title: fastMEF_3

first: Vince

last: Schulz

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

description:
fastMEF_3
cytosolic RNA

data_processing:
Multiple samples were indexed and loaded to the Hi-Seq2000 for sequencing performed with 50bp single end reads.  Base-calling was performed using the Illumina Casava 1.8.2 pipeline.
The first 8 bases of each fastq sequence read were removed using the fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) to remove bases introduced during random priming. Sequences were mapped to the mouse mm9 genome using the splice aware tophat version 2.0.4 alignment software.
The number of reads in each mouse gene was counted using the htseq-count software (http://wwwhuber.embl.de/users/anders/HTSeq/doc/overview.html).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited .txt files reports tag counts for each mouse gene for each sample.

source_name: Mouse embryonic fibroblasts

growth_protocol: Bulk MEFs were maintained in DMEM with 10% FBS and Pen/Strep. Fast and slow MEFs were grown for a total of 6 days in complete mESC medium (DMEM with 15% Hyclone FBS, Non-essential amino-acids, Pen/Strep, L-glutamine, β-mercaptoethanol and 1000U/ml LIF) plus 2 ug/ml od docycycline. GMPs were grown in 100 ng/ml mSCF, 50 ng/ml mIL3, 50 ng/ml Flt3L and 50 ng/ml mTPO (all from PeproTech) with a serum free base medium X VIVO15 (BioWhittaker). iPS cells were grown in complete mESC medium as above without doxycycline.

extract_protocol:
Cells were directly sorted into an RNase-free 96-well PCR plate (USA Scientific) followed by cell lysis, cytoplasmic content separation and total RNA preparation. Prior to collecting sorted cells, the 96-well PCR plate was kept on ice and each of wells was loaded with 20U RNaseOut (Invitrogen) and 0.5ul dithiothreitol (DDT) (Invitrogen). 1,000 cells of each population of interest were sorted in each well using a SONY Reflection or BD Aria instrument. The cells were quickly spun down (2,000rpm, 2min) in the wells and then RNase-free phosphate-buffered saline (PBS) was added to bring the total volume to 2.5ul. Next, 2.5ul of 2x cell membrane selected lysis buffer was added and the cells were lysed by pipetting up and down for 5 times. The entire lysate solution was transferred to a 1.5ml Eppendorf tubes and spun at 8,000rpm for 5 min in a chilled centrifuge (4C). The supernatant, which contains the total mature RNA from cytoplasm, was transferred to PCR tubes on ice. Finally 5µl of total RNA was obtained from each sorted cell sample.
The mRNA selection and reverse transcription was performed as described previously with some modifications (Pan et al., 2013). Briefly, 5'-phosphorylated oligo-GdT24 (pGdT24) primer was used to selectively reverse transcribe mRNAs. Before reverse transcription, the total RNA sample was mixed with dNTPs (0.5 mM) and pGdT24 (4 µM) and denatured on a pre-heated 68C PCR machine for 5 minutes, then rapidly cooled down by immediately placing it on ice. Subsequently, the first strand cDNA was synthesized with addition of the cocktail containing the First Strand Buffer, DDT, RNaseOut, and 10u/µl Superscript Reverse Transcriptase III (all from Invitrogen). Then, the double-stranded cDNA (dscDNA) was generated in a 50µl of reaction mix. The product was purified with the Genomic DNA Clean and Concentrator kit (Zymo). Afterwards, several steps including DNA end-blunting, 5'-end phosphorylation and ligation were performed with the End-It DNA End-Repair Kit (Epicentre) with T4 DNA ligase (Epicentre). With no further purification or deactivation of enzyme, the product was directly amplified by adding a mixture of the Reaction Buffer and DNA polymerase (15:1) from REPLI-g UltraFast Mini Kit (QIAGEN). When the reaction was completed, the amplification product was purified using the Genomic DNA Clean and Concentrator kit (Zymo) column as mentioned above. Finally, 3 to 5 µg (up to 8 µg) of amplified cDNA derived from mature mRNA was obtained, which was then evaluated by PCR using a set of primers as described in (Pan et al., 2013). This product was fragmented for sequencing library construction as described below.

treatment_protocol: No treatment was performed for bulk MEF and iPS cells. Fast and slow GMPs were isolated following 24 hours of CFSE dye dilution. Fast and slow MEFs were isolated after 48 hours of CFSE dye dilution after a total of 6 days of Yamanaka factor induction by doxycycline.

value: Mouse embryonic fibroblasts

tag: sort characteristic

value: CFSE sorted

tag: cycle speed

value: Fast


title: fastMEF_4

status: Public on Feb 12 2014

type: SRA

city: New Haven

state: CT

country: USA

description:
fastMEF_4
cytosolic RNA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type


title: WDR5_empty_RIPseq_IP_rep2

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

description: library strategy: RIP-seq

data_processing:
Sequencing reads were mapped to the mouse genome using TopHat (version 1.1.3) (Trapnell et al., 2009). Each sample generated 13.6 to 51.1 million mapped sequences, recorded in BAM/SAM format.
A non-redundant mm9 transcriptome was assembled from UCSC RefSeq genes, UCSC genes, and predictions from (Ulitsky et al., 2011) and (Guttman et al., 2011). Gene expression in the form of log2d RPKM was calculated.
Genome_build: mm9
Supplementary_files_format_and_content: The processed file is in txt format with RPKMs.

source_name: embryonic stem cells

growth_protocol: Embryonic stem cells were cultured under standard feeder-free conditions with LIF supplementation.

extract_protocol:
RIPiT was performed as described previously (Singh et al., 2013) with the following modifications. WDR5 tagged constructs contained a FLAG and HA epitope which were used for sequential purification of WDR5 bound RNAs. No RNaseI elution step was included. Full length WDR5 bound RNAs were isolated by Trizol extraction and first converted into dsDNA with a NuGen Ovation v2 kit. This dsDNA was converted into a deep sequencing library using the NEBNext ChIP-seq Library Prep Kit from NEB. WDR5 empty represents ESCs infected with a lentivirus containing no tagged WDR5. WDR5 wild type represents ESCs infected with a lentivirus containing a FLAG-HA tagged WDR5 wild type sequence expression construct. WDR5 F266A represents ESCs infected with a lentivirus containing a FLAG-HA tagged WDR5 mutated at position F266 (to an alanine) expression construct.
The isolated RNA was DNase treated and purified using Qiagen miRNeasy columns.
For sequencing libraries we first amplified the RNA with the NuGEN Ovation v2 kit and then followed Illumina’s protocol.

treatment_protocol: Formaldehyde crosslinked RIP-seq was carried out as previously described (Yong et al. 2010)

value: embryonic stem cells

tag: infection

value: lentivirus containing no tagged WDR5

tag: strain

value: 129/B6 F1 hybrid

tag: chip antibody

value: Anti-FLAG-M2 Affinity Gel (Sigma, Cat# A2220) and Anti-HA Agarose (Pierce, Cat# 26181)


title: fastMEF_2

description:
fastMEF_2
cytosolic RNA


title: D4C

city: New York

first: liang

last: zhang

state: NY

address: 1230 york Avenue

department: fuchs

institute: the Rockefeller University

data_processing:
Galaxy Webtools: Groomer data, based on MM9 female ref genome
Galaxy Webtools: Trimming 3 nt from each end of all reads
Galaxy Webtools: Filter Fastq, filtering any reads with any base quality <20
Galaxy Webtools: Tophat mapping, all default settings, use MM9 female as refer genome
Galaxy Webtools: Cufflink transcript analysis, all default settings, use MM9_gene.gtf from the MM9 data base as reference annotation. Use refmrna.fa file from the MM9 database for bias correction
Genome_build: MM9
Supplementary_files_format_and_content: Tabular file, content including: tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status FPKM FPKM_conf_lo FPKM_conf_hi

source_name: miR-125b addicted tumor initiating cells Off Dox day 4, replicate 3

growth_protocol: For Histone-H2BGFP expression in DTG tumor cells, the U6 promoter was deleted in the PLKO-PGK-H2B-GFP vector {Beronja, 2010 #68}throughNdeI-AgeI digestion, Quick Blunting Kit treatment (NEB), and self-ligation. The resulting PLNA-PGK-H2BGFP plasmid was packaged into lentivirus and used to infect ~1x106freshly sorted α6hiβ1hi DTG tumor cells. After 30 min, cells were then extensively washed and immediately engrafted onto backskins of Nude mice by intradermal transplantation. GFP+α6hiβ1hicells were FACS-isolated from resulting tumors and then serially transplanted as above

extract_protocol:
Total RNAswere extracted from the FACS-sorted cells using the miRNeasy Mini Kit (Qiagen) according to the vender’s protocol.
RNA samples were submitted to the Genomics Resources Core Facility of the Weill Cornell Medical College for library construction using IlluminaTruSeq Stranded mRNA Sample Prep Kit and then sequencing using Illumina HiSeq2000.

treatment_protocol: For RNA seq analysis of the miR-125b addicted tumor regression process, H2BGFP labeled DTG tumor cells were intradermally engrafted onto backskins of Nude mice (1x104cells/site). Tumors were allowed to grow to ~1cm diameter. Mice were then taken Off Dox by transferring them to regular food {Zhang, 2011 #96} for 0, 4, 7 days. GFP+α6hiβ1hiwere then FACS-isolated from the tumors. Two or three independent replicates were collected for each time point.

tag: time

value: Day 4

tag: genetic background

value: FVB


title: eCenH3 RNA-seq Replicate 3

city: Paris

first: Genevieve

last: Almouzni

state: Ille De France

address: 26 Rue D'Ulm

department: Nuclear Dynamics and Genome Plasticity

country: France

institute: Institut Curie

description: Strand specific RNA-seq

data_processing:
Reads were mapped onto the human reference genome (hg19) using STAR mapper v2.1 (https://code.google.com/p/rna-star/) with default settings.
SAM files were converted to BAM files, sorted and indexed using Samtools
Read counts for each gene were calculated using htseq-count from the HTSeq package using gene annotation from Gencode v12 (http://www.gencodegenes.org/)
Differential expression analysis was carried out using the R package DESeq.
Genome_build: hg19
Supplementary_files_format_and_content: Read counts for each gene across all cell lines and replicates (merged output from HTSeq)

organism: Homo sapiens

source_name: eCenH3 RNA-seq

growth_protocol: HeLa S3 overexpressing eCenH3 or the parental cell line (WT) are grown in spinner flask to a concentration of 1.106 cells/ml with a viability of at least 97%.

extract_protocol:
5x10^6 cells were used in each case. Total RNA was extracted using the Qiagen Rneasy Mini-kit.
Libraries were prepared using the Epicenter ScriptSeq Strand-specific Library preparation kit with Ribo-Zero and then sequenced on an Illumina Hi-Seq2000 machine.

