title: Female liver nuclear RNA pool 2

description:
G86_M2
nuclear RNA pooled from 4 mouse livers
poly-A selected, unstranded library

data_processing:
Sequence reads were mapped to mm9 using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
Reads were counted along gene bodies of lincRNA for each sample and normalized using the geometric mean normalization method (Anders et  al, Genome Biol, 2010).
Genome_build: mm9
Supplementary_files_format_and_content: A Microsoft Excel sheet containing normalized read counts of lincRNAs across all samples is provided. Bigwig files for each sample are also included, where each score represents the normalized gene expression level. Gene models for liver-expressed lincRNAs can be found at GEO series GSE65444.

molecule: nuclear RNA

growth_protocol: Untreated female CD-1 mice (Charles River Laboratories), 8 weeks old, were euthanized and their livers were extracted.

extract_protocol:
Nuclei was extracted from female mouse liver tissue by homogenization and sucrose purification. RNA was extracted from purified nuclei using Trizol following standard protocol.
Poly-A-enriched nuclear RNA was prepared for Illumina sequencing using non strand-specific sample preparation protocol

value: female


title: M3

status: Public on Oct 23 2015

type: SRA

city: Tallahassee

first: Mohamed

last: Kabbaj

state: Florida

address: 1115 W Call St

department: Biomedical Sciences

country: USA

institute: Florida State University

description:
DESeq2_normalized_counts.txt
edgeR_normalized_counts.txt

library_source: transcriptomic

data_processing:
Illumina Casava1.9 software used for basecalling.
Trimmomatic v0.32 was used to remove adapter sequences, and quality filtering using the following parameters: LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36. Reads shorter than 36 bp after trimming were thus removed from the study.
Filtered reads were then aligned to the reference genome using tophat v2.0.11 and the --b2-very-sensitive Bowtie2 (v2.1.0) preset, guided by GTF file. Of note, reads were aligned to the reference genome to which theERCC spike-ins were added.
The number of reads mapping uniquely to each gene was counted by HTSeq-count v0.6.1p1, and processed for statistical analysis using the R Bioconductor packages edgeR (v3.6.7), and DESeq2 (v1.4.5).
Genome_build: Rnor_5.0 Ensembl Release 76 (August 2014)
Supplementary_files_format_and_content: DESeq2_normalized_counts.txt: Tab-delimited text file contain normalized read counts for each sample, as computed by DESeq2.
Supplementary_files_format_and_content: edgeR_normalized_counts.txt: Tab-delimited text file contain normalized read counts for each sample, as computed by edgeR.

molecule: total RNA

organism: Rattus norvegicus

source_name: medial prefrontal cortex

extract_protocol:
Brains were dissected out, flash frozen, and stored at -80C until sectioning on a cryostat at -20C for tissue-punching of the medial prefrontal cortex. Total RNA was then extracted using TRI-Reagent according to the manufacturer's protocol (Molecular Research Center, #TR 118), followed by DNAse I treatment to remove any eventual DNA contamination and clean-up (RNA Clean & Concentrator, Zymo Research, Irvine, CA, USA) .
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina with poly(A) mRNA purification from one microgram of total RNA based on magnetic beads, cDNA synthesis using random hexamers, and final amplification using barcoded primers following the manufacturer’s protocol (#E7530, New England Biolabs, Ipswich, MA, USA). In order to determine the lower limit of detection and verify the linearity of quantification during the statistical analysis of the sequencing data, synthetic RNA Spike-Ins (#4456739, ERCC ExFold RNA Spike-In Mixes, Life technologies, Carlsbad, CA) were added to each sample prior to poly(A) mRNA purification following the recommended dilutions (2 µL of a 1:100 dilution). Of note, Mix 1 and Mix 2 of the ERCC ExFold RNA Spike-Ins were equally distributed among samples in an exclusive manner. The resulting barcoded and unstranded libraries were quantified using a KAPA qPCR library quantification kit (KAPA Biosystems, Boston, MA, USA) with three serial dilutions ran in duplicates on a CFX96 real-time PCR instrument (Bio-Rad). Finally, the absence of adapters or primers contamination was verified on a Bioanalyzer using a DNA High Sensitivity chip (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Following five days of habituation and handling under pair-housing, the estrous cycle of female rats was monitored by daily vaginal smearing and subsequent cytological analysis for a minimum of two cycles.

tag: strain

value: Sprague-Dawley

tag: tissue

value: medial prefrontal cortex

tag: gender

value: Male

tag: estrous cycle


title: Female liver nuclear RNA pool 3

status: Public on Oct 21 2015

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description:
G86_M3
nuclear RNA pooled from 4 mouse livers
poly-A selected, unstranded library

organism: Mus musculus

source_name: liver tissue

value: CD-1 (Charles River)

tag: Sex

tag: age

value: 8 weeks old

value: liver


title: MEFs-Input-DRB-ChIPseq

status: Public on Oct 22 2015

city: La Jolla

first: Xiang-Dong

last: Fu

state: CA

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

description: ChIP-seq

library_source: genomic

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 mouse genome by using Bowtie (version 0.12.7), with parameters "--best --strata -l25 -n2'. Only uniquely mapped reads were kept.
For ChIP-seq, the reads mapped to the same location were kept up to 4.  The heart RBFox2 and input ChIP reads were trimmed 3 bp at 5'-end before mapping because of low sequencing qualities. The genomic coverage signal were counted from reads on both strands and normalized to 1 million total reads. The normalized signal from input samples were subtracted from those corresponding IPed samples and negative values were reset as 0.
For Gro-seq, the replicated samples were combined together. The genomic coverage signal were counted in forward and reverse strands separately and normalized to 1 million total reads.
For CLIP-seq, the reads mapped to the same location with same random barcode sequence (attached to read name) were kept to 1. The genomic coverage signal were counted in forward and reverse strands separately, and then normalized to 1 million total reads.
For 3'-end RNA-seq, the reads mapped to the same location were kept up to 4, and only reads in exons were counted. The counts for different samples were normalized to 10 million total reads.
For RASL-seq, the reads were mapped to targetd exon-exon junctions with up to two mismatches.
Genome_build: mm9
Supplementary_files_format_and_content: The bigWig files are genomic signals for ChIP-seq, Gro-seq and CLIP-seq samples. The Excel file for RASL-seq samples are counts for targeted isoforms.  The Excel file for 3'-end RNA-seq samples are normalized abundance measurements.

molecule: genomic DNA

source_name: MEFs-Input-DRB-ChIPseq

growth_protocol: DMEM plus 10% FBS

extract_protocol: MEFs were fixed with 1% Formaldehyde at room temperature for 10 min. After the treatment, cross linking was quenched with 0.125 M glycine for 10 min. ~50 million cells were used for each ChIP.

treatment_protocol: MEFs were treated with 100μM DRB for 3 hours.

tag: cell type

value: MEF cell line

tag: passages

tag: treated with

value: DRB


title: Hypophysectomized male liver pool 2_G85_M4

description:
total RNA pooled from 4 mouse livers
poly-A selected, unstranded library
G85_M4

data_processing:
Sequence reads were mapped to mm9 using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
Reads were counted along lincRNA gene bodies for each sample and normalized using the geometric mean normalization method (Anders et  al, Genome Biol, 2010).
DESeq (Anders et  al, Genome Biol, 2010) and edgeR (Robinson et al, Bioinformatics, 2010) were used to compute differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: A Microsoft Excel sheet containing normalized counts of lincRNAs across all samples and differential expression results comparing intact to hypophysectomized male and intact to hypophysectomized female samples is provided. Bigwig files for each sample are also included, where each score represents the normalized gene expression level. Gene models for liver-expressed lincRNAs can be found in GEO series GSE65444.

growth_protocol: Untreated and hypophysectomized male and female CD-1 mice (Charles River Laboratories), 8 weeks old, were euthanized and their livers were then extracted.

extract_protocol:
Trizol reagent was used to prepare total liver RNA using standard protocols.
Poly-A-enriched  RNA was prepared for Illumina sequencing using a non strand-specific sample preparation protocol

value: male

value: 10 weeks old


title: Intact female liver pool 1_G85_M5

description:
total RNA pooled from 4 mouse livers
poly-A selected, unstranded library
G85_M5


title: Intact female liver pool 2_G85_M6

description:
total RNA pooled from 5 mouse livers
poly-A selected, unstranded library
G85_M6


title: Male liver with continuous GH treatment for 1 day - liver 1

description:
total RNA from individual liver
poly-A selected, unstranded library
G88_M1

data_processing:
Sequence reads were mapped to mm9 using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
Reads were counted along lincRNA gene bodies for each sample and normalized using the geometric mean normalization method (Anders et  al, Genome Biol, 2010).
DESeq (Anders et  al, Genome Biol, 2010) and edgeR (Robinson et al, Bioinformatics, 2010) were used to compute differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: A Microsoft Excel file containing normalizedread  counts of lincRNAs across all samples and differential expression results comparing intact to continuous GH-treated mouse livers is provided. Bigwig files for each sample are also included, where each score represents the normalized gene expression level. Gene models for liver-expressed lincRNAs can be found at GEO series GSE65444.

growth_protocol: Vehicle (control)-treated and 1 to 7 days continuous GH-treated male CD-1 mice (Charles River Laboratories), 8 weeks old, were euthanized and their livers were extracted.

extract_protocol:
Trizol reagent was used to prepare total liver RNA using standard protocols.
Poly-A-enriched RNA was prepared for Illumina sequencing using a non strand-specific sample preparation protocol

treatment_protocol: Continuous GH treatment was carried out as described in G. Ling et al, Mol. Cell. Biol, 2010 (PMID: 20876297).


title: Control male liver - day 7

description:
total RNA pooled from 3 mouse livers
poly-A selected, unstranded library
G88_M12


title: Male liver nuclear RNA (2 PM)

description:
G81_M8
nuclear RNA pooled from 2 mouse livers
poly-A selected, unstranded library

data_processing:
Sequence reads were mapped to mm9 using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
Reads were counted along lincRNA gene bodies for each sample and normalized using the geometric mean normalization method (Anders et  al, Genome Biol, 2010).
Genome_build: mm9
Supplementary_files_format_and_content: A Microsoft Excel sheet containing normalized read counts of lincRNA across the four samples is provided. Bigwig files for each sample are also included, where each score represents the normalized gene expression level. For the two samples that were sequenced using strand-specific RNA-seq (G81_M1 and G81_M2), there are two bigwig files: one contains gene expression level for the forward strand and another one for the reverse strand.

growth_protocol: Untreated male and female CD-1 mice (Charles River Laboratories), 8 weeks old, were euthanized and their livers were extracted.

extract_protocol:
Nuclei was extracted from male and female mouse liver tissue by homogenization and sucrose purification. RNA was extracted from purified nuclei using Trizol following standard protocol.
Poly-A-enriched RNA was prepared for Illumina sequencing using either strand specific, as indicated under Sample Description


title: Female liver nuclear RNA

description:
nuclear RNA pooled from 6 mouse livers
poly-A selected RNA, strand-specific library
G78_M12

data_processing:
Sequence reads were mapped to mm9 using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
Reads were counted along lincRNA gene bodies for each sample and normalized using the geometric mean normalization method (Anders et  al, Genome Biol, 2010).
DESeq (Anders et  al, Genome Biol, 2010) was used to compute differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: A Microsoft excel file containing normalized counts of lincRNA across the two samples and differential expression results comparing male to female samples is provided. There are two bigwig files for each sample, where one bigwig file contains gene expression level for the forward direction and another one for the reverse direction. Each score in the bigwig file represents the normalized gene expression level. Gene models for liver-expressed lincRNAs can be found within GEO series GSE65444.

growth_protocol: Untreated male and female CD-1 mice (Charles River Laboratories), 8 weeks old, were euthanized and their livers were then extracted.

