title: IMP2_M_R267_3

city: Boston

first: John

middle: G

last: Flanagan

address: 240 Longwood Avenue

department: Cell Biology

institute: Harvard Medical School

description: RNA interacting with IMP2

data_processing:
The quality of raw sequence reads (36 nt) was analyzed using fastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapter sequences were trimmed, and reads with more than 2 undetermined bases (Ns) were removed. The sum of base Phred quality scores of each read was calculated, and reads with the lowest 1% sum of Phred scores were filtered. The rest reads were trimmed from the 3’- end to retain 28 nt of high quality. After filtering and trimming, reads were aligned to mouse genome (NCBI37/mm9 assembly) using Bowtie (Langmead et al., 2009) (http://bowtie- bio.sourceforge.net/index.shtml), allowing up to 2 mismatches. Reads aligned to multiple positions in the genome were filtered. RefSeq mRNA database was used to build the exon junction index to align reads that overlap the exon junction sites. Those reads that were not aligned to genome were aligned to exon junctions, and only uniquely aligned reads were retained. Reads that aligned to the same genomic locations were collapsed to remove potential duplicates resulting from PCR amplifications. The control mRNA-seq data were aligned to the mouse genome and exon junction sites by the same procedure. The aligned reads were annotated based on RefSeq mRNA database.
Peak identification: To identify IMP2 binding sites, we combined and analyzed reads from all four CLIP replicates. Overlapping reads were grouped into clusters, and each cluster was assigned two values, peak height and fold change. Peak height was defined as the maximum number of overlapping reads in the cluster, and median fold change was calculated by comparing to the randomly sampled background from mRNA-seq data. To differentiate significantly enriched IMP2 binding sites from false positives, we generated mock CLIP data sets by randomly sampling the same number of sequence reads as in the IMP2 CLIP samples from the control mRNA-seq data. The false discovery rate was calculated as the ratio of the number of peaks identified from mock CLIP data to that from CLIP data using the same cutoff. We selected high-confidence peaks on mature mRNAs, based on the following criteria: (a) a minimal peak height of 18 in pooled CLIP samples, which is greater than the maximal peak height in five different sets of mock CLIPs, (b) a minimal median fold change of 2, (c) reproducible peaks requiring that within a peak region, at least 4 overlapping reads be present in the four replicates. Additionally, in order to eliminate occasional mRNAs with high read coverage along the transcript but no prominent peaks, we required that the peak height should be at least 1.2x the highest peak in the introns, and at least 10x the average read coverage in the introns.
Genome_build: mm9

source_name: Embryonic (E14) brain

extract_protocol:
HITS-CLIP was performed essentially as described previously (Licatalosi et al., 2008; Preitner et al., 2014) on E14 Swiss Webster mouse brains. Briefly, embryonic brain tissues were partially dissociated before UV irradiation (UV at 254 nm, 3X 300 mJ/cm2 in a Stratalinker). Cell lysates were sonicated, treated with DNase, and digested with benzonase (Sigma E8263; at a final dilution of 1:2000; 10 min at 37°C) to produce protein-bound RNAs of ~40 nt fragments. Then pre-cleared lysates were mixed with 30 μl Sepharose beads and 30 μg antibody (mouse polyclonal anti-IMP2 antibody, Abnova H00010644-A01; rabbit anti-IMP2 antibody, Proteintech 11601-1-AP), and rotated for 3 hours at 4°C. Immunoprecipitated protein-RNA complexes were stringently washed with SDS- containing buffer and dephosphorylated, and the radiolabeled RNA adapter (5’- UCGUAUGCCGUCUUCUGCUUGU-3’) were ligated at the 3’ end of the RNA fragments. Protein-RNA complexes were then phosphorylated at the 5’ end, separated on a 4-12% denaturing NuPAGE gel (Invitrogen), transferred to a nitrocellulose membrane, and exposed on a film. Narrow bands corresponding to the size of the specific protein-RNA complexes were then excised from the membrane. RNA fragments were extracted, ligated to the 5’ adapter (5’- GUUCAGAGUUCUACAGUCCGACGAUC-3’) and amplified by RT-PCR (primers: AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA, and CAAGCAGAAGACGGCATACGA). The purified PCR products were sequenced on Illumina sequencing platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: stain

value: Swiss Webster

tag: development stage

value: brain


title: IMP2_R_R267_2

status: Public on Aug 02 2016

type: SRA

state: MA

country: USA

description: RNA interacting with IMP2

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue


title: 1.K4R-K36me3-H3

city: Jerusalem

first: Nir

last: Friedman

address: Givat Ram

department: School of Engineering

country: Israel

institute: The Hebrew University of Jerusalem

library_source: genomic

data_processing:
Pair-end reads were mapped to the yeast genome (sacCer3) using bowtie2 with maximal fragment size of 1000bp.
We treated duplicate fragments as potential PCR artifacts. We thus treated the set of unique fragments found as the read-set. We defined mononucleosome fragments as these shorter than 220bp.
We used the nucleosome location atlas defined by Weiner et al(Weiner et al., 2015). We measured nucleosome coverage by counting the number of fragments overlapping a window of size 50bp around the center of the nucleosome.
Genome_build: sacCer3
Supplementary_files_format_and_content: csv file containing read counts for each nucleosome location in each combinatorial ChIP sample