tag: cell line

value: HeLa S3

value: Cervical cancer

tag: genotype/variation

value: wild type


title: WDR5_empty_RIPseq_Input

description: library strategy: RIP-seq


title: eCenH3 RNA-seq Replicate 2

description: Strand specific RNA-seq


title: eCenH3 RNA-seq Replicate 1

description: Strand specific RNA-seq


title: slowMEF_4

description:
slowMEF_4
cytosolic RNA

value: Slow


title: Hela S3 WT RNA-seq Replicate 3

description: Strand specific RNA-seq

source_name: Hela S3 WT RNA-seq


title: slowMEF_2

description:
slowMEF_2
cytosolic RNA


title: Heterotypic CenH3 (CenH3/H3) ChIP-seq

library_source: genomic

data_processing:
Merged reads were mapped to the RepeatMasked human genome (Hg19) using Bowtie (v0.12.7) allowing up to 3 mismatches and requiring only unique matches (-v 3, -m 1) using the first 50bp of each read.
Peaks were called for ChIP datasets using SICER (v1.0.3) using 200bp sliding windows and merging islands located with 400bp with FDR of 1e-5.
Read density wig files were created using FindPeaks4 (v4.0.13)
Genome_build: hg19
Supplementary_files_format_and_content: Wig files contain read density across the human genome. Enriched peaks are in BED format

molecule: genomic DNA

source_name: Heterotypic CenH3 (CenH3/H3) ChIP-seq

extract_protocol:
Cells are harvested by a low speed centrifugation (500g, 5min, 4°C), washed twice in cold PBS and resuspended in three cell volumes of cold NB buffer (15mM Tris HCl pH 7,5, 15mM NaCl, 60mM KCl, 300mM Sucrose, 1X complete EDTA free (roche diagnostic), 25ng/ml trichostatin A, 10mM beta glycerophosphate, 5mM sodium fluoride, 0,2mM sodium orthovanadate). Four pellet volumes of NB buffer containing 1% NP40 is then added to the cell suspension and incubated 10 min at 4°C on a wheel. After centrifugation at 1200g for 5 min at 4°C nuclei are washed with 3 nuclei volumes of NB buffer and resuspended in ½ nuclei volume of NB buffer. After adding CaCl2 to a final concentration of 2mM nuclei are partially digested with MNase (Nuclease S7 roche diagnostic) to give a range of oligonucleosome. Nuclei are centrifuged 5 min at 16 000g 4°C and the supernatant is dialyzed at least 3h against 1L of lies buffer (Tris HCl pH 7,5 1mM, EDTA pH 8 0,2mM, 1X complete EDTA free (roche diagnostic), 25ng/ml trichostatin A, 10mM beta glycerophosphate, 5mM sodium fluoride, 0,2mM sodium orthovanadate). To extract as much chromatin as possible from the remaining pellet, it is resuspended in one pellet volume of Lysis buffer and dialyzed for at least 3h against 1L of dialysis buffer. After centrifugation 16 000g 4°C 5 min the supernatant of the resuspended pellet is mixed with the first supernatant. The extract is loaded on top of a 5-30% sucrose gradient made in the lies buffer and centrifuged for 16h 29000rpm at 4°C in the SW32 rotor (Beckman Coulter). 1ml fractions are made and 50l is analyzed by agarose gels to determine the nucleosome composition of each fractions. After increasing NaCl concentration to 300mM, Tris/HCl pH 8 to 10mM and NP40 to 0,1%, fractions containing mononucleosomes are pooled and histone are immunoprecipitated with Flag M2 Agarose beads (Sigma Aldrich) for 4h at 4°C or with protein A/G magnetic beads (Thermo scientific) coated with CENP-A (3-19) antibody (Enzo life sciences) overnight at 4°C on a wheel. Beads are washed 3 times with the IP buffer (20mM Tris HCl pH7,5, 300mM NaCl, 0,2mM EDTA pH 8, 0,1% NP40, glycerol 10%, 1X complete EDTA free (roche diagnostic), 25ng/ml trichostatin A, 10mM beta glycerophosphate, 5mM sodium fluoride, 0,2mM sodium orthovanadate) and elute 2 times 1h at 4°C for the flag IP with ½ beads volumes of elution buffer (IP buffer containing 0,4g/ml flag peptide, Sigma Aldrich)  2 times 3h at 4°C for the CENP-A IP with ½ beads volumes of elution buffer (IP buffer containing 0,5g/ml CENP-A 3-19 peptide).
Libraries were prepared according to standard Illumina protocols for paired-end sequencing on the HiSeq2000 machine

value: eCenH3 HeLa S3

value: CenH3 over-expression

value: CenH3 (Enzo life science, ADI-KAM-CC006-E) + H3 (Sigma Aldrich, H9289)


title: Homotypic CenH3 (CenH3/CenH3) ChIP-seq

source_name: Homotypic CenH3 (CenH3/CenH3) ChIP-seq

value: CenH3 (Enzo life science, ADI-KAM-CC006-E)


title: Hela S3 WT RNA-seq Replicate 2

description: Strand specific RNA-seq


title: Hela S3 WT RNA-seq Replicate 1

description: Strand specific RNA-seq


title: fastGMP_5

description:
fastGMP_5
cytosolic RNA

source_name: Granulocyte monocyte progenitors

value: Granulocyte monocyte progenitors


title: slowMEF_1

description:
slowMEF_1
cytosolic RNA

value: Mouse embryonic fibroblasts

value: CFSE sorted


title: slowMEF_3

description:
slowMEF_3
cytosolic RNA


title: eCenH3 ChIP-seq (replicate 2)

description: Partial MNase digested chromatin followed by sucrose gradient purification of mononucleosomes followed by ChIP

data_processing:
Paired-end reads were merged into a single read using the program SeqPrep (v0.4) (https://github.com/jstjohn/SeqPrep) using a minimum overlap of 15bp and only reads >=100bp were retained (representing ~99% of the total).
Merged reads were mapped to the RepeatMasked human genome (Hg19) using Bowtie (v0.12.7) allowing up to 3 mismatches and requiring only unique matches (-v 3, -m 1) using the first 50bp of each read.
Peaks were called for ChIP datasets using SICER (v1.0.3) using 200bp sliding windows and merging islands located with 400bp with FDR of 1e-5.
Read density wig files were created using FindPeaks4 (v4.0.13)
Genome_build: hg19
Supplementary_files_format_and_content: Wig files contain read density across the human genome. Enriched peaks are in BED format

source_name: eCenH3 ChIP

extract_protocol:
Cells are harvested by a low speed centrifugation (500g, 5min, 4°C), washed twice in cold PBS and resuspended in three cell volumes of cold NB buffer (15mM Tris HCl pH 7,5, 15mM NaCl, 60mM KCl, 300mM Sucrose, 1X complete EDTA free (roche diagnostic), 25ng/ml trichostatin A, 10mM beta glycerophosphate, 5mM sodium fluoride, 0,2mM sodium orthovanadate). Four pellet volumes of NB buffer containing 1% NP40 is then added to the cell suspension and incubated 10 min at 4°C on a wheel. After centrifugation at 1200g for 5 min at 4°C nuclei are washed with 3 nuclei volumes of NB buffer and resuspended in ½ nuclei volume of NB buffer. After adding CaCl2 to a final concentration of 2mM nuclei are partially digested with MNase (Nuclease S7 roche diagnostic) to give a range of oligonucleosome. Nuclei are centrifuged 5 min at 16 000g 4°C and the supernatant is dialyzed at least 3h against 1L of lies buffer (Tris HCl pH 7,5 1mM, EDTA pH 8 0,2mM, 1X complete EDTA free (roche diagnostic), 25ng/ml trichostatin A, 10mM beta glycerophosphate, 5mM sodium fluoride, 0,2mM sodium orthovanadate). To extract as much chromatin as possible from the remaining pellet, it is resuspended in one pellet volume of Lysis buffer and dialyzed for at least 3h against 1L of dialysis buffer. After centrifugation 16 000g 4°C 5 min the supernatant of the resuspended pellet is mixed with the first supernatant. The extract is loaded on top of a 5-30% sucrose gradient made in the lies buffer and centrifuged for 16h 29000rpm at 4°C in the SW32 rotor (Beckman Coulter). 1ml fractions are made and 50l is analyzed by agarose gels to determine the nucleosome composition of each fractions. After increasing NaCl concentration to 300mM, Tris/HCl pH 8 to 10mM and NP40 to 0,1%, fractions containing mononucleosomes are pooled and histone are immunoprecipitated with Flag M2 Agarose beads (Sigma Aldrich) for 4h at 4°C or with protein A/G magnetic beads (Thermo scientific) coated with CENP-A (3-19) antibody (Enzo life sciences) overnight at 4°C on a wheel. Beads are washed 3 times with the IP buffer (20mM Tris HCl pH7,5, 300mM NaCl, 0,2mM EDTA pH 8, 0,1% NP40, glycerol 10%, 1X complete EDTA free (roche diagnostic), 25ng/ml trichostatin A, 10mM beta glycerophosphate, 5mM sodium fluoride, 0,2mM sodium orthovanadate) and elute 2 times 1h at 4°C for the flag IP with ½ beads volumes of elution buffer (IP buffer containing 0,4g/ml flag peptide, Sigma Aldrich)  2 times 3h at 4°C for the CENP-A IP with ½ beads volumes of elution buffer (IP buffer containing 0,5g/ml CENP-A 3-19 peptide).
Libraries were prepared according to standard Illumina protocols for sequencing on the HiSeq2000 machine

value: Flag M2 Agarose beads (Sigma Aldrich)


title: eCenH3 MNase input (replicate 2)

description: Partial MNase digested chromatin followed by sucrose gradient purification of mononucleosomes

source_name: eCenH3 MNase input


title: eCenH3 ChIP-seq (replicate 1)


title: fastGMP_3

description:
fastGMP_3
cytosolic RNA

value: Fast


title: eCenH3 MNase input (replicate 1)


title: WT CenH3 ChIP-seq (replicate 1)

source_name: WT CenH3 ChIP

value: CENP-A (Enzo life science, ADI-KAM-CC006-E)


title: fastGMP_2

description:
fastGMP_2
cytosolic RNA


title: WT MNase input (replicate 1)

source_name: WT MNase input


title: fastGMP_1

description:
fastGMP_1
cytosolic RNA


title: WT MNase input (replicate 2)


title: slowGMP_3

description:
slowGMP_3
cytosolic RNA


title: fastMEF_1

description:
fastMEF_1
cytosolic RNA


title: slowGMP_1

description:
slowGMP_1
cytosolic RNA


title: slowGMP_2

description:
slowGMP_2
cytosolic RNA


title: iPS_4

description:
iPS_4
cytosolic RNA

source_name: Factor independent induced pluripotent stem cells

value: Bulk Oct4:GFP+


title: iPS_3

description:
iPS_3
cytosolic RNA

value: Factor independent induced pluripotent stem cells


title: MEF_4

description:
MEF_4
cytosolic RNA

value: Bulk, unsorted


title: MEF_3

description:
MEF_3
cytosolic RNA


title: iPS_1

description:
iPS_1
cytosolic RNA


title: MEF_2

description:
MEF_2
cytosolic RNA


title: 1199_SP

first: Gerold

last: Bongers

address: 1425 Madison Ave, 12-26A

department: Immunology Institute

institute: Icahn School of Medicine at Mount Sinai

description: Serrated polyp tissue from HBUS mouse 1199

data_processing:
Paired-end sequencing reads were aligned to the M. musculus genome using Tophat (v2.0.7) with the –bowtie1 argument (bowtie v0.12.9). Read counts were extracted using htseq-count (v0.5.3p9).
Genome_build: MGSCv37
Supplementary_files_format_and_content: Read counts extracted using htseq-count (v0.5.3p9).

growth_protocol: HBUS mice were reared as described (Bongers et al., 2010; Bongers et al., 2012) and cecal polyp/surrounding tissue was isolated after 60 weeks. All experiments involving mice were performed in accordance with the guidelines of the Animal Care and Use Committee of Mount Sinai School of Medicine.

extract_protocol:
Approximately 200 mg tissue sample was placed in 1.5 ml RNAlater buffer (Ambion) and snap-frozen in liquid nitrogen. At time of extraction, samples were centrifuged for 10 min at 16.000g at room temperature. Pellets were resuspended in 150 μl of Lysis Buffer (Tris/HCl pH 8, 1 mM EDTA, 15 mg/mL Lysozyme (Sigma), 15 μl Proteinase K (20 mg/mL)) and incubated at room temperature for 10 min with brief mixing every 2 min. Following addition of 1.2 mL QIAGEN RLT buffer containing 1% v/v β-mercaptoethanol, 1 mL of 0.1 mm glass beads (BioSpec) were added and samples were homogenized in a FastPrep at setting 5 (4 pulses of 20 sec). Samples were kept on ice for 1 min between pulses. Lysates were then homogenized with a QIAshredder spin columns and RNA was isolated using the AllPrep mini kit (Qiagen), according to the manufacturers protocols, which included an on-column digestion with DNase I. 25 μg of RNA from each tissue sample was processed with the MICROBEnrich kit (Ambion) and 5 μg of processed RNA was further depleted of rRNAs using the Meta-Bacteria RiboZero rRNA removal kit (Epicentre).
rRNA depleted RNA was prepared for Illumina paired-end sequencing using the NEB Next mRNA Library Prep Master Mix Set for Illumina (NEB, E6110S); manufacturer’s protocols were followed with the following modifications. RNA was fragmented for 10 minutes, and then purified with Qiagen RNeasy MinElute spin columns. Reverse transcription was performed with SuperScript III (Invitrogen). Library preparation reactions were cleaned up using Agencourt AMPure XP beads. Size selection was performed before ligation mediated PCR using Invitrogen E-Gel 2% with SYBR Safe staining. Excised gel fragments were purified with Qiagen QIAQuick Gel Extraction kit. Adapters and primers were synthesized by IDT following published Illumina sequences. Enrichment PCR was performed with Kapa HiFi HotStart ReadMix. Primers were used at a final concentration of 500 nM; cycling parameters were as follows: 94 oC for 5 min, 15 cycles of 94 oC 1 min, 62 oC for 30 sec, 72 for 45 sec and then 72 oC for 10 min. Libraries were quantified using the Agilent BioAnalyzer DNA 1000 chips, diluted to 12 pM and sequenced for 100 cycles (paired-end) on the Illumina HiSeq 2000 using standard methods.

