title: HiSeq_H3K9ac_lo_CB_DMSO3

description:
ChIP-seq
processed data file: H3K9ac_CB_DMSO.tdf


title: HiSeq_H3_hi_BM_DMSO2

status: Public on Nov 02 2015

type: SRA

city: Boston

first: Peter

last: van Galen

state: Massachusetts

address: 4 Blackfan Circle

department: Hematology

country: USA

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

description: ChIP-seq

library_source: genomic

data_processing:
Provided fastq files are already demultiplexed according to adapter barcode and trimmed.
Alignment: BWA paired-end alignment to hg19
Filter1: Remove all unmapped reads and reads with X0 > 2 from bam files
Filter2: Remove all PCR duplicates using PicardTools MarkDuplicates with REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT
Filter3: Of pairs with identical R1 starting position alignment, keep only the pair with the longest fragment size.
Make tdf files using igvtools count --includeDuplicates --pairs
Genome_build: hg19
Supplementary_files_format_and_content: For visualization in IGV, tdf files are provided.

molecule: genomic DNA

organism: Homo sapiens

source_name: Bone marrow

extract_protocol:
Mint-ChIP: Cells were lysed and native chromatin was digested using Mnase. Subsequently, nucleosomes were indexed by adapter ligation and pooled for immunoprecipiation of H3K9ac (Active Motif, 39917), H3K9me2 (Abcam, ab1220) and total H3 (Abcam, ab1791).
Mint-ChIP: Immunoprecipitated DNA was amplified by in vitro transcription, followed by reverse transcription. Resulting fragments, tagged on both ends, were amplified by PCR using primers compatible with Illumina sequencing.

tag: tissue

value: Bone marrow

tag: immunprecipitation

value: Total H3

tag: mnase for chromatin digestion

value: High

tag: treatment

value: DMSO


title: HiSeq_H3_hi_BM_UNC3

description: ChIP-seq


title: HiSeq_H3_lo_BM_DMSO3

description: ChIP-seq

value: Low


title: HiSeq_H3K9ac_lo_CB_DMSO2

source_name: Cord blood

value: Cord blood


title: HiSeq_H3_lo_CB_DMSO1

description: ChIP-seq


title: HiSeq_H3K9ac_lo_CB_DMSO1


title: HiSeq_H3_lo_CB_DMSO3

description: ChIP-seq


title: HiSeq_H3K9ac_lo_BM_UNC2

description:
ChIP-seq
processed data file: H3K9ac_BM_UNC.tdf


title: HiSeq_H3K9ac_lo_BM_UNC3


title: HiSeq_H3K9ac_lo_BM_UNC1


title: HiSeq_H3K9ac_lo_BM_DMSO2

description:
ChIP-seq
processed data file: H3K9ac_BM_DMSO.tdf


title: HiSeq_H3_hi_BM_UNC2

description: ChIP-seq


title: HiSeq_H3_hi_BM_DMSO1

description: ChIP-seq


title: HiSeq_H3K9ac_hi_CB_DMSO3


title: HiSeq_H3K9ac_lo_BM_DMSO1


title: HiSeq_H3K9ac_hi_CB_DMSO1


title: HiSeq_H3K9ac_hi_CB_DMSO2


title: HiSeq_H3K9ac_hi_BM_UNC1


title: HiSeq_H3K9ac_hi_BM_DMSO3


title: HiSeq_H3K9ac_hi_BM_DMSO2


title: HiSeq_H3K9ac_hi_BM_UNC3


title: HiSeq_H3K9ac_hi_BM_UNC2


title: t6_inf_rep2

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

library_source: transcriptomic

data_processing:
Fastq file were mapped using STAR version 2.3.1n
sam files were sorted using picard-tools-1.90
raw counts were generated with htseq-count version 0.6.0 and UCSC gtf file for hg19
raw counts were combined in a table using a R script
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file containing raw counts

molecule: total RNA

source_name: human bronchial epithelial cells

growth_protocol: Primary NHBE cells from single healthy donor were obtained from Clonetics-BioWhittaker, San Diego, CA. Briefly, cells were cultured on transwell membrane supports at ALI to trigger differentiation. At 28 d post-ALI, cultures which formed a pseudostratified mucociliary epithelium with beating cilia and mucus production

extract_protocol:
Total RNA was isolated from Hi176 infected WD-NHBE cells at 1, 6, 24 and 72 h post infection using Trizol reagent, as well as mock-infected cells and Hi176 conditioned in infection medium for 1 h.
The strand-specific cDNA library was generated with ScriptSeq- Complete Gold Kit – Epidemiology, Low Input from Epicentre after ribosomal RNA depletion using Ribo-Zero Gold – Epidemiology kit

treatment_protocol: after 28 day of culture cells were infected with Hi176 at MOI of 100:1. NTHi strain 176,is an isolate obtained from the middle ear and was a part of a Finnish otitis media outbreak cohort study (kindly provided by Derek Hood, University Oxford, UK)

tag: time

value: 6 hour infection

value: infected Hi176 at MOI of 100:1


title: t72_NHBE_rep1

value: 72 hour control sample


title: t72_inf_rep3

value: 72 hour infection


title: t72_inf_rep2


title: t72_inf_rep1


title: t24_inf_rep3

value: 24 hour infection


title: t6_inf_rep3


title: t24_inf_rep1


title: t6_inf_rep1


title: t72_NHBE_rep3


title: HiSeq_H3K9ac_hi_BM_DMSO1


title: t24_inf_rep2


title: HiSeq_H3K9ac_lo_BM_DMSO3


title: t24_NHBE_rep2

value: 24 hour control sample


title: t1_inf_rep2

value: 1 hour infection


title: t24_NHBE_rep3


title: t1_NHBEctr_rep2

value: 1 hour control sample


title: Pre-xeno DNA

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
Reads were aligned to the human genome and to the human repetitive elements from UCSC using the Helicos Digital Gene Expression pipeline. Pubmed ID 19581875
For each sample, read counts for the repetitive elements were multiplied by 1,000,000 and divided by the total number of reads that aligned to the genome.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of aligned read counts multiplied by 1,000,000 and divided by total number of genomic alignments. Rownames identify repetitive element region of the genome and column names identify sample.

source_name: SW620 colon cancer cell line

growth_protocol: Tissue culture in RPMI1640 10%FBS media

extract_protocol:
Dneasy Blood and Tissue Kit (Qiagen)
Helicos single molecule sequencing DNA protocol

tag: cell line

tag: environment

value: 2D culture conditions


title: Xeno DNA

growth_protocol: Xenograft subcutaneous in Nu/Nu mouse

value: Mouse xenograft


title: Post-xeno DNA


title: t1_inf_rep1


title: Xeno RNA

extract_protocol:
TRIzol RNA purrification
Helicos single molecule sequencing DGE protocol: Pubmed ID 18388294, 20133332


title: t24_NHBE_rep1


title: t1_Hi726ctr_rep3

organism: Haemophilus influenzae

source_name: Gram-negative bacteria

value: bacterial control


title: t1_inf_rep3


title: Post-xeno RNA


title: Pre-xeno RNA


title: t72_NHBE_rep2


title: t1_NHBEctr_rep3


title: t1_Hi726ctr_rep1


title: t1_Hi726ctr_rep2


title: NextSeq_H3_lo_BM_DMSO1

description: ChIP-seq

value: Bone marrow


title: NextSeq_H3_lo_BM_UNC2

description: ChIP-seq

value: Total H3


title: NextSeq_H3_lo_BM_DMSO3

description: ChIP-seq


title: NextSeq_H3_lo_CB_DMSO1

description: ChIP-seq


title: NextSeq_H3_lo_CB_DMSO3

description: ChIP-seq


title: NextSeq_H3_lo_BM_UNC1

description: ChIP-seq


title: NextSeq_H3_lo_BM_UNC3

description: ChIP-seq


title: NextSeq_H3_hi_CB_DMSO3

description: ChIP-seq

value: High


title: NextSeq_H3_lo_CB_DMSO2

description: ChIP-seq

value: DMSO


title: Drosophila_larvae_WT_CDK12_input_DNA_rep2

city: Beijing

first: Li

middle: xia

last: Pan

state: Beijing

address: North Zhongguancun Street

department: School of medicine

country: China

institute: Tsinghua university

data_processing:
The ChIP-seq reads were mapped to Drosophila melanogaster genome (dm3) using Bowtie2 with parameters -t -q -N 1 -L 25.
All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed.
The occupancy profile of CDK12 was recorded into files in wiggle track format (WIG) for analyzing the data in UCSC Genome Browser
Genome_build: dm3
Supplementary_files_format_and_content: wig files for input in replicate 2.

organism: Drosophila melanogaster

source_name: third instar larvae

growth_protocol: Larvae were cultured on standard medium (cornmeal/agar/sugar) in 18 degrees.

extract_protocol:
Using a ceramic mortar and pestle chilled with liquid N2, frozen larvae were ground to a powder and transferred to a homogenizer in ice-cold PBS. At room temperature, the homogenized cell suspensions were cross-linked with 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min and filtered through Miracloth. Chromatin pellets were collected and resuspended in ice-cold RIPA buffer, followed by sonicating in a Branson Digital Sonifer with 25% output for 10 min (2s on, 4 s off). For immunoprecipitation, Protein A Sepharose™ Fast Flow (GE Healthcare 17-5280-01) was pre-blocked, 4μl CDK12 polyclonal antibody were used for each immunoprecipitation. The input DNA and the IP DNA were purified with a PCR purification Kit (Qiagen28104) and eluted in TE buffer.
DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads according to the DNA amount after each step. Library DNA was amplified by Phusion HF (NEB, Cat. M0530L). 2% agarose gel was used to select 200-500bp DNA fragments after PCR amplification.

treatment_protocol: The w1118 strain was crossed with the actin-Gal4 strain as a wild type sample. For total larval chromatin preparation, approximately 3500 third instar larvae were collected, frozen in liquid nitrogen and stored at -80 °C.

tag: developmental stage

value: third instar

value: whole larvae

tag: genotype

value: wild type

tag: chip antibody


title: Drosophila_larvae_WT_CDK12_ChIP-Seq_rep2

description: CDK12 polyclonal antibodies are kindly provided by Dr. Arno L. Greenleaf

data_processing:
The ChIP-seq reads were mapped to Drosophila melanogaster genome (dm3) using Bowtie2 with parameters -t -q -N 1 -L 25.
All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed.
The occupancy profile of CDK12 was recorded into files in wiggle track format (WIG) for analyzing the data in UCSC Genome Browser
Genome_build: dm3
Supplementary_files_format_and_content: wig files, binding profile of CDK12 in replicate 2.

value: CDK12 polyclonal (rabbit)


title: NextSeq_H3_hi_CB_DMSO2

description: ChIP-seq

value: Cord blood


title: NextSeq_H3_hi_BM_UNC2

description: ChIP-seq


title: NextSeq_H3_hi_BM_UNC3

description: ChIP-seq


title: t1_NHBEctr_rep1


title: NextSeq_H3_hi_BM_UNC1

description: ChIP-seq


title: Drosophila_larvae_WT_CDK12_input_DNA_rep1

data_processing:
The ChIP-seq reads were mapped to Drosophila melanogaster genome (dm3) using Bowtie2 with parameters -t -q -N 1 -L 25.
All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed.
The occupancy profile of CDK12 was recorded into files in wiggle track format (WIG) for analyzing the data in UCSC Genome Browser
Genome_build: dm3
Supplementary_files_format_and_content: wig files for input in replicate 1.

value: whole tissue


title: Drosophila_larvae_WT_CDK12_ChIP-Seq_rep1

data_processing:
The ChIP-seq reads were mapped to Drosophila melanogaster genome (dm3) using Bowtie2 with parameters -t -q -N 1 -L 25.
All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed.
The occupancy profile of CDK12 was recorded into files in wiggle track format (WIG) for analyzing the data in UCSC Genome Browser
Genome_build: dm3
Supplementary_files_format_and_content: wig files, binding profile of CDK12 in replicate 1.