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Yeast cells were grown in YPD media at 30ºC with constant shaking to OD 0.6-0.8.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes at room temperature with occasional shaking, quenched with 0.125 M glycine for 5 minutes at room temperature with occasional shaking, collected by centrifugation, (4000 g, 5 minutes), washed with cold ddH2O supplemented with EDTA-free protease inhibitors cocktail (Roche) and the pellet was resuspended in buffer Z (1 M sorbitol, 50 mM Tris 7.4, 10 mM β-mercaptoethanol) with zymolyase (Seikagaku) at 0.3 - 1 units per 1 ml of original cell volume. Cells were gently rotated at 30ºC for 25 minutes until > 95% of cells were spheroplasted. Spheroplasts were pelleted (6500 g, 10 minutes) and resuspended in NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail) at final concentration of 200 OD/ml. Chromatin was digested with 12.5 units/ml MNase (Worthington) for 20 minutes at 37ºC, and digestion was stopped by removing the tubes into ice and addition of 1 volume of ice cold MNase stop buffer ( 220 mM NaCl, 0.2% SDS, 0.2% DOX, 10 mM EDTA, 2%,Triton X-100, EDTA-free protease inhibitor cocktail). Tubes were kept on ice for 10 minutes, vortexed 3 x 10 seconds, centrifuged (16,000 g, 10 minutes, 4ºC), and the supernatant containing the nucleosomes was removed to a fresh tube.
See attached paper - http://biorxiv.org/content/early/2016/06/27/060962

tag: strain

tag: library

value: Histone mutation library

tag: 1st ip

tag: 2nd ip / input


title: 1.K4R-K79me3-K4me3


title: 1.K4R-K18ac-K18ac


title: P60 Cerebellum H3K27ac ChIP-seq Rep 1

city: Durham

first: Christopher

middle: L

last: Frank

state: NC

address: 101 Science Dr.

institute: Duke University

data_processing:
Basecalls performed using CASAVA v1.8
ChIP-seq mapped to NCBI37/mm9 with Bowtie v1.0.0;  Up to 2 mismatches were allowed
Putative PCR artifacts filtered from mapped ChIP-seq reads prior to peak calls
ChIP-seq peaks called with MACS v1.4
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq .bed files contain all MACS peak calls and scores with default significance threshold

source_name: whole cerebellum

extract_protocol: Chromatin Immunoprecipitation (anti histone H3K27Ac, Abcam Ab4729). NEB Library Preparation Kit ( NEB 6240S and NEB E7335s)

tag: developmental stage

value: Postnatal day 60 (P60)

tag: antibody

value: H3K27Ac, Abcam Ab4729


title: 1.K4R-K18ac-K36me3


title: P7 Cerebellum H3K27ac ChIP-seq Rep 2

value: Postnatal day 7 (P7)


title: P60 Cerebellum H3K27ac ChIP-seq Rep 2


title: IMP2_R_R270_2

description: RNA interacting with IMP2


title: 1.K4R-H3-Input

value: Input


title: 1.K4R-K18ac-Input


title: 1.K4R-K18ac-K4me3


title: H3K27ac_TKO3b1

city: Los Angeles

first: Andrew

last: King

state: CA

address: Gonda Bldg Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

data_processing:
Fastq files were demultiplexed and generated using bcl2fastq version 1.8.4
Reads were mapped to mm9 genome using bowtie version 1.1.0 with options -m1 --best -v2
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph data displays ChIP-seq sequencing reads normalized to a depth of 1e7. Each read is extended by the predicted sequencing fragment length.

source_name: Embryonic stem cell (ESC)

growth_protocol: Mouse embryonic stem cells (mESCs) were grown on irradiated mouse embryonic fibroblasts and maintained in DMEM supplemented with 15% fetal bovine serum, 1 mM GlutaMAX, 1X Non-essential amino acids, 1X Penicillin/Streptomycin, mLIF, and 0.001% β-mercaptoethanol.