extract_protocol:
Nuclei was extracted from male and female mouse liver tissue by homogenization and sucrose purification. RNA was extracted from purified nuclei using Trizol following standard protocol.
Poly-A-enriched nuclear RNA was prepared for Illumina sequencing using a strand-specific sample preparation protocol


title: Hypophysectomized female liver pool 1_G85_M7

description:
total RNA pooled from 3 mouse livers
poly-A selected, unstranded library
G85_M7


title: Female total RNA pool 2

description:
poly-A selected
G83_M4_FemaleTotal2

data_processing:
Sequence reads were mapped to mm9 using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
Reads were counted along gene bodies of lincRNA for each sample and normalized using the geometric mean normalization method (Anders et  al, Genome Biol, 2010).
DESeq (Anders et  al, Genome Biol, 2010) and edgeR (Robinson et al, Bioinformatics, 2010) were used to compute differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: A Microsoft excel containing normalized counts of lincRNA across the four samples and differential expression results comparing male to female samples is provided. Bigwig files for each sample are also provided, where each score represents the normalized gene expression level. Gene models for hepatic lincRNAs are given in a GTF file format.

source_name: female_liver tissue

extract_protocol:
Trizol reagent was used to prepare total liver RNA using standard protocols.
Poly-A-enriched RNA was prepared for Illumina sequencing using non strand-specific sample preparation protocol


title: Male total RNA pool 2

description:
poly-A selected
G83_M2_MaleTotal2

source_name: male_liver tissue


title: unc_18_3

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

data_processing:
Base calls were performed using CASAVA-1.8.2
Reads were aligned using bowtie with the following parameters: --best --strata -v 2 -m 5 to a set of 36,035 S. mediterranea transcripts assembled from various sources including a previous transcriptome used in microarrays studies (Adler et al.,2014), trinity assemblies from lab generated data involving whole animals, embryos, and sorted X1 cells, a transcriptome from the Bartscherer lab (Boser et al., 2013), and the Dresden transcriptome assembly from PlanMine (http://planmine.mpi-cbg.de), reduced as a collection to unique representations of loci via CD-HIT (Fu et al., 2012).
Read counts to genes were tallied from the SAM files with a custom script. RPKM values were generated using the rpkm function from the edgeR library from Bioconductor in R.
Genome_build: Schmidtea_mediterranea_3.1
Supplementary_files_format_and_content:
rpkm.txt contains tab-delimited RPKM vales for each sample.
smed_20140614.fa contains the sequences of the 36,035 alignment targets described above. Each sequence defline contains a unique identifier for the sequence, the originating transcriptome identifier, and the source of the sequence.

molecule: polyA RNA

organism: Schmidtea mediterranea

source_name: whole worm_18 days after unc22 RNAi

growth_protocol: Schmidtea mediterranea CIW4 asexual strain was maintained in 1X Montjuic salts supplemented with 50 ug/ml Gentamicin and fed homogenized calf liver paste as previously described (Gurley at al., Science 2008, PMID: 18063757; Reddien et al., Dev. Cell 2005, PMID: 15866156).

extract_protocol:
Three biological replicates of 10 worms each were collected for RNA isolation. Replicates for each time point were stored in Trizol (Life Technologies) at –80C until ready for chloroform extraction. RNA was precipitated with isopropanol and washed with 75% ethanol. Pellet was air-dried and resuspended in nuclease-free water.
Libraries were prepared for RNA Seq analysis from 500ng-1ug per whole worm sample or 100ng of sorted cell Total RNA by polyA selection and conversion to strand-specific libraries using the Illumina TruSeq kit.

treatment_protocol: Animals were given RNAi food every 3 days, with the first day designated as Day 0. For RNA Seq analysis, control (unc 22 RNAi), chd4(RNAi) and p53(RNAi) animals were fed RNAi food 3 times.

tag: time after rnai treatment

value: 18 days

tag: RNAi

value: Whole Worm Tissue

tag: replicate


title: Hypophysectomized male liver pool 1_G85_M3

description:
total RNA pooled from 4 mouse livers
poly-A selected, unstranded library
G85_M3


title: Female liver nuclear RNA pool 1

description:
G86_M1
nuclear RNA pooled from 4 mouse livers
poly-A selected, unstranded library


title: unc_18_1


title: Intact male liver pool 2_G85_M2

description:
total RNA pooled from 5 mouse livers
poly-A selected, unstranded library
G85_M2


title: Hypophysectomized female liver pool 2_G85_M8

description:
total RNA pooled from 4 mouse livers
poly-A selected, unstranded library
G85_M8


title: Male liver nuclear RNA (11 AM)

description:
G81_M7
nuclear RNA pooled from 2 mouse livers
poly-A selected, unstranded library


title: Male liver total RNA (11 AM)

description:
G81_M1
total RNA pooled from 6 mouse livers
poly-A selected RNA, strand-specific library


title: Male liver nuclear RNA

description:
nuclear RNA pooled from 6 mouse livers
poly-A selected RNA, strand-specific library
G78_M8


title: Male total RNA pool 1

description:
poly-A selected
G83_M1_MaleTotal1


title: unc_15_3

source_name: whole worm_15 days after unc22 RNAi

value: 15 days


title: unc_15_1


title: Intact male liver pool 1_G85_M1

description:
total RNA pooled from 4 mouse livers
poly-A selected, unstranded library
G85_M1


title: unc_18_2


title: unc_9_1

source_name: whole worm_9 days after unc22 RNAi

value: 9 days


title: unc_9_2


title: unc_15_2


title: unc_12_3

source_name: whole worm_12 days after unc22 RNAi

value: 12 days


title: unc_12_2


title: Male liver total RNA (2 PM)

description:
G81_M2
total RNA pooled from 6 mouse livers
poly-A selected RNA, strand-specific library


title: unc_12_1


title: unc_3_3

source_name: whole worm_3 days after unc22 RNAi

value: 3 days


title: unc_3_1


title: unc_9_3


title: unc_3_2


title: Female total RNA pool 1

description:
poly-A selected
G83_M3_FemaleTotal1

value: female


title: p53_18_3

source_name: whole worm_18 days after p53 RNAi


title: p53_15_2

source_name: whole worm_15 days after p53 RNAi


title: p53_15_3


title: D3

description:
DESeq2_normalized_counts.txt
edgeR_normalized_counts.txt

value: Sprague-Dawley

value: Female

value: Diestrus


title: p53_15_1


title: p53_18_2


title: p53_12_3

source_name: whole worm_12 days after p53 RNAi


title: p53_12_1


title: p53_9_1

source_name: whole worm_9 days after p53 RNAi


title: p53_6_3

source_name: whole worm_6 days after p53 RNAi

value: 6 days


title: p53_9_3


title: unc_6_3

source_name: whole worm_6 days after unc22 RNAi


title: unc_6_2


title: p53_3_3

source_name: whole worm_3 days after p53 RNAi


title: p53_6_2


title: p53_3_2


title: p53_3_1


title: p53_6_1


title: unc_6_1


title: CHD4_15_3

source_name: whole worm_15 days after CHD4 RNAi


title: CHD4_15_2


title: CHD4_15_1


title: CHD4_12_3

source_name: whole worm_12 days after CHD4 RNAi


title: CHD4_12_2


title: CHD4_9_3

source_name: whole worm_9 days after CHD4 RNAi


title: CHD4_12_1


title: CHD4_9_2


title: CHD4_9_1


title: CHD4_6_2

source_name: whole worm_6 days after CHD4 RNAi


title: p53_12_2


title: CHD4_6_1


title: CHD4_6_3


title: CHD4_3_3

source_name: whole worm_3 days after CHD4 RNAi


title: CHD4_3_2


title: p53_9_2


title: CHD4_3_1


title: Male liver nuclear RNA pool 3

description:
nuclear RNA pooled from 4 mouse livers
poly-A selected, unstranded library
G95_M3

data_processing:
Sequence reads were mapped to mm9 using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
Reads were counted along gene bodies of lincRNA for each sample and normalized using the geometric mean normalization method (Anders et  al, Genome Biol, 2010).
Genome_build: mm9
Supplementary_files_format_and_content: A Microsoft Excel sheet containing normalized read counts of lincRNAs across all samples is provided. Gene models for liver-expressed lincRNAs can be found in GEO series GSE65444.

source_name: liver tissue

growth_protocol: Untreated male CD-1 mice (Charles River Laboratories), 8 weeks old, were euthanized and their livers were then extracted.

extract_protocol:
Nuclei were extracted from male mouse liver tissue by homogenization and isolated by sucrose purification. RNA was extracted from purified nuclei using Trizol following a standard protocol.
Poly-A-enriched liver nuclear RNA was prepared for Illumina sequencing using a non strand-specific sample preparation protocol

value: CD-1 (Charles River)

value: 8 weeks old


title: Male liver nuclear RNA pool 1

description:
nuclear RNA pooled from 4 mouse livers
poly-A selected, unstranded library
G95_M1

value: liver


title: IL1b 2

city: Bath

first: Mark

middle: Andrew

last: Lindsay

address: Claverton Down

department: Pharmacy and Pharmacology

country: United Kingdom

institute: University of Bath

data_processing:
Tophat 2 (version 0.6) alignment
Differential expression of protein coding genes (Gencode v19) was evaluated between control and IL1b treated human chondrocytes using using CuffDiff (0.0.6) (Table 1)
Alignments files from control and IL1b treated sample were merged and transcripts assembled using Cufflinks (0.0.6)
Cuffcompare (0.0.5) was employed identify lncRNAs (from cufflink assembled transcripts) by comparison with Gencode v18 (Table 2)
Differential expression of long non-coding RNAs was evaluated between control and IL1b treated human chondrocytes using using CuffDiff (0.0.6) (Table 1)
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

organism: Homo sapiens

source_name: Chondrocyte cells

growth_protocol: Primary chondrocytes were isolated from cartilage by collagenase digestion, and cultured in DMEM supplementated with 10% FCS, penicillin (100U/ml), streptomycin (100µg/ml), L-glutamine (2mM), non-essential amino acids (5%v/v) and amphotericin (2µg/ml) and grown to 70-80% confluence

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen) and further purified using RNAeasy columns (Qiagen).
ScriptSeq Complete Gold Kit protocol was used to deplete total RNA of ribosomal RNA and prepare strand-specific libraries

value: Cartilage

tag: passage

tag: treatment

value: 4h IL-1beta


title: IL1b 1


title: Male liver nuclear RNA pool 2

description:
nuclear RNA pooled from 4 mouse livers
poly-A selected, unstranded library
G95_M2

value: male


title: IL1b 3


title: Control 3

value: No stimulation


title: Control 2


title: A5SS_RNA

city: Seattle, WA 98195

first: Alexander

middle: B

last: Rosenberg

state: WA

address: 4000 15th Ave NE

department: Electrical Engineering

institute: University of Washington

data_processing:
The fastq files were processed using custom python scripts. All of the analysis is available at https://github.com/Alex-Rosenberg/cell-2015
Genome_build: NA
Supplementary_files_format_and_content: For each library we have a file with all the barcode – intronic sequence associations, as well as a matrix with the number of spliced reads at each position for each library member.
Supplementary_files_format_and_content: [A5SS_spliced_reads.txt] Counts of spliced reads at each position for each library member in the alternative 5' library

growth_protocol: HEK293 cells were cultured in in DMEM (Cellgro) + 10% FBS and L-glutamine/penicillin/streptomycin on coated plates. Plates were coated for 24 hours with 8mL of 100x diluted extracellular matrix gel (Sigma-Aldrich) before HEK293 cells were added to the plates.