title: NextSeq_H3_hi_BM_DMSO2

description: ChIP-seq


title: NextSeq_H3K9me2_lo_CB_DMSO2

description:
ChIP-seq
processed data file: H3K9me2_CB_DMSO.tdf

value: Low


title: NextSeq_H3_hi_BM_DMSO3

description: ChIP-seq


title: NextSeq_H3_hi_BM_DMSO1

description: ChIP-seq


title: NextSeq_H3K9me2_lo_CB_DMSO1


title: NextSeq_H3K9me2_lo_CB_DMSO3


title: NextSeq_H3_lo_BM_DMSO2

description: ChIP-seq


title: NextSeq_H3_hi_CB_DMSO1

description: ChIP-seq


title: NextSeq_H3K9me2_hi_CB_DMSO2


title: NextSeq_H3K9me2_lo_BM_UNC1

description:
ChIP-seq
processed data file: H3K9me2_BM_UNC.tdf


title: NextSeq_H3K9me2_lo_BM_DMSO1

description:
ChIP-seq
processed data file: H3K9me2_BM_DMSO.tdf


title: NextSeq_H3K9me2_hi_BM_UNC3


title: NextSeq_H3K9me2_hi_BM_UNC1


title: NextSeq_H3K9me2_lo_BM_DMSO3


title: NextSeq_H3K9me2_hi_CB_DMSO3


title: NextSeq_H3K9me2_lo_BM_DMSO2


title: NextSeq_H3K9me2_lo_BM_UNC3


title: NextSeq_H3K9me2_hi_BM_UNC2


title: NextSeq_H3K9me2_lo_BM_UNC2


title: NextSeq_H3K9me2_hi_BM_DMSO3


title: NextSeq_H3K9me2_hi_CB_DMSO1


title: heterotrophy 72h sample2

city: Shanghai

first: Jianhua

last: Fan

address: 130 Meilong Road

institute: East China University of Science & Technology

data_processing:
Default parameters were used to pass reads using Illumina quality-control pipeline. All the filtered reads were trimmed to 50 bp. The processed sequence files (total of 187, 503, 403 reads) were then mapped to the assembled genome by TopHat 1.3.3 with a tolerance of up to 2 mismatches and 3 indels.
The Cufflinks was used to assemble the read into transcripts and a set of transcripts was generated for each condition.
Genome_build: de novo assembly
Supplementary_files_format_and_content: FASTA
Supplementary_files_format_and_content: gff3

organism: Auxenochlorella pyrenoidosa

growth_protocol: Chlorella cells were cultivated heterotrophically to achieve high cell density, heterotrophic growth with glucose and urea as organic carbon source and nitrogen source.

extract_protocol: the total RNA was isolated using TRIzol Reagent (Invitrogen) according to manufacturer’s instructions. The RNA samples were cleaned up using RNeasy columns (Qiagen, http://www.qiagen.com) following the manufacturer’s instruction.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: After glucose consumption was complete, the broth was then diluted to ~2 g/L dry biomass and transferred to light environment for photoautotrophy.

tag: strain

value: whole cells


title: heterotrophy 72h sample3


title: phototrophy 2h sample1


title: phototrophy 2h sample2


title: NextSeq_H3K9me2_hi_BM_DMSO1


title: heterotrophy 24h sample3


title: phototrophy 2h sample3


title: heterotrophy 72h sample1


title: heterotrophy 0h sample3


title: heterotrophy 24h sample1


title: NextSeq_H3K9me2_hi_BM_DMSO2


title: heterotrophy 0h sample2


title: At_JKD_YFP_2

city: Pozuelo de Alarcon

first: Miguel

middle: Angel

last: Moreno-Risueno

state: Madrid

department: Biotechnology

country: Spain

institute: Center for Plant Biotechnology and Genomics

data_processing:
Illumina Casava software used for basecalling
ChIP sequencing tags were aligned against the TAIR9 assembly using Bowtie
Tag counts at each position across the genome were processed using F-seq. We refer to this transformed data as the density signal for IP samples and control. We normalized the signal for each chromosome by the total number of ChIP-seq tags to counter the effects of differing library depths for each experiment. Control density signal was subtracted from IP density signal to factor out sequencing biases and other chromatin effects. We used this differential density signal to look for regions where there was high enrichment of IP signal across the genome, termed ChIP-seq peaks. Each peak was assigned a fold enrichment score, which was the ratio of aggregate density signal between IP and control.
After peak discovery, we performed IDR analysis for ChIP-seq experiments with two biological replicates. IDR analysis measures reproducibility between two experiments and peak pairs from two replicates are assigned an IDR value, measuring reproducibility of peaks in multiple experiments. We ranked our peaks using fold enrichment scores, as suggested by ENCODE IDR pipeline. Following IDR analysis, each peak pair was assigned an IDR value, which can be used as threshold to filter out peak pairs that are not reproducible.
Genome_build: TAIR9
Supplementary_files_format_and_content: Tab-delimited bed files which include chromosome information, peak start and end coordinates, peak length, peak summit, densisty signal for IP replicates and IDR value

organism: Arabidopsis thaliana

source_name: Roots

growth_protocol: Arabidopsis plants were vertically grown on plates containing MS, pH:5.7, 1% sucrose medium at 22 °C under 16 hours daily illumination.

extract_protocol:
Roots were collected on nylon mesh and fixed for 15 min with 1.6% formaldehyde in PBS-EDTA. Roots were rinsed, dried, ground with mortar and pestle in liquid N, and dissolved in same volume of 50 mM Tris-Cl pH 7.5, 150 mM NaCl, 2.5 mM EDTA, 2mM PMSF, 2x Complete Protease Inhibitors, 0.5% Sarkosyl. This mixture was processed in Bioruptor for 15 min at 4 °C. Supernatant was diluted 6 times with 50 mM Tris-Cl pH 7.5, 150 mM NaCl, 2.5 mM EDTA, 2mM PMSF, 2x Complete Protease Inhibitors and immunoprecipitated with a-GFP AbCam290 at 4 °C o/n, Pierce Protein G beads and Pierce Spin Cups. DNA purification was performed by standard RNAse-A and proteinase K treatments followed by Qiagen MinElute kit
Immunoprecipitated purified DNA was linearly amplified and processed with Nextera DNA Sample Prep kit.  Briefly, genomic regions were fragmented and adaptors ligated using Nextera transposon insertion system. These fragments were make into libraries of ~100 bp insert size. Adaptors cointain barcodes and thus samples weredistincly barcoded. Libraries were mixed and sequenced in one lane.  50 bp of single ends were sequenced through Illumina High Sequencing.

treatment_protocol: Plants were grown on standard medium with any supplementation

tag: ecotype

value: Columbia

tag: cell types expressing ip proteins

value: Ground tissue and stem cell organizer (QC)

tag: antibody


title: At_BLJ_YFP_2

value: Ground tissue


title: heterotrophy 0h sample1


title: At_Control


title: Drosophila_larvae_WT_input_DNA_rep2

data_processing:
The ChIP-seq reads were mapped to Drosophila melanogaster genome (dm3) using the software BWA with default parameters.
 After reads alignment, peak calling was performed by software MACS (version 1.4.2).
 In addition to the default parameters, some advanced parameters of MACS were set considering that HP1a and H3K9me2 associated with repetitive elements, which are no model, shift size=73 and maximum duplicate tags at the same position=5.
 Enrichments of HP1a and H3K9me2 signal were calculated against input.
The occupancy profiles of HP1a and H3K9me2 were recorded into files in wiggle track format (WIG) for analyzing the data in UCSC Genome Browser
 Genome_build: dm3
Supplementary_files_format_and_content: wig files for input in replicate 2.

extract_protocol:
Using a ceramic mortar and pestle chilled with liquid N2, frozen larvae were ground to a powder and transferred to a homogenizer in ice-cold PBS. At room temperature, the homogenized cell suspensions were cross-linked with 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min and filtered through Miracloth. Chromatin pellets were collected and resuspended in ice-cold RIPA buffer, followed by sonicating in a Branson Digital Sonifer with 25% output for 10 min(2s on, 4 s off). For immunoprecipitation, Protein A Sepharose™ Fast Flow (GE Healthcare 17-5280-01) was pre-blocked, 4μl HP1a polyclonal antibody or 3μl H3K9me2 antibody (Ab1220) were used for each immunoprecipitation. The input DNA and the IP DNA were purified with a PCR purification Kit (Qiagen28104 ) and eluted in TE buffer.
Libraries were constructed according to Hiseq 2500 rapid SR50 one flowcell sequencing instructions

treatment_protocol: CDK12 RNAi virgin females were crossed with actin-Gal4 males to drive the ubiquitous knockdown, and the larvae were raised at 18°C. The w1118 strain was crossed with the same Gal4 strain as a wild type control. For total larval chromatin preparation, approximately 3500 third instar larvae were collected, frozen in liquid nitrogen and stored at −80 °C.


title: heterotrophy 24h sample2


title: Drosophila_larvae_CDK12-KD_input_DNA_rep2

value: CDK12 knockdown


title: Drosophila_larvae_WT_HP1a_ChIP-Seq_rep2

description: HP1a polyclonal antibodies are kindly provided by S.C.R. Elgin

data_processing:
The ChIP-seq reads were mapped to Drosophila melanogaster genome (dm3) using the software BWA with default parameters.
After reads alignment, peak calling was performed by software MACS (version 1.4.2).
In addition to the default parameters, some advanced parameters of MACS were set considering that HP1a and H3K9me2 associated with repetitive elements, which are no model, shift size=73 and maximum duplicate tags at the same position=5.
Enrichments of HP1a and H3K9me2 signal were calculated against input.
The occupancy profiles of HP1a and H3K9me2 were recorded into files in wiggle track format (WIG) for analyzing the data in UCSC Genome Browser
Genome_build: dm3
Supplementary_files_format_and_content: wig files, binding profile of HP1a in replicate 2.

value: HP1a polyclonal (rabbit)


title: At_JKD_YFP_1


title: Drosophila_larvae_CDK12-KD_HP1a_ChIP-Seq_rep2


title: SNL_rep1

city: Philadelphia

first: matteo

last: cesaroni

state: PA

address: 3307 N. Broad S, Rm 220, PAHB

institute: Temple University

description: Experiment, Spinal nerve Ligated, left side

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to the rn4 genome assembly using TopHat 2.0.9 with these parameters: -p 28 --b2-fast -G /UCSC/rn4/Annotation/Genes/genes.gtf --segment-length 20
Fragments Per Kilobase of exon per Megabase of library size (FPKM) and DE genes were calculated using cuffdiff v 2.1.1 with default parameters
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Rattus norvegicus

source_name: nervous system

extract_protocol:
DRGs were removed, flash frozen on dry ice, andtotal  RNA wasextracted  using either Trizol reagent(Life Technologies) or RNeasy (Qiagen). Illumina TruSeq Stranded Total RNA with Ribo-zero Gold kits  (RS-122-2301 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague-Dawley

value: Dorsal root ganglion (DRG)


title: Sham_rep2

description: Control, right side

value: Control, right side


title: SNL_rep2

value: Experiment, Spinal nerve Ligated, left side


title: SNL_rep4


title: Sham_rep1

description: Control, right side


title: Sham_rep3

description: Control, right side


title: Drosophila_larvae_CDK12-KD_H3K9me2_ChIP-Seq_rep2

data_processing:
The ChIP-seq reads were mapped to Drosophila melanogaster genome (dm3) using the software BWA with default parameters.
After reads alignment, peak calling was performed by software MACS (version 1.4.2).
In addition to the default parameters, some advanced parameters of MACS were set considering that HP1a and H3K9me2 associated with repetitive elements, which are no model, shift size=73 and maximum duplicate tags at the same position=5.
Enrichments of HP1a and H3K9me2 signal were calculated against input.
The occupancy profiles of HP1a and H3K9me2 were recorded into files in wiggle track format (WIG) for analyzing the data in UCSC Genome Browser
Genome_build: dm3
Supplementary_files_format_and_content: wig files, binding profile of H3K9me2 in replicate 2.