extract_protocol:
mESCs were pre-plated to deplete MEF feeders before collection. Cells were fixed with 1% formaldehyde after which chromatin was isolated and sonicated to 150-300 bp using Bioruptor (Diagenode). Sonicated chromatin was precleared with Protein A/G Dynabeads then incubated in antibody overnight. Chromatin was then immunoprecipitated with Protein A/G Dynabeads for > 2 hours. ChIP was washed successively by two rounds of low-salt buffer, two rounds of high-salt buffer, two rounds of LiCl buffer, and finally two rounds of TE buffer. ChIP DNA was eluted in TE, reverse crosslinked overnight, treated with RNase A, then proteinase K, and finally extracted with phenol-chloroform and ethanol precipitation.
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit per manufacturer's recommendations. Libraries were quantified using Qubit Fluorometer and Bioanalyzer High Sensitivity DNA Analysis Kit individually. Libraries were pooled and sequenced using the Illumina HiSeq 2000 machine as either 50-bp or 100-bp single-end sequencing reads.

tag: cell type

value: ESC

tag: line

tag: genotype

value: H3K27ac (Active Motif 39133)


title: 1.K4R-H3-K79me3


title: H3K27ac_TKO3a2


title: 1.K4R-K36me3-Input


title: 1.K4R-K18ac-H3


title: 1.K4R-H3-K4me3


title: H3K27ac_TKO3a1


title: H3K27ac_DKO3b1

value: J1 ESC


title: 1.K4R-H3-K36me3


title: IMP2_M_R270_3

description: RNA interacting with IMP2


title: H3K27ac_TKO

value: TKO


title: 1.K4R-H3-K18ac


title: H3K27ac_DKO3a2


title: H3K4me1_TKO3a2

value: H3K4me1 (Abcam ab8895)


title: H3K4me1_TKO


title: H3K27ac_J1

value: WT


title: 1.K36R-K79me3-Input


title: H3K4me1_TKO3b1


title: 1.K36R-K79me3-K79me3


title: H3K4me1_DKO3b1


title: H3K4me1_DKO3a2


title: 1.K4R-H3-H3


title: H3K27me3_TKO3b1

value: H3K27me3 (Active Motif 39155)


title: H3K4me1_J1


title: H3K27me3_TKO3a2


title: 1.K36R-K79me3-K4me3


title: 1.K36R-K79me3-K18ac


title: 1.K36R-K79me3-H3


title: H3K27ac_DKO3a1


title: H3K27me3_TKO3a1


title: H3K27me3_TKO-r2


title: H3K27me3_DKO3b1mut


title: H3K27me3_TKO


title: H3K27me3_DKO3b1


title: 1.K36R-K79me3-K36me3


title: 1.K36R-K4me3-Input


title: H3K27me3_DKO3a2


title: 1.K36R-K4me3-K79me3


title: H3K4me1_DKO

value: DKO


title: H3K27me3_DKO


title: H3K27me3_J1-r2


title: 1.K36R-K4me3-K4me3


title: H3K4me1_DKO3a1


title: H3K4me3_TKO3b1

value: H3K4me3 (Abcam ab8580)


title: H3K4me3_TKO3a2


title: H3K27me3_J1


title: RRBS_TKO3b1-r2

data_processing:
Fastq files were trimmed using Trim Galore version 0.4.1 with options --rrbs and --phred33 or --phred64 depending on quality score encoding.
Reads were mapped to mm9 genome using Bismark version 0.14.4 specifying either --phred33-quals or --phred64-quals depending on quality score encoding.
Methylation state of individual CpGs were determined using bismark_methylation_extractor specifying --cutoff 5 --comprehensive
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph data displays fraction of methylated cytosine in CpG context supported by minimally 5 reads.

extract_protocol:
Genomic DNA was purified from mESCs using standard phenol-chloroform-isoamyl alcohol extraction followed by ethanol precipitation.
RRBS libraries were generated starting from 400-800 ng of genomic DNA as previously described by Meissner et al. with minor modifications. MspI- generated fragments were end-repaired and adenylated before being ligated with Illumina TruSeq adapters. DNA purifications after each enzymatic reaction as well as size-selection of adapter-ligated fragments ranging from 200-350 bp were carried out using AMPure XP beads (Beckman Coulter). Bisulfite conversion was performed with Qiagen EpiTect kit. In order to optimize the efficiency, bisulfite conversion, carried out as described by the manufacturer, was performed twice. Bisulfite-converted libraries were amplified using MyTaq Mix (Bioline).