value: HBUS

tag: tissue

value: Serrated polyp


title: fastGMP_4

description:
fastGMP_4
cytosolic RNA


title: MEF_1

description:
MEF_1
cytosolic RNA


title: JIL-1_null _mutant_Z2_2 Sample 4

city: Ames

first: Jorgen

last: Johansen

state: Iowa

address: MBB3142, Iowa State Univeristy

department: BBMB

institute: Iowa State Universtiy

data_processing:
Remove low quality nucleotides from raw reads using Data2Bio's trimming script
GSNAP (Genomic Short-read Nucleotide Alignment Program, version 2013-10-12) was used to map trimmed reads to the reference genome (BDGP 5.72/dm3).
75th percentile normalization method was used to normalize wild-type and mutant RNA-Seq reads
Identification of genes with different expression

organism: Drosophila melanogaster

source_name: Salivary Glands

growth_protocol: 25°C Incubator

extract_protocol:
Total RNA was isolated by UltraClean Tissue and Cells RNA isolation Kit
Libraries were prepared according to Illumina's instructions

treatment_protocol: Salivary gland cells were isolated from wild type and JIL-1 null mutant 3rd instar larvae of Drosophila Melanogaster

tag: developmental stage

value: Third instar larvae

value: Salivary Gland Cells

tag: genotype


title: JIL-1_null _mutant_Z2_1 Sample 3


title: WT CenH3 ChIP-seq (replicate 2)

value: HeLa S3

value: Cervical cancer

value: wild type


title: H3K9me2_Z2_2 Sample 13

data_processing:
ChIP-seq reads were aligned to the dm3(BDGP5.72) Drosophila genome assembly using  Bowtie V0.12.7
SAMtools  V0.1.18  and BEDtools V2.14.3 were used to sort and transfer files.
peaks were called using SICER V1.1  with the following setting: 200 bp window size, 200 bp gap size, and an effective genome size of 72% of the Drosophila genome

growth_protocol: Salivary gland cells were isolated from wild type and JIL-1 null mutant 3rd instar larvae of Drosophila Melanogaster

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions

value: Abcam Anti-Histone H3 (di methyl K9) antibody [mAbcam 1220]


title: 1192_NM

description: Normal surrounding (distal) cecum tissue from HBUS mouse 1192

value: Normal surrounding (distal) cecum


title: WT_2 Sample 2

value: Wild Type


title: Z2_input_2 Sample 12


title: 1199_NM

description: Normal surrounding (distal) cecum tissue from HBUS mouse 1199


title: 1192_SP

description: Serrated polyp tissue from HBUS mouse 1192


title: 1119_NM

description: Normal surrounding (distal) cecum tissue from HBUS mouse 1119


title: Input3 Sample 10


title: iPS_2

description:
iPS_2
cytosolic RNA


title: 1119_SP

description: Serrated polyp tissue from HBUS mouse 1119


title: Developmentally competent embryo conditioned media Salker_B3

status: Public on Feb 11 2014

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited general transfer format cufflinks output files include FPKM values

source_name: uterus

extract_protocol:
Uteri were removed, flash frozen on dry ice. Total RNA extraction was performed using RNA STAT-60, according to manufacturer's instructions.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Immature female (25 d C57BL/6) mice were given a hormone treatment of a single dose 1 mg progesterone and 10 mg/kg/day β-estradiol for a total of 3d to prime the uterus for embryo transfer. The uterine horns of control and study mice were injected with an equal volume (50 μl) of either unconditioned embryo culture medium (ECM), serving as controls, or pooled conditioned media from competent (n = 9) or arresting embryos (n = 18)

value: uterus

tag: treatment

value: developmentally competent embryo conditioned media


title: Arrested embryo conditioned media Salker_C3

value: arrested embryo conditioned media


title: Developmentally competent embryo conditioned media Salker_B2


title: Control Salker_A3

value: control embryo culture media (unconditioned)


title: H3K9me2_WT_2 Sample 11


title: Control Salker_A1


title: Developmentally competent embryo conditioned media Salker_B1


title: Control Salker_A2


title: S2ph pol2_ChIPSeq Rep2

city: RTP

first: ruifang

last: li

state: NC

address: 111 T.W. Alexander Drive

institute: NIEHS

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7 with parameters -m 1 -v 2
Only reads that were mapped to an unambiguous ‘best’ genomic location with no more than 2 mismatches were accepted
Duplicate reads were removed to limit PCR amplification bias, and all alignments were extended at the 3’ end to a length of 150 bases
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph files were generated from these mapped, non-duplicate, extended reads for visualization of aggregate genomic coverage.

source_name: S2ph pol2_ChIPSeq

extract_protocol:
30 mg of liver tissue was pulverized then incubated in 1% formaldehyde in PBS for 15 min at room temperature. Cross-linking was terminated by addition of glycine. The cells were spun down and rinsed in ice-cold PBS two times. The cell lysates were sonicated using a Bioruptor (Diagenode) to generate 150–350 bp fragments for immunoprecipitation. The following antibodies were used for ChIP: H3K36me3 (Abcam), S5ph pol2 (Abcam), S2ph pol2 (Abcam).
libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kits v1 following the manufacturer’s instructions.

treatment_protocol: Liver was dissected and washed in PBS then was snap frozen on dry ice.

value: Liver

tag: age

value: 8 weeks

tag: gender

value: male

value: S2ph pol2 (Abcam, ab5095)


title: input DNA

source_name: input DNA


title: S2ph pol2_ChIPSeq Rep1


title: S5ph pol2_ChIPSeq Rep1

source_name: S5ph pol2_ChIPSeq

value: S5ph pol2 (Abcam, ab5131)


title: H3K36me3_ChIPSeq Rep1

value: H3K36me3 (Abcam, ab9050)


title: H3K36me3_ChIPSeq Rep2


title: S5ph pol2_ChIPSeq Rep2


title: RNA-seq - Rich Media

city: Collegeville

first: David

last: Mayhew

state: PA

address: 1250 South Collegeville Road

department: Target Sciences, Computation Biology, R&D

institute: GlaxoSmithKline

description: Expression data

data_processing:
Illumina sequence reads were filtered by requiring the correct 17 bp LTR sequence in the first 17 bases of sequence from the read and an appropriate 8 bp barcode sequence. Reads were mapped using a seeded hash approach. The first 12 genomic bases of each read were mapped to the yeast genome.  The remaining genomic fragments of each read were then aligned to the seeds using an ungapped alignment and allowing up to 2 mismatches on each read.  Only insertions with unique reads were accepted.
genome build: Σ1278b

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast were grown in synthetic low ammonium media

extract_protocol: Calling Card Illumina libraries were prepared by harvesting all His+ FOAr colonies and extracting their genomic DNA. Each DNA sample was divided into three aliquots and digested with Hinp1I or HpaII or TaqI. Digested DNA was ligated overnight at 15°C in dilute solution (<10ng/ul) to encourage self-circularization. After ethanol precipitation, self-ligated DNA was resuspended in ddH2O and used as template in an inverse PCR. Primers that anneal to Ty5 sequences (OM8714: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTAATTCACTACGTCAACA; OM8827: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATC) were used to amplify the genomic regions flanking Ty5 integrations and the bar codes within Ty5, as well as adding adapter sequences that allow the PCR products to be sequenced on the Illumina HiSeq 2000. The PCR products were purified using the QIAquick PCR Purification Kit (Qiagen) and diluted to 10nM.

treatment_protocol: Transposon induction occurred in media with 2% galactose

tag: growth

value: Rich Media


title: RNA-seq - Nitrogen Starved Media

description: Expression data

value: Nitrogen Starved Media


title: Calling Cards - Rgm1 insertions

description:
library strategy: Calling Card
Transposon insertions

tag: transposon

tag: transcription factor


title: Calling Cards - Gcn4 insertions


title: Calling Cards - Msn2 insertions


title: Arrested embryo conditioned media Salker_C1


title: Arrested embryo conditioned media Salker_C2


title: Calling Cards - Msn4 insertions


title: U343 RIPSeq miR137 transfection Rep2

city: Los Angeles

first: Philip

middle: James

last: Uren

address: 1050 Childs Way, RRI201

institute: University of Southern California

description: library strategy: RIP-Seq

data_processing:
Read alignment performed using RMAP
Read counts obtained against a transcriptomic reference created from RefSeq by collapsing isoforms and producing one super-transcript per gene; in-house software used
Genome_build: hg18
Supplementary_files_format_and_content: BED file. Read counts per gene

source_name: U343 cells

growth_protocol: U251 and U343 were grown in DMEM media supplemented with 10% fetal bovine serum in standard cell culture conditions (5% carbon dioxide) and incubator.

extract_protocol:
For RNAseq experiments, cells were harvested after 48 hours for total RNA extraction using TRIzol. For RIPSeq, cell extracts were prepared from U251 and U343 transfected cells (miR-137 and control mimics) in polysomal lysis buffer, diluted in NT2 buffer and incubated for 3 hours with protein A-sepharose 4 Fast flow from GE conjugated with a mix of PABP antibodies. Beads were washed in NT2 buffer five times and subsequently digested with Proteinase K. RNA was extracted with phenol-chloroform, precipitated with isopropanol and kept at -80 degrees Celsius until usage.
Total RNA was purified from control and miR-137 transfected cells with Trizol. Total RNA and RIP samples were depleted of 28S, 18S, 5.8S and 5S rRNA using RiboZero rRNA removal kit from Epicentre as per manufacters instructions. The rRNA depleted samples from U251 cells (16μl) were then mixed with 1μL random hexamers (500ng) and 1μL 10X MMLV Buffer, heated to 65oC for 2 minutes and placed on ice. To this mixture was added 2.5mM DTT, 0.5 mM dNTPs, 40 units of Riboguard and 50 units of EpiScript RT. First strand cDNA was then synthesized by incubation for 10 minutes at 25oC, 30 minutes at 42oC and 15 minutes at 70oC, then held at 4oC in a thermocycler with a heated lid. Second strand cDNA was synthesized by addition of 30 mM Tris pH 7.5, 5 mM MgCl2, 5 mM DTT, 0.3 mM each dNTP, 2.5 units of E. coli RNase H and 20 units of E. coli DNA polymerase I. The mixtures were then incubated for one hour at 16oC, followed by 15 minutes at 80oC. The reactions were then purified using Zymo DNA Clean kit and the samples were eluted with 16μL of nuclease-free water. The double-stranded cDNA was then fragmented and tagged using the Nextera DNA library kit from Epicentre as per the protocol supplied by the manufacturer and PCR amplified for 9 cycles. The samples were purified using Zymo DNA Clean kit and quantitated by using a bioanalyzer and Qubit methods, then sequenced on an Illumina GAIIx instrument for 36 cycles. After Ribo-Zero treating the RNA samples from the U343 cells, 50 ng were converted into double-stranded cDNA using the TotalScript cDNA kit as per the supplied protocol and purified using the Zymo DNA Clean and Concentrator kit. The cDNA was then tagmented and amplified using the Nextera DNA sample prep kit and purified using the Zymo DNA clean kit. The samples were quantitated by bioanalyzer and Qubit methods, then sequenced on an Illumina GAIIx instrument for 36 cycles.

treatment_protocol: MicroRNA mimics were transfected into cells in 10cm dishes using Invitrogen Lipofectamine RNAiMax reagent by reverse transfection according to the manufacturer’s instructions. Transfection complexes were prepared and added directly to the cell at a final concentration of 25nM.