value: H3K9me2 monoclonal (Abcam ab1220)


title: Sham_rep4

description: Control, right side


title: UNC0638_rep1

description: UNC0638 tretaed after, Spinal nerve Ligated, left side


title: SNL_rep3


title: Drosophila_larvae_WT_H3K9me2_ChIP-Seq_rep2


title: Drosophila_larvae_WT_input_DNA_rep1

data_processing:
The ChIP-seq reads were mapped to Drosophila melanogaster genome (dm3) using the software BWA with default parameters.
After reads alignment, peak calling was performed by software MACS (version 1.4.2).
In addition to the default parameters, some advanced parameters of MACS were set considering that HP1a and H3K9me2 associated with repetitive elements, which are no model, shift size=73 and maximum duplicate tags at the same position=5.
Enrichments of HP1a and H3K9me2 signal were calculated against input.
The occupancy profiles of HP1a and H3K9me2 were recorded into files in wiggle track format (WIG) for analyzing the data in UCSC Genome Browser
Genome_build: dm3
Supplementary_files_format_and_content: wig files for input in replicate 1.

extract_protocol:
Using a ceramic mortar and pestle chilled with liquid N2, frozen larvae were ground to a powder and transferred to a homogenizer in ice-cold PBS. At room temperature, the homogenized cell suspensions were cross-linked with 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min and filtered through Miracloth. Chromatin pellets were collected and resuspended in ice-cold RIPA buffer, followed by sonicating in a Branson Digital Sonifer with 25% output for 10 min (2s on, 4 s off). For immunoprecipitation, Protein A Sepharose™ Fast Flow (GE Healthcare 17-5280-01) was pre-blocked, 4μl HP1a polyclonal antibody or 3μl H3K9me2 antibody (Ab1220) were used for each immunoprecipitation. The input DNA and the IP DNA were purified with a PCR purification Kit (Qiagen28104) and eluted in TE buffer.
Libraries were constructed according to Hiseq 2500 rapid SR50 one flowcell sequencing instructions


title: Drosophila_larvae_WT_HP1a_ChIP-Seq_rep1

data_processing:
The ChIP-seq reads were mapped to Drosophila melanogaster genome (dm3) using the software BWA with default parameters.
After reads alignment, peak calling was performed by software MACS (version 1.4.2).
In addition to the default parameters, some advanced parameters of MACS were set considering that HP1a and H3K9me2 associated with repetitive elements, which are no model, shift size=73 and maximum duplicate tags at the same position=5.
Enrichments of HP1a and H3K9me2 signal were calculated against input.
The occupancy profiles of HP1a and H3K9me2 were recorded into files in wiggle track format (WIG) for analyzing the data in UCSC Genome Browser
Genome_build: dm3
Supplementary_files_format_and_content: wig files,  binding profile of HP1a in replicate 1.


title: Drosophila_larvae_CDK12-KD_HP1a_ChIP-Seq_rep1


title: At_BLJ_YFP_1


title: Drosophila_larvae_CDK12-KD_H3K9me2_ChIP-Seq_rep1

data_processing:
The ChIP-seq reads were mapped to Drosophila melanogaster genome (dm3) using the software BWA with default parameters.
After reads alignment, peak calling was performed by software MACS (version 1.4.2).
In addition to the default parameters, some advanced parameters of MACS were set considering that HP1a and H3K9me2 associated with repetitive elements, which are no model, shift size=73 and maximum duplicate tags at the same position=5.
Enrichments of HP1a and H3K9me2 signal were calculated against input.
The occupancy profiles of HP1a and H3K9me2 were recorded into files in wiggle track format (WIG) for analyzing the data in UCSC Genome Browser
Genome_build: dm3
Supplementary_files_format_and_content: wig files,  binding profile of H3K9me2 in replicate 1.

value: H3K9me2 monoclonal (ab1220)


title: Drosophila_larvae_WT_H3K9me2_ChIP-Seq_rep1

value: wild type


title: UNC0638_rep2

value: UNC0638 tretaed after, Spinal nerve Ligated, left side


title: UNC0638_rep3


title: Drosophila_larvae_CDK12-KD_input_DNA_rep1


title: Dere_FC_mRNA

status: Public on Nov 01 2015

city: BOSTON

first: NELSON

middle: C

last: LAU

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

institute: Boston University Chobanian & Avedisian School of Medicine

data_processing:
The adapter sequence based on the standard Illumina linkers were only removed on the small RNA reads.  The full sequence of this adapter linker is CGTCGTATGCCGTCTTCTGCTTGT.
The linker sequence was first removed by fastx_clipper program from FASTX Toolkit(0.0.13) with the parameters: "-a CGTCGTATGCCG -M 9 -n -l 20"
The shorter linkers on remaining reads were removed by searching for where the last 2 to 8 base pairs matches perfactly to the first 2 to 8 base pairs of the adapter sequence (CGTCGTATGCCG)
The final filtering step removed reads if its entire sequence contained more than 12 base pairs of poly(A/C/G/T).
No additional processing was performed on mRNA reads.
Supplementary_files_format_and_content: text files of sequences for each RNA read

organism: Drosophila erecta

extract_protocol:
Mouse, rat and rabbit testes were homogenized as described in Lau et al, Science. 2006 Jul 21;313(5785):363-7., and this extract was used only for the Mili (Piwil2) IP experiments.  For total RNA, testes were pulverized into powder while frozen and thawed into Tri-reagent solution to extract RNA according to the manufacterur (MRC) instructions
Small RNA libraries were constructed using the custom protocol described in Matts et al. Methods Mol Biol. 2014;1093:123-36.  Messenger RNA libraries were constructed with the Epicentre ScriptSeq v2 kits.

tag: genotype/variation

tag: age

value: adult

tag: Sex

value: female

value: ovary follicle cells

tag: molecule subtype

value: messenger RNA


title: Dere_FC_sRNA

tag: tissue

value: small RNA


title: nb004

city: Moscow

first: Alexander

last: Tanas

address: Moskvorechie St., 1

country: Russia

institute: Research Centre for Medical Genetics

data_processing:
Basecalls performed using Ion Torrent Suite 4.0
XmaI-RRBS reads were aligned to the hg19 genome assembly using Bismark v0.12.2 with bowtie2 v2.2.3 with settings --non_directional -L 24 --rdg 0,3 --rfg 0,3.
Data were filtered to remove artificial methylation using custom script
Methylation state called using bismark_methylation_extractor
Genome_build: hg19
Supplementary_files_format_and_content: .cov files were generated using bismark_methylation_extractor

source_name: Breast

extract_protocol:
DNA was purified using standard phenol-chloroform extraction method after treatment with PrK.
XmaI-RRBS

value: normal breast


title: nb001


title: Rabbit_Adult_testes_sRNA

organism: Oryctolagus cuniculus

value: male

value: testes


title: nb003


title: MCF-7


title: Rabbit_Adult_testes_Mili_IP_sRNA

tag: ip antibody

value: custom rabbit polyclonal anti-Mili antibody


title: nb005


title: nb006


title: DBbMBF1Ctrl

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

institute: Zhejiang University

data_processing:
Illumina HiSeq™ 2000 used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 49 bp tag fragments were mapped to the sequenced genome of Beauveria bassiana ARSEF2860 with the precision of no more than two nucleotide mismatch.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Screening of differentially expressed genes in WTCtrl/BbMBF1Ctrl set and WTTS9h/BbMBF1TS9h set. FDR (False Discovery Rate) is a method to determine the threshold of P-value in multiple tests (Benjamini, Y. and Yekutieli D. The Annals of Statistics. 2001, 29: 1165-1188).
Genome_build: Beauveria bassiana ARSEF 2860/GCA_000280675.1
Supplementary_files_format_and_content: Excel files, including Gene ID, gene length, RPKM values, log2(fold change) and false discovery rate (FDR)  for each paired sample.

organism: Beauveria bassiana ARSEF 2860

growth_protocol: Conidia suspension (100 μl,107 conidia ml-1) of WT and ΔBbMBF1 of Beauveria bassiana were smeared on the SDAY plate (4% glucose, 1% peptone, 1% yeast extract and 1.5% agar), and the plates were incubated at 25 °C for 3 day.

extract_protocol:
Resultant mycelia of each strain were harvested and ground into powder in liquid nitrogen. Total RNA was isolated from mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA).
The double-stranded cDNA were prepared with the Illumina gene expression sample prep kit for Illumina arrays.

treatment_protocol: For the thermal stress, the mycelia (on the plates) were put into the incubator at 40°C for 9 hours. The unstressed mycelia were used as control.

tag: culture time

value: 3 days

value: mycelia

tag: treatment

value: control


title: WTTS9h

source_name: BbWT

value: thermal stress


title: WTCtrl


title: B6WT-129KO PrP:IP pool1 (SNP)

city: Bonn

first: Clemens

last: Krost

address: Sigmund-Freud-Str. 25

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

description:
RNA co-purified with PrP
processed data file: B6WT-129KO_PrP-IP_pool1_variants.txt

data_processing:
mapping: CLC Genomics Workbench
Probabilistic Variant Detection
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-limited txt files contain information regarding "Mapping", "Reference Position", "Type", "Length", "Reference", "Allele", "Linkage", "Zygosity", "Count", "Coverage", "Frequency", "Forward/reverse balance", "Average quality", "Overlapping annotations", "Coding region change" and "Amino acid change" for all variants discovered

organism: Mus musculus

source_name: brain

extract_protocol:
After dissection brains were instantly weighed and homogenized in 10 volumes of Polysome Lysis Buffer (PLB) (Keene et al., 2006) containing 1 mM DTT, 400 µM vanadylribonucleoside complexes solution, 1x protease inhibitor cocktail (both Sigma) and 100 U/ml RNase inhibitor (Thermo Fisher Scientific) with 10 strokes of a dounce homogenizer at 800 rpm. Homogenates were subsequently centrifuged for 15 min at 16,000 g and 4°C. For each immunoprecipitation, 200 µl of the supernatant (input) was added to 760 µl of PLB and incubated with 1 µl DNase (New England Biolabs) on ice for 15 min. After the treatment, 40 µl 0.5 M EDTA, pH 8.0 (20 mM total) and 5 µl Triton-X-100 (0.5 % total) were added to each sample. Two preclearing steps of the lysate were performed by adding 0.9 mg of washed (PBST) and equilibrated (PLB) Dynabeads® Protein G (Life Technologies) and rotation for 30 min at 4°C. Double precleared lysates were incubated with 5 µg of a mouse isotype control antibody (Biolegend) for 45 min at 4°C before unspecific immunoprecipitates were removed by addition of 1.2 mg Dynabeads® Protein G (45 min, 4°C). PrP immunoprecipitation was done by incubation with 2 µg of SAF61 antibody (Cayman Chemical) for 1 h, 4°C and addition of 1.5 mg Dynabeads® Protein G (1 h, 4°C). The beads were then washed with 0.5 ml PLB without supplements for 5 times. For RNA cleanup, washed beads were resuspended in 200 µl PLB containing 0.1 % SDS and 0.4 µg/ml Proteinase K and incubated on a shaker at 700 rpm for 30 min and 50°C. RNA was extracted using phenol:chloroform:isoamylacohol (25:24:1), chloroform:isoamylacohol (24:1) and precipitated by adding 20 µl 3 M NaOAc pH 5.2, 1 µl glycogen (20 mg/ml) and 500 µl EtOH abs. Samples were incubated at -20°C over night and centrifuged in a precooled (4°C) tabletop centrifuge at maximum speed for 1 h. RNA pellet was washed with 500 µl 70 % EtOH, air-dried and resolved in 10 µl H20.
RNA libraries were prepared according to Illumina's instructions, barcoded (Sample 1 - ACAGTG; Sample 2 - GCCAAT; Sample 3 - GTGAAA; Sample 4 - GTGGCC; Sample 5 - ATCACG; Sample 6 - CGATGT; Sample 7 - TTAGGC; Sample 8 - TGACCA), multiplexed (Sample 1,2,5-8 and 3-4, respectively) and run on an Illumina HiSeq2000™ (50 bp single end sequencing)