extract_protocol:
Total RNA was extracted using RNeasy (Qiagen) kits 24 hours after transfection. The optional on column DNaseI digest was performed with the RNase-Free DNase Set (Qiagen). Total RNA quality and purity was tested by measuring the A260/A280 ratio on a NanoDrop 1000 Spectrophotometer, and in some cases by measuring the ratio of the 18S and 28S rRNA bands on a native 1% agarose gel. mRNA was separated from 35-48ug total RNA using polyA Spin mRNA Isolation Kits (New England Biolabs). Isolated mRNA was again digested by DNaseI for 30 minutes using the Turbo DNA-free kit (Ambion). cDNA was then synthesized from 109-374ng mRNA using MultiScribe Reverse Transcriptase (Ambion) and Oligo d(T)16 (Ambion). cDNA synthesis was performed by holding reactions at 25°C for 10 min, 42°C for 110 min, and 85°C for 5 min. The quality of cDNA and presence of DNA contamination were checked through qPCR: Citrine, mCherry, and TBP were compared using cDNA, No Reverse Transcription Controls (NRTC) and a No Template Control (NTC). The results indicated that there was no plasmid or genomic DNA carryover into the cDNA reactions.
The resulting cDNA was then amplified by PCR to generate products compatible with the Illumina HiSeq2000 Flow Cell. PCR reactions were performed in 100uL with 2x Phusion HF Master Mix (New England Biolabs), 50pmol forward primer and 50pmol reverse primer with sample specific barcodes and 20% of each cDNA reaction. Cycling was done on a BioRad T100TM Thermal Cycler with the following protocol: 98°C for 5 min, then 7 cycles of 98°C for 10s, 67.5°C for 15s, 72°C for 30s, and a final extension step at 72°C for 5 min. The necessary number of cycles was determined for each sample by first running PCR reactions with EvaGreen in a Biorad CFX and determining when fluorescence began to plateau. Following PCR, 10% of the products were run on a 2% agarose gel to determine if the expected bands were present. The remainder of the PCR products was purified using the QIAquick PCR Purification kit (Qiagen) and eluted into 30uL of EB. Concentrations as well as A260/280 and A260/230 ratios were measured on a NanoDrop 1000 Spectrophotometer.  Illumina compatible PCR products were also generated from the DNA plasmid library with the same protocol as above except the cDNA template was replaced with 10ng of plasmid library DNA and the PCR reaction was performed with 20 cycles.

treatment_protocol: For transfection of a complex pool of plasmids, 1.2 million cells were seeded in a 10cm dish 24 hours before transfection. We mixed 10ug of the plasmid library in 1ml of Opti-MEM Reduced Serum Medium (Life Technologies) with 30ul of Lipofectamine LTX and 10ul of Plus Reagent (Life Technologies), before transfecting into the 10cm dish. The DMEM was was replaced 5 hours after transfection.

tag: cell line

tag: transfection

value: A5SS_DNA plasmid library


title: Danio_rerio_SnapC_MUT

city: Seattle

first: Russell

last: Berg

data_processing:
Base calling was performed using Real-Time Analysis Software v1.17
CASAVA v1.8.2 was employed for demultiplexing and fastq file generation
Fastq files were filtered by keeping only those reads that passed Illumina's default Chastity threshold of >= 0.6
Reads were aligned using the default settings in TopHat v2.0.5 (running bowtie 0.12.8)
Cuffmerge and Cuffdiff: as described in PMID 23299976
Genome_build: Zv9r71;
http://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.4
Supplementary_files_format_and_content: Cuffdiff output file
http://www.broadinstitute.org/webservices/gpModuleRepository/download/prod/module/?file=/Cufflinks.cuffdiff/broad.mit.edu:cancer.software.genepattern.module.analysis/00236/3/Cufflinks_cuffdiff.pdf

organism: Danio rerio

source_name: snapc1b mutation at 13: 37996163 (T->C)

growth_protocol: zebrafish embryos and larvae were maintained by standard husbandry protocol. See Tobin, et al.

extract_protocol:
Individual larvae were euthanized at 6dpf and a small piece of tissue from the head of each animal removed with forceps. The head was placed in HotShot DNA extraction buffer. The corpse was placed in 50ul Trizol for RNA isolation (Invitrogen). gDNA was genotyped by HRM and mutant RNA pooled. Trizol extraction followed as per manufacturer’s protocol. RNA was purified with LiCl extraction.
Genotyping primers:
snapc1b_HRM Forward: 5’ - CCACAAATTCCAAATGACATTGA -3’
snapc1b_HRM Reverse: 5’ - CCTTTTCTCTCTTGGCTCTTGTTT -3’
RNA quality control: Total RNA integrity was checked using an Agilent 2200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA).
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina, Inc., San Diego, CA, USA) and a Sciclone  NGSx Workstation (PerkinElmer, Waltham, MA, USA).  Library size distributions were validated using an Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).  Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).  RNA-seq libraries were pooled (2-plex) and clustered onto a flow cell lane using an Illumina cBot.  Sequencing was performed using an Illumina HiSeq 2500 Rapid mode employing a paired-end, 50 base read length (PE50) sequencing strategy.

tag: strain background

value: ABxWIK

tag: developmental stage

value: 7 days post fertilization

tag: genotype/variation

tag: tisue

value: whole larvae


title: Flag-DKC1

city: Sherbrooke

first: Michelle

middle: S

last: Scott

state: Quebec

address: 3201 Jean Mignault

department: Biochemistry

country: Canada

institute: University of Sherbrooke

data_processing:
Cutadapt was used to remove tags and adaptors from the raw reads obtained from the fastq files for each sequencing experiment. Because read lengths are longer than the RNAs sequenced, adapters are present at both ends of the reads.  Cutadapt was thus run twice to remove adapters at both ends, with parameter values -g CTGGAATTCGCGGTTAAA -a ANANCGGAANANCACACGTCTGAACTCCAGTCNC for the first run and -g TGGNGTTNGACGTGTGCTCTTCCGATCT -a TTTANCCGCGAATTCCAN for the second run. Other parameters were set to --minimum-length 10 --match-read-wildcards --times 5 -q 20 --paired-output.
The resulting reads were aligned using Bowtie2 to an index consisting of all non-coding RNAs annotated on build hg38 of the human genome by Ensembl. Bowtie parameter values used were –local, -I 13.
The resulting SAM file was processed using a custom python script which captures a regular expression present in the hTR sequences, namely the ACA box found 3 residues from the 3’ end of hTR, and calculates the number of non-genomic consecutive As following the 3’ end of the molecule. Using this strategy, the script counts the number of reads aligned to hTR, not aligned to hTR, having less than 3 nucleotides between the 3’ end and the ACA box, and the number of reads for each length of polyadenylated tail.
Genome_build: hg38
Supplementary_files_format_and_content: Excel file compiling the abundances of all forms of hTR

growth_protocol: Cells were grown in DMEM containing 10% tetracycline-free FBS, Hygromycine (75 µg/ml), and Blasticidin (15 µg/ml), and were passaged until they reached 90% confluency.

extract_protocol:
RNA co-immunoprecipitation (RIP) assays and extraction of RNA from beads were carried out as previously described (Bergeron et al. 2015, Mol. Cell. Biol., 35: 2503-2517).
Preparation of human telomerase RNA-specific libraries was based on the RNA ligase-mediated 3’ RACE approach described by Goldfarb and Cech (BMC Mol Biol. 2013, 14: 23). Barcoded libraries were combined and analyzed on an Illumina MiSeq instrument.

treatment_protocol: Expression from the tetracycline-sensitive promoter was induced using 500 ng/ml doxycycline.

value: human embryonal kidney cells

value: Flag-DKC1 with tetracycline-sensitive promoter

tag: induced with

value: 500 ng/ml doxycycline

tag: rip antibody

value: Anti-Flag M2

tag: rip antibody vendor

value: Sigma-Aldrich

tag: rip antibody cat.#

tag: rip antibody lot #

tag: molecule subtype

value: human telomerase RNA


title: Flag-PABPN1

tag: cell type

value: Flag-PABPN1 with tetracycline-sensitive promoter


title: Flag-hTERT

value: Flag-hTERT with tetracycline-sensitive promoter


title: Danio_rerio_SnapC_WT

source_name: snapc1b wild type


title: A3SS_DNA

description:
Plasmid DNA
synthetic sequences

data_processing:
The fastq files were processed using custom python scripts. All of the analysis is available at https://github.com/Alex-Rosenberg/cell-2015
Genome_build: NA
Supplementary_files_format_and_content: For each library we have a file with all the barcode – intronic sequence associations, as well as a matrix with the number of spliced reads at each position for each library member.
Supplementary_files_format_and_content: [A3SS_seq.txt] Sequences in alternative 3' library

molecule: other

organism: synthetic construct

source_name: plasmid prep

value: A3SS_DNA (alternative 3' library)


title: A3SS_RNA

data_processing:
The fastq files were processed using custom python scripts. All of the analysis is available at https://github.com/Alex-Rosenberg/cell-2015
Genome_build: NA
Supplementary_files_format_and_content: For each library we have a file with all the barcode – intronic sequence associations, as well as a matrix with the number of spliced reads at each position for each library member.
Supplementary_files_format_and_content: [A3SS_spliced_reads.txt] Counts of spliced reads at each position for each library member in the alternative 3' library

value: A3SS_DNA plasmid library


title: HD_iPSC_8

status: Public on Oct 20 2015

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

data_processing:
RNAseq reads were aligned to the human genome assembly using STAR 2.3.0 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample
Supplementary_files_format_and_content: rawReadCounts.csv is linked as a supplementary file on the Series record

growth_protocol: All lines of iPSCs were grown on Matrigel (BD Biosciences) in mTeSR1 defined medium (Stemcell Technologies). Optimal passaging occurred at 70-80% confluency and was performed by treatment for 1 h with 1 mg/ml collagenase. For RNA-Seq sample preparation, comparison lines were grown and expanded in tandem for 3 passages before collection of total RNA.

extract_protocol:
Total RNA was purified from iPSCs or NSCs using RNeasy Mini kit (Qiagen). For RNA-Seq samples, an additional 350 ul RLT/-mercaptoethanol solution were added to each tube, followed by vortexed and centrifuged to lyse the cells. A Qiacube instrument was then used to extract the RNA using the RNase Micro protocol. The samples were eluted in 25 ul PCR grade H20. Sample OD was obtained by nanodrop for QC and then diluted to 4ng/40 ul.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq by IIlumina library preparation on a Hiseq 2000 was performed by the core genomics facility at the University of Minnesota. The samples were sequenced on a 50bp PE run. 32 libraries prepared and barcoded using TruSeq RNA Library preparation kits.

treatment_protocol: NSCs were generated with STEMdiff Neural Induction Medium from Stemcell Technologies according to manufacturer’s manual.

tag: region

value: HD

value: iPSC

tag: group


title: HD_iPSC_2


title: HD_iPSC_6


title: HD_iPSC_5


title: HD_iPSC_3


title: HD_iPSC_4


title: HD_NSC_8

value: NSC


title: HD_iPSC_1


title: HD_NSC_7


title: HD_NSC_5


title: HD_NSC_4


title: C116_iPSC8


title: HD_NSC_3


title: HD_NSC_2


title: C116_iPSC_7


title: HD_NSC_1


title: Control 1

tag: tissue

value: Cartilage

tag: passage

value: No stimulation


title: HD_iPSC_7


title: C116_iPSC_1


title: C116_iPSC_4


title: C116_NSC_8


title: C116_NSC_5


title: C116_iPSC_3


title: C116_NSC_7


title: C116_NSC_6


title: C116_NSC_3


title: C116_NSC_4


title: C116_NSC_1


title: C116_NSC_2


title: HD_NSC_6


title: mutHEK293_Input

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Embryonic Kidney (HEK)

growth_protocol: H293T cells were cultured in DMEM + 10% serum at 37°C / 5% CO2

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

tag: chip antibody

value: Input

tag: antibody manu.