tag: transfection


title: U343 RIPSeq miR137 transfection Rep1

description: library strategy: RIP-Seq


title: Calling Cards - Yap6 insertions


title: Calling Cards - Hms2 insertions


title: U343 RIPSeq control transfection Rep1

description: library strategy: RIP-Seq

value: control


title: U343 RIPSeq control transfection Rep2

description: library strategy: RIP-Seq


title: Calling Cards - Hot1_insertions


title: Calling Cards - Msn1 insertions


title: U343 RNASeq miR137 transfection Rep2


title: Calling Cards - Dig1 insertions


title: U343 RNASeq miR137 transfection Rep1


title: Calling Cards - Hms1 insertions


title: U251 RIPSeq miR137 transfection Rep2

description: library strategy: RIP-Seq

source_name: U251 cells


title: Calling Cards - Fkh1 insertions


title: Calling Cards - Rtg1 insertions


title: Calling Cards - Rlm1 insertions


title: Calling Cards - Smp1 insertions


title: U251 RIPSeq miR137 transfection Rep1

description: library strategy: RIP-Seq


title: U251 RIPSeq control transfection Rep2

description: library strategy: RIP-Seq


title: U343 RNASeq control transfection Rep1


title: Calling Cards - Rim101 insertions


title: Calling Cards - Sfl1 insertions


title: Calling Cards - Skn7 insertions


title: U251 RNASeq miR137 transfection Rep1


title: U251 RNASeq control transfection Rep2


title: U251 RIPSeq control transfection Rep1

description: library strategy: RIP-Seq


title: U343 RNASeq control transfection Rep2


title: Calling Cards - Phd1 insertions


title: Calling Cards - Gln3 insertions


title: Calling Cards - Nrg1 insertions


title: Root methylation 2

city: los angeles

first: matteo

last: pellegrini

address: 610 charles young drive east

institute: UCLA

description:
BS59
Col roots light-grown genomic DNA, pre-methylated Illumina adapter, one PCR amplification (15 cycles), dCTP used in end repair, single-end library.
Processed data files:
ATHr_M_CGm.wig.gz
ATHr_M_CHGm.wig.gz
ATHr_M_CHHm.wig.gz
ATHr_M_Cm.wig.gz
ATHr_P_CGm.wig.gz
ATHr_P_CHGm.wig.gz
ATHr_P_CHHm.wig.gz
ATHr_P_Cm.wig.gz
ATHr_M_BSCcov.wig.gz
ATHr_P_BSCcov.wig.gz

data_processing:
BS-seq: Aligned to TAIR7 using BS-Seeker allowing up to two mismatches.
MNase: Aligned to TAIR7 using Bowtie.
Pipeline: Illumina Solexa 1.3
Genome_build: TAIR7
Supplementary_files_format_and_content: ATHr_M_CGm, ATHr_M_CHGm, ATHr_M_CHHm, ATHr_M_Cm, ATHr_P_CGm, ATHr_P_CHGm, ATHr_P_CHHm, ATHr_P_Cm, ATHr_M_BSCcov, ATHr_P_BSCcov: C*m: (C count)/(C+T count) with minimum of 5 C+T count at every cytosine (Cm), or only measured at each cytosine within a specific sequence context (CGm, CHGm, CHHm) +/- strands (P and M), BSCcov: C+T count.
Supplementary_files_format_and_content: ATHr_Nuc: Nucleosome count normalized to 1,000,000 genome-wide (weight of each nucleosome start position = 1000000 / # of aligned MNase reads), each weighted nucleosome start site extended for 147bp downstream (average nucleosome length).

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Arabidopsis root cultures were grown in liquid solution.

extract_protocol:
DNA and chromatin was extracted using standard protocols.
Bisulfite libraries (BS16 & BS59) were prepared by sonicating DNA, adenylation and ligation of Illumina adapters followed by bisulfite conversion and PCR amplification.
MNase libraries (Nuc5p) were prepared by digesting chromatin and isolating mononucleosome fractions, followed by adapter ligation and PCR amplification.

treatment_protocol: No treatment.

tag: ecotype

value: Columbia

value: wild type

value: root


title: Calling Cards - Tec1 insertions


title: Root methylation 1

description:
BS16
At BS lib from roots with low low nuc technique, fewer PCR cycles were used (15+15 instead of 18+18).
Processed data files:
ATHr_M_CGm.wig.gz
ATHr_M_CHGm.wig.gz
ATHr_M_CHHm.wig.gz
ATHr_M_Cm.wig.gz
ATHr_P_CGm.wig.gz
ATHr_P_CHGm.wig.gz
ATHr_P_CHHm.wig.gz
ATHr_P_Cm.wig.gz
ATHr_M_BSCcov.wig.gz
ATHr_P_BSCcov.wig.gz


title: Calling Cards - Ste12 insertions


title: Calling Cards - Mit1 insertions


title: Calling Cards - Sok2 insertions


title: Calling Cards - Mga1 insertions


title: Root nucleosome

description:
Nuc5p
Root mononucleosome DNA from wild type Columbia (prepared by Yana), MNase digestion 1/10, concentration 8.8ng/ul, paired-end library.


title: Calling Cards - Flo8 insertions


title: U251 RNASeq control transfection Rep1


title: NICM+LVAD2_miRNASeq

status: Public on Feb 10 2014

city: Taipei

first: Kai-Chien

last: Yang

address: No.1, Sec. 1, Jen-Ai Rd, 1150R

department: Graduate Institute and Department of Pharmacology

country: Taiwan

institute: National Taiwan University

data_processing:
Demultiplexing and basecalling performed using CASAVA version 1.6
(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.
(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.
Genome_build: hg9
Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file

source_name: human left ventricle apex tissue

extract_protocol:
LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80℃; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8)
RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits

value: left ventricle apex tissue

tag: diagnosis

value: non-ischemic cardiomyopathy

tag: lvad support

value: Post-LVAD


title: NICM+LVAD5_miRNASeq


title: NICM+LVAD4_miRNASeq


title: NICM+LVAD3_miRNASeq


title: NICM+LVAD6_miRNASeq


title: NICM+LVAD8_miRNASeq


title: Calling Cards - Mfg1 insertions


title: NICM+LVAD7_miRNASeq


title: Library1U_run2

city: University Park

first: Michael

last: Axtell

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

description: smallRNA-seq

data_processing:
Raw FASTQ data was adapter trimmed using trim_illumina_sRNA_fastq.pl version 0.4 (http://axtell-lab-psu.weebly.com/tools.html) with settings -a TGGAATTC -e 1 -q N to recover 15-42 nt trimmed reads in FASTA format. Trimmed reads were then condensed to report tallies of unique sequences
Genome_build: N/A
Supplementary_files_format_and_content: Tab-delimited text showing unique small RNA sequences and their frequencies in the library

organism: Nicotiana benthamiana

source_name: Leaves

growth_protocol: Nicotiana benthamiana plants were grown on soil at 22°C under 24h-light condition. One plant per 3.5 inches pot. Plants were grown to 1-month old before RNA extraction.

extract_protocol:
Around 50mg leaf samples were ground to a fine powder in liquid nitrogen followed by RNA extraction using miRNeasy Mini Kit (QIAGEN Cat. No. 217004). Total RNAs were extracted per the manufacturer's instructions.
Illumina TruSeq Small RNA kit, per manufacturer's instructions

tag: strain

value: wild-type

value: uninoculated


title: NICM+LVAD1_miRNASeq


title: Library1V_run1

description: smallRNA-seq


title: Library1U_run1

description: smallRNA-seq


title: ICM+LVAD8_miRNASeq

value: ischemic cardiomyopathy


title: ICM+LVAD3_miRNASeq


title: Calling Cards - Mss11 insertions


title: ICM+LVAD6_miRNASeq


title: ICM+LVAD7_miRNASeq


title: ICM+LVAD4_miRNASeq


title: NICM8_miRNASeq

value: pre-LVAD


title: Library1V_run2

description: smallRNA-seq


title: ICM+LVAD1_miRNASeq


title: ICM+LVAD2_miRNASeq


title: NICM7_miRNASeq


title: NICM6_miRNASeq


title: NICM5_miRNASeq


title: NICM3_miRNASeq


title: ICM+LVAD5_miRNASeq


title: WT_1 Sample 1

value: Third instar larvae

tag: cell type

value: Salivary Gland Cells

value: Wild Type


title: NICM1_miRNASeq


title: ICM3_miRNASeq


title: ICM8_miRNASeq


title: NICM2_miRNASeq


title: ICM6_miRNASeq


title: ICM5_miRNASeq


title: NF6_miRNASeq

value: non-failing


title: ICM4_miRNASeq


title: ICM1_miRNASeq


title: ICM2_miRNASeq


title: NF8_miRNASeq


title: NF7_miRNASeq


title: NF5_miRNASeq


title: NF4_miRNASeq


title: NICM+LVAD8_RNASeq


title: NF2_miRNASeq


title: NICM4_miRNASeq


title: NICM+LVAD6_RNASeq


title: NICM+LVAD7_RNASeq


title: NICM+LVAD3_RNASeq


title: NICM+LVAD5_RNASeq


title: ICM7_miRNASeq


title: NICM+LVAD2_RNASeq


title: NICM+LVAD1_RNASeq


title: ICM+LVAD6_RNASeq


title: ICM+LVAD5_RNASeq


title: ICM+LVAD4_RNASeq


title: ICM+LVAD3_RNASeq


title: ICM+LVAD2_RNASeq


title: ICM+LVAD8_RNASeq


title: NICM8_RNASeq


title: NF3_miRNASeq


title: NICM6_RNASeq


title: NF1_miRNASeq


title: NICM4_RNASeq


title: NICM3_RNASeq


title: NICM5_RNASeq


title: NICM2_RNASeq


title: NICM+LVAD4_RNASeq


title: NICM7_RNASeq


title: ICM8_RNASeq


title: ICM7_RNASeq


title: ICM6_RNASeq


title: ICM4_RNASeq


title: ICM2_RNASeq


title: ICM3_RNASeq


title: ICM1_RNASeq


title: NF8_RNASeq


title: ICM+LVAD7_RNASeq


title: ICM+LVAD1_RNASeq


title: NF5_RNASeq


title: NF7_RNASeq


title: NF3_RNASeq


title: NF2_RNASeq


title: H3K4me3 ChIP–seq Rag2(–/–) Ikzf1(∆/–) pro-B 15842

status: Public on Feb 09 2014

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
Peak calling of ChIP-seq data and target gene assignment: Peaks were called using the MACS program version 1.3.6.1 (ref. 19) with default parameters, a read length of 36 for ChIP-seq and 76 for DHS-seq, a genome size of 2,654,911,517 bp (mm9) and the appropriate input control sample. Peaks were filtered for p-values of < 10-10. This stringent cutoff efficiently removed false positive (unique) peaks of technical replicas. Ikaros peaks were assigned to target genes exactly as described15. Ikaros Bio-ChIP-sequencing resulted in ~180 million reads. To make these data comparable with other, less deeply sequenced ChIP-seq data, we implemented a subsampling procedure as follows: Both the input and Ikaros ChIP-seq data were down-sampled randomly 10 times to 27.3 and 22.5 million reads, respectively. These read numbers were selected to match those of the DHS-seq data and previously used input sequences. Peaks were then called for all Ikaros ChIPseq and input subsample combinations (10x10), as described above. The 9878 Ikaros peaks, which were called in 80% of all combinations, were used for multiple peak overlap analysis based on the Multovl program20.
Analysis of RNA-seq data: For analysis of differential gene expression, the RNA-seq samples were cut down to a read length of 30 or 44 bp (depending on the RNA-seq experiments to be compared) and aligned to the mouse transcriptome using the TopHat version 1.4.1 (ref. 22). The number of reads per gene was counted using the HTseq version 0.5.3 (http://www-huber.embl.de/users/anders/HTSeq) with the overlap resolution mode option set to "union". As two independent RNA-seq experiments were available for each cell type analyzed in Fig. 3f-h and Fig. 8b,e, the corresponding RNA-seq data were compared by using the R package DESeq version 1.8.3 (ref. 23) to calculate the significance level of differential expression. To this end, the samples were normalized, and the dispersions were estimated using the default DESeq settings. Genes with an adjusted p-value of < 0.1 were called as differentially expressed.
Genome_build: MM9

source_name: Pro-B cell

extract_protocol:
phenol-chloroform extraction
2-5 ng of cDNA, ChIP-precipitated DNA were used as starting material for the generation of single-end sequencing libraries as described by Illumina’s ChIP Sequencing sample preparation protocol. DNA fragments of the following sizes were selected for the different experiments: 200–350 bp for ChIPseq and 150–700 bp for RNA-seq. For strand-specific RNA-sequencing, the uridines present in one cDNA strand were modified with uracil-N-glycosylase (New England Biolabs) unable to generate second strand. The barcode containing adaptor was used for tagging and PCR amplification. Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS library quantification kit.  library construction protocol