value: brain

value: 4 months

tag: rip antibody

value: SAF61 antibody (Cayman Chemical, catalog# CM189755, lot# 0113)


title: DBbMBF1TS9h


title: 129WT-B6KO PrP:IP pool1 (SNP)

description:
RNA co-purified with PrP
processed data file: 129WT-B6KO_PrP-IP_pool1_variants.txt


title: 129WT-B6KO PrP:IP pool2 (SNP)

description:
RNA co-purified with PrP
processed data file: 129WT-B6KO_PrP-IP_pool2_variants.txt


title: Mouse_Adult_Kidney_Asb1_AO36(KO)_mRNA

tag: strain background

value: kidney


title: nb002


title: Mouse_Adult_Testes_Asb1_AO36(KO)_mRNA

value: adult


title: Mouse_Adult_Kidney_Asb1_AO34(Het)_mRNA


title: Mouse_Adult_Testes_Asb1_AO34(Het)_mRNA


title: Mouse_Adult_Testes_Asb1_AO33(KO)_mRNA


title: Rabbit_Testes_mRNA_Lau

value: wild type


title: Mouse_Adult_Testes_Asb1_AO31(Het)_mRNA


title: B6WT-129KO PrP:IP pool2 (SNP)

description:
RNA co-purified with PrP
processed data file: B6WT-129KO_PrP-IP_pool2_variants.txt


title: Mouse_Adult_testesAsb1_ao34(Het)_sRNA


title: Mouse_10dpp_testes_sRNA

value: 10dpp pups


title: Mouse_Adult_testes_Asb1_ao31(Het)_sRNA


title: Mouse_Adult_testes_Asb1_ao32(KO)_sRNA


title: Dyak_FC_sRNA

organism: Drosophila yakuba

value: female

value: ovary follicle cells


title: FFI control

description:
Sample 8
total RNA

data_processing:
mapping: STAR 2.3.0e (Dobin et al., 2013)
analysis: samtools-0.1.18 (Li et al., 2009)
analysis: FastQC V0.10.1
counting: HTSeq-count 0.5.4p5 (Anders et al., 2014)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-limited txt files contain Ensembl gene IDs and gene counts; Excel file contains DESeq2 analysis of mRNAs co-purified with PrP and enrichment analysis of WT, CJD and FFI

extract_protocol:
After dissection brains were instantly weighed and homogenized in 10 volumes of Polysome Lysis Buffer (PLB) (Keene et al., 2006) containing 1 mM DTT, 400 µM vanadylribonucleoside complexes solution, 1x protease inhibitor cocktail (both Sigma) and 100 U/ml RNase inhibitor (Thermo Fisher Scientific) with 10 strokes of a dounce homogenizer at 800 rpm. Homogenates were subsequently centrifuged for 15 min at 16,000 g and 4°C. For each immunoprecipitation, 200 µl of the supernatant (input) was added to 760 µl of PLB and incubated with 1 µl DNase (New England Biolabs) on ice for 15 min. After the treatment, 40 µl 0.5 M EDTA, pH 8.0 (20 mM total) and 5 µl Triton-X-100 (0.5 % total) were added to each sample. Two preclearing steps of the lysate were performed by adding 0.9 mg of washed (PBST) and equilibrated (PLB) Dynabeads® Protein G (Life Technologies) and rotation for 30 min at 4°C. Double precleared lysates were incubated with 5 µg of a mouse isotype control antibody (Biolegend) for 45 min at 4°C before unspecific immunoprecipitates were removed by addition of 1.2 mg Dynabeads® Protein G (45 min, 4°C). PrP immunoprecipitation was done by incubation with 2 µg of SAF61 antibody (Cayman Chemical) for 1 h, 4°C and addition of 1.5 mg Dynabeads® Protein G (1 h, 4°C). The beads were then washed with 0.5 ml PLB without supplements for 5 times. For RNA cleanup, washed beads were resuspended in 200 µl PLB containing 0.1 % SDS and 0.4 µg/ml Proteinase K and incubated on a shaker at 700 rpm for 30 min and 50°C. RNA was extracted using phenol:chloroform:isoamylacohol (25:24:1), chloroform:isoamylacohol (24:1) and precipitated by adding 20 µl 3 M NaOAc pH 5.2, 1 µl glycogen (20 mg/ml) and 500 µl EtOH abs. Samples were incubated at -20°C over night and centrifuged in a precooled (4°C) tabletop centrifuge at maximum speed for 1 h. RNA pellet was washed with 500 µl 70 % EtOH, air-dried and resolved in 10 µl H20.
RNA libraries were prepared according to Illumina's instructions, barcoded (Sample 1 - GAGTGG; Sample 2 - ACTGAT; Sample 3 - ATCACG; Sample 4 - ATTCCT; Sample 5 - ATGTCA; Sample 6 - AGTTCC; Sample 7 - CCGTCC; Sample 8 - AGTCAA), multiplexed (Sample 1-4 and 5-8, respectively) and run on an Illumina HiSeq2000™ (50 bp single end sequencing)

value: 12 months


title: CJD PrP:IP pool

description:
Sample 5
RNA co-purified with PrP


title: FFI PrP:IP pool

description:
Sample 7
RNA co-purified with PrP


title: CJD control

description:
Sample 6
total RNA


title: HMVEC_LY_3

city: Seattle

first: Terri

last: DiMaio

state: WA

address: 750 Republican St.

department: Microbiology

institute: University of Washington

data_processing:
perform image analysis and base calling with Illumina's RTA v1.17 Software
demultiplex and generate files in FASTQ format, using Illumina's CASAVA v1.8.2 Software
remove reads that didn't pass Illumina's base call quality threshold
align reads, using TopHat v2.08b ( http://tophat.cbcb.umd.edu/ ) along with Bowtie 1.0.0 ( http://bowtie-bio.sourceforge.net/index.shtml ), using Ensembl's GRCh37 release 70 as the reference genome.
generate counts for each gene using htseq-count v0.5.3p9 (using the intersection-strict overlapping mode)
Genome_build: Ensembl's GRCh37 release 70
Supplementary_files_format_and_content: tab-delimited text file includes CPM (counts per million reads) for each sample

source_name: neonatal dermal microvasculature

extract_protocol:
RNA was isolated using the RNA isolation kit by Macherey-Nagel. Samples were cleaned and concentrated, where necessary, using Zymogen kit
RNA-seq libraries were generated using Illumina TruSeq RNA Sample Prep Kit v2 following the manufactures protocol.

tag: cell type

value: Primary lymphatic-specific endothelial cells

tag: passage


title: Mouse_Adult_testes_Asb1_ao36(KO)_sRNA

value: male

value: testes

value: small RNA


title: zcf21 deletion mutant in YPD broth with 15 mM caffeine at 30C

city: Würzburg

first: Christian

last: Pérez

address: Joseph-Schneider-Straße 2

department: Institute for molecular Infection Biology

institute: Center for Infectious Biology

data_processing:
The base quality of each sequence read was inspected for low-quality calls (average quality below 15) and subsequently removed before proceeding with further processing.
High-quality reads were mapped to the whole reference genome using BWA version 0.5.9-r16 (Li and Durbin, 2009, Bioinformatics 25:1754-1760) with default parameters.
Bowtie was used to map reads to the reference transcriptome and Cufflinks was used to quantify transcripts from the RNA-Seq alignment-assembly.
Alignments generated from the mapping to the whole reference genome are provided as SAM (BAM) files.
BAM files were converted to WIG files which are visualized using MochiView (Homann and Johnson, 2010, BMC Biology 8:49).
Genome_build: Candida albicans SC5314 Assembly 21 (available at www.candidagenome.org)
Supplementary_files_format_and_content: wig files
Supplementary_files_format_and_content: C_albicans_SC5314_A21_current_chromosomes.fasta: Chromosomal annotations used for C. albicans.

organism: Candida albicans

source_name: yeast cells, zcf21 deletion mutant, YPD broth with 15 mM caffeine, 30C

growth_protocol: Wild-type reference strain and zcf21 deletion mutant were grown to late exponential phase in YPD broth at 30°C or on Todd-Hewitt agar at 37°C for 24 h.

extract_protocol:
About 1x10^8 cells were collected from the liquid cultures or from colonies scraped off the plates, and total RNA was extracted using RiboPure™ RNA purification kit for yeast (Ambion, Life Technologies) following the manufacturer's recommended protocol.
RNA sequencing, including library preparation, were carried out by GATC Biotech (Konstanz, Germany) following standard operating procedures. The protocol involved poly(A)+ RNA selection, mRNA fragmentation, random primer cDNA synthesis, adapter ligation and Illumina (HiSeq 2500) sequencing (single read mode, 1 x 50 base pair read length).

treatment_protocol: Cells were grown in the presence or absence of 15 mM or 5 mM caffeine.

tag: strain/background

value: zcf21 deletion

tag: culture medium

value: YPD broth

value: 15 mM caffeine

tag: culture temperature


title: zcf21 deletion mutant in TH agar without 5 mM caffeine at 37C

source_name: yeast cells, zcf21 deletion mutant, TH agar, 37C

value: TH agar


title: zcf21 deletion mutant in TH agar with 5 mM caffeine at 37C

source_name: yeast cells, zcf21 deletion mutant, TH agar with 5 mM caffeine, 37C

value: 5 mM caffeine


title: input-L1

city: La Jolla

first: Xiang-Dong

last: Fu

state: CA

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

data_processing:
Sequencing reads were trimmed by using cutadapt program (version 1.2.1). Trimmed reads smaller than 16 nt were discarded.
Reads were mapped to the C. elegans genome (UCSC version ce10) by using Bowtie (version 0.12.7), with parameters "--best --strata -l25 -n2'. Only uniquely mapped reads were kept.
Reads were extended downstream 100 bp to generate the genomic coverage signals. For each sample, the coverage singals were normalized to 1 million total count of reads.
Genome_build: ce10
Supplementary_files_format_and_content: The bigWig files are normalized genomic signals.

organism: Caenorhabditis elegans

source_name: wild type worms

growth_protocol: synchronized worms were maintained at room temperature

extract_protocol:
Larvae were cross-linked at RT for 30 min in 2% formaldehyde (Fisher). Crosslinking was quenched with 0.25 M glycine for another 30 min at RT. For each immunoprecipitation, 10 mg 4H8 antibody was coupled to 50 ml Dynabeads (Invitrogen) coated with protein A and G (25 ml protein A plus 25 ml protein G). After sonication and centrifugation, 1.5 ml supernatant (around 30 mg protein) was pre-cleared by rotating for 2 hrs with 30 ml empty Dynabeads (15 ml protein A plus 15 ml protein G) before incubating with 4H8-coupled Dynabeads at 4°C overnight.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: wild type and deletion mutant worms

tag: Stage

tag: strain

tag: chip antibody

value: supernatant lysates


title: HMVEC_LY_2


title: ssup-L2

source_name: ssup-72(0) worms


title: N2-L1


title: input-L2


title: ssup-sydn-L2

source_name: ssup-72(0); sydn-1(0) worms


title: ssup-sydn-L1


title: sydn-L2

source_name: sydn-1(0) worms


title: N2-L2


title: sydn-L1


title: HMVEC_LY_1


title: zcf21 deletion mutant in YPD broth without 15 mM caffeine at 30C

source_name: yeast cells, zcf21 deletion mutant, YPD broth, 30C

tag: genotype/variation


title: HMVEC_BL_2

value: Primary blood-specific endothelial cells


title: Reference strain in TH agar without 5 mM caffeine at 37C

source_name: yeast cells, reference, TH agar, 37C

value: wild-type


title: WT PrP:IP pool 2

description:
Sample 3
RNA co-purified with PrP

value: mixed C57BL/6,129S4

value: brain

tag: age

value: 10 months

value: SAF61 antibody (Cayman Chemical, catalog# CM189755, lot# 0113)


title: WT PrP:IP pool 1

description:
Sample 1
RNA co-purified with PrP
linearly amplified

value: 2 months


title: WT control 1

description:
Sample 2
total RNA


title: HMVEC_BL_3


title: WT control 2

description:
Sample 4
total RNA


title: Reference strain in YPD broth without 15 mM caffeine at 30C

source_name: yeast cells, reference, YPD broth, 30C


title: Reference strain in YPD broth with 15 mM caffeine at 30C

source_name: yeast cells, reference, YPD broth with 15 mM caffeine, 30C


title: HMVEC_BL_1


title: Reference strain in TH agar with 5 mM caffeine at 37C

source_name: yeast cells, reference, TH agar with 5 mM caffeine, 37C


title: T21_Obese

city: Tempe

first: Samantha

middle: Elaine

last: Day

state: AZ

address: University Dr. and Mill Ave.