tag: antibody catalog


title: HEK293_CTCF

value: CTCF

value: Millipore


title: HEK293_Input


title: mutHEK293_CTCF


title: C116_iPSC_6


title: Thy6 sample 1

first: Gay

middle: Miriam

last: Crooks

state: California

address: 610 Charles E. Young Drive, East

department: Pathology & Laboratory Med

institute: University of California Los Angeles

description: CD8+ T cells purified from thymus

data_processing:
The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in paired-end mode. We followed a 2-pass alignment strategy: in the first round, reads were aligned to a genome index that included both the genome sequence (GRCh37 primary assembly) and the exon/intron structure of known gene models (Ensembl GRCh37.71). Novel splice junctions were then included in the junction database to generate a new genome index for re-alignment. Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%, minimum intron length=21, minimum alignment overhang for novel junctions=10, infinite penalty for non-canonical splice sites
Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-nonemtpy” mode for version v0.6.1p2). The reference annotation was built using Gencode protein coding genes (GRCh37.71) and an in-house database of long non-coding RNAs (see Supplementary Table 1 in manuscript website).
Expression estimates in units of FPKMs (fragments per kilobase of mappable gene length and million reads) were obtained after normalizing the counts matrix with sequencing depth and gene effective length. These expression levels, which are expected to correlate with mRNA relative abundance within each sample (within-sample normalization), were used for rank-order classifier in comparative analyses for individual samples. Differential expression or global clustering across samples was always carried out after inter-sample normalization.
Genome_build: GRCh37
Supplementary_files_format_and_content: Expression estimates in units of FPKMs. Format: Gene id / Average expression estimates for each cell type.

source_name: CD3+CD4neg CD8+

growth_protocol: Anonymous normal human thymi and bone marrow were obtained from donors via the UCLA Translational Pathology Core Laboratory and ALLCELLS, Alameda, CA respectively, in accordance with UCLA Institutional Review Board guidelines. The magnetic activated cell sorting (MACS) system (Miltenyi Biotec, San Diego, CA) was used to enrich CD34+ cells from bone marrow and thymus prior to isolation of CD34+ subsets by flow cytometry.. Bone marrow CD34+ cells were incubated with the following antibodies: CD34-APC-Cy7 (581), CD38-APC (HIT2), CD10-PE-Cy7 (HI10a), CD62L-PE (DREG-56), CD45RA Percpcy5.5 (all from Biolegend, San Diego, CA), as well as the following FITC-labeled lineage depletion antibodies: CD3 (SK7), CD14 (M2E2), CD19 (4G7), CD56 (MY31), and CD235a (GA-R2)(Becton Dickinson [BD], San Jose, CA). CD19 was not included in the lineage depletion cocktail used for sorting BCP. An unstained control was used to set gates. The following CD34+ enriched thymic cells were incubated with CD34 percp-cy5.5 (8G12), CD7 FTIC (4H9), CD1a PE (HI149) and APC-labeled CD4 (RPA-T4) and CD8 (SK1). To isolate DP and SP thymocytes, non-CD34 enriched thymic cells were incubated with CD3 APC (UCHT1), CD4 FTIC (RPA-T4), and CD8 Percp (SK1) (all from BD). Dead cells were gated out using 4’,6-diamidino-2-phenylindole (DAPI). FMO (fluorescence minus one) controls were used to set gates for isolating thymic cells.

extract_protocol:
The Trizol method (Mirneasy RNA extraction mini kit, Qiagen, Valencia, CA) was used to extract RNA from all samples.
The Ovation RNA‑Seq System V2 (NuGen, San Carlos, CA) was used to convert 6-10 ng of RNA into amplified cDNA (linear amplification). The cDNA was sheared using a S220 focused ultrasonicator (Covaris, Woburn, MA) to generate an average fragment size of 350 base pairs. 900 ng of sheared cDNA was converted into sequencing libraries using the Encore Rapid DR Multiplex kit (NUGen)

treatment_protocol: The following immunophenotypic definitions were used to isolate progenitors from 1) bone marrow CD34+ cells: CD34+CD38neglinneg  (HSC), CD34+CD45RA+CD38+CD10neg CD62Lhi linneg (LMPP), (CD34+ CD38+CD10+CD45RA+ linneg (CLP) and CD34+ CD38+CD19+linneg (BCP); 2) thymic CD34+ cells: CD34+CD7negCD1anegCD4negCD8neg (Thy1), CD34+CD7+CD1anegCD4negCD8neg (Thy2), CD34+CD7+CD1a+CD4negCD8neg (Thy3); and 3) thymic CD34neg cells: CD4+CD8+ (Thy4), CD3+CD4+CD8neg  (Thy5), and CD3+CD4neg CD8+ (Thy6) (Supplemental Fig.1b). All populations were isolated on a FACSAria (355, 405, 488, 561 and 633 nm lasers) (BD Immunocytometry Systems). Progenitor populations were isolated from 2 donors (2 biological replicates) for bone marrow and thymus (separate donors for bone marrow and thymus). Fresh samples were used for both replicates of the bone marrow and for one replicate of the thymus. Cells cryopreserved post MACS were thawed and used for isolation of subsets by flow cytometry for the other replicate of the thymus.

value: Thymus

tag: cell markers

value: CD3+CD4neg CD8+


title: Thy6 sample 2

description: CD8+ T cells purified from thymus


title: Thy5 sample 2

description: CD4+ T cells purified from thymus


title: Thy4 sample 2

description: Double positive thymocytes purified from thymus


title: Thy5 sample 1

description: CD4+ T cells purified from thymus


title: C116_iPSC_5


title: C116_iPSC_2


title: Thy3 sample 2

description: Thy3 thymic progenitors purified from thymus


title: Thy4 sample 1


title: Thy2 sample 2

description: Thy2 thymic progenitors purified from thymus

source_name: CD34+CD7+CD1aneg CD4negCD8neg

value: CD34+CD7+CD1aneg CD4negCD8neg


title: Thy3 sample 1


title: Thy2 sample 1


title: Thy1 sample 2

description: Thy1 thymic progenitors purified from thymus

source_name: CD34+CD7neg CD1aneg CD4negCD8neg

value: CD34+CD7neg CD1aneg CD4negCD8neg


title: Thy1 sample 1


title: BCP sample 1

description: B-committed progenitors purified from bone marrow

value: Bone marrow


title: CLP sample 2

description: Common lymphoid progenitors purified from bone marrow


title: BCP sample 2


title: CLP sample 1


title: LMPP sample 2

description: Lymphoid-primed multipotent progenitors purified from bone marrow

source_name: CD34+CD45RA+CD38+CD10neg CD62Lhilinneg

value: CD34+CD45RA+CD38+CD10neg CD62Lhilinneg


title: HSC sample 1

description: Hematopietic stem cells purified from bone marrow


title: HSC sample 2


title: LMPP sample 1


title: M5

data_processing:
Illumina Casava1.9 software used for basecalling.
Trimmomatic v0.32 was used to remove adapter sequences, and quality filtering using the following parameters: LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36. Reads shorter than 36 bp after trimming were thus removed from the study.
Filtered reads were then aligned to the reference genome using tophat v2.0.11 and the --b2-very-sensitive Bowtie2 (v2.1.0) preset, guided by GTF file. Of note, reads were aligned to the reference genome to which theERCC spike-ins were added.
The number of reads mapping uniquely to each gene was counted by HTSeq-count v0.6.1p1, and processed for statistical analysis using the R Bioconductor packages edgeR (v3.6.7), and DESeq2 (v1.4.5).
Genome_build: Rnor_5.0 Ensembl Release 76 (August 2014)
Supplementary_files_format_and_content: DESeq2_normalized_counts.txt: Tab-delimited text file contain normalized read counts for each sample, as computed by DESeq2.
Supplementary_files_format_and_content: edgeR_normalized_counts.txt: Tab-delimited text file contain normalized read counts for each sample, as computed by edgeR.

source_name: medial prefrontal cortex

tag: strain

value: Sprague-Dawley

value: medial prefrontal cortex

tag: gender

value: Male

tag: estrous cycle


title: CL_L_27

city: Dunsany

first: Paul

last: Cormican

state: Meath

address: Grange

country: Ireland

institute: Teagasc

data_processing:
base calls using using CASAVA v1.9
quality control checks on raw sequence data with FASTQC v0.10.0
adaptor sequences and low quality bases from the 3’ end of the sequence reads removed using Trim Galore;(http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/); reads less than 20 bases in length were then discarded
The remaining reads were aligned to the bovine genome (UMD3.1 assembly) [doi:10.1186/gb-2009-10-4-r42] using STAR v2.3.0 [doi: 10.1038/nmeth.1363.] allowing two mismatches to account for sequencing errors and SNP
Only uniquely mapped reads were retained for downstream analysis.
featureCounts [doi: 10.1093/bioinformatics/btt656] was used to assign uniquely aligned reads to Ensembl (v73) annotated exons; Reads mapping to multiple features or overlapping genes were discarded.
Genome_build: UMD3.1 assembly
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

organism: Bos taurus

source_name: Corpus Luteum

growth_protocol: See Cummins et al doi:10.3168/jds.2011-4742

extract_protocol:
Standard trizol extraction see Chomczynski doi:10.1016/0003-2697(87)90021-2
Illumina TruSeq RNA Sample Preparation Kit v2

treatment_protocol: Washed in PBS, connective tissue removed, snap-frozen in liquid nitrogen, stored -80 freezer

value: Corpus Luteum tissue biopsy

tag: timepoint

value: day 13 of oestrous cycle

tag: genotype

value: Fert- (low fertility)

tag: batch

tag: parity


title: CL_L_17


title: CL_H_24

value: Fert+ (high fertility)


title: CL_L_25


title: CL_H_21


title: CL_H_23


title: CL_L_20


title: MB_TGFB_3_RNA-Seq

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: MBNL1 with recombinant porcine TGFβ - Input RNA-Seq

data_processing:
FASTQ sequence files were aligned to the rat genome version 5 using TopHat2 with de novo junction discovery.
Alternative splicing, alternative polyadenylation and differential gene expression analyses along with all visualized pathways, heatmaps and Venn 14 diagrams were obtained using AltAnalyze version 2.0.9 (Emig et al., 2010), and the Ensembl 77 / UCSC mRNA rn5 database filtering on genes with an RPKM>1. Alternative splicing events were identified using a reciprocal isoform percent spliced difference of at least 25% and putative alternative polyadenylation using a splicingindex difference > 2 or ASPIRE δI value > 0.2, occurring in the last of exon of the gene.
For all RNAseq experiments pathways and ontology enrichment analyses were performed with ToppGene (Chen et al., 2009) and GO-Elite (Zambon et al., 2012). All heatmaps from AltAnalyze were created using the HOPACH package via a connection to R (Salomonis et al., 2005).
Genome_build: rat genome version 5

source_name: Neonatal Rat Cardiac Fibroblasts

extract_protocol:
The resin was washed and RNA extracted using a Magna RIP kit (Millipore) and phenol-chloroform precipitation. For cardiac fibroblast experiments RNA was isolated and prepared with an RNAeasy kit (Qiagen).
Eluted RNAs were detected by RNAseq analysis using paired-end 100 nucleotide (nt) sequencing and 40 million reads for input-RNAs and RIP-RNAs. RNA Seq libraries were generated with Illumina TruSeq Stranded mRNA HT kits

treatment_protocol: To determine the mRNAs that directly bind to MBNL1 a Flag-epitope tagged MBNL1 was adenovirally overexpressed in cardiac fibroblasts. Fibroblast lysates were collected 36 hr later and then incubated with Flag-M2 affinity resin (Sigma) overnight at 4°C.