value: Pro-B cell

tag: chip antibody

value: anti H3K4me3, Diagenode pAb-003-050, Lot.:A5051-001P


title: NF1_RNASeq


title: H3K4me3 ChIP–seq Rag2(–/–) Ikzf1(∆/+) pro-B 15840


title: NICM1_RNASeq


title: H3K9ac ChIP–seq Rag2(–/–) Ikzf1(∆/–) pro-B 15834

value: anti H3K9ac, Millipore 07-352, Lot:DAM1813175


title: H3K4me3 ChIP–seq Rag2(–/–) Ikzf1(∆/–) pro-B 15841


title: H3K4me3 ChIP–seq Rag2(–/–) Ikzf1(∆/+) pro-B 15839


title: H3K9ac ChIP–seq Rag2(–/–) Ikzf1(∆/+) pro-B 15832


title: H3K9ac ChIP–seq Rag2(–/–) Ikzf1(∆/–) pro-B 15833


title: H3K9ac ChIP–seq Rag2(–/–) Ikzf1(∆/+) pro-B 15831


title: ICM5_RNASeq


title: RNA-seq Ikaros KD Ik4056 pre-pro-B 15290

description: SuperScript® VILO™ cDNA Synthesis, strand-specific

source_name: Pre-pro-B cell

extract_protocol:
Rneasy Plus Mini Kit, Dynabeads mRNA purification kit
2-5 ng of cDNA, ChIP-precipitated DNA were used as starting material for the generation of single-end sequencing libraries as described by Illumina’s ChIP Sequencing sample preparation protocol. DNA fragments of the following sizes were selected for the different experiments: 200–350 bp for ChIPseq and 150–700 bp for RNA-seq. For strand-specific RNA-sequencing, the uridines present in one cDNA strand were modified with uracil-N-glycosylase (New England Biolabs) unable to generate second strand. The barcode containing adaptor was used for tagging and PCR amplification. Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS library quantification kit.  library construction protocol

value: Pre-pro-B cell


title: ChIP input pro-B 10195


title: Ikaros Bio-ChIP-seq DP-T 11263

description: Dynabeads M-280 Streptavidin, stringent wash

source_name: DP-T cell

value: DP-T cell

value: Ikzf1(ihCd2/ihCd2) R26(BirA/BirA)


title: RNA-seq Ikaros KD Ik2709 pre-pro-B 15291


title: RNA-seq Ikaros KD empty vector control pre-pro-B 15288


title: RNA-seq Ikaros KD Ik2709 pre-pro-B 15285


title: ChIP input DN3 9908

source_name: DN3 cell

value: DN3 cell


title: IRF4 ChIP-seq pro-B 8844

value: anti IRF4 (M-17), Santa Cruz sc-6059x, lot:E0608


title: RNA-seq Ikaros KD Ik4056 pre-pro-B 15284


title: RNA-seq Ikaros KD Ren713 control pre-pro-B 15283


title: NF6_RNASeq

value: left ventricle apex tissue


title: EBF1 V5-ChIP-seq pro-B 8659

value: anti V5 (clone V5-10)-agarose, Sigma A7345


title: RNA-seq Ikaros KD empty vector control pre-pro-B 15282


title: RNA-seq Ikaros KD Ik2709 pre-pro-B 15279


title: RNA-seq Ikaros KD Ik4056 pre-pro-B 15278


title: RNA-seq Ikaros KD Ik2709 pre-pro-B 15273


title: RNA-seq Ikaros KD Ik4056 pre-pro-B 15272


title: RNA-seq Ikaros KD Ren713 control pre-pro-B 15271


title: RNA-seq Ikaros KD Ren713 control pre-pro-B 15277


title: 8-cell_replicate3

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

country: Germany

institute: Ludwig-Maximilians-Universität München

description: pools of 10 embryos

data_processing:
CASAVA 1.6 software was used for basecalling.
Adaptor sequences and the first 5 bases were removed. Additionally, reads were trimmed from the 3'- and 5'-end with a quality cutoff of 20. Reads below a length of 30 were discarded.
Filtered reads were mapped with Tophat2 (v.2.0.3) to the bovine UMD3.1 reference genome with default parameters.
The number of reads falling into exons of genes were counted using HTSeq-count. Read counts were normalized by library size and by a variance stabilizing transformation with DESeq and differential abundances were calculated with an adj. p-value < 0.05.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: tab-delimited text file include normalized values for each gene and sample.

organism: Bos taurus

source_name: embryos

growth_protocol: IVP of bovine embryos was done as described previously . Briefly, cumulus-oocyte complexes (COCs) were aspirated from German Simmental ovaries obtained in a local abattoir and washed twice in preincubated (39°C, 5% CO2 in air) Tissue Culture Medium 199 (TCM 199; Invitrogen) supplemented with l-glutamine (100 mg/L), NaHCO3 (3 g/L), Hepes (1400 mg/L), sodium pyruvate (250 mg/L), l-lactic-Ca-salt (600 mg/L), gentamicin (55 mg/L), and 10% (v/v) estrous cow serum (ECS). For in vitro maturation (IVM) COCs were washed in TCM 199 supplemented with 0.01 U/ml of bovine FSH and bovine LH (both Sioux Biochem), transferred to four-well plates (Nunc), and matured in 400 μl of this medium for 20–24 h at 39°C in an atmosphere of 5% CO2 in humidified air. For in vitro fertilization (IVF) the matured COCs were transferred to 400 μl of Tyrode albumin lactate pyruvate (TALP) medium containing 2.2 mg/ml of sodium pyruvate, 10 μg/ml of heparin sodium salt, and 6 mg/ml of BSA, after three washes in the same medium. Then, the COCs and spermatozoa (artificial insemination straws from a commercially available Zebu bull, subjected to a 90 min swim-up after thawing) were co-incubated for 18 h at 39°C in an atmosphere of 5% CO2 in humidified air. Presumptive zygotes were mechanically denuded by vortexing and gentle pipetting; washed three times in synthetic oviduct fluid (SOF) culture medium enriched with 5% ECS, 20 μl/ml of 100× basal medium (Invitrogen), and 10 μl/ml of 100× minimum essential medium (Invitrogen). Batches of app. 20 embryos were transferred to 400-μl droplets of medium covered with mineral oil and cultured until reaching the respective stages. The culture atmosphere was 5% CO2, 5% O2, and 90% N2 at 39°C and maximum humidity. Pools of ten embryos were picked after visual inspection and snap frozen in liquid nitrogen after washing in PBS. Stages collected for sequencing were: denuded oocytes before and after maturation and embryos at the 4-cell, 8-cell, 16-cell, and blastocyst stages.

extract_protocol:
Frozen pools of ten oocytes or embryos were thawed and lysed in 10 µl of Lysis Buffer (Prelude kit from NuGEN, San Carlos USA). cDNA was generated and amplified with the ovation RNAseq v2 kit (NuGEN, San Carlos, USA).
In brief 1 µl of the lysate was used for mixed random-/polyA-primed first-strand cDNA synthesis. After second strand synthesis the double-stranded cDNA was amplified by single primer isothermal amplification and the amplified cDNA was bead-purified (AmpureXP, Beckman-Coulter, Brea, USA) and fragmented by sonication (Bioruptor, Diagenode, Liege Belgium; 25 cycles 30 sec on/30 sec off). 500 ng of fragmented cDNA were used for preparation of Illumina-compatible sequencing libraries using the NuGEN Rapid library kit according to the manufacturer’s protocol. Adapter ligation was done with sample-specific barcodes. The resulting library was amplified (KAPA hifi polymerase, 8 cycles, 95°C 80 sec, 55°C 30 sec, 72°C 60 sec) and quantified on a Bioanalyzer 2100 (Agilent, Santa Clara, USA). Barcoded libraries were pooled at 10 nM concentration for multiplexed sequencing. Three replicates of each stage were sequenced on an Illumina GAIIx to a mean coverage of 20 Mio reads each. Sequencing runs were done in single-read mode with an 80 base read-length.

tag: Stage

tag: breed

value: German Simmental x Brahman


title: RNA-seq Ikaros KD Ren713 control pre-pro-B 15289


title: 4-cell_replicate2

description: pools of 10 embryos


title: 8-cell_replicate2

description: pools of 10 embryos


title: 4-cell_replicate3

description: pools of 10 embryos


title: 8-cell_replicate1

description: pools of 10 embryos


title: RNA-seq pro-B 15262


title: RNA-seq pro-B 15261


title: RNA-seq pro-B 15260


title: IKDNlargepreB 8

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

institute: Harvard Medical School

data_processing:
Basecalls performed using CASAVA versions 1.4-1.8
RNAseq reads were aligned to the mm9 genome assembly using the Burrows-Wheeler Aligner
Differential expression of WT and mutant large preB and WT adherent and WT nonadherent preB cells was performed using the DeSeq algorithm implemented through R
Genome_build: mm9
processed data file content: The columns labelled raw show raw read count and the columns labelled normalized show log 2 transformed normalized raw read counts.

source_name: Bone marrow

growth_protocol: cultured cells grown

extract_protocol:
Trizol extraction followed by Pure Link RNA minikit from Ambion
Protocols as described in Illumina-Truseq RNA  and Nugene Ovation RNASeq kits

tag: genotype/variation

value: IKDN

tag: cell phenotype

value: sorted culture adherent

tag: kit used

value: Nugene-Ovation

value: mixed background of 129sv c57black6


title: Mi-2b (CHD4) ChIP-seq Ikzf1(∆/–) pro-B 13310

description: DSG plus HCHO double crosslink

tag: genotype

value: Ikzf1(fl/-) Cd79(cre/+)

value: Anti-CHD4 (clone 3F2/4), Abcam AB70469, lot:GR104037-2


title: WTlargepreB 7

value: wild type

value: sorted culture adherent-2


title: Mi-2b (CHD4) ChIP-seq Ikzf1(∆/+) pro-B 13309

description: DSG plus HCHO double crosslink

value: Pro-B cell

value: Ikzf1(fl/+) Cd79(cre/+)


title: PU.1 Bio-ChIP-seq pro-B 8677

value: Spi1(ihCd2/ihCd2) R26(BirA/BirA)


title: WTlargepreB 6

value: sorted culture non-adherent-1


title: RNA-seq pro-B (c-Kit high) 12806

source_name: pro B cell

value: pro B cell

value: Ikzf1(fl/+) Cd79a(Cre/+)


title: 4-cell_replicate1

description: pools of 10 embryos


title: WTlargepreB 5

value: sorted culture adherent-1


title: RNA-seq pre-B (total) 12079

source_name: Pre-B cell

value: Pre-B cell

value: Wild-type


title: RNA-seq Ikaros KD empty vector control pre-pro-B 15270

value: Pre-pro-B cell


title: MII_oocyte_replicate2

description: pools of 10 oocytes

source_name: ooyctes

value: MII oocytes

value: German Simmental


title: IKDNlargepreB 4

value: IKDN

value: sorted primary

value: Illumina-Trueseq

value: mixed background of 129sv c57black6


title: RNA-seq pro-B (c-Kit high) 12073


title: NF4_RNASeq

tag: tissue

value: left ventricle apex tissue

value: non-failing


title: Ikaros Bio-ChIP-seq pre-pro-B 11890

value: Ikzf1(ihCd2/ihCd2) R26(BirA/+) Ebf1(fl/fl) Vav-Cre


title: RNA-seq pro-B 11601

value: Pro-B cell

value: Ikzf1(fl/-) Cd79a(Cre/+)


title: IKDNlargepreB 3


title: RNA-seq Ikaros KD empty vector control pre-pro-B 15276


title: GV_oocyte_replicate3

description: pools of 10 oocytes

value: GV oocytes


title: WTlargepreB 2

value: wild type


title: RNA-seq pro-B 11598

value: Ikzf1(fl/+) Cd79a(Cre/+)


title: RNA-seq pro-B 15263


title: WTlargepreB 1


title: GV_oocyte_replicate1

description: pools of 10 oocytes


title: MII_oocyte_replicate3

description: pools of 10 oocytes


title: RNA-seq pro-B 11600


title: RNA-seq pro-B 11599


title: RNA-seq pro-B (c-Kit high) 11597


title: GV_oocyte_replicate2

description: pools of 10 oocytes


title: U251 RNASeq miR137 transfection Rep2

tag: cell line


title: Ikaros Bio-ChIP-seq pro-B 9102


title: GAF n-ChIP S2 rep1

status: Public on Feb 08 2014

city: Boston

first: Guillermo

middle: A

last: Orsi

state: Massachusetts

address: 240 Longwood Ave.