institute: Arizona State University

data_processing:
Data was collected using HiSeq data collection version 1.5.15.1 software, and the bases were called using Illumina’s RTA version 1.13.48.
Briefly, FASTQ were trimmed to remove adaptor sequences, and any reads with less than 15bp were discarded. Trimmed Fastqs were then aligned against the reference genome Hg19 using BSMAP
Samtools was used to get mpileup and custom PERL scripts were used to determine CpG methylation and bisulfite conversion ratios
To determine differences in methylation between groups, the aligned data was imported into the free open source R package, methylSig.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig data files were generated using custom scripts and score represent the methylation level at that loci.

source_name: Vastus lateralis muscle

extract_protocol:
Homogenization of the muscle biopsy was performed in 1X PBS with the Bullet Blender (Integrated Scientific Solutions). DNA was isolated using QIAamp DNA mini kit (Qiagen).
Briefly, DNA was digested with Msp1 (New England Biolabs) and purified using QIAquick Nucleotide Removal Kit (Qiagen).  End-repair A tailing was performed (New England Biolabs) and TruSeq methylated indexed adaptors (Illumina) were ligated with T4 DNA ligase (New England Biolabs). Size selection was performed with Agencourt AMPure XP beads (Beckman Coulter). Bisulfite conversion was performed using EZ-DNA Methylation Kit (Zymo Research) as recommended by the manufacturer with the exception that incubation was performed using 55 cycles of 95 ̊C for 30 seconds and 50°C for 15 minutes.  Following bisulfite treatment, the DNA was purified as directed and amplified using Pfu Turbo C Hotstart DNA Polymerase (Agilent Technologies). The final libraries from RRBS were prepared for sequencing as per the manufacturer’s instructions in the Illumina cBot and HiSeq Paired end cluster kit version 3. The flow cell was then loaded into the Illumina cBot for generation of cluster densities. After cluster generation, the flow cells were sequenced as 51 x 2 paired end reads using Illumina HiSeq 2000 with TruSeq SBS sequencing kit version 3.

treatment_protocol: Participants underwent euglycemic hyperinsulinemic clamps with muscle biopsies. The biopsies were immediately frozen in liquid nitrogen.

tag: Sex

value: Male

tag: obese status

value: Obese


title: B6WT-129KO control2 (SNP)

description:
total RNA
processed data file: B6WT-129KO_control2_variants.txt

tag: tissue

value: 4 months

tag: genotype


title: B-ALL

city: columbia

first: Jianlin

middle: Jack

last: Cheng

state: MO

address: Engineering Building West 109

department: Computer Science Department

institute: University of Missouri,columbia

data_processing:
Library strategy: Hi-C seq
These libraries were sequenced using an Illumina HiSeq 2000
Software Maq was used to map each read-pair to the reference human genomes (NCBI build 36.3), where parameter “sum of mismatching base qualities (-e)” controlling the tolerance of mismatches was set to 150 in most experiments.
Data were filtered using the following specifications…
Maq outputs the base pair positions in the reference genomes where each DNA read is mapped to. The mapped positions were analyzed by our method to generate chromosomal contacts
An in-house bioinformatics software pipeline was developed and applied to map sequence reads to the human reference genome, producing a large data set of high-quality and high-resolution chromosome contacts
Genome_build: NCBI build 36.3
Supplementary_files_format_and_content: The processed data file is tab delimited with five columns. The column headers are; Mapping ID, chromosome number 1, chromosome location 1, chromosome number 2, chromosome location 2. The Mapping ID is the key assigned during Mapping for each sequence. The chromosome number and location respectively correspond to the id and location of the chromosome being mapped.

source_name: Primary TumorB-cell acute lymphocytic leukemia

extract_protocol:
Hundreds of millions of Hi-C paired-end sequence reads for three different human cells (RL follicular lymphoma cell line, primary tumor B-cells from an acute lymphoblastic leukemia patient, and MHH-CALL-4 B-cell acute lymphoblastic leukemia cell line) using the Hi-C technique.
Hi-C libraries were created  for a case of primary human B-acute lymphoblastic leukemia (B-ALL), the MHH-CALL-4 B-ALL cell line (CALL4), and the follicular lymphoma cell-line (RL). These libraries were sequenced using an Illumina HiSeq 2000. High-quality paired-end reads of 39M, 79M, and 33M were obtained for these cells, respectively.

tag: cell line

value: B-ALL

tag: cell line source

value: B cells


title: 129WT-B6KO control1 (SNP)

description:
total RNA
processed data file: 129WT-B6KO_control1_variants.txt


title: B6WT-129KO control1 (SNP)

description:
total RNA
processed data file: B6WT-129KO_control1_variants.txt


title: T19_Obese


title: RL

source_name: B-cell Follicular  Lymphoma

value: RL

value: B-cell Follicular  Lymphoma


title: CALL4

source_name: MHH-CALL- 4 B-cell acute lymphocytic leukemia


title: T22_Obese

value: Female


title: T17_Obese


title: T10_Obese


title: T13_Obese


title: T11_Obese


title: T15_Obese


title: T24_Lean

value: Lean


title: T20_Lean


title: T27_Lean


title: T08_Lean


title: T06_Lean


title: T18_Lean


title: T16S_Lean


title: T09_Lean


title: T05_Lean


title: T04_Lean


title: T14_Obese


title: T03_Lean


title: MB-157

city: Foster City

first: Daniel

last: Hogan

state: California

address: private address

description: rRNA depleted total RNA

data_processing:
Raw sequencing results in the form of FASTQ files were used as input for alignment of the sequencing data to the human ENSEMBL reference RNA database GRCh37 using Tophat2 --no-coverage-search.
Tophat2 generated BAM files were converted to CXB files with Cufflinks and used as input into Cuffdiff2 to generate normalized FPKM values and for differential expression analyses.
HTSeq was used to calculate the number of reads that mapped to each transcript.
Genome_build: hg19
Supplementary_files_format_and_content: Htseq output and Cuffnorm ouput

source_name: breast medullary carcinoma

growth_protocol: Cells were grown in indicated media plus 10% FBS (Hyclone Lab Inc, Omaha, NE), 1 mM Sodium Pyruvate (Hyclone Lab Inc, Omaha, NE), and 2 mM Glutamax (Life Technologies, Grand Island, NY). All cells were cultured at 37°C in a humidified 5% CO₂ incubator, except MB-157 which was cultured at 37°C in a humidified atmospheric (no supplemental CO2) incubator

extract_protocol:
Media was removed and cells were lysed on the plate by addition of 1 mL of Trizol. The Trizol solution was transferred to 1.5 mL microfuge tubes and RNA was extracted by addition of chloroform to 30% final concentration. Tubes were centrifuged at 12,000 x g for 15 minutes. The aqueous phase was removed and RNA was further purified using Maxwell® 16 Total RNA Purification Kit (Promega, Madison, WI, Cat.# AS1050)
Ovation Human FFPE RNA-Seq kit (Nugen, San Carlos, CA, Cat.# 0340 and 0341)

tag: growth media

value: L-15 Leibovitz

value: breast medullary carcinoma


title: COLO 205

description: rRNA depleted total RNA

source_name: human colorectal metastatic adenocarcinoma

value: COLO 205

tag: cell type


title: NCI-H508

description: rRNA depleted total RNA

source_name: colorectal metastatic adenocarcinoma

value: colorectal metastatic adenocarcinoma


title: AU565

description: rRNA depleted total RNA

source_name: breast adenocarcinoma

value: breast adenocarcinoma


title: 42-MG

description: rRNA depleted total RNA

source_name: glioblastoma

value: DMEM

value: glioblastoma


title: HTB-38

description: rRNA depleted total RNA

source_name: colorectal primary adenocarcinoma

value: McCoy’s 5A

value: colorectal primary adenocarcinoma


title: 8-MG

description: rRNA depleted total RNA


title: T98G

description: rRNA depleted total RNA


title: U-87

description: rRNA depleted total RNA


title: dilated cardiomyopathy 4

city: Naples

first: Valerio

last: Costa

state: Italy

address: Via P. Castellino, 111

department: Institute of Genetics and Biophysics

institute: National Research Council

data_processing:
Sequenced reads were trimmed for adaptor sequence, and for low-quality sequence, then mapped to hg19 whole genome using TopHat2 v2.0.10 with parameters: -p 8 -N 2 -g 10 -r 200 -a 15 -m 1 -i 100 --library-type fr-unstranded --segment-mismatches 3 --read-edit-dist 2 -G
Gene expression was performed by using SummarizeOverlap function implemented in RNASeqGUI
Differential expression analysis was performed by using NOISeqBIO method
Genome_build: hg19
Supplementary_files_format_and_content: text file with normalized counts

source_name: Heart

extract_protocol:
Tissue samples were homogenized in TRIzol reagent by TissueLaser Disruption system (Qiagen), flash frozen on dry ice, and total RNA was isolated according to manufacturer's protocol of TRIzol Reagent. RNA quality assessment was performed by Experion System (Bio-Rad) and 4 ug of total RNA was used for the construction of sequencing libraries by Illumina TruSeq RNA Sample Preparation Kit.
cDNA libraries were prepared for sequencing according to TruSeq RNA Sample Preparation Guide. The quantity and quality of libraries were checked by Qubit (Life Technologies) and Experion Sistems (Bio-Rad).

value: Heart

tag: diagnosis

value: dilated cardiomyopathy


title: restrictive cardiomyopathy 5

value: restrictive cardiomyopathy


title: restrictive cardiomyopathy 3


title: Control 4

value: healthy


title: Control 5


title: dilated cardiomyopathy 6


title: Control 6


title: Control 3


title: 129WT-B6KO control2 (SNP)

description:
total RNA
processed data file: 129WT-B6KO_control2_variants.txt

source_name: brain

value: brain

value: 4 months


title: Overexpression of U2AF1_v1_wildtype after U2AF1 knockdown, replicate 2

city: Goyaongsi

first: Charny

last: Park

state: Gyeonggi-do

address: 323 Ilsan-ro,

country: South Korea

institute: National Cancer Center

description: 4. 1W Rep2

data_processing:
Quality trimming using Trimmomatic-v0.30
Alignment using Tophat v2.0.12 to GRCh37
Alternative splicing analysis using MATS 3.0.8
Genome_build: GRCh37
Supplementary_files_format_and_content: Text file of MATS output format

source_name: lung carcicoma cell line

growth_protocol: Growth condition; adherent; This cell line was grown in RPMI-1640 Medium with 10% fetal bovine serum.

extract_protocol:
By using Qiagen RNeasy kit
The 1ug of total RNA was started for library construction.

