 millions of cells.  To test the quality of isolated DNA the fractionation in the pulsed-field gels was performed as described before (Tchurikov and Ponomarenko, 1992). Portions of the original agarose-DNA plugs (5-50 microliters) containing 1-10 microgramms of DNA were used for electrophoresis without any restriction enzyme digestion. The DNA samples were run in 0.8% agarose gels on an LKB Pulsaphor system using hexagonal electrode and switching times of 25 or 450 sec.  For elution of DNA preparations the fractionation in 1% agarose conventional mini-gel was performed. One-half of DNA-agarose plug was washed in 1xTE 3 times (for 15 min each) following by 3 times washing in the same solution containing 17.4 microgramms/ml PMSF in ethanol. After fractionation in the mini-gel, the ethidium-bromide stained DNA band was excised and electoeluted inside the dialysis cellulose membrane bag. After overnight dialysis without stirring against 1 liter of 0.01 x TE at 4°C, the DNA was concentrated with PEG (4°C) and redialyzed.  Rapid amplification of forum domains termini (RAFT) procedure:  About 1.5 microgramms of isolated DNA (see above) was ligated with 70 ng of double-stranded oligonucleotide (25 bp long 5’-phosphorylated 5’ pCCCCTGCAGTATAAGGAGAATTCGGG 3’ oligonucleotide annealed with 26 bp long 5’ biotinylated 5’ bio-CCGAATTCTCCTTATACTGCAGGGG 3’ oligonucleotide) in 150 microliters of solution containing 0.1 M NaCl, 50 mM Tris HCl (pH 7.4), 8 mM MgCl2, 9 mM 2-mercaptoethanol, 7 microM ATP, 7.5 % PEG, and 40 units of T4 DNA ligase at 20°C for 16 hr. After heating at 65°C for 10 min the DNA preparation was digested with Sau3A enzyme to shorten the forum domain to the termini attached to the ligated oligonicleotide. The selection of such termini was performed in 0.5 ml eppendorf tubes using 300 microliters of suspension containing streptavidin magnespere paramagnetic particles, SA-PMP (Promega) according to the manufacturer's recommendations. After extensive washing with 0.5xSSC removing DNA fragments corresponding to internal parts of forum domains, the forum termini (FT) DNA preparation was eluted from the SA-PMP using digestion with EcoRI enzyme in final volume of 50?mictolitres (double-stranded FT). The FT were then ligated with 100x molar excess of double-stranded Sau3A adaptor (5’-phosphorylated 5’ pGATCGTTTGCGGCCGCTTAAGCTTGGG 3’ oligonucleotide annealed with 5’ CCCAAGCTTAAGCGGCCGCAAAC 3’ oligonucleotide). In some experiments (FT) DNA preparation was eluted from the SA-PMP using heating by incubation at 100°C for 3 min in 50 microliters of 0.01xTE (single-stranded FT). Before heating the FT preparation was ligated with100x molar excess of double-stranded Sau3A adaptor in suspension with SA-PMP (see above). Both final DNA samples (double-stranded FT or single-stranded FT) were used for PCR amplifications. 35 cycle PCR amplification in 30 microlitersl of a solution containing 67 mM Tris-HCl (pH 8.4); 6 mM MgCl2; 10 mM 2-mercaptoethanol; 16.6 mM ammonium sulfate; 6.7 microM EDTA; 5 microg/ml BSA; 1 mM dNTPs; 1.5 microg of primer corresponding to Sau3A adaptor (5’ CCCAAGCTTAAGCGGCCGCAAAC 3’); 1.5 microg of primer corresponding to biotinilated oligonucleotide (5’ CCGAATTCTCCTTATACTGCAGGGG 3’) and 1 u of Taq polymerase was performed using Eppendorf Mastercycler Personal. Amplification conditions were 90°C for melting, 65°C for annealing and 72°C for extension, for 1 min each.  After purification using MiniElute PCR purification Kit (Qiagen) the DNA preparation was used for preparation of libraries. The libraries were prepared using TruSeq RNA Sample Preparation Kit v2 (Illumina). The final DNA was separated in 2% agarose gels, and two DNA fractions - 200-500 bp (short) and higher 500 bp (long) were eluted using QIAqiuck gel extraction kit (Quigen). The short and long DNA samples were sequenced using Genome Analyzer IIx or MiSeq (Illumina), respectively.
The libraries were prepared using TruSeq RNA Sample Preparation Kit v2 (Illumina)   following the manufacturer's protocols.