department: BCMP

data_processing:
bedgraph files were generated by counting the number of mapped paired-end reads from fragments <76bp or >120bp overlapping each 10bp bin in the genome. Normalized scores are obtained by dividing read counts covering each 10bp bin by the total number of reads, and multiplying by the size of the genome.
Genome_build: dmel r5.32

source_name: GAF n-ChIP S2

extract_protocol:
ChIP was performed as described in CM Weber, JG Henikoff & S Henikoff, H2A.Z nucleosomes enriched over active genes are homotypic, Nat Struct Mol Bio 2010 Dec;17(12):1500-7, PMID 21057526 and SS Teves & S Henikoff Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide. Genes Dev. 2011 Nov 15;25(22):2387-97. PubMed PMID: 22085965
A modified Solexa Illumina library construction protocol was used as previously described in SS Teves & S Henikoff Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide. Genes Dev. 2011 Nov 15;25(22):2387-97. PubMed PMID: 22085965


title: Adf1 n-ChIP S2 rep1

source_name: Adf1 n-ChIP S2


title: Pho n-ChIP S2 rep1

source_name: Pho n-ChIP S2


title: Adf1 n-ChIP S2 rep2


title: RNA-seq pro-B (c-Kit high) 12072


title: IgG_RIPSeq

city: shanghai

first: shu-han

last: sun

address: 800 Xiang-Yin Road

country: China

institute: Second Military Medical University

data_processing:
The samples were single-end sequenced with a read length of 50 bp on an Illumina HiSeq 2500 sequencer.
Sequencing reads were mapped against the human reference genome version 19 using the TopHat algorithm version 2.0.9 supplying Ensembl gene annotations version GRCh37.65 and default settings.
Further analysis was performed using the R statistical programming language version 2.15.0.
After alignment to the genome, the expression level of genes was determined based on the value of RPKM (reads per kilobase per million reads), which was calculated by cuffdiff (version: 2.1.1).
Genome_build: human reference genome version 19

source_name: HCC cells SMMC-7721

extract_protocol:
After 48 hrs, cells were used to perform RNA immunoprecipitation (RIP) experiments using a GFP antibody or nonspecific mouse IgG and the Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore, Bedford, MA) according to the manufacturer’s instructions.
The sequencing libraries were generated using 100 ng of RNA and the TruSeq Stranded Total RNA kits from Illumina according to the manufacturer’s instructions.

treatment_protocol: SMMC-7721 cells were co-transfected with pcDNA3.1-MS2-ATB and pMS2-GFP.

tag: rip antibody

value: Normal Mouse IgG (Millipore, CS200621)

value: hepatocellular carcinoma


title: RNA-seq pre-B (total) 12078

value: Pre-B cell

value: Wild-type


title: MII_oocyte_replicate1

description: pools of 10 oocytes

value: MII oocytes

value: German Simmental


title: Pc n-ChIP BG3-c2 rep2

source_name: Pc n-ChIP BG3-c2


title: Pc n-ChIP BG3-c2 rep1


title: Pc n-ChIP S2 rep2

source_name: Pc n-ChIP S2


title: Pho n-ChIP S2 rep2


title: AntiGFP_RIPSeq


title: H3K27Me3 n-ChIP S2R+ rep2

source_name: H3K27Me3 n-ChIP S2R+


title: H3K27Me3 n-ChIP S2R+ rep1


title: Degradome

city: Beijing

first: Yijun

last: Qi

state: Bejing

address: Biotech. Building

department: School of Life Sciences

institute: Tsinghua University

description: Sample 4

data_processing:
Adaptor sequences in the sequencing reads were removed using vectorstrip from EMBOSS package v6.3.1.
Trimmed reads with a length of 19-27nt were aligned to Volvox carteri genome using bowtie v1.0.0.
Genome_build: Volvox_v1 (http://www.ncbi.nlm.nih.gov/assembly/GCA_000143455.1/)
Supplementary_files_format_and_content: Counts

organism: Volvox carteri

source_name: Whole colony degradome

growth_protocol: Volvox carteri (NIES-865) was obtain from National Institute for Environmental Studies (NIES) and cultured in MG liquid medium (http://mcc.nies.go.jp/) at 23℃, 48μE/m2sec.

extract_protocol:
Gonidia and somatic cells were separated by Dounce homogenizer. Total RNAs were extracted from Volvox whole colonies, gonidia and somatic cells using TRIzol reagent (Invitrogen). Small RNAs were isolated from total RNA.
Small RNAs were fractionated on a 15% PAGE gel. 18-28 nt small RNAs were purified and ligased to 3’ RNA linker-1 (IDT). 3’ ligation products were fractionated on 15% PAGE gel and 36~44 nt ligation products were purified and ligased to 5’ RNA linker. Ligation products were reverse transcribed by Supersript III (Invitrogen) and amplified by PCR.
Poly(A)+ RNA were purified from total RNA by oligodT resin (Qiagen) and ligased to 5’ RNA linker. Ligation products were purified and reversed transcribed with RACER RT primer by Superscript III (Invitrogen). First strand cDNA were amplified by linker and RACER primers and digested by MmeI (NEB). Digestion products were purified and ligased to dsDNA linker. Ligation products were amplified by linker and dsDNA linker primers.

value: Whole colony


title: Pc n-ChIP S2 rep1


title: Somatic Cell Small RNA Seq

description: Sample 3

source_name: Somatic cell sRNA

value: Somatic cells


title: Gonidia Small RNA Seq

description: Sample 2

source_name: Gonidia sRNA

value: Gonidia


title: Pho n-ChIP S2R+ rep1

source_name: Pho n-ChIP S2R+


title: Pho n-ChIP S2R+ rep2


title: Adf1 n-ChIP S2R+ rep2

source_name: Adf1 n-ChIP S2R+


title: GAF n-ChIP S2R+ rep1

source_name: GAF n-ChIP S2R+


title: Whole Cell Small RNA Seq

description: Sample 1

source_name: Whole cell sRNA


title: Adf1 n-ChIP S2R+ rep1


title: Pc n-ChIP S2R+ rep2

source_name: Pc n-ChIP S2R+


title: GAF n-ChIP S2 rep2


title: HL-ASE-WCEH7_Ind19-Aug18

status: Public on Feb 07 2014

city: La Jolla

first: Kun

last: Zhang

address: 9450 Gilman Drive

department: Bioengineering

institute: UCSD

description:
Whole-cell Extract of polyclonal cell line GM12878 clone H7
SRX400142

data_processing:
library strategy: padlock probe targeted library (digital RNA allelotyping method; ultra-deep sequencing of padlock captured SNPs from the transcriptome)
Basecalls performed using RTA version 1.13
Sequencing reads were trimmed to remove the targeting arms of padlock probes
Mapped to reference genome using samtools version 0.1.18
Variant called using GATK version 1.4-1
hg18
processed data files format and content: allelic table text tile

source_name: polyclonal cell line GM12878

extract_protocol:
DNA - Qiagen Blood Mini kit, RNA - Nuclei PURE Prep Sigma Aldrich NUC201, ChIP as described in PMID 16630819; 17603471. Antibodies used are AB9050 from Abcam for H3K36me3 mark and ABE44 from Millipore for H3K27me3 mark. cDNA synthesis was done after Turbo Dnase treatment according to manufacturer instruction for SuperScript III
To capture the targeted coding SNPs, mixture containing Padlock probes targeting 36,456 common coding SNPs and 200 ng of genomic DNA (or cDNA, ChIPed-DNA) was prepared in 1X Ampligase Buffer (Epicentre) (Zhang et al., 2009). The mixture was denatured at 95°C, gradually cooled and then hybridized at 60°C for 24 hours. The product was circularized after adding AmpliTaq Stoffel (Life Technology), and Ampligase (Epicentre), in presence of dNTPs, and incubating at 60°C for 18 hours. Following this exonuclease I (USB) and exonuclease III (USB) was added to cleave the linear DNA by incubating at 37°C for 2 hours and followed by heat inactivation at 90°C. The circularization product was amplified using primer AmpF6.3Sol: AATGATACGGCGACCACCGACACTCTCAGATGTTATCGAGGTCCGAC), AmpR6.3Ind  in Kapa SYBR FAST qPCR master mix (Kapa Biosystems) using the following program: 95 °C for 2 minutes, and then 6 cycles at 98°C for 20 seconds, 58°C for 20 seconds, 72°C for 20 seconds followed by 20 cycles at 98°C for 10 seconds and 72°C for 20 seconds. PCR reaction was terminated before the real time PCR curve reached plateau to avoid over-amplification. The amplicons were purified using Qiaquick PCR purification kit (Qiagen), and products in the expected size range (180bp) were selected using polyacrylamide (PAGE) gel. The libraries were sequenced on an Illumina Genome Analyzer IIx.
PMID 19620972

tag: cell line source

value: polyclonal cell line GM12878

tag: clone id

tag: molecule subtype

value: Whole-cell Extract


title: HL-ASE-WCEH16_Ind21-Aug18

description:
Whole-cell Extract of polyclonal cell line GM12878 clone H16
SRX400141


title: HL-ASE-WCEH0_Ind18-Aug18

description:
Whole-cell Extract of polyclonal cell line GM13130 clone H0
SRX400162

source_name: polyclonal cell line GM13130

value: polyclonal cell line GM13130


title: HL-ASE-WCEH14_Ind20-Aug18

description:
Whole-cell Extract of polyclonal cell line GM12878 clone H14
SRX400140


title: HL-ASE-H7gDNA_Ind1-Jun26

description:
gDNA of polyclonal cell line GM13130 clone H7
SRX400161
processed data file: H7.txt

value: gDNA


title: HL-ASE-DF1cDNA_Ind7-Jun26

description:
cDNA of polyclonal cell line GM12878 clone DF1
SRX400134

value: cDNA


title: HL-ASE-DF1gDNA_Ind10-Jun26

description:
gDNA of polyclonal cell line GM12878 clone DF1
SRX400135


title: HL-ASE-H0gDNA_Ind12-Jun26

description:
gDNA of polyclonal cell line GM13130 clone H0
SRX400159


title: HL-ASE-H14gDNA_Ind2-Jun26

description:
gDNA of polyclonal cell line GM13130 clone H14
SRX400160


title: HL-ASE-GMgDNA_Ind9-Jun26

description:
gDNA of polyclonal cell line GM12878
SRX400133


title: HL-ASE-WCEDF1_Ind16-Aug18

description:
Whole-cell Extract of polyclonal cell line GM12878 clone DF1
SRX400143


title: HL-ASE-WCEDF2_Ind17-Aug18

description:
Whole-cell Extract of polyclonal cell line GM12878 clone DF2
SRX400138


title: HL-ASE-gDNAH16_Ind29-Aug18

description:
gDNA of polyclonal cell line GM13130 clone H16
SRX400157
processed data file: H16.txt


title: HL-ASE-gDNAH14_Ind28-Aug18

description:
gDNA of polyclonal cell line GM13130 clone H14
SRX400156
processed data file: H14.txt


title: HL-ASE-gDNAH7_Ind27-Aug18

description:
gDNA of polyclonal cell line GM13130 clone H7
SRX400158


title: Pc n-ChIP S2R+ rep1


title: GAF n-ChIP S2R+ rep2


title: HL-ASE-DF2gDNA_Ind11-Jun26

description:
gDNA of polyclonal cell line GM12878 clone DF2
SRX400131


title: HL-ASE-DF2cDNA_Ind8-Jun26

description:
cDNA of polyclonal cell line GM12878 clone DF2
SRX400130


title: HL-ASE-ChipK36DF2_Ind4-Jun26

value: ChIPed material (DNA)

tag: chip antibody vendor

value: abcam

tag: chip antibody cat. #

tag: chip antibody lot #

value: mixed


title: HL-ASE-WCEGM12878_Ind15-Aug18

description:
Whole-cell Extract of polyclonal cell line GM12878
SRX400139


title: HL-ASE-ChIPK36me3H7_Ind3-Aug18

description:
SRX400155
processed data file: H7.txt


title: HL-ASE-ChipK27DF1_Ind5-Jun26

value: Millipore


title: HL-ASE-ChipK36DF1_Ind3-Jun26


title: HL-ASE-ChIPK36me3H14_Ind4-Aug18

description:
SRX400153
processed data file: H14.txt


title: HL-ASE-ChIPK36me3H0_Ind2-Aug18

description:
SRX400152
processed data file: H0.txt


title: HL-ASE-ChIPK27me3H7_Ind12-Aug18

description:
SRX400151
processed data file: H7.txt


title: HL-ASE-ChIPK27me3H16_Ind14-Aug18

description:
SRX400150
processed data file: H16.txt


title: HL-ASE-ChIPK27me3H14_Ind13-Aug18

description:
SRX400149
processed data file: H14.txt


title: HL-ASE-ChIPK27me3H0_Ind11-Aug18

description:
SRX400148
processed data file: H0.txt


title: HL-ASE-GmgDNA_H0gDNA_1_1_gDNA_Ind13-Jun26

description:
gDNA of polyclonal cell line GM12878/GM13130
SRX400132

source_name: polyclonal cell line GM12878/GM13130

value: polyclonal cell line GM12878/GM13130


title: HL-ASE-cDNAH16_Ind26-Aug18

description:
cDNA of polyclonal cell line GM13130 clone H16
SRX400146
processed data file: H16.txt


title: HL-ASE-cDNAH7_Ind24-Aug18

description:
cDNA of polyclonal cell line GM13130 clone H7
SRX400147
processed data file: H7.txt


title: HL-ASE-ChIPK27me3GM12878_Ind10-Aug18

description:
SRX400085
processed data file: GM12878.txt


title: HL-ASE-ChIPK36me3H16_Ind9-Aug18

description:
SRX400154
processed data file: H16.txt


title: YPR057W

city: Rehovot

first: Noam

last: Ohana

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
The software that I used was not yet published (Jaitin and Voichek in press)
Align the reads to the genome: using bowtie we find the coordinate in the genome for which each read aligns
Cleaning PCR amplification: the primers had a sequence that allowed the correction of PCR amplification bias.
Reads aligning more than once:  Some of the reads aligned more than once (two places in the genome fit just as good), usually we throw these cases. In this case, some gene comes in orthologs couples, for example RP genes, and reads coming from them will be separated between the two genes. We separate the reads weight which are aligned to two places according to the reads that where aligned uniquely
Sum the signal over the genes: As we filter RNAs using the poly-A selection and we do so after cutting the RNA molecules, our signal will be condensed near the 3’ end of the gene.  To get a score for each gene, we sum the signal for 400bp before the 3’ to 200bp after the 3’ of the gene.  We take the 3’ position from TSS data  and for genes that doesn’t have TSS data we use the ORF 3’. The border of -400 -> +200 were taken as the protocol is calibrated to give segments of size ~200bp and as we are not sure about the TSS end we take a larger range.
normalization and conversion to log2 scale: all samples to 10^6 reads, by dividing each sample by the total number of reads and multiplying by 10^6. converting all values to log2 scale
substracting the log2 values of wildtype strain (control) of each gene from all the samples
Genome_build: Saccharomyces Genome Database (SGD) version 64
Supplementary_files_format_and_content: tab-delimited text files contain value of log2 number of reads for each sample, according to a list of genes in our lab that contains 6701 genes.