treatment_protocol: Overexpression of U2AF1 was performed by infecting U2AF1 wildtype or mutant virus

value: lung carcinoma cell line


title: Overexpression of U2AF1_v3_wildtype after U2AF1 knockdown, replicate 1

description: 6. 3W Rep1


title: A549, untreated cells, replicate 2

description: 1. Normal control Rep2


title: Overexpression of U2AF1_v1_S34F after U2AF1 knockdown, replicate 2

description: 5. 1M Rep2


title: Negative control (empty vector, control siRNA), replicate 2

description: 2. EV_siC Rep2


title: Overexpression of U2AF1_v1_S34F after U2AF1 knockdown, replicate 1

description: 5. 1M Rep1


title: Overexpression of U2AF1_v3_S34F after U2AF1 knockdown, replicate 1

description: 7. 3M Rep1


title: Overexpression of U2AF1_v1_wildtype after U2AF1 knockdown, replicate 1

description: 4. 1W Rep1


title: U2AF1 knockdown (Overexpression of empty vector after U2AF1 knockdown), replicate 1

description: 3. EV_siU Rep1


title: U2AF1 knockdown (Overexpression of empty vector after U2AF1 knockdown), replicate 2

description: 3. EV_siU Rep2


title: Overexpression of U2AF1_v3_S34F after U2AF1 knockdown, replicate 2

description: 7. 3M Rep2


title: A549, untreated cells, replicate 1

description: 1. Normal control Rep1


title: Negative control (empty vector, control siRNA), replicate 1

description: 2. EV_siC Rep1


title: HE4

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing: Supplementary_files_format_and_content: A text file has been provided that contains normalized read counts within the non-overlapping 50bp windows genome wide. Windows with all zero values or all values below a noise cutoff have been removed, so only windows considered to have signal remain. Each row represents one 50bp window. The genomic coordinates (hg19) are provided in the first three columns. The remaining columns contain the read counts for each sample, and are labeled the same as the "title" labels provided in this GEO submission.

source_name: prostate adenocarcinoma

extract_protocol:
DNA was extracted from formalin-fixed paraffin embedded samples. First, paraffin was removed by treatments with xylene and ethanol. Second, protein was digested using Proteinase K treatment, RNA was removed by RNase A treatment, and protein was removed by 6M NaCl precipitation. DNA was then precipitated by ethanol and re-suspended in water.
The library was constructed by enriching for methylated DNA fragments using MiGS (MBD-isolated Genome Sequencing, Serre 2010). After enrichment, library was prepared using the Illumina ChIP-seq preparation protocol (2007).

tag: histology

value: high grade

tag: ancestry

value: european american


title: HE6


title: Overexpression of U2AF1_v3_wildtype after U2AF1 knockdown, replicate 2

description: 6. 3W Rep2


title: BA2

source_name: prostate

value: benign

value: african american


title: HA3


title: HA2


title: BA1


title: HN

city: shanghai

first: Pei

middle: Hai

last: yan

address: No. 130, meilong road, Shanghai

institute: East China University of Science and Technology

description: Serratia sp. ZM

data_processing:
Primary sequencing data was produced by Illumina HiSeqTM 2000.
Sequenced reads were subjected to quality control, then mapped to Serratia sp. SCBI whole genome with SOAPaligner/SOAP2.
The gene expression level is calculated by using RPKM method (Reads per kilobase transcriptome per million) mapped reads.
Genome_build: Serratia sp. SCBI (CP003424.1)
Supplementary_files_format_and_content: Files include RPKM values for each Sample.

organism: Serratia sp. ZM

source_name: Serratia, low nitrogen

growth_protocol: Growth in low nitrogen (2mM (NH4)2SO4) or high nitrogen (10mM (NH4)2SO4) conditions.

extract_protocol:
After 10 hours, cells were processed for total RNA extraction using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: ZM

value: wild type

tag: growth condition

value: high nitrogen

tag: growth time

value: 10 hours


title: WT_lung_2

city: Boston

first: James

last: Bradner

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: WT normal lung replicate 2

data_processing:
alignment: TopHat2 using default settings
expression levels: Gene-level expression measurements for 23,021 Ensembl mouse genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples.  Cufflinks command line-cufflinks --GTF <gtf_file> -q -p 3 -u -b <genome.fa> -o <output directory> <bam_file_from_tophat>
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM files for each sample

source_name: Lung tissue

growth_protocol: Fresh murine lung tumor nodules were minced and cultured in 100-mm dishes with RPMI-1640/10% FBS/1% penicillin–streptomycin. H661 and H292 cells (obtained from American Type Culture Collection) were cultured in RPMI-1640/10% FBS/1% penicillin–streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent followed by RNA cleanup (Qiagen, #74204).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: normal Lung


title: LN

description: Serratia sp. ZM

source_name: Serratia, high nitrogen

value: low nitrogen


title: WT_lung_1

description: WT normal lung replicate 1


title: EZH2OE_lung_tumor_1

description: EZH2 overexpressing lung tumor replicate 1

value: Lung tumor

value: EZH2 overexpression


title: HA1


title: Lung_HZ54_input

description: WCE control for HZ54 EZH2 overexpressing lung tumor

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences processed through MACS 1.4.2 and fragment pileup was outputted in .wig format

source_name: Lung

extract_protocol:
Mouse lung tissue was pulverized using Covaris Tissue Smasher model CP02 by following the CryoPrep Dry Pulverization Manuel. Lung tissue was smashed 1-2 times on setting 4 in the tissueTUBE (Covaris #520071). Approximately 50mg of pulverized lung tissue was cross-linked with prewarmed 1% formaldehyde (ThermoScientific  #28906 diluted in PBS) for 20 minutes at 37°C.  The tissue was spun down at 1,000rpm for 2 minutes and quenched with 0.125M glycine in PBS + 0.5% BSA for 20 minutes at room temperature, spun down at 1,000rpm for 2 minutes and washed with PBS + 2x Protease Inhibitor Cocktail (PIC) (Roche #11873580001) + 5mM Sodium Butyrate (Millipore #19-137) then spun down at 1,000rpm for 2 minutes. The cross-linked tissue was then lysed with 390uL ChIP Lysis Buffer (1% SDS, 10nM EDTA pH8.0, 50mM Tris-HCl pH 8.0, 2x PIC and 5mM Sodium Butyrate) on ice for one hour. The lysate was split into 3 microTUBEs (Covaris #520045) and sheared on the Covaris E210 Series with 5% Duty Cycle, 5 Intensity, 200 Cycles per Burst for a total of 27 minutes. The sheared chromatin was spun down at 14,000rpm for 15 minutes at 4°C. An aliquot of input was saved while the remaining chromatin was snap frozen and stored at -80°C. Input was brought up to 100ul with TE, 10ug of RNAseA (Roche) added and incubated for 30 minutes at 37°C followed by addition of 100ug of Proteinase K (Roche) and incubation at 65°C overnight. Input was purified with Qiagen PCR Purification Kit (#28104) and quantified
The prepared chromatin was thawed on ice while 10ug of antibodies against either H3K27ac (Abcam #Ab4729) or H3K27me3 (Cell Signaling #CS9733S) were conjugated to a mix of magnetic Protein A and Protein G coupled beads (Invitrogen #100.02D and #100.04D respectively) in the presence of 0.5% BSA in PBS with rotation at 4°C for 2 hours. Beads were washed 3 times with 0.5%BSA in PBS and either 5ug of chromatin was added to the H3K27ac ChIP or 10ug of chromatin was added to the H3K27me3 ChIP and rotated overnight at 4°C. The beads were washed 2 times with Tris based RIPA buffer (0.1% SDS, 1% Triton X-100, 10mM Tris-HCl pH 7.4, 1mM EDTA pH 8.0, 0.1% Sodium Deoxycholate), 2 times with 0.3M NaCl RIPA (0.1% SDS, 1% Triton X-100, 10mM Tris-HCl pH 7.4, 1mM EDTA pH 8.0, 0.1% Sodium Deoxycholate, 0.3M NaCl), 2 times with LiCl Buffer (250mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA pH 8.0, 10mM Tris-HCl pH 8.0) and 2 times with TE buffer pH 7.6 (Fisher Scientific cat. no. BP2474-1). The beads were resuspended in 100uL of TE and RNAseA and PK digested/reverse crosslinked and purified as described in the chromatin prep.

value: lung tumor

value: EZH2 overexpressing


title: EZH2OE_lung_tumor_3

description: EZH2 overexpressing lung tumor replicate 3


title: EZH2OE_normal_lung_2

description: EZH2 overexpressing normal lung replicate 2


title: HE2


title: EZH2OE_normal_lung_1

description: EZH2 overexpressing normal lung replicate 1


title: Dmel_FC_TJ-2_mutant_sRNA

data_processing:
The adapter sequence based on the standard Illumina linkers were only removed on the small RNA reads.  The full sequence of this adapter linker is CGTCGTATGCCGTCTTCTGCTTGT.
The linker sequence was first removed by fastx_clipper program from FASTX Toolkit(0.0.13) with the parameters: "-a CGTCGTATGCCG -M 9 -n -l 20"
The shorter linkers on remaining reads were removed by searching for where the last 2 to 8 base pairs matches perfactly to the first 2 to 8 base pairs of the adapter sequence (CGTCGTATGCCG)
The final filtering step removed reads if its entire sequence contained more than 12 base pairs of poly(A/C/G/T).
No additional processing was performed on mRNA reads.
Supplementary_files_format_and_content: text files of sequences for each RNA read

extract_protocol:
Mouse, rat and rabbit testes were homogenized as described in Lau et al, Science. 2006 Jul 21;313(5785):363-7., and this extract was used only for the Mili (Piwil2) IP experiments.  For total RNA, testes were pulverized into powder while frozen and thawed into Tri-reagent solution to extract RNA according to the manufacterur (MRC) instructions
Small RNA libraries were constructed using the custom protocol described in Matts et al. Methods Mol Biol. 2014;1093:123-36.  Messenger RNA libraries were constructed with the Epicentre ScriptSeq v2 kits.

tag: strain background

value: Oregon-R

value: adult

value: female

value: ovary follicle cells

tag: molecule subtype

value: small RNA


title: Dmel_FC_sRNA

tag: genotype/variation

tag: age


title: EZH2OE_lung_tumor_2

description: EZH2 overexpressing lung tumor replicate 2


title: HE1

value: high grade

value: european american


title: HE3


title: LA2

value: low grade

value: african american


title: Lung_HZ54_H3K27me3

description: Chromatin IP against H3K27me3 in EZH2 overexpressing lung tumor


title: Lung_HZ54_H3K27ac

description: Chromatin IP against H3K27ac in EZH2 overexpressing lung tumor


title: Cd2

city: Madurai

first: Velmurugan

last: Ganesan

state: Tamilnadu

address: Palkalainagar

department: Department of Molecular Biology, School of Biological Sciences

country: India

institute: Madurai Kamaraj University

description: Small RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 via miRdeep* program
Using miRdeep* RPKM of miRNAs were identified
Differential expression studied by DeSeq
Genome_build: mm10
Supplementary_files_format_and_content: .txt files with miRNA read count

source_name: Whole blood

growth_protocol: Balb/c mice were grown under normal conditions and provided feed and water  ab libithum

extract_protocol:
After experimental period, both group of animals were sacrificed and the blood is harvested. Total RNA isolated using miRNEasy kit (Qiagen).
Small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cadmium group of animals were fed with cadmium mixed drinking water ab libithum

tag: strain

value: Balb/c

tag: agent

value: cadmium

value: Whole blood

value: 180 days


title: HE5


title: Cd1

description: Small RNA

tag: tissue


title: Lung_HZ545_input

description: WCE control for HZ545 EZH2 overexpressing lung tumor

tag: genotype


title: LA1


title: Dmel_FC_TJ1_mutant_sRNA

value: wild type

tag: Sex


title: Con2

description: Small RNA

value: control


title: LE3


title: Lung_HZ545_H3K27me3

value: lung tumor


title: Con1

description: Small RNA


title: LE2


title: LE1


title: Lung_HZ1746_input

description: WCE control for HZ1746 EZH2 overexpressing normal lung

value: normal lung

value: EZH2 overexpressing


title: Lung_HZ1746_H3K27ac

description: Chromatin IP against H3K27ac in EZH2 overexpressing normal lung


title: Lung_HZ545_H3K27ac


title: Lung_HZ1746_H3K27me3

description: Chromatin IP against H3K27me3  in EZH2 overexpressing normal lung


title: BE5

value: benign


title: LA3


title: BE2


title: Rat_10dpp_testes_sRNA

value: Sprague-Dawley

value: 10dpp pups

value: male

value: testes


title: H9c2 A2M treated cells

first: Subbiah

last: Ramasamy

department: Molecular Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn5 whole genome using bowtie v0.12.2 via miRdeep* program
Using miRdeep* itself the RPKM and differential expression was studied
Genome_build: rn4
Supplementary_files_format_and_content: txt files with read count

growth_protocol: H9c2 cardiomyoblast cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % fetal bovine serum and antibiotics 10 µg/ml Streptomycin and 0.25 µg/ml  Amphotericin under a humidified atmosphere of 95 % air, 5 % CO2 at 37 ºC.