treatment_protocol: HEK 293 cells were seeded in 10 cm culture plates 1-2 days before experiment in DMEM containing 10% FBS, and used at approximately 60-80% confluency.

tag: tissue

value: kidney

tag: age

value: embryo


title: EGFR5


title: EGFR4


title: ChIP-seq_Input_siCTRL_E2+TNF_rep2


title: MEK_EGFR4


title: MEK4


title: ChIP-seq_ER_siCTRL_E2+TNF_rep1


title: Control4


title: ChIP-seq_FoxA1_E2+TNF_rep2

description: ChIP-enriched DNA from MCF7 cells after 40min of E2+TNFα treatment

value: FoxA1 (Abcam ab23738)


title: ChIP-seq_FoxA1_E2+TNF_rep1


title: MEK_EGFR3


title: ChIP-seq_FoxA1_TNF_rep1

description: ChIP-enriched DNA from MCF7 cells after 40min of TNFα treatment

value: TNFa


title: 3h

description: fungal cell

source_name: 3h acriflavine


title: ChIP-seq_Input_siCTRL_E2+TNF_rep1


title: EGFR3


title: MEK3


title: Control3


title: MEK_EGFR2


title: ChIP-seq_FoxA1_E2_rep2

description: ChIP-enriched DNA from MCF7 cells after 40min of E2 treatment


title: ChIP-seq_FoxA1_Vehicle_rep2

description: ChIP-enriched DNA from MCF7 cells after 40min of Vehicle  treatment

value: Vehicle


title: ChIP-seq_FoxA1_E2_rep1


title: EGFR2


title: Control2


title: ChIP-seq_p65_E2+TNF_rep2

value: p65  (Abcam ab7970)


title: ChIP-seq_FoxA1_Vehicle_rep1

description: ChIP-enriched DNA from MCF7 cells  after 40min of Vehicle treatment


title: ChIP-seq_p65_TNF_rep2


title: EGFR1


title: ChIP-seq_p65_E2_rep2


title: ChIP-seq_p65_TNF_rep1


title: MEK1


title: ChIP-seq_FoxA1_TNF_rep2


title: Control1


title: ChIP-seq_p65_E2_rep1


title: ChIP-seq_ER_E2+TNF_rep2


title: ChIP-seq_p65_Vehicle_rep2


title: GRO-seq_E2+TNFα_40m_rep2

description: GRO-seq in MCF-7 cells treated for 40 minutes with E2+TNFα prior to nuclear run-on reaction

data_processing:
library strategy: GRO-seq
Alignment: Short-reads were aligned to the human reference genome (hg19), including autosomes, X-chromosome, and one complete copy of an rDNA repeat (GenBank ID: U13369.1).  The BWA software package (Li et al., 2009) was used to align reads and the output was processed using custom Perl scripts, and imported into R for most the analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bed