source_name: cells

growth_protocol: The cells were grown in a liquid media over night. Then they were diluted to OD 0.05 and allowed to undergo 2-3 divisions.

extract_protocol:
The extraction was made using Macherey-Nagel nucleospin© kit, for extraction of RNA in 96 well format
For each 96 well plate, a 50ml lysis buffer was made. The buffer contained 9.11gr sorbitol (SIGMA-ALDRICH) to a final concentration 1M, 10 ml EDTA 0.5M to a final concentraion100mM and 50ul lyticase (10IU/ul). To each well 450ul were added, and mixed with pellet. The plate was put in 30°C of 30' in order to break the cell wall. Then, the plate was centrifuged for 10' 2500rpm, and soup was transfer to a new 96 well plate, that provided by the nucleospin® 96 RNA kit. From that stage on the extraction continued using this kit. From RNA extracts, labelled cDNA was made for each sample. The cDNA of each samples were run in the highsec 2500 of the illumina company, using Truseq SR Cluster Kit v3 -cBot-HS cluster kit and Truseq SBS Kit v3-HS run kit (50 cycles).

treatment_protocol: Growth in exponential phase

tag: strain


title: YPR164W


title: HL-ASE-cDNAGM_Ind22-Aug18

description:
cDNA of polyclonal cell line GM12878
SRX400083

data_processing:
library strategy: padlock probe targeted library (digital RNA allelotyping method; ultra-deep sequencing of padlock captured SNPs from the transcriptome)
Basecalls performed using RTA version 1.13
Sequencing reads were trimmed to remove the targeting arms of padlock probes
Mapped to reference genome using samtools version 0.1.18
Variant called using GATK version 1.4-1
Genome_build: hg18
processed data files format and content: allelic table text tile


title: HL-ASE-cDNAH14_Ind25-Aug18

description:
cDNA of polyclonal cell line GM13130 clone H14
SRX400145
processed data file: H14.txt


title: HL-ASE-cDNAH0_Ind23-Aug18

description:
cDNA of polyclonal cell line GM13130 clone H0
SRX400144
processed data file: H0.txt


title: YPL129W


title: YPL161C


title: YPL260W


title: HL-ASE-ChIPK36me3GM12878_Ind1-Aug18

description:
SRX400088
processed data file: GM12878.txt

tag: chip antibody


title: YOR221C


title: YPL079W


title: YPL080C


title: YOR070C


title: YOL112W


title: YOR010C


title: YOR123C


title: YOR025W


title: YOR001W


title: YOL118C


title: HL-ASE-ChipK27DF2_Ind6-Jun26


title: YPL120W


title: YOL109W


title: YOL098C


title: YOL018C


title: YOL072W


title: YOL014W


title: YOL004W


title: YOL064C


title: YOL013C


title: YNR006W


title: YOR182C


title: YNR067C


title: YOL006C


title: YNL323W


title: YOL041C


title: YOL001W


title: YNL302C


title: YOL013WA


title: YNR071C


title: YNL227C


title: YOL110W


title: YNL229C


title: YNL236W


title: YNL316C


title: YNR010W


title: YNL250W


title: YNL169C


title: YNL198C


title: YNL197C


title: YNL199C


title: YNL241C


title: YNL206C


title: YNL226W


title: YNR051C


title: YNL120C


title: YNL107W


title: YNL098C


title: YNL193W


title: YNL171C


title: YNL080C


title: YNL156C


title: YMR312W


title: YMR230W


title: YNL069C


title: YMR243C


title: YNL064C


title: YNL041C


title: YMR207C


title: YMR183C


title: YMR202W


title: YMR179W


title: YMR116C


title: YMR205C


title: YMR086CA


title: YNL141W


title: YMR078C


title: YMR224C


title: YML097C


title: YMR060C


title: YMR143W


title: YML063W


title: YML054C


title: YML041C


title: YML035C


title: YML026C


title: YMR307W


title: YML013CA


title: YLR448W


title: YLR441C


title: YLR422W


title: YLR418C


title: YLR405W


title: YLR414C


title: YLR402W


title: YLR388W


title: YMR003W


title: YLR384C


title: YLR372W


title: YLR371W


title: YLR370C


title: YLR373C


title: YLR360W


title: YLR337C


title: YLR342W


title: YMR269W


title: YLR338W


title: YLR287CA


title: YLR264W


title: YLR329W


title: YLR268W


title: YLR410W


title: YLR242C


title: YLR190W


title: YLR185W


title: YLR193C


title: YLR435W


title: YLR182W


title: YLR184W


title: YLR357W


title: YML032C


title: YLR096W


title: YLR125W


title: YLR089C


title: YMR004W


title: YLR087C


title: YLR073C


title: YLR052W


title: YLR082C


title: YLL010C


title: YKR082W


title: YLR032W


title: YLL002W


title: YLR261C


title: YKR020W


title: YLR235C


title: YKR019C


title: YKR055W


title: YLR079W


title: YKR057W


title: YKL197C


title: YKL212W


title: YKL149C


title: YKL185W


title: YKL110C


title: YKL091C


title: YLL029W


title: YKL069W


title: YLR234W


title: YKR074W


title: YKL055C


title: YKL048C


title: YKL113C


title: YKL139W


title: YKL057C


title: YKL200C


title: YKL041W


title: YKR007W


title: YJR119C


title: YJR117W


title: YJR060W


title: YJR074W


title: YJR082C


title: YJL218W


title: YJL204C


title: YJR118C


title: YJR015W


title: YKL020C


title: YJL197W


title: YJL171C


title: YJL199C


title: YJL135W


title: YKL064W


title: YJL133W


title: YJL152W


title: YJL115W


title: YJL117W


title: YJL130C


title: YKL096WA


title: YJR059W


title: YJR032W


title: YJR107W


title: YJL053W


title: YJL175W


title: YJL029C


title: YIL165C


title: YIL125W


title: YIR023W


title: YIL110W


title: YIL119C


title: YIL149C


title: YIL134W


title: YIL087C


title: YIL076W


title: YIL013C


title: YHR178W


title: YJL101C


title: YHR081W


title: YHR203C


title: YIL040W


title: YIL008W


title: YHR034C


title: YHR021C


title: YHR111W


title: YHR066W


title: YHR014W


title: YHR041C


title: YGR237C


title: YJL016W


title: YHL033C


title: YIR005W


title: YIL139C


title: YHR012W


title: YGR200C


title: YGR118W


title: YGR085C


title: YGR188C


title: YGL253W


title: YGR184C


title: YGR077C


title: YGR157W


title: YGR163W


title: YGR027C


title: YGL218W


title: YGL244W


title: YGL219C


title: YGL196W


title: YGR105W


title: YGL212W


title: YGL173C


title: YGL168W


title: YGL124C


title: YGL163C


title: YGL147C


title: YGL105W


title: YGL110C


title: YGL127C


title: YGL084C


title: YGR101W


title: YGL024W


title: YFR040W


title: YGL043W


title: YGL007W


title: YGL066W


title: YFR030W


title: YFL052W


title: YGL081W


title: YFR032CA


title: YFL023W


title: YFL036W


title: YER151C


title: YER145C


title: YER095W


title: YER083C


title: YFL001W


title: YER155C


title: YER139C


title: YER019W


title: YDR532C


title: YER060WA


title: YER020W


title: YDR508C


title: YDR439W


title: YDR500C


title: YDR443C


title: YDR455C


title: YDR388W


title: YDR382W


title: YDR392W


title: YDR359C


title: YER074W


title: YDR369C


title: YDR363W


title: YDR207C


title: YDR270W


title: YDR332W


title: YDR245W


title: YDR335W


title: YDR276C


title: YDR200C


title: YDR159W


title: YDR174W


title: YDR244W


title: YDR146C


title: YER061C


title: YDR123C


title: YDR128W


title: YDR024W


title: YDR076W


title: YDR004W


title: YDR378C


title: YDL174C


title: YDL115C


title: YDL100C


title: YDL020C


title: YDL082W


title: YCR081W


title: YCR077C


title: YDL033C


title: YCR075C


title: YCL062W


title: YCR033W


title: Small RNAs from ovaries of y[1]; cn[1] bw[1] sp[1] strain

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

data_processing:
The reads with clipped 3'-adapter were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie to dm3 genome assembly with requiring of perfect mathcing.
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited files include the frequencies of clipped read occurrences in each library.

source_name: ovaries

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
Total RNA was isolated by Trizol (Invitrogene) and size-fractioned by PAGE (19-29 nt)
Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012)

value: ovaries


title: YCR008W


title: YCR071C


title: YCL026C


title: YCR001W


title: YCL063W


title: YCL016C


title: YCL010C


title: YBR231C


title: YBR171W


title: YBR189W


title: YDR025W


title: YDL127W


title: YBR122C


title: YBR126C


title: YBR106W


title: YDL081C


title: YBR093C


title: YBR076W


title: YBR084CA


title: YBR082C


title: YBL054W


title: YBL007C


title: YBR266C


title: YBL083C


title: YBL027W


title: YAL014C


title: YAL056W


title: YAL026C


title: YAR043C


title: HCV RNA / RNase A / 5.0 min

city: Aurora

first: Daphne

middle: A.

last: Cooper

state: CO

department: Department of Microbiology

institute: University of Colorado

description:
HCV RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from HCV RNA incubated for 5.0 min with RNase A.

data_processing:
Reads were trimmed for contaminating linker sequence.
Reads were aligned using Bowtie with -m1 --best --strata options
The 8-base UMI at the 5'-end of the raw read was counted to remove PCR over-amplification bias.
Signal from No 2-5A and No RNase A timepoints was subtracted from 0, 2.5, 5, 10, and 20 minute timepoints in RNase L and RNase A data (except for PV RNase L), these processed data samples include "baseline" in the file name.
The 3'-dinucleotide from the read was obtained to characterize RNase specificity, and # of UMI reads were plotted against genome postion using R to map cleavage sites across the genome/sequence.
Genome_build: HCV: Hepatits C virus subtype 1A polyprotein gene complete cds (AF009606.1)
Genome_build: PV: Human poliovirus 1 Mahoney, complete genome (V01149.1)
Genome_build: 28S: Homo sapiens RNA, 28S ribosomal 1 (RN28S1), ribosomal RNA (NR_003287.2)
Genome_build: 18S: Homo sapiens RNA, 18S ribosomal 1 (RN18S1), ribosomal 1 (NR_003286.2),
Genome_build: 5.8S: Homo sapiens RNA, 5.8S ribosomal 1 (RN5-8S1), ribosomal RNA (NR_003285.2)
Genome_build: 5S: Homo sapiens RNA, 5S ribosomal 9 (RN5S9), ribosomal RNA (NR_023371.1)
Genome_build: U6: Homo sapiens RNA, U6 small nuclear 33 (RNU6-33), small nuclear RNA (NR_046491.1)
Supplementary_files_format_and_content: text files include tab delimited columns [genome, cleavage site, cleavage site+1, # of UMI reads, and dinucleotide]

organism: hepatitis C virus genotype 1a

source_name: Hepatitis C virus RNA

extract_protocol:
Total cellular RNA was extracted using 4M guanidine thiocyanate with acid phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation.
Illumina TruSeq RNA linker with 8-base Unique Molecular Identifier (UMI) was attached with Arabidopsis thaliana tRNA ligase (recognizes RNAs with terminal 2', 3'-cyclic phosphates). cDNA was generated using a DNA primer specific to the Illumina linker, and the IDT miRNA cloning linker 1 was attached to the 3'-end of the cDNA. cDNAs were PCR amplified, pooled, and sequenced.
2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing were used to identify and quantify metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs

tag: experimental condition

value: HCV RNA incubated with RNase A

tag: exptl time

value: 5.0 min


title: Polio RNA / RNase L & 2-5A / 2.5 min

description:
Polio RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from polio RNA incubated for 2.5 min with RNase L and 2-5A.