extract_protocol:
After 24 hours of treatment, the induction of hypertrophy was confirmed by microscopy and the total RNA was isolated using miRNEasy kit (Qiagen Inc., USA)
Small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After the cells reached 50-60% confluence, they were treated with 50 μg/ ml alpha-2 macroglobulin and incubated for 24 hours

value: 16 weeks

tag: tissue source

value: Embyronic heart

tag: cell line

value: cardiomyoblast cells

tag: treated with

value: 50 μg/ml alpha-2 macroglobulin for 24hrs


title: BE1

tag: histology

value: european american


title: Dvir_FC_sRNA

first: NELSON

last: LAU

organism: Drosophila virilis

value: adult

value: female

value: ovary follicle cells

value: small RNA


title: Rat_Adult_testes_sRNA

value: wild type


title: Lung_HZ1745_input

description: WCE control for HZ1745 EZH2 overexpressing normal lung

value: normal lung


title: Lung_HZ1745_H3K27ac

value: EZH2 overexpressing


title: BE4

value: benign

tag: ancestry


title: Rat_Adult_testes_Mili_IP_sRNA

value: Sprague-Dawley

tag: ip antibody

value: custom rabbit polyclonal anti-Mili antibody


title: H9c2 Control cells

tag: cell type

value: none (control)


title: BE3


title: Lung_HZ1745_H3K27me3

description: Chromatin IP against H3K27me3 in EZH2 overexpressing normal lung


title: Apo IMR90 H3K36 me3

status: Public on Oct 31 2015

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

description: E1A/RasG12V overexpressing  IMR90 anti Histone H3K36me3 CMA333 ChIP Seq

data_processing:
Single-end reads were aligned against the Human Reference Genome (assembly hg18, NCBI Build 36) using BWA version 0.5.5. Reads were filtered by removing those with a BWA alignment quality score less than 15. A further filtration was carried out by removing reads falling into the 'blacklist' regions identified by ENCODE.
Genome_build: hg18
Supplementary_files_format_and_content: tdf  (converted from wig files) containing data that has been preprocessed for faster display in IGV

source_name: human diploid fibroblast

growth_protocol: cultured in 5%O2 in DMEM with 10% FBS and Pen/Strep and Glutamine

extract_protocol: immunoprecipitated DNA was end-repaired, A-tailed, ligated to the sequencing adapters, amplified by 18 cycles of PCR and size selected (200-300 bp) followed by single end 4 sequencing on an Illumina Genome Analyzer according to the manufacturer’s recommendationas described in Chandra, T. et al. Independence of Repressive Histone Marks and ChromatinCompaction during Senescent Heterochromatic Layer Formation. Mol Cell 47, 203–214 (2012)

treatment_protocol: 24 hours Etoposide (100microM),pBabe-Puro H-RasG12V, pWXL-Hygro E2A, H-RasG12V, pLNCX-Neo ER:H-RasG12V overexpression

value: human diploid fibroblast

value: overexpressing E1A/RasG12V

tag: histone marks to be tested

tag: condition

value: pApo; pro-apoptotic (overexpression of E1A/RasG12V)

tag: chip antibody

value: mouse monoclonal H3K36me3 antibody, clone CMA333 (PMID:20824077)


title: Apo IMR90 H3K4me3

description: E1A/RasG12V overexpressing IMR90 anti Histone H3K4me3 CMA304 ChIP Seq

tag: genotype/variation

value: mouse momoclonal H3K4me3 antibody, clone CMA304 (PMID:18227620)


title: Dvir_FC_mRNA

city: BOSTON

address: 72 E Concord St K219, Dept of Biochemistry

tag: age

tag: molecule subtype

value: messenger RNA


title: HEK293T_smRNA_rep2

city: Philadelphia

first: Lee

middle: Elliott

last: Vandivier

address: 433 S. University Ave Rm 104

institute: University of Pennsylvania

description: 16 to 50nt RNAs (smRNAs)

data_processing:
3' adapter sequences were trimmed using cutadapt (version 1.4.2 with parameters -e 0.06 -O 6 -m 14)
Trimmed reads were aligned to the Arabidopsis genome (TAIR10) human genome (hg19) using Tophat (version 2.0.9 with parameters --read-mismatches 3 --read-edit-dist 3 --max-multihits 1 --b2-very-sensitive --transcriptome-max-hits 1 --no-coverage-search --no-novel-juncs)
RNA modifications were predicted and classified using the High Throughput Annotation of Modified Ribonucleotides (HAMR) pipeline (Ryvkin et al. 2013).
Genome_build: TAIR10; hg19
Supplementary_files_format_and_content: HAMR-predicted modifications (BED format)

source_name: HEK293T cells

growth_protocol: Arabidopsis plants were grown under 16hr light 8hr dark days, and buds were harvested at approximately 4 weeks of age. HEK293T and HeLa cells were seeded in 15-cm standard Corning tissue-culture treated culture dishes (Sigma, St Louis, MO), grown to 90% confluence (approximately 18 million cells) in DMEM media (Life Technologies, San Diego, CA) supplemented with L-glutamine, 4.5 g/L D-glucose, 10% fetal bovine serum (FBS (Atlanta Biologics, Atlanta, GA)) and Pen/Strep (Fisher Scientific, Waltham, MA).

extract_protocol:
For Arabidopsis, bud tissue was ground with a mortar and pestle. Human cells were pelleted and homogenized.  RNA was extracted with Qiazol (Qiagen; Valencia, CA) and then further purified with the Qiagen miRNeasy RNA isolation kit following the included protocol (Qiagen; Valencia, CA).
TruSeq small RNA sequencing kit [illumina, Valencia, CA]), as previously described (Willmann et al. 2014; Li et al. 2012).

treatment_protocol: Both plants and human cells were not otherwise treated

tag: rna fraction

tag: replicate

value: Illumina Hi-Seq2000 50 nt strand-specific


title: HEK293T_smRNA_rep1

description: 15 to 50nt RNAs (smRNAs)


title: Checkpoint IMR90 H3K36me3

description: 24 hour Etoposide treated IMR90 anti Histone H3K36me3 CMA333 ChIP Seq

value: Etoposide for 24hrs

value: DDR; acute DNA damage response (24 hour Etoposide treated)


title: HeLa_smRNA_rep2

description: 16 to 50nt RNAs (smRNAs)

source_name: HeLa cells

value: HeLa

value: small RNA


title: HeLa_smRNA_rep1

description: 15 to 50nt RNAs (smRNAs)


title: Ras IMR90 H3K4me3

description: RasG12V overexpressing IMR90 anti Histone H3K4me3 CMA304 ChIP Seq

value: overexpressing RasG12V

value: RIS; RAS-induced senescence (overexpression of RasG12V)


title: Checkpoint IMR90 H3K4me3

description: 24hour Etoposide treated IMR90 anti Histone H3K4me3 CMA304 ChIP Seq


title: Growing IMR90 H3K4me3

description: Growing IMR90 anti Histone H3K4me3 CMA304 ChIP Seq

value: Growing


title: induced-adult-cardiac-Parkin-KO-5

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

data_processing:
Illumina Casava1.6 and Casava1.8 software was used for basecalling. All 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the transcriptome, defined by annotation based on the UCSC mm10 genes.gtf and associated bowtie2 index provided by Illumina iGenomes, using tophat v2.0.10.
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the supplied gtf, based on UCSC mm10 genes.gtf
htseq-count data allows each user maximum flexibility in performing sample (library) depth normalization and differential gene expression using software such as DESeq or edgeR.
Additionally, we used Cufflinks v2.1 to calculate FPKM for each gene entry in each library.  However, this was merely done for later graph display.  Actual calculations of differential gene expression used htseq-count data as input to DESeq.
Genome_build: mm10
Supplementary_files_format_and_content: single tab-delimited text files include htseq-count values for each gene, or FPKM values for each gene.

molecule: polyA RNA

source_name: induced-adult-cardiac-Parkin-KO

extract_protocol:
Hearts were removed and ventricular apexes were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per Methods Mol Biol. 2015;1299:27-49, PMID 25836573.
non-strand-specific, single-end RNA-Seq

tag: strain background

value: floxed, MERCreMer (induced)

value: adult

tag: time point

value: 9-10 weeks after tamoxifen induction

tag: tissue

value: whole heart


title: induced-adult-cardiac-Parkin-KO-6


title: Growing IMR90 H3K36me3

description: Growing IMR90 anti Histone H3K36me3 CMA333 ChIP Seq

tag: cell line

value: human diploid fibroblast


title: induced-adult-cardiac-Parkin-KO-3


title: induced-adult-cardiac-Parkin-KO-2


title: noninduced-adult-heart-6

source_name: noninduced-adult-heart

value: floxed, non-Cre (noninduced)


title: induced-adult-cardiac-Parkin-KO-4


title: mouse-germline-KO-parkin-heart-4

source_name: mouse-germline-KO-parkin-heart

value: germline Parkin knockout


title: noninduced-adult-heart-1


title: mouse-germline-KO-parkin-heart-3


title: noninduced-adult-heart-3


title: noninduced-adult-heart-5


title: mouse-germline-KO-parkin-heart-2


title: mouse-wt-heart-5

source_name: mouse-wt-heart

value: wild type


title: noninduced-adult-heart-2


title: mouse-wt-heart-3


title: Ras IMR90 H3K36me3

description: RasG12V overexpressing IMR90 anti Histone H3K36me3 CMA333 ChIP Seq

value: mouse monoclonal H3K36me3 antibody, clone CMA333 (PMID:20824077)


title: mouse-wt-heart-4


title: mouse-wt-heart-2


title: mouse-wt-heart-1


title: Input of ES cell-derived granule cells at Day 15 treated with vitamin C (2)

city: New York

first: Michelle E.

last: Ehrlich

state: NY

address: 1 Gustave L. Levy Pl, New York, NY 10029

department: Department of Psychiatry

institute: Icahn School of Medicine at Mount Sinai

description:
tar archive of wig files: D15vitc_hmc2_control_all.tar
processed data file: D15vitc_hmc2_summits.bed

data_processing:
Library strategy: hMe-Seal-seq
The 5hmC filtered and unfiltered reads were mapped to the mm10 mus musculus genome using the program bowtie2, and the 5hmC summits were calculated using Model-based Analysis of ChIP-Seq (MACS). To explore the enhancer region activity for each exon, the 5hmC summit landscape +/- 5000bp relative to exon start sites were considered. These summit landscapes, centered at the exon start site for each exon, were averaged together to obtain a condensed view for each gene. Similarly, the mean of the condensed 5hmC summit landscape for each gene in relevant gene sets were calculated and used to analyze concordant 5hmC across pathways.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using MACS, and contain represent 5hmC pileups. Bed files were generated using MACS, and contain the peak summits locations for every peak.  Wig files are available in tar archives on the series record.

source_name: ES cell-derived granule cells

growth_protocol: GFP-positive ES cell-derived granule cells and cerebellar granule cells were sorted in a BD FACSAria cell sorter. Genomic DNA was isolated from sorted cells and purified P7 GCs using DNeasy Blood & Tissue Kit.