title: CL_H_16


title: CL_H_19


title: CL_L_28


title: MBNL_3_RNA-Seq

description: MBNL1 murine cDNA adenoviral - Input RNA-Seq


title: Endo_L_14

source_name: Endometrium

value: ipsilateral uterine horn biopsy


title: CL_H_18


title: Control_3_RNA-Seq

description: b-Galactosidase control adenoviral - Input RNA-Seq


title: MBNL_1_RNA-Seq


title: MB_TGFB_3_RIP

description: MBNL1 with recombinant porcine TGFβ - RIP-Seq


title: MB_TGFB_1_RIP


title: Endo_H_13


title: MBNL_1_RIP

description: MBNL1 murine cDNA adenoviral - RIP-Seq


title: MBNL_3_RIP

description: MBNL1 murine cDNA adenoviral - RIP-Seq


title: Control_1_RIP

description: b-Galactosidase control adenoviral - RIP-Seq


title: Endo_L_11


title: Endo_H_12


title: Endo_L_8


title: Endo_H_7


title: CL_H_15


title: Endo_L_6


title: Endo_H_5


title: A3-1 RNA-seq

city: Seoul

first: Jun

last: Cho

address: Building 504 Room 509, School of Biological Sciences, Seoul National University, 1 Gwanangno, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description:
RNA-seq
mES_RPF_RNA-seq.csv

data_processing:
Basecalls performed using Illumina Pipeline CASAVA v1.8.2
The first few steps in the sequence analysis were done using Assaf Gordon's FASTX-Toolkit. The reads was trimmed from the 3'-end so that the remaining reads were 27-nt in length. After trimming, the reads were collapsed to generate a set of unique sequences.
The collapsed reads were aligned to were aligned to non-redundant RefSeq transcript sequences (constructed from UCSC mm9 assembly) using Bowtie version 1.1.1 with options for unique mapping that allows a maximum 1-nt of mismatch.
To quantify translation and mRNA abundance of individual genes, the number of the RPF and RNA-seq tags aligned to each individual mRNA transcript were counted. The transcripts with low read counts in RPF and RNA-seq (i.e., < 50 raw reads in all of the libraries) were excluded to reduce noise.
Each read count per individual mRNA transcript was normalized by the median values of the read counts in the RPF or RNA-seq libraries ("ncount" in mES_RPF_RNA-seq.csv).
Genome_build: mm9
Supplementary_files_format_and_content: The .csv files report read counts for individual genes/transcripts.

source_name: embryonic stem cell

growth_protocol: Mouse embryonic stem cells were incubated in DMEM media containing 20% FBS, non-essential amino acid, nucleosides and LIF at 37℃.

extract_protocol:
The cells were lysed with the buffer of 10 mM Tris-HCl at pH 7.4, 100 mM KCl, 5 mM MgCl2, 2mM DTT,  1% Triton X-100, 100 µg/mL cycloheximide with 1 µL protease inhibitor cocktail (Calbiochem), 2 µL RNasin (Promega) and 2 µL SUPERase In (Ambion) to maintain bindings between the ribosomes and mRNAs. the ribosome-mRNA complexes were purified by using Sephacryl S-400 columns
The preparation method of libraries were based on the standard protocol of Illumina Truseq small RNA library prep.

treatment_protocol: The cells were treated with siRNA for luciferase and incubated for 48 hours.

tag: cell line

value: ES cell line A3-1

tag: sirna sequence for luciferase


title: Endo_H_2


title: Endo_H_1


title: Endo_L_3


title: TP - SPD 1745 (tprA) and SPD 1746 (phrA) deletion strain, IU6118 rep2

city: Bloomington

first: Ho-Ching

middle: Tiffany

last: Tsui

state: IN

address: 1001 E. Third St.

department: Biology

institute: Indiana University

description:
processed data file: DEG_list_TP_WZ.txt, totalcounts15samples.tsv
TP 2

data_processing:
Trimming using Trimmomatic version 0.17
java -classpath trimmomatic-0.17.jar org.usadellab.trimmomatic.TrimmomaticSE -phred33 FILENAME ./run307.PN1_GTAGAG_L002_R1.trimmed.fastq ILLUMINACLIP:vec.fa:2:40:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:75
Mapping using bowtie2 and Streptococcus pneumoniae D39 reference
NC_008533,NC_005022 with default options
Gene counts using in house script and Streptococcus pneumoniae D39 reference
Differential expression using DESeq
estimateDispersions:method="blind", sharing-mode="fit-only"
Genome_build: NC_008533,NC_005022
Supplementary_files_format_and_content: DEG_list*.txt: differential expression using DESeq

organism: Streptococcus pneumoniae

growth_protocol: Strains IU1781, IU4955, IU4957 and IU6118 were grown exponentially in BHI media at 37°C to OD620 ≈0.15 to 0.2 (exponential phase).

extract_protocol:
To isolate RNA for RNA-sequencing analysis, starter cultures were used to inoculate 30 ml cultures of BHI broth in 50 mL conical tubes. RNA was extracted from 23 mL of exponentially growing culture (OD620 of ~0.15) using the FastRNA Pro Blue Kit (MP Bio) according to the manufacturer’s guidelines. Briefly, cells were isolated by centrifugation at 14,500 x g for 5 minutes at 4°C.  The cells were resuspended in 1 ml RNApro (MP Bio) and processed twice in the Fast Prep Instrument (MP Bio) for 40 seconds at a setting of 6.0. Chloroform and 100% ethanol were used to extract and precipitate the RNA from the resulting lysate and the miRNeasy minikit (Qiagen) and on-column DNase I treatments were used to purify the RNA as above. The amount and purity of all RNA samples isolated were assessed by NanoDrop spectroscopy (Thermo Fisher). RNA integrity was assessed using the Agilent 2100 BioAnalyzer (Aligent Technologies).
cDNA libraries were prepared from total RNA by the University of Wisconsin-Madison Biotechnology Center.  The mRNA was enriched from two micrograms total RNA using RiboZeroTM rRNA Removal (Gram-positive bacteria) Kit (EpiCentre Inc.). rRNA-depleted mRNA samples were purified by ethanol precipitation and quantified by fluorometry with the Qubit® RNA assay kit (Invitrogen). Double stranded cDNA synthesis was performed following ScriptSeqTM v2 RNA-Seq Library Preparation guide (EpiCentre Inc.) in accordance with the manufacturer’s standard protocol. Thirty nanograms of enriched mRNA were fragmented using divalent cations via incubation for 5 min at 85°C. The first strand of cDNA was synthesized by reverse transcription using random-sequence primers containing a tagging sequence at their 5’ ends. Di-tagged cDNA was synthesized by random annealing of a terminal-Tagging Oligo (TTO) to the 3’ end of the cDNA for extension of the cDNA by DNA polymerase. Di-tagged cDNA was purified using Agencourt AMPure® XP beads (Beckman Coulter) followed by PCR amplification for 15 cycles using FailsafeTM PCR enzyme and ScriptSeq Index DNA primer set (EpiCentre Inc.). This step generated the second strand of cDNA and completed the addition of Illumina adapter sequences incorporating a user-defined barcode. The amplified libraries were purified using Agencourt AMPure® XP beads. Quality and quantity were assessed using an Agilent DNA 1000 chip (Agilent) and Qubit® dsDNA HS assay kit (Invitrogen), respectively. Libraries were standardized to 2 μM. Cluster generation was performed using standard Cluster kits (v3) and Illumina Cluster Station.

treatment_protocol: For SG sample, IU1781 was grown to OD620 of 0.03, treated with 10 µM 10-residue synthetic PhrA,  and then allowed to incubate to OD620 ≈0.15 to 0.2 before harvesting.

tag: strain background

tag: genotype/variation


title: SG - wild type cells treated with 10-residue synthetic PhrA peptide rep3

description:
processed data file: DEG_list_SG_WZ.txt, totalcounts15samples.tsv
SG 3

value: wild type

tag: treated with

value: 10 µM 10-residue synthetic PhrA


title: SG - wild type cells treated with 10-residue synthetic PhrA peptide rep1

description:
processed data file: DEG_list_SG_WZ.txt, totalcounts15samples.tsv
SG 1


title: TP - SPD 1745 (tprA) and SPD 1746 (phrA) deletion strain, IU6118 rep3

description:
processed data file: DEG_list_TP_WZ.txt, totalcounts15samples.tsv
TP 3


title: TP - SPD 1745 (tprA) and SPD 1746 (phrA) deletion strain, IU6118 rep1

description:
processed data file: DEG_list_TP_WZ.txt, totalcounts15samples.tsv
TP 1


title: PA - SPD 1746 (phrA) deletion strain, IU4957 rep3

description:
processed data file: DEG_list_PA_WZ.txt, totalcounts15samples.tsv
PA 3

value: SPD 1746 (phrA) deletion strain


title: PA - SPD 1746 (phrA) deletion strain, IU4957 rep2

description:
processed data file: DEG_list_PA_WZ.txt, totalcounts15samples.tsv
PA 2


title: Control_3_RIP


title: Endo_H_10

tag: tissue


title: TA - SPD 1745 (tprA) deletion strain, IU4955 rep3

description:
processed data file: DEG_list_TA_WZ.txt, totalcounts15samples.tsv
TA 3

value: SPD 1745 (tprA) deletion strain


title: TA - SPD 1745 (tprA) deletion strain, IU4955 rep2

description:
processed data file: DEG_list_TA_WZ.txt, totalcounts15samples.tsv
TA 2


title: PA - SPD 1746 (phrA) deletion strain, IU4957 rep1

description:
processed data file: DEG_list_PA_WZ.txt, totalcounts15samples.tsv
PA 1


title: Endo_L_9


title: CG1091 KO-replicate3

status: Public on Oct 19 2015

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

data_processing:
Basecalls performed using RTA 1.18.64.0
The strand specific reads were screened for ribosomal RNA by aligning with BWA (v0.6.1) against known rRNA sequences (RefSeq). Non matching reads were considerd downstream.
The rRNA subtracted were aligned with TopHat (v1.4.1) against the Drosophila melanogaster genome (FlyBase r5.44) and a maxiumum of 6 missmatches.  Introns between 20-150000 bp are allowed which is based on FlyBase statistics. Maximum multihits was set to 1 and InDels as well as Microexon-search was enabled. Additionally, a gene model was provided as GTF (FlyBase r5.44).
Aligned reads are subjected to FPKM estimation with Cufflinks (v1.3.0). In this step bias detection and correction was performed. Furthermore, only those fragments compatible with FlyBase annotation (r5.44) were allowed and counted towards the number of mapped hits used in the FPKM denominator.  snRNA, rRNA, tRNA, snoRNA and pseudogenes are masked.
The aligned reads were counted with HTSeq (0.6.1p1) and the polyA containing transcripts were subjected to differential expression analysis with DESeq (v1.10.1)
Genome_build: FlyBase dmel_r5.44
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (Standard output cufflinks); tab-delimited text file with differentially expressed genes for the whole analysis (standard output DESeq). DESeq_1.10.1.txt headers: Condition A: CG1091 KO; Condition B: WT.

organism: Drosophila melanogaster

source_name: Drosophila Schneider 2 cells

extract_protocol:
Total RNA extraction performed with Trizol (Life Technologies)
PolyA selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) followed by library preparation using NEBNext® Ultra Directional RNA Library Prep Kit for Illumina® (NEB). Following barcodes were used: 26052=CGATGT, 26051=ATCACG, 26056=GCCAAT, 26055=ACAGTG, 26054=TGACCA, 26053=TTAGGC.