organism: Poliovirus 1

source_name: Poliovirus RNA

value: Polio RNA incubated with RNase L & 2-5A

value: 2.5 min


title: HCV RNA / RNase A / 20 min

description:
HCV RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from HCV RNA incubated for 20 min with RNase A.

value: 20 min


title: Polio RNA / RNase L & 2-5A / 20 min

description:
Polio RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from polio RNA incubated for 20 min with RNase L and 2-5A.


title: HCV RNA / RNase A / 2.5 min

description:
HCV RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from HCV RNA incubated for 2.5 min with RNase A.


title: HCV RNA / RNase A / 0 min

description:
HCV RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from HCV RNA incubated for 0 min with RNase A.

value: 0 min


title: Polio RNA / RNase L & 2-5A / 10 min

description:
Polio RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from polio RNA incubated for 10 min with RNase L and 2-5A.

value: 10 min


title: HCV RNA / RNase A / 10 min

description:
HCV RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from HCV RNA incubated for 10 min with RNase A.


title: Polio RNA / RNase L & 2-5A / 5.0 min

description:
Polio RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from polio RNA incubated for 5.0 min with RNase L and 2-5A.


title: Polio RNA / RNase L & 2-5A / 0 min

description:
Polio RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from polio RNA incubated for 0 min with RNase L and 2-5A.

source_name: Poliovirus RNA (Polio RNA)


title: HCV RNA / RNase L & 2-5A / 5.0 min

description:
HCV RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from HCV RNA incubated for 5.0 min with RNase L and 2-5A.

value: HCV RNA incubated with RNase L & 2-5A


title: HCV RNA / RNase L & 2-5A / 10 min

description:
HCV RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from HCV RNA incubated for 10 min with RNase L and 2-5A.


title: HCV RNA / RNase L & 2-5A / 2.5 min

description:
HCV RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from HCV RNA incubated for 2.5 min with RNase L and 2-5A.


title: HCV RNA / RNase L / No 2-5A / 20 min

description:
HCV RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from HCV RNA incubated for 20 min with RNase L but no 2-5A.

source_name: Hepatitis C virus RNA (HCV RNA)

value: HCV RNA incubated with RNase L


title: HCV RNA / RNase L & 2-5A / 0 min

description:
HCV RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from HCV RNA incubated for 0 min with RNase L and 2-5A.


title: HCV RNA / no RNase A / 20 min

description:
HCV RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from HCV RNA incubated for 20 min without  RNase A.

value: HCV RNA incubated without RNase A


title: YBR026C


title: YBR025C


title: Polio-Infected / M25 HeLa cells / 6 hpa

description:
Total RNA from polio-infected M25 HeLa cells
2', 3'-cyclic phosphate cDNA library derived using RNA from Polio-Infected / M25 HeLa cells / 6 hpa

source_name: Polio-Infected / M25 HeLa cells / 6 hpa

value: M25 HeLa / dominant-negative mutant RNase L

value: Polio-Infected / M25 HeLa cells / 6 hpa

value: 6 hr post-adsorption (hpa)


title: YAL002W


title: Polio-Infected / M25 HeLa cells / 4 hpa

description:
Total RNA from polio-infected M25 HeLa cells
2', 3'-cyclic phosphate cDNA library derived using RNA from Polio-Infected / M25 HeLa cells / 4 hpa

source_name: Polio-Infected / M25 HeLa cells / 4 hpa

value: Polio-Infected / M25 HeLa cells / 4 hpa

value: 4 hr post-adsorption (hpa)


title: Mock-Infected / M25 HeLa cells / 8 hpa

description:
Total RNA from mock-infected M25 HeLa cells
2', 3'-cyclic phosphate cDNA library derived using RNA from Mock-Infected / M25 HeLa cells / 8 hpa

source_name: Mock-Infected / M25 HeLa cells / 8 hpa

value: Mock-Infected / M25 HeLa cells / 8 hpa

value: 8 hr post-adsorption (hpa)


title: Polio-Infected / M25 HeLa cells / 0 hpa

description:
Total RNA from polio-infected M25 HeLa cells
2', 3'-cyclic phosphate cDNA library derived using RNA from Polio-Infected / M25 HeLa cells / 0 hpa

source_name: Polio-Infected / M25 HeLa cells / 0 hpa

value: Polio-Infected / M25 HeLa cells / 0 hpa

value: 0 hr post-adsorption (hpa)


title: Polio-Infected / W12 HeLa cells / 8 hpa

description:
Total RNA from polio-infected W12 HeLa cells
2', 3'-cyclic phosphate cDNA library derived using RNA from Polio-Infected / W12 HeLa cells / 8 hpa

source_name: Polio-Infected / W12 HeLa cells / 8 hpa

value: W12 HeLa / wildtype RNase L

value: Polio-Infected / W12 HeLa cells / 8 hpa


title: Mock-Infected / M25 HeLa cells / 0 hpa

description:
Total RNA from mock-infected M25 HeLa cells
2', 3'-cyclic phosphate cDNA library derived using RNA from Mock-Infected / M25 HeLa cells / 0 hpa

source_name: Mock-Infected / M25 HeLa cells / 0 hpa

value: Mock-Infected / M25 HeLa cells / 0 hpa


title: Polio-Infected / W12 HeLa cells / 0 hpa

description:
Total RNA from polio-infected W12 HeLa cells
2', 3'-cyclic phosphate cDNA library derived using RNA from Polio-Infected / W12 HeLa cells / 0 hpa

source_name: Polio-Infected / W12 HeLa cells / 0 hpa

value: Polio-Infected / W12 HeLa cells / 0 hpa


title: Polio-Infected / W12 HeLa cells / 4 hpa

description:
Total RNA from polio-infected W12 HeLa cells
2', 3'-cyclic phosphate cDNA library derived using RNA from Polio-Infected / W12 HeLa cells / 4 hpa

source_name: Polio-Infected / W12 HeLa cells / 4 hpa

value: Polio-Infected / W12 HeLa cells / 4 hpa


title: Polio RNA / RNase A / 10 min

description:
Polio RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from polio RNA incubated for 10 min with RNase A.

value: Polio RNA incubated with RNase A

value: 10 min


title: Polio-Infected / W12 HeLa cells / 2 hpa

description:
Total RNA from polio-infected W12 HeLa cells
2', 3'-cyclic phosphate cDNA library derived using RNA from Polio-Infected / W12 HeLa cells / 2 hpa

source_name: Polio-Infected / W12 HeLa cells / 2 hpa

value: Polio-Infected / W12 HeLa cells / 2 hpa

value: 2 hr post-adsorption (hpa)


title: Polio RNA / RNase A / 5.0 min

description:
Polio RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from polio RNA incubated for 5.0 min with RNase A.

value: 5.0 min


title: Polio-Infected / M25 HeLa cells / 8 hpa

description:
Total RNA from polio-infected M25 HeLa cells
2', 3'-cyclic phosphate cDNA library derived using RNA from Polio-Infected / M25 HeLa cells / 8 hpa

source_name: Polio-Infected / M25 HeLa cells / 8 hpa

value: M25 HeLa / dominant-negative mutant RNase L

value: Polio-Infected / M25 HeLa cells / 8 hpa


title: Polio RNA / no RNase A / 20 min

description:
Polio RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from polio RNA incubated for 20 min without  RNase A.

value: Polio RNA incubated without RNase A

value: 20 min


title: Mock-Infected / W12 HeLa cells / 0 hpa

description:
Total RNA from mock-infected W12 HeLa cells
2', 3'-cyclic phosphate cDNA library derived using RNA from Mock-Infected / W12 HeLa cells / 0 hpa

source_name: Mock-Infected / W12 HeLa cells / 0 hpa

value: Mock-Infected / W12 HeLa cells / 0 hpa


title: Seq13

status: Public on Feb 06 2014

city: New York

first: Gabriel

last: Rosenfeld

address: 1300 York Ave. Rm. LC711

department: Cell and Developmental Biology

institute: Weill Cornell

data_processing:
Basecalls, demultiplexing, and filtering of reads was  performed using Casava 1.7.0.
Read alignment was performed with the BWA alignment algorithm with native goby support using gobyweb, version: development (20110921150240) with the following parameters: Ambiguity threshold = 1, Max Number Gap Opens = 1, Max Number Gap Extensions = -1.
Differential expression was generated with the DESEQ package with native goby support using gobyweb, version: development (20110921150240) with the following parameters: q-value threshold = 1.0, weight adjustment = none, Gene counts box checked.
Data were filtered according to geneID's demonstrating a p-adjusted < 0.1, a log2 fold change > 1 for WT/G4, and Average RPKM in the comparison group > 1.
Genome_build: Zv9.61
Supplementary_files_format_and_content: Wig files were generated using gobyweb, version: development(20110921150240).  Additional supplementary .xlsx file containing RPKM, counts, and statistical values was exported from gobyweb and processed in excel.

organism: Danio rerio

source_name: sorted cardiomyocytes

growth_protocol: Embryos were grown in 1x E3 buffer for 24 hours at 28.5 degrees Celsius in petri dishes.  25 ml of E3 buffer was used per 50-60 embryos in each dish.

extract_protocol:
RNA was isolated by Trizol except that after addition of 1.5 volumes of 100% ethanol to the aqueous phase, the solution was transferred to an RNeasy minElute column (Qiagen).  On-column DNase digestion, subsequent washing, and RNA elution was performed according to the Qiagen's recommended protocol for RNeasy micro kit.
100ng of total RNA was used to prepare the libraries.  Libraries were prepared for RNA sequencing using the mRNA-Seq (seq1, seq5, and seq11) or TruSeq Kit (seq13, seq14, and seq15) according to the Illumina's recommended protocol.

treatment_protocol: Embryos were injected with morpholino before the 4-cell stage of development.  2nl of a 0.7mM concentration of Gata4 morpholino (5'-TCCACAGGTGAGCGATTATTGCTTC-3') were injected per individual embryo.  At 24 hours post fertilization (hpf), batches of approximately 200 embryos were pooled into 1.5 ml tube.  Embryos were dissociated by manual agitation with a pellet pestle (Fisher) and trypsinized with pre-heated TrypLE (Life Technologies) at 32C for 15 min on a rotator. Trypsinized samples were pipetted through a 35um cell strainer into a 5ml tube, trypsin inhibited by addition of 4ml FACS buffer (L-15 medium supplemented with 1% heat inactivated FCS, 0.8mM CaCl2, 50U/ml penicillin, and 0.05 mg/ml streptomycin) followed by addition of FCS to 7.5% final concentration. Cells were pelleted at 300 RCF for 5 min and then washed with FACS buffer. Dissociated embryonic cells were resuspended at 7.5x106 cells/ml in FACS buffer. FACS was performed on a Vantage cell sorter (BD) into Trizol LS (Life Technologies), and stored at -80C until RNA isolation.

tag: developmental stage

tag: transgenic line

tag: experimental group

value: Wildtype


title: Seq14

value: Gata4 morphant


title: Polio-Infected / W12 HeLa cells / 6 hpa

description:
Total RNA from polio-infected W12 HeLa cells
2', 3'-cyclic phosphate cDNA library derived using RNA from Polio-Infected / W12 HeLa cells / 6 hpa

source_name: Polio-Infected / W12 HeLa cells / 6 hpa

value: W12 HeLa / wildtype RNase L

value: Polio-Infected / W12 HeLa cells / 6 hpa

value: 6 hr post-adsorption (hpa)


title: Seq15


title: HCV RNA / RNase L & 2-5A / 20 min

description:
HCV RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from HCV RNA incubated for 20 min with RNase L and 2-5A.

source_name: Hepatitis C virus RNA

value: HCV RNA incubated with RNase L & 2-5A