extract_protocol:
The 5hmC-enriched genomic DNA collection was performed with a selective labeling strategy known as hMe-Seal.
Libraries were prepared using TruSeq DNA HT Sample Prep Kit according to Illumina's instructions. Briefly, purified double stranded DNA was fragmented into approximately 200 bp using Covaris-S2 system. These fragments were end-repaired and ligated with adapters for Illumina HiSeq 2500 technology using TruSeq DNA HT Sample Prep Kit (Illumina) and following manufacturer‘s instructions.

value: ES cell-derived granule cells


title: Input of ES cell-derived granule cells at Day 15 without treatment (1)

description:
tar archive of wig files: D15_hmc2_control_all.tar
processed data file: D15_hmc2_summits.bed


title: Input of ES cell-derived granule cells at Day 15 treated with vitamin C (1)


title: noninduced-adult-heart-4


title: induced-adult-cardiac-Parkin-KO-1


title: 5hmC seq of ES cell-derived granule cells at Day 15 without treatment (1)

description:
tar archive of wig files: D15_hmc2_treat_all.tar
processed data file: D15_hmc2_summits.bed


title: 5hmC seq of ES cell-derived granule cells at Day 15 without treatment (2)


title: 5hmC seq of P7 cerebellar granule cells (2)

description:
tar archive of wig files: P7_hmc2_treat_all.tar
processed data file: P7_hmc2_summits.bed

source_name: cerebellar granule cells

value: cerebellar granule cells


title: mouse-germline-KO-parkin-heart-1


title: 5hmC seq of ES cell-derived granule cells at Day 15 treated with vitamin C (2)

description:
tar archive of wig files: D15vitc_hmc2_treat_all.tar
processed data file: D15vitc_hmc2_summits.bed


title: Input of P7 cerebellar granule cells (1)

description:
tar archive of wig files: P7_hmc2_control_all.tar
processed data file: P7_hmc2_summits.bed


title: Input of P7 cerebellar granule cells (2)


title: Input of ES cell-derived granule cells at Day 15 without treatment (2)


title: 5hmC seq of P7 cerebellar granule cells (1)


title: Arabidopsis_RNA_rep3

description: polyA-selected RNA

source_name: Arabidopsis immature inflorescence

value: immature inflorescence

value: polyA-selected RNA

value: Illumina Hi-Seq2000 50 nt strand-specific


title: Sw_Hy

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn5 whole genome using bowtie v0.12.2 via miRdeep* program
Using miRdeep* itself the RPKM and differential expression was studied
Genome_build: rn4
Supplementary_files_format_and_content: Excel files with read count

source_name: Heart

growth_protocol: The animals are grown under normal conditions and provided feed and water  ab libithum

extract_protocol:
After experimental period, both group of animals were sacrificed and the heart was dissected. Total RNA isolated using miRNEasy kit (Qiagen).
Small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The Sw_Hy group of animals were allowed to swim for 90 minutes twice per day for 8 weeks

tag: strain

value: Wistar

value: Left ventricle

value: 16 weeks


title: Arabidopsis_GMUCT_rep1

description: polyA-selected, uncapped RNA

data_processing:
Library strategy: GMUCT
3' adapter sequences were trimmed using cutadapt (version 1.4.2 with parameters -e 0.06 -O 6 -m 14)
Trimmed reads were aligned to the Arabidopsis genome (TAIR10) human genome (hg19) using Tophat (version 2.0.9 with parameters --read-mismatches 3 --read-edit-dist 3 --max-multihits 1 --b2-very-sensitive --transcriptome-max-hits 1 --no-coverage-search --no-novel-juncs)
RNA modifications were predicted and classified using the High Throughput Annotation of Modified Ribonucleotides (HAMR) pipeline (Ryvkin et al. 2013).
Genome_build: TAIR10; hg19
Supplementary_files_format_and_content: HAMR-predicted modifications (BED format)

value: polyA-selected uncapped RNA


title: Arabidopsis_RNA_rep2

description: polyA-selected RNA


title: Sw_Con

description: control


title: Arabidopsis_GMUCT_rep2

description: polyA-selected, uncapped RNA


title: Arabidopsis_smRNA_rep2

description: 16 to 50nt RNAs (smRNAs)

value: small RNA


title: Arabidopsis_RNA_rep4

description: polyA-selected RNA


title: Arabidopsis_smRNA_rep1

description: 15 to 50nt RNAs (smRNAs)


title: 16 psu treated

city: Shanghai

first: Xu

last: Zhixin

address: 500 Dongchuan Rd.,Shanghai 200241

institute: East China Normal University

description: 8 healthy Nile tilapia

data_processing:
The clean reads were then aligned to tilapia genome (version: GCA_000188235.2) using the MapSplice program (v2.1.6). In alignment, preliminary experiments were performed to optimize the alignment parameters (-s 22 -p 15 --ins 6 --del 6 --non-canonical) to provide the largest information on the AS events.
We applied HTseq to calculate the mRNA counts based on the mapping result
Genome_build: Orenil1.1 (GCA_000188235.2)
Supplementary_files_format_and_content: Counts file

organism: Oreochromis niloticus

source_name: Nile Tilapia_16 psu treated

growth_protocol: Nine tanks of Nile tilapia (initial weight 2.2 ± 0.47 g) were reared in freshwater, with 30 fish in each tank. During the experiment, 1/3 of the water was replaced every day with aerated fresh water or saline water. Tilapias were fed twice per day, at 08:00 h and 16:00 h, with a commercial diet that contained 36% crude protein and 5.6% crude lipid. The diet was extruded in the form of 2-mm diameter pellets that were air dried. Daily rations were adjusted to a feeding level that was slightly over satiation, and feed that was not consumed was removed every day with a siphon tube.

extract_protocol:
Total RNA was extracted from Hepatopancreas by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies).

treatment_protocol: Two sets of three tanks were acclimated to the salinities of 8 and 16 psu, respectively, by increasing the salinity of 4 psu per day. The fish were then reared for 5 weeks.

tag: developmental stage

value: juvenile

tag: disease state

value: healthy

value: Hepatopancreas

value: Histiocytes of hepatopancreas

tag: salinity

value: 16 psu


title: 0396 2-3

city: Oak Ridge

first: Charlotte

last: Wilson

state: Tennessee

address: 1 Bethel Valley Road

department: Biosciences Bldg 1520

country: New Zealand

institute: ORNL

data_processing:
Demultiplexing and file conversion performed by bcl2fastq version bcl2fastq-1.8.3
RNAseq reads were aligned to the C. thermocellum DSM1313 (NC_017304.1) genome assembly using Fastq files imported into the CLCBio RNA-sequencing pipeline. Default settings were used for mismatch, insertion, and deletion costs.
Total gene counts from the CLCBio mapping were used for DESeq2 analysis to normalise and determine significant gene expression differences
Supplementary_files_format_and_content: Tab deliminated file includes read counts for each gene across the 36 samples used in this study

organism: Acetivibrio thermocellus DSM 1313

source_name: Bacterial fermentation

growth_protocol: Strains of Clostridium thermocellum were grown in pH controlled 1L Q-Plus bioreactors (Sartorius) using MTC growth medium and cellobiose (5g/L) as the substrate (58°C, 100 rpm).  Cells were harvested from 50 ml samples taken from the fermenter at mid-exponential, late exponential and stationary growth phases.  Each fermentation was performed in triplicate.

extract_protocol:
Cells pelleted from a 50 mL sample drawn from each fermenter were resuspended in 3 mL of TRIzol (Invitrogen, CA). A 1 ml aliquot of the TRIzol cell suspension was used for cell lysis by bead beating with 0.8 g of 0.1mm glass beads (Biospec Products) with 3 X 20 s bead beating treatments at 6,500 rpm in a Precellys 24 high-throughput tissue homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France). The RNA from each cell lysate was purified and DNaseI treated using the Qiagen RNeasy kit. The RNA quantity and quality assessed by Nanodrop and Bioanalyzer respectively. Purified RNA was depleted of rRNA using the Ribo-Zero rRNA Removal kit for Gram Positive Bacteria (Epicentre/Illumina). The sample was then concentrated with RNA Clean & Concentrate-5 (Zymo Research, CA) following the manufacturer’s protocol.
Depleted RNA was used as the starting material for the Epicentre ScriptSeq™ mRNA-Seq Library preparation kit (Illumina compatible) utilising Epicentres Fail Safe PCR Enzyme mix (Epicentre, WI) and following the manufacturer’s protocol. cDNA, tagged with ScriptSeq adaptors (1-12), was eluted with 20 µl of Buffer EB provided in the Min-Elute PCR purification kit (Qiagen) according to the ScriptSeq™ mRNA-Seq Library preparation kit protocol. Twelve PCR cycles were used during library amplification and samples were purified using the Min-Elute PCR purification kit and eluted with 20 µl of buffer EB. The final mRNA Seq library was quantified with a Qubit Fluorometer (Invitrogen, CA) and library quality was assessed with an Agilent Bioanalyzer High Sensitivity Chip for DNA (Agilent, CA). Samples were pooled into three groups to make a stock of 20 nM in 72 ul.  A 40 ul aliquot of each of the three pooled libraries was sent to HudsonAlpha Genomic Serices Laboratory for a SR50 sequencing run on an Illumina Hiseq 2500 platform.

tag: time point sampled

value: Stationary phase


title: 8 psu treated

description: 8 healthy Nile tilapia

source_name: Nile Tilapia_8 psu treated

tag: cell type

value: 8 psu


title: 0396 1-3


title: 0396 3-3


title: 0 psu treated

description: 8 healthy Nile tilapia

source_name: Nile Tilapia_0 psu treated

value: 0 psu (freshwater)


title: 5hmC seq of ES cell-derived granule cells at Day 15 treated with vitamin C (1)

value: ES cell-derived granule cells


title: 0396 3-1

value: Mid-exponential growth phase


title: 0396 1-2

value: Late-exponential growth phase


title: 2023 1-3


title: 2023 3-2


title: 2023 3-3


title: Arabidopsis_RNA_rep1

description: polyA-selected RNA

value: immature inflorescence

value: polyA-selected RNA

value: Illumina Hi-Seq2000 50 nt strand-specific


title: 2023 2-3


title: 2023 2-2


title: 2023 3-1


title: hpt 3-3

value: delta-hpt


title: 2023 1-2


title: hpt 1-3


title: hpt 3-2


title: 2023 1-1


title: hpt 1-2


title: 2023 2-1


title: hpt 2-3


title: hpt 3-1


title: 0396 2-2


title: 0396 3-2


title: 0089 2-3


title: hpt 1-1


title: 0089 3-3


title: 0089 1-3


title: 0089 3-2


title: hpt 2-1


title: 0396 1-1


title: 0396 2-1


title: 0089 2-2


title: 0089 1-2


title: 0089 1-1


title: hpt 2-2


title: 0089 2-1


title: 0089 3-1


title: iv2022-in vivo

status: Public on Oct 30 2015

city: Guelph

first: Valeria

middle: Regina

last: Parreira

state: ON

address: 50 Stone Rd E

department: Pathobiology

country: Canada

institute: University of Guelph

data_processing:
Illumina Casava1.8.2. software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to C. perfringens strain CP4 whole genome using bowtie2 version 2.1.0 using default parameters.
Raw reads counts were generated for each gene using HTSeq software version 0.5.4p1, using the HTSeq counting mode “union”
Estimates of absolute expression (rpkm, reads per kilobase per million read) were generated using the edgeR function rpkm
Genome_build: C. perfringens CP4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Clostridium perfringens

source_name: chicken intestinal contents

extract_protocol:
RNAlater was added to chicken intestinal contentes and bacterial cultures and  frozen at -70C. RNA from C. perfringens were isolated using silica column kits.
RNA libraries were prepared using Illumina HiSeq 2500 with TruSeq v3 chemistry

tag: features

value: virulent


title: CP4-2-in vitro

source_name: lab culture


title: iv1217-in vivo