extract_protocol:
MCF-7 cells were seeded at 2.5 million cells per 15 cm dish and treated with Vehicle, E2, TNFα, or E2 + TNFα, as described above.  The cells were washed three times with ice-cold PBS, swollen in hypotonic buffer, and collected in ice-cold lysis buffer [10 mM Tris•HCl, pH 7.4, 0.5% NP-40, 10% Glycerol, 3 mM CaCl2, 2 mM MgCl2, 1 mM DTT, 1X protease inhibitor cocktail (Sigma-Aldrich), and SUPERase-In (Ambion)] at 1000 x g for 10 min at 4°C.  The cells were then resuspended in 1.5 ml of lysis buffer and pipetted up and down through a narrow opening 30 to 50 times to release the nuclei.  The nuclei were pelleted again by centrifugation and washed once with 1 mL of lysis buffer.  The nuclear pellets were resuspended in 500 μL of freezing buffer (50 mM Tris•HCl, pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, and 4 units of SUPERase-In per mL), counted, and stored in 100 μl aliquots containing 5 x 106 nuclei.
Nuclear run-on and library preparation was performed as previously described (Danko et al., 2013; Hah et al., 2011), with modifications.  Briefly, cells were treated for 40 min with 100 nM E2, 25 ng/ml TNFα, or both E2 + TNFα and libraries were prepared from two biological replicates using a circularized ligation-based protocol for adaptor addition used to improve the efficiency of library preparation, reduce sequence bias, and allow for barcoding.  The libraries were amplified with indexed primers containing barcodes according to the Illumina TrueSeq small-RNA library prep kit, then sequenced using an Illumina HiSeq 2000.  A more detailed protocol is available from the corresponding author (W.L.K.).

tag: treated with

value: 100 nM 17β-estradiol + 25 ng/mL TNFα for 40min

tag: molecule subtype

value: nascent RNA


title: ChIP-seq_ER_E2+TNF_rep1

tag: cell type

tag: chip antibody


title: GRO-seq_TNFα_40m_rep3

description: GRO-seq in MCF-7 cells treated for 40 minutes with TNFα prior to nuclear run-on reaction

value: 25 ng/mL TNFα for 40min


title: ChIP-seq_p65_Vehicle_rep1


title: ChIP-seq_ER_E2_rep2


title: GRO-seq_TNFα_40m_rep1


title: GRO-seq_E2_40m_rep3

description: GRO-seq in MCF-7 cells treated for 40 minutes with E2 prior to nuclear run-on reaction

value: 100 nM 17β-estradiol (E2) for 40min


title: ChIP-seq_ER_E2_rep1


title: GRO-seq_TNFα_40m_rep2


title: ChIP-seq_ER_TNF_rep2


title: GRO-seq_Veh_40m_rep3

description: GRO-seq in MCF-7 cells treated for 40 minutes with Vehicle prior to nuclear run-on reaction

value: Vehicle for 40min


title: MEK2

value: Non-tumorigenic immortalized breast epithelia line


title: GRO-seq_E2_40m_rep1


title: ChIP-seq_p65_E2+TNF_rep1


title: MEK_EGFR1

value: infection with adenovirus with MEK and EGFR


title: GRO-seq_E2+TNFα_40m_rep3

value: ER Positive Breast Cancer Cells


title: ChIP-seq_ER_TNF_rep1

value: ER alpha (rabbit polyclonal generated in the Kraus Lab)


title: ChIP-seq_ER_Vehicle_rep2


title: GRO-seq_E2_40m_rep2


title: GRO-seq_E2+TNFα_40m_rep1


title: GRO-seq_Veh_40m_rep2


title: GRO-seq_Veh_40m_rep1


title: ChIP-seq_ER_Vehicle_rep1


title: ChIP-seq_Input_E2+TNF_rep2

description: ChIP 5% Input from MCF7 cells  after 40min of E2+TNF treatment

value: input


title: ChIP-seq_Input_TNF_rep2

description: ChIP 5% Input from MCF7 cells  after 40min of TNF treatment


title: ChIP-seq_Input_E2+TNF_rep1


title: ChIP-seq_Input_TNF_rep1


title: DSBs-short

description: DNA fraction 200-400 bp

source_name: DSBs-short

tag: genotype

value: wild type


title: ChIP-seq_Input_E2_rep1

description: ChIP 5% Input from MCF7 cells  after 40min of E2 treatment