value: Schneider 2 cells

value: CG1091 knockout


title: TA - SPD 1745 (tprA) deletion strain, IU4955 rep1

description:
processed data file: DEG_list_TA_WZ.txt, totalcounts15samples.tsv
TA 1


title: Wild-type (strain used IU1781 – D39 rpsL1) rep1

description:
processed data file: totalcounts15samples.tsv
WZ 1


title: Wild-type (strain used IU1781 – D39 rpsL1) rep3

description:
processed data file: totalcounts15samples.tsv
WZ 3


title: CG1091 KO-replicate2


title: CG1091 KO-replicate1


title: WT-replicate3

value: wildtype


title: SG - wild type cells treated with 10-residue synthetic PhrA peptide rep2

description:
processed data file: DEG_list_SG_WZ.txt, totalcounts15samples.tsv
SG 2


title: A3-1 RPF

description:
ribosome profiling
mES_RPF_RNA-seq.csv


title: WT-replicate2


title: WT-replicate1


title: whole flies_CG1091 rep 2 -/-

description:
Sample name: 22226
18-30 nt size selection for miRNA seq

data_processing:
Basecalling RTA v1.17.21.3
The adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG) was cut once with cutadapt (v1.2.1).
The random 4mers on 5' and 3' were removed with fastx_trimmer of the fastx-toolkit (v0.0.13). The in vitro tailing samples were only cut on 3'. The processed reads were filtered in respect of their size selection (see sample description).
Putative contamination was filtered out by aligning to sequences of S2 viruses (derived from Genbank) with tailor (v1.0b1).
All reads were aligned to the drosophila genome (Flybase r5.55) with tailor (v1.0b1). The minimum length of exact match was 18 (miRNA) and 36 (pre-miRNA).
Counts were calculated with htseq-count (v0.6.1p1). The parameters were stranded=yes and “intersection-nonempty”. A GTF containing pre-miRNAs annotations (FlyBase r5.55) was used. The annotation was split in two halves assigned to 5' an andd 3' of each miRNA region, respectively.
Counts were normalized by the total count of miRNAs in each sample (RPM).
Instead of aligning, the in vitro tailing samples were split into substrate (first 4 nuclteotides) and tail (following sequence). Untrimmed reads and reads containing nucleotides with a quality smaller 20 (PHRED) were discarded. Counts were calculated and corrected by the input since the input sample was not expected to contain tailed substrates.
Genome_build: Flybase r5.55
Supplementary_files_format_and_content: TAB delimited text files containing the reads per million (RPM) of genome matching (GM) and prefix matching (PM) 5' fixed pre-miRNA/miRNA species; TAB delimited text files containing the in vitro substrate and their counts, input subtracted counts, fraction of untailed substrate and fraction of tailed substrate

source_name: whole flies

extract_protocol:
Total RNA extraction performed with the miRVana miRNA Isolation Kit (#AM1560, Ambion). Small RNA sequencing libraries were constructed from an input ot 20ug total RNA.
RNA libraries were constructed as described in Newman et al. (2011)

tag: treatment

value: 7 base-pair frame-shift deletion in the third exon of CG1091, homozygous

tag: age

value: 0-5 day old

value: male


title: whole flies_W1118

description:
Sample name: 22230
18-30 nt size selection for miRNA seq

value: control sample


title: whole flies_CG1091 rep 1 -/+

description:
Sample name: 22225
18-30 nt size selection for miRNA seq

value: 7 base-pair frame-shift deletion in the third exon of CG1091, heterozygous


title: whole flies_CG1091 rep 2 -/+

description:
Sample name: 22227
18-30 nt size selection for miRNA seq


title: S2 cells_GFP

description:
Sample name: 20142
40-100 nt size selection for pre-miRNA seq; material from sample 4 and 5 pooled together (i.e., S2 cells_GFP reps 1-2)

source_name: S2 cells

value: dsRNA GFP treatment control sample


title: S2 cells_CG1091

description:
Sample name: 20129
40-100 nt size selection for pre-miRNA seq; material from sample 8, 9 and 10 pooled together (i.e., S2 cells_CG1091 reps 1-3)

value: dsRNA CG1091 treatment sample


title: S2 cells_GFP/Luc

description:
Sample name: 20128
40-100 nt size selection for pre-miRNA seq; material from sample 6 and 7 pooled together (i.e., S2 cells_GFP/Luc reps 1-2)

value: dsRNA GFP/Luc treatment control sample


title: S2 cells_CG1091 rep 3

description:
Sample name: 19655
18-30 nt size selection for miRNA seq


title: S2 cells_UT

description:
Sample name: 20141
40-100 nt size selection for pre-miRNA seq; material from sample 1, 2 and 3 pooled together (i.e., S2 cells_UT reps 1-3)

value: untreated sample


title: Wild-type (strain used IU1781 – D39 rpsL1) rep2

description:
processed data file: totalcounts15samples.tsv
WZ 2


title: S2 cells_CG1091 rep 2

description:
Sample name: 19648
18-30 nt size selection for miRNA seq


title: Endo_H_4

value: ipsilateral uterine horn biopsy

value: day 13 of oestrous cycle

value: Fert+ (high fertility)


title: S2 cells_CG1091 rep 1

description:
Sample name: 19639
18-30 nt size selection for miRNA seq

value: wild type


title: S2 cells_GFP rep 2

description:
Sample name: 19646
18-30 nt size selection for miRNA seq


title: S2 cells_UT rep 3

description:
Sample name: 19654
18-30 nt size selection for miRNA seq


title: S2 cells_UT rep 2

description:
Sample name: 19645
18-30 nt size selection for miRNA seq


title: S2 cells_GFP rep 1

description:
Sample name: 19637
18-30 nt size selection for miRNA seq


title: S2 cells_GFP/Luc rep 2

description:
Sample name: 19647
18-30 nt size selection for miRNA seq


title: S2 cells_GFP/Luc rep 1

description:
Sample name: 19638
18-30 nt size selection for miRNA seq


title: ProB_H3K4me1_rep_3

city: Basel

first: Mohamed-Amin

last: choukrallah

address: Maulbeerstrasse 66

department: Epigenetic

country: Switzerland

institute: FMI

data_processing:
Sequencing Reads were mapped to the mouse genome (mm9) using qAlign function, which internally uses Bowtie (http://bowtie-bio.sourceforge.net/  ) from the QuasR R package (http://www.bioconductor.org) with default settings.  Alignments were shifted by 60 bases, corresponding to an estimated fragment length of 120 bp
library-size normalized wig files were generated with the qExportWig function (default parameters) from QuasR package
Genome_build: mm9
Supplementary_files_format_and_content: wig

source_name: Pro B

growth_protocol: NUP98–HOXB4-HSC (abbreviated HSC) correspond to BM cells that were transduced with retrovirus encoding an NUP98–HOXB4 fusion protein and cultured in SCF/IL6 containing media. These cells have stem-cell properties and are able to reconstitute all hematopoietic compartments in sublethally irradiated Rag2-deficient mice, including long term HSCs (LT-HSC), short-term HSC (ST-HSC) and all hematopoietic cells. Pro B cells were sorted from the bone marrow (BM) with  the following markers ( ckit+, B220+, CD19-, CD25-, IgM-). Pro B cells were expanded in the presence of IL7 and OP9 feeder cells for 1 week.  Mature B cells were sorted from the spleen as CD19 positive cells using MACS kit and CD19 beads (#130-052-201). Mature B cells were cultured in the presence of LPS for 2 days.

extract_protocol:
Cells were fixed with 1% formaldehyde in PBS (20 ml vol./ ~1 × 108 cells) for 10 min, followed by quenching with 2.5 M glycine for 5 min. Cells were lysed for 10 min in 1 ml lysis buffer A (10 mM HEPES, pH 8.0, 10 mM EDTA, 0.5 mM EGTA, 0.25 % Triton X-100 + PI). The supernatant was discarded and the nuclei were incubated for 10 min in buffer B (10 mM HEPES, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.01 % Triton X-100 + PI). Next, the nuclei were suspended in chromatin lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0.5 % SDS) for 30 min. Sonication was performed using Bioruptor Next Gen (Diagenode) at high output intensity for 25 cycles (30on/30off). Finally the collected supernatant was diluted 5x with chromatin dilution buffer (250 mM NaCl, 1.67 % Triton X-100). The chromatin (25-50 µg) was subjected to the IP with the above mentioned antibodies and incubated overnight. The IPs were incubated with either protein A or G coupled to magnetic beads for 1 h. The beads were washed with the following buffers, twice with low salt (0.10% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 15 mM NaCl), high salt (0.10% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 50 mM NaCl), LiCl (250 mM LiCl, 1 M EDTA, 10 mM Tris pH8.0, 1% NP-40, 1% Na Deoxychholate) and once with TE (20 mM Tris-HCl, pH8.9, 2 mM EDTA). The protein-DNA complexes were eluted from the beads with 500 µl elution buffer (10mM Tris-HCl, pH7.5, 1mM EDTA, 1% SDS, 100 mM NaHCO3) and reverse cross-linked overnight at 65°C with Proteinase K. ChIPed DNA was isolated by phenol/ chloroform extraction and ethanol precipitated. 10ng of ChIPed DNA were processed for Illumina  high-seq analyzer according to the manufacturer’s protocol.
Sequencing libraries were prepared using bar-coded adapters following standard Illumina library preparation protocol. Four samples carrying different barcodes were pooled at equal molar ratios and subjected for sequencing on Illumina HiSeq 2000 sequencer according to Illumina standards.

tag: antibody

value: H3K4me1 (abcam ab8895)

tag: cell type

value: Pro B


title: ProB_H3K4me1_rep_4

tag: strain


title: ProB_H3K27ac_rep2

value: H3K27ac (Cell Signaling 8173)


title: HSC_H3K4me1_rep_3

source_name: HSC

value: HSC


title: Mat_B_H3K27ac_rep2

source_name: mature B cells

value: mature B cells


title: HSC_H3K27ac_rep2


title: whole flies_CG1091 rep 1 -/-

description:
Sample name: 22224
18-30 nt size selection for miRNA seq

value: 7 base-pair frame-shift deletion in the third exon of CG1091, homozygous

value: 0-5 day old

tag: gender


title: S2 cells_UT rep 1

description:
Sample name: 19636
18-30 nt size selection for miRNA seq


title: D2_input_ChIP-seq

city: Oxford

first: Arne

middle: Wyndham

last: Mould

state: Oxfordshire

address: Warneford Hospital

department: Psychiatry

institute: Oxford University

description:
Input
D1_D2merged_for_Wig_control_afterfiting_all.wig

data_processing:
ChIP-seq reads were mapped to mm9 using Stampy with default parameters
Peaks were called using MACS-1.4.2 with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: Wig files contains the track for the 2 merged Lhx1 ChIPs of stably Lhx1 transfected D1 and D2 clones and the parent P19 Lhx1 ChIP control.

source_name: Stably transfected P19 embryonic carcinoma cells

extract_protocol: Lysates were precleared with Protein G Dynabeads.  Complexes were then isolated with 15µg anti-Lhx1 polyclonal antibody  (Santa Cruz sc-19341,goat IgG) prebound to Protein G Dynabeads.  Sequencing libraries were then prepared using the Illumina ChIP-seq DNA Sample Prep Kit.  Libraries were size selected at ~200bp and 13 libraries were multiplexed per lane on a HiSeq 2000.

tag: cell types


title: D1_input_ChIP-seq

value: Stably transfected P19 embryonic carcinoma cells


title: P19_Lhx1_ChIP-seq

description:
ChIP
P19new_for_Wig_treat_afterfiting_all.wig

value: Anti-Lhx1 (Santa Cruz sc-19341,goat IgG)


title: D1_Lhx1_ChIP-seq

description:
ChIP
D1_D2merged_for_Wig_treat_afterfiting_all.wig


title: D2_Lhx1_ChIP-seq


title: Mat_Bcell_RNA_seq_rep1

data_processing: Sequencing Reads were mapped to the mouse genome (mm9) using qAlign function, which internally uses Bowtie (http://bowtie-bio.sourceforge.net/ ) from the QuasR R package (http://www.bioconductor.org) with default settings. Alignments were shifted by 60 bases, corresponding to an estimated fragment length of 120 bp

extract_protocol:
Cells were fixed with 1% formaldehyde in PBS (20 ml vol./ ~1 × 108 cells) for 10 min, followed by quenching with 2.5 M glycine for 5 min. Cells were lysed for 10 min in 1 ml lysis buffer A (10 mM HEPES, pH 8.0, 10 mM EDTA, 0.5 mM EGTA, 0.25 % Triton X-100 + PI). The supernatant was discarded and the nuclei were incubated for 10 min in buffer B (10 mM HEPES, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.01 % Triton X-100 + PI). Next, the nuclei were suspended in chromatin lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0.5 % SDS) for 30 min. Sonication was performed using Bioruptor Next Gen (Diagenode) at high output intensity for 25 cycles (30on/30off). Finally the collected supernatant was diluted 5x with chromatin dilution buffer (250 mM NaCl, 1.67 % Triton X-100). The chromatin (25-50 µg) was subjected to the IP with the above mentioned antibodies and incubated overnight. The IPs were incubated with either protein A or G coupled to magnetic beads for 1 h. The beads were washed with the following buffers, twice with low salt (0.10% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 15 mM NaCl), high salt (0.10% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 50 mM NaCl), LiCl (250 mM LiCl, 1 M EDTA, 10 mM Tris pH8.0, 1% NP-40, 1% Na Deoxychholate) and once with TE (20 mM Tris-HCl, pH8.9, 2 mM EDTA). The protein-DNA complexes were eluted from the beads with 500 µl elution buffer (10mM Tris-HCl, pH7.5, 1mM EDTA, 1% SDS, 100 mM NaHCO3) and reverse cross-linked overnight at 65°C with Proteinase K. ChIPed DNA was isolated by phenol/ chloroform extraction and ethanol precipitated. 10ng of ChIPed DNA were processed for Illumina HiSeq analyzer according to the manufacturer's protocol. Total RNA was extracted from 3 different cultures of HSCs, Pro B cells and LPS activated mature B cells using RNeasy Mini Kit #Qiagen 74104. Every cell culture is a pool of cells extracted from 3 mice. 10 ng of RNA were used for library preparation (ScriptSeq v2 RNA-Seq Library Preparation Kit) and sequenced according to the Illumina protocol.
Sequencing libraries were prepared using bar-coded adapters following standard Illumina library preparation protocol. Four samples carrying different barcodes were pooled at equal molar ratios and subjected for sequencing on Illumina HiSeq 2000 sequencer according to Illumina standards.


title: ProB_RNA_seq_rep2

value: ProB


title: Mat_Bcell_RNA_seq_rep2


title: Mat_Bcell_RNA_seq_rep3


title: ProB_RNA_seq_rep1


title: HSC_RNA_seq_rep3


title: HSC_RNA_seq_rep2


title: P19_input_ChIP-seq

description:
Input
P19new_for_Wig_control_afterfiting_all.wig


title: HSC_RNA_seq_rep1


title: Mat_Bcell_input


title: Mat_Bcell_H3K4me1_rep2


title: Mat_Bcell_H3K4me1_rep1


title: Mat_Bcell_H3K27ac


title: ProB_H3K27ac


title: ProB_H3K4me1_rep2


title: ProB_H3K4me1_rep1


title: HSC_input


title: HSC_H3K9me2_rep2


title: HSC_H3K9me2_rep1


title: HSC_H3K4me1_rep2


title: HSC_H3K4me1_rep1


title: HSC_H3K27ac


title: In vitro tailing randomized substrate (Input)

description:
Sample name: 15148
30-60 nt size selection for 3´ adapter ligation
synthetic randomized RNA NNNN3´

source_name: synthetic RNA oligo NNNN-3´

value: Input in the presence of rNTPs


title: In vitro tailing randomized substrate (5 min CG1091 treatment)

description:
Sample name: 15154
30-60 nt size selection for 3´ adapter ligation
synthetic randomized RNA NNNN3´

value: 5 min treatment with FLAG-Tailor in the presence of rNTPs


title: HSC_H3K4me3

value: H3K4me3 (Millipore 07-473)


title: dCas9_KRAB_HS2_CR10_rep3

city: Durham

first: Charles

last: Gersbach

state: NC

address: 101 Science Dr

department: Biomedical Engineering

institute: Duke University

data_processing:
Trim reads to 50 bp using fastx_trimmer (FASTX-Toolkit)
Filter out delivered lentiviral vector sequences using bowtie2
Alignment to reference transcriptome using bowtie2
Reads were converted from .sam to .bam using samtools view -bS
Sort reads using samtools sort
Index reads using samtools index
Duplicate reads were removed using picard-tools MarkDuplicates
Bam files were re-indexed after duplicates were removed using Samtools Index
Reads were counted using samtools idxstats
Differential expression was computed using R version 3.1.2 using the Deseq package  with default settings
Genome_build: RefSeq transcripts from hg19
Supplementary_files_format_and_content: Counts of the number of reads aligned to each RefSeq transcript

source_name: Cultured K562 cells

growth_protocol: K562 cells were obtained from the American Tissue Collection Center (ATCC) through the Duke University Cel Culture Facilities and were maintained in RPMI1640 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
1-2 million cells were washed with PBS and then lysed using Qiagen RLT buffer. Total RNA was extracted using Qiagen RNeasy mini-columns with 1% β-mercaptoethanol in RLT buffer and a 15 min on column DNase digestion. mRNA was purified using oligodT Dynabead (Invitrogen).
First-strand cDNA was synthesized using the SuperScript VILO cDNA Synthesis Kit (Invitrogen) and second-strand cDNA was synthesized using DNA polymerase I (New England Biolabs). cDNA was purified using Agencourt AMPure XP beads (Beckman Coulter). Purified cDNA was treated with Nextera transposase (Illumina) for 5 min at 55 °C to simultaneously fragment and insert sequencing primers into the double-stranded cDNA. Transposase activity was halted using QG buffer (Qiagen) and fragmented cDNA was purified on AMPure XP beads.

treatment_protocol: K562 cells were transduced with lentivirus to stably express dCas9 or dCas9-KRAB and HS2 targeted gRNA.  To facilitate transduction, the cationic polymer polybrene was added at a concentration of 4 µg/mL to the viral media.  The lentivirus contained a puromycin resistance gene, and 1 µg/ml puromycin was used to initiate selection for transduced cells approximately 96 hours after transduction.

tag: transduced gene

tag: grna target

value: globin HS2 enhancer


title: dCas9_KRAB_HS2_CR10_rep2


title: dCas9_KRAB_HS2_CR4_rep3


title: dCas9_HS2_CR10_rep3


title: dCas9_HS2_CR10_rep1


title: dCas9_KRAB_HS2_CR10_rep1


title: dCas9_HS2_CR10_rep2


title: dCas9_KRAB_HS2_CR4_rep1


title: dCas9_KRAB_HS2_CR4_rep2


title: dCas9_HS2_CR4_rep2


title: dCas9_HS2_CR4_rep3


title: dCas9_HS2_CR4_rep1


title: dCas9_KRAB_rep3


title: dCas9_KRAB_rep2


title: HSC_H3K4me1_rep_4


title: dCas9_KRAB_rep1


title: In vitro tailing randomized substrate (2 min CG1091 treatment)

description:
Sample name: 15149
30-60 nt size selection for 3´ adapter ligation
synthetic randomized RNA NNNN3´

value: 2 min treatment with FLAG-Tailor in the presence of rNTPs

tag: genotype


title: dCas9_KRAB_HS2_CR10_H3K9me3_rep2

first: Mudit

last: Chaand

address: 35 Cambridgepark Drive

institute: Syros Pharmaceuticals

data_processing:
Reads aligning to lentiviral sequence were filtered out using Bowtie2 (v2.1.0) with default parameters.
Remaining reads were aligned to hg19 reference genome using Bowtie2 (v2.1.0) with default parameters.
Aligned reads were sorted using samtools (v1.2).
PCR Duplicates were removed using samtools (v1.2).
Reads aligning to ENCODE blacklist regions were removed using BEDTools (v2.23.0, intersectBed).
Read normalized (reads per million mapped reads) bedgraph files were made using BEDTools (v2.23.0, genomeCoverageBed).
BigWig files were made from bedgraph files using bedGraphToBigWig (v4).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files containing RPM normalized read signal

extract_protocol:
For each replicate, 2 ×10^7 nuclei were re-suspended in 1 mL of RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS in PBS at pH 7.4). Samples were sonicated using a Diagenode Bioruptor XL sonicator at 4°C to fragment chromatin to 200-500 bp segments. Insoluble  components were removed by centrifugation for 15 min at 15000 rpm. We conjugated 5  µg of anti-FLAG (Sigma-Aldrich, F1804), or anti-H3K9me3 (Abcam,  ab8898) to 200 µl of either sheep anti-rabbit or sheep anti-mouse IgG magnetic beads  (Life Technologies 11203D/11201D). Sheared chromatin in RIPA was then added to the  antibody-conjugated beads and incubated on a rotator overnight at 4°C. After incubation,  beads were washed five times with a LiCl wash buffer (100 mM Tris at pH 7.5, 500 mM  LiCl, 1% NP-40, 1% sodium deoxycholate), and remaining ions were removed with a  single wash with 1 mL of TE (10 mM Tris-HCl at pH 7.5, 0.1 mM Na2EDTA) at 4°C.  Chromatin and antibodies were eluted from beads by incubating for 1 h at 65°C in IP  elution buffer (1% SDS, 0.1 M NaHCO3), followed by incubating overnight at 65°C to  reverse formaldehyde cross-links. DNA was purified using MinElute DNA purification  columns (Qiagen).
Illumina TruSeq adapted libraries were constructed using an Apollo 324 NGS Library  Prep System with a PrepX Complete ILMN DNA Library Kit (WaferGen Biosystems  Inc). ChIP products were amplified with 15 cycles of PCR, and fragments 150-700 bp in  length were selected using an AxyPrep MAG PCR Clean-Up Kit (Axygen MAG-PCRCL-50).  Libraries were sequenced using single end 50 bp reads on an Illumina HiSeq.

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: dCas9_HS2_CR10_H3K9me3_rep3

tag: cell line


title: dCas9_KRAB_HS2_CR10_H3K9me3_rep3


title: dCas9_KRAB_HS2_CR4_H3K9me3_rep3


title: dCas9_KRAB_HS2_CR10_H3K9me3_rep1


title: dCas9_HS2_CR4_H3K9me3_rep2


title: dCas9_KRAB_HS2_CR4_H3K9me3_rep2


title: dCas9_HS2_CR4_H3K9me3_rep3


title: dCas9_KRAB_HS2_CR4_H3K9me3_rep1


title: dCas9_HS2_CR4_H3K9me3_rep1


title: dCas9_KRAB_H3K9me3_rep3

source_name: Cultured K562 cells_dCas9_KRAB_H3K9me3


title: dCas9_KRAB_H3K9me3_rep1


title: dCas9_KRAB_HS2_CR10_FLAG_rep1

value: anti-FLAG

value: Sigma-Aldrich


title: dCas9_KRAB_H3K9me3_rep2


title: Mat_Bcell_H3K27me3_rep1


title: Mat_Bcell_H3K9me2


title: dCas9_HS2_CR10_FLAG_rep3

source_name: Cultured K562 cells_dCas9_HS2_CR10_FLAG


title: Mat_Bcell_H3K27me3_rep2


title: Mat_Bcell_H3K4me3


title: dCas9_KRAB_HS2_CR10_FLAG_rep3


title: dCas9_KRAB_HS2_CR10_FLAG_rep2


title: dCas9_HS2_CR10_FLAG_rep2


title: dCas9_HS2_CR10_FLAG_rep1


title: dCas9_HS2_CR10_H3K9me3_rep2


title: dCas9_KRAB_HS2_CR4_FLAG_rep3


title: ProB_input

value: Pro B


title: ProB_H3K27me3_rep2


title: dCas9_KRAB_HS2_CR4_FLAG_rep2


title: ProB_H3K27me3_rep1


title: dCas9_HS2_CR4_FLAG_rep3

source_name: Cultured K562 cells_dCas9_HS2_CR4_FLAG


title: ProB_H3K9me2


title: ProB_H3K4me3


title: dCas9_HS2_CR4_FLAG_rep2


title: endosperm HT rep1

city: hangzhou

first: ying

last: zhu

address: 198, Shiqiao Rd

country: China

institute: Zhejiang Academy of Agricultural Sciences

organism: Oryza sativa Japonica Group

source_name: endosprem

growth_protocol: Rice plants (Oryza sativa sp. Japonica, Nipponbare) were grown under control temperature (28°C/ 22°C, 12-h-day/12-h-night cycle).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Five days after pollination rice plants were then transferred to either a 35°C /28°C or 28°C / 22°C artificial climate room for high temperature or control treatment

tag: Stage

value: grain-filling stage

value: endosprem

value: high temperature


title: endosperm RT rep2

tag: tissue

value: control


title: dCas9_HS2_CR4_FLAG_rep1


title: dCas9_KRAB_FLAG_rep3

source_name: Cultured K562 cells_dCas9_KRAB_FLAG


title: endosperm HT rep2

tag: treatment


title: dCas9_HS2_CR10_H3K9me3_rep1


title: endosperm RT rep1


title: No_lentivirus_control_rep3


title: dCas9_KRAB_FLAG_rep2


title: ChIP: Input_BE2C_012615 [lab: Look-DFCI]

status: Public on Oct 18 2015

source_name: Neuroblastoma

growth_protocol: Cells were grown in RPMI with 10% FBS and 1% penn/strep.

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

tag: system

value: Brain

tag: antibody manu.

tag: antibody catalog


title: leo1_2

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

data_processing:
Trimmed reads by cutadapt, to remove adaptor and length at least 15nt (-a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC -m 15)
Aligned to S. Pombe genome using Bowtie 2 (default parameters)
SAM files read into Podbat (strand-specific, resolution 25nt)
Reads normalized to tRNAs (Podbat-calculated averages)
Genome_build: ASM294v2
Supplementary_files_format_and_content: wig format, variable step

organism: Schizosaccharomyces pombe

source_name: leo1 rep2

growth_protocol: Cells were grown to mid-log phase at 30 °C.

extract_protocol:
Total RNA was extracted with hot acid phenol and chloroform.
1 µg of total RNA from each sample used to prepare library with TruSeq Small RNA Library preparation kit (Illumina).

tag: strain


title: leo1_1

source_name: leo1 rep1


title: htb1K119R_2

source_name: htb1K119R rep2


title: No_lentivirus_control_rep1


title: ChIP: H3K27ac_ab4729_BE2C _012615 [lab: Look-DFCI]


title: HuC FP+

city: Berkeley

first: Ehud

last: Isacoff

address: 279 Life Sciences Addition

department: MCB

institute: UC Berkeley

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to Zv9 using Tophat v1.4.0
FPKMs were generated using Cufflinks v2.1.1 and compared using Cuffdiff
Genome_build: Zv9
Supplementary_files_format_and_content: tab delimited text file with FPKM for each sample

source_name: spinal neurons

growth_protocol: 20 hpf embryos were used

extract_protocol:
Fluorescent neural cell bodies were FACS sorted into Trizol and flash frozen before total RNA extraction and polyA selection.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tails dissected free at the level of the 3rd somite and dissociated with trypsin/collagenase before FACS

tag: gal4 driver

value: HuC

tag: population

value: panneuronal


title: htb1K119R_1

source_name: htb1K119R rep1


title: dCas9_KRAB_HS2_CR4_FLAG_rep1

tag: transduced gene


title: ChIP: Input_NGP_012615 [lab: Look-DFCI]

value: NGP


title: rrp6_2

source_name: rrp6 rep2


title: ChIP: GATA3_sc-22206X_NGP_012615 [lab: Look-DFCI]

description: young_id: 20150206_3521

value: Santa Cruz


title: ChIP: H3K27ac_ab4729_NGP_012615 [lab: Look-DFCI]

description: young_id: 20150206_3520


title: ChIP: Input_BE2_012615 [lab: Look-DFCI]


title: ago1_1

source_name: ago1 rep1


title: rrp6_1

source_name: rrp6 rep1


title: ago1_2

source_name: ago1 rep2


title: ChIP: H3K27ac_ab4729_BE2_012615 [lab: Look-DFCI]


title: No_lentivirus_control_rep2

tag: grna target


title: wt_H3K9me2 rep1

description: ChIP-exo

data_processing:
Read alignment using Bowtie 2 (default parameters)
SAM files loaded into Podbat 0.6.0 (www.podbat.org) with options "first base only", "resolution"=25, "strand-specific" unchecked, MAPQ>0
Normalized to total  # reads
Exported to wig.
Genome_build: ASM294v2
Supplementary_files_format_and_content: wig format, variable step

growth_protocol: Liquid cultures were grown in YES media shaking at 180 rpm at 30°C.

extract_protocol:
Immunoprecipitation was done using indicated antibody from chromatin extracts prepared from mid-logarithmic phase cells. Briefly, cells were fixed in 1% formaldehyde for 30 minutes, quenched with 125 mM glycine, and washed twice in PBS. Cells were resuspended in lysis buffer (0.1% SDS, 50 mM Hepes-KOH, 1 % Triton X-100, 0.1 % sodium deoxucholate, 1 mM EDTA and 150 mM NaCl) and lysed with glass beads in a FastPrep homogenizer. The lysate was sonicated and soluble chromatin fragments with an average size of 300 bp were collected. Chromatin was immunoprecipitated with indicated antibody and protein A magnetic beads overnight. The beads were washed.
With the immunoprecipitate still on the beads, the DNA was polished, A-tailed, and ligated to an Illumina sequencing library adaptor. Digestion lambda exonuclease (final concentration 2.5U/reaction) removed nucleotides from 5′ ends of double-stranded DNA until blocked by the formaldehyde induced protein-DNA crosslink. The crosslinks were reversed (4h at 65°C) and DNA was eluted from the beads. The single-stranded DNA was subsequently made double-stranded by primer annealing and extension. A second sequencing adaptor was ligated. Using indexing primers, the fragments were PCR amplified and gel purified (Qiagen MinElute). Samples were quantified on using Qubit (HS dsDNA).

tag: genotype

value: WT

value: H3K9me2 (Abcam ab1220)


title: ChIP: GATA3_sc-22206X_Be2c_103014

description: young_id: 20141126_3340

data_processing:
Sample(s) 20141126_3337, 20141126_3340, 20141126_3342 aligned to the hg19 reference genome using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
Sample(s) 20141124_3330, 20141124_3332, 20141124_3333 aligned to the hg19 reference genome using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 46
Supplementary_files_format_and_content: WIG files represent counts of aligned reads in 50 bp bins with each read being extended 200 in the direction of alignment using MACS. Counts are in reads-per-million and floored at 0.1

growth_protocol: Kelly/SHSy5Y/BE2C was grown in RPMI with 10% FBS and 1% penn/strep.

treatment_protocol: No

value: Blood

tag: chip antibody


title: WT_2

source_name: WT rep2


title: dCas9_KRAB_FLAG_rep1

value: globin HS2 enhancer

tag: chip antibody vendor


title: 1020 FP+

value: olig2+ subpopulation


title: Input for ChIP:SHSY5Y_103014


title: Input for ChIP:Be2c_103014

description: young_id: 20141126_3342


title: ChIP: GATA3_sc-22206X_SHSY5Y_103014

description: young_id: 20141124_3330


title: leo1_H3K9me2 rep2

description: ChIP-exo


title: zebrafish_RPE_V3

status: Public on Oct 17 2015

city: Saint Louis

first: Jennifer

last: Enright

address: 660 S. Euclid, Box 8118

institute: Washington University School of Medicine

data_processing:
bullfrog de novo transcriptome assembly using Trinity (version r2013-11-10)
de novo transcritome assembly filtered to include only predicted open frames > 100 aa, trinity TransDecoder plugin
bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome (PLoS One, 2013. 8(7): p. e67801) using bowtie-build
reads aligned to transcriptome using bowtie (version 0.12.7)
count table constructed from bowtie output file using custom perl script
differential gene expression called using edgeR
Genome_build: bullfrog_RPE_Trinity.fasta (included with this dataset), curated zebrafish transcriptome with cyp27 family transcripts added (PLoS One, 2013. 8(7): p. e67801, included with this dataset)
Supplementary_files_format_and_content: excel spreadsheets contain raw counts and RPKM for each transcript, as well as the output from edgeR
Supplementary_files_format_and_content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data

source_name: retinal pigment epithelium (RPE)

growth_protocol: Zebrafish were treated for three weeks with TH or a vehicle control.

extract_protocol:
Zebrafish RPE was isolated by dissection, and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection, and RNA was isolated using phenol/chloroform extraction and treated with DNase.
Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA-Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI-Seq. Bullfrog RNA was depleted of rRNA using a Ribo-Zero rRNA Removal Kit, and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI-Seq.

value: Vehicle control

tag: region of rpe

value: retinal pigment epithelium


title: bullfrog_RPE_V3

organism: Aquarana catesbeiana

value: ventral


title: bullfrog_RPE_V2


title: bullfrog_RPE_V1


title: ChIP: H3K27ac_ab4729_SHSY5Y_103014


title: zebrafish_RPE_V1


title: bullfrog_RPE_D3

value: dorsal


title: zebrafish_RPE_T3

value: Thyroid hormone


title: ChIP: GATA3_sc-22206X_BE2_012615 [lab: Look-DFCI]

description: young_id: 20150206_3511

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1


title: bullfrog_RPE_D2


title: WT_1

source_name: WT rep1


title: wt_H3K9me2 rep2

description: ChIP-exo


title: bullfrog_RPE_D1


title: zebrafish_RPE_T1


title: leo1_H3K9me2 rep1

description: ChIP-exo


title: Ovary Replicate 3 sRNAseq

status: Public on Oct 16 2015

city: Singapore

first: Vivek

last: Tanavde

state: Singapore

address: 30 Biopolis Street, #07-01, Matrix

department: Genome and Gene Expression Data Analysis Division

country: Singapore

institute: Bioinformatics Institute, A*STAR, Singapore

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
The sequenced reads were first subjected to adapter removal through the cutadapt program (Martin 2011). The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package (Friedländer et al. 2012).
The unique reads fasta file was then put through an elimination pipeline module (Vaz et al. 2010) comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database, finally culminating into an un-annotated pool of reads that served as a source of novel miRNAs and novel sRNAs.
The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl -p <zebrafish precursor miRNA fasta file> -m <zebrafish mature miRNA fasta file> -r <unique reads fasta file> -t Zebrafish
The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M-values (TMM) normalisation using the Bioconductor package edgeR (Robinson et al. 2010).
Genome_build: ZV9
Supplementary_files_format_and_content: 1. 'Danio-rerio-known-miRNA-Rel19-profile-Raw.txt': Tab-delimited text file that includes the raw counts for the known mature miRNA (miRBase Release 19).
Supplementary_files_format_and_content: 2. 'Danio-rerio-known-miRNA-Rel19-profile-Normalised.txt': Tab-delimited text file that includes the Trimmed Mean of M-values (TMM) normalised counts for the known mature miRNA (miRBase Release 19). One of the replicate of Heart (MZH008) failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.

source_name: Ovary

growth_protocol: Fishes were purchased from a local supplier and acclimatized before tissue extraction.

extract_protocol:
Total RNA were extracted using mirVana™ miRNA Isolation Kit (AM1560, Life Technologies). Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol.
Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit ( RS-200-0012, Illumina, Inc.). Libraries were prepared according to manufacturer instructions. Briefly, 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel (Life Technologies) and bands corresponding to adapter-ligated constructs derived from 22-30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser (Agilent Technologies) before sequencing.

tag: gender

value: Female

value: Ovary

tag: genetic background

value: Wild type - Singapore strain


title: zebrafish_RPE_V2


title: Eye Replicate 2 sRNAseq

description: gender: not specified

source_name: Eye

value: Eye


title: Eye Replicate 3 sRNAseq

description: gender: not specified


title: Eye Replicate 1 sRNAseq

description: gender: not specified


title: Heart Replicate 1 sRNAseq

description: gender: not specified

source_name: Heart

value: Heart


title: Ovary Replicate 1 sRNAseq


title: Heart Replicate 3 sRNAseq

description: gender: not specified


title: Ovary Replicate 2 sRNAseq


title: Testis Replicate 3 sRNAseq

source_name: Testis

value: Male

value: Testis


title: Heart Replicate 2 sRNAseq

description: gender: not specified


title: Testis Replicate 2 sRNAseq


title: ChIP: GATA3_sc-22206X_Kelly_103014

description: young_id: 20141126_3337

source_name: Neuroblastoma

tag: cell line

value: Kelly

value: Santa Cruz


title: Female Liver Replicate 1 sRNAseq

source_name: Female Liver

tag: tissue

value: Liver


title: Female Liver Replicate 3 sRNAseq


title: Male Liver Replicate 2 sRNAseq

source_name: Male Liver


title: Male Liver Replicate 1 sRNAseq


title: Female Liver Replicate 2 sRNAseq


title: Female Gut Replicate 3 sRNAseq

source_name: Female Gut

value: Gut


title: Male Liver Replicate 3 sRNAseq


title: zebrafish_RPE_T2

tag: treatment


title: Female Gut Replicate 2 sRNAseq