title: H3K4me3_J1


title: Input


title: 1.K36R-K4me3-K36me3


title: 1.K36R-K4me3-K18ac


title: 1.K36R-K4me3-H3


title: RRBS_TKO3a2-r2


title: H3K4me3_TKO


title: RRBS_TKO3a1-r2


title: RRBS_TKO3b1


title: 1.K36R-K36me3-K79me3


title: RRBS_TKO


title: RRBS_TKO3a2


title: RRBS_DKO3b1


title: RRBS_TKO3a1


title: 1.K36R-K36me3-K4me3


title: H3K27me3_DKO3a1


title: RRBS_DKO3a2


title: 1.K36R-K36me3-H3


title: 1.K36R-K36me3-K18ac


title: RRBS_DKO3a1


title: 1.K36R-K18ac-K79me3


title: RRBS_DKO


title: 1.K36R-K18ac-K4me3


title: RRBS_J1


title: RRBS_J1-r2


title: 1.K36R-K36me3-Input


title: RRBS_TKO-r2


title: 1.K36R-K18ac-Input


title: 1.K36R-K18ac-H3


title: SUZ12_247_AEBP2_KO_rep2_ChIPSeq

city: Oxford

first: Michal

middle: R.

last: Gdula

address: South Parks Road

country: United Kingdom

institute: Oxford University

data_processing:
Single‐end tags were mapped to the mouse genome (mm9) using Map with Bowtie for Illumina (version 1.1.2) (Langmead et al., 2009). By setting the “-m” parameter to 1, reads which could align to more than one place in the genome were excluded from further analysis.
Reads were ordered by the “Convert SAM to BAM (version 2.0.0)” tool and PCR duplicates and unmapped reads were removed using SAMtools (Li et al., 2009).
Samples were downsampled by randomly discarding reads using Picard tools (http://picard.sourceforge.net) where appropriate.
Subsequently, peaks were called using Model‐based Analysis of ChIP‐Seq (MACS2 version 2.0.10.2). Peaks were detected with a q-value cut-off at 0.05 and using the broad setting (Zhang et al., 2008).
MACS2 also generated a sequencing trace which was visualized in the Integrated Genome Browser (Nicol et al., 2009)
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files generated by MACS2
Supplementary_files_format_and_content: bed files with enrichment peaks generated by MACS2

source_name: ESCs

growth_protocol: ES cells were grown in ES cell medium, which consisted of Dulbecco's Modified Eagle Medium (DMEM, Life Technologies) supplemented with 10% foetal calf serum (FCS, Seralab), 2 mM L-glutamine, 1x non-essential amino acids, 50 μM 2-mercaptoethanol, 50 μg/ml penicillin/streptomycin (all Life Technologies) and LIF-conditioned medium, made in-house, at a concentration equivalent to 1000 U/ml. Non-differentiating ES cells were grown on tissue culture dishes coated with PBS+1% gelatine. Cells were grown at 37°C in a humid atmosphere with 5% CO2. Cells were passaged using 0.05% trypsin-EDTA (Life Technologies) with 2% Chicken Serum (Life Technologies) and frozen in FCS + 10% dimethyl sulphoxide (DMSO, Sigma).

extract_protocol:
ChIP for FS2-tagged AEBP2 was performed as described (Farcas et al., 2012) except that we used rProtein A Sepharose beads (GE Healthcare) that had been blocked for 1 hr at 4 °C with 1 mg/ml Bovine Serum Albumin (BSA) and 1 mg/ml yeast tRNA (Sigma). ChIP for endogenous proteins was performed as described (Stock et al., 2007), except approximate concentration after sonication was measured by measuring absorbance using the Nanodrop ND-1000 (ThermoScientific) and 200 μg of chromatin was used per IP and after the washes DNA was purified using ChIP DNA Clean & concentration™ columns (Zymo 13 Research) and eluted in 10 μl volume.
NEB Next® DNA Library Prep Master Mix Set for Illumina

tag: cell line

value: 129/1 XY ES cell line

value: AEBP2 KO

tag: chip antibody

value: anti-SUZ12 (Cell Signalling, catalog# 3737)


title: AEBP2_244_wild_type_rep2_ChIPSeq

value: wild-type

value: anti-AEBP2 (generated in this study)


title: H3K27_246_AEBP2_KO_rep2_ChIPSeq

value: anti-H3K27 (Diagenode, catalog# pAb-069-050)


title: 1.K36R-H3-K79me3

value: Histone mutation library


title: H3K27_242_wild_type_rep2_ChIPSeq


title: 1.K36R-H3-Input

value: Input


title: input_AEBP2_KO_rep2_245


title: 1.K36R-H3-K36me3


title: 1.K36R-K36me3-K36me3


title: 1.K36R-H3-K4me3


title: 1.K18R-K79me3-Input


title: input_AEBP2_KO_rep1_205


title: 1.K36R-H3-K18ac


title: 1.K36R-K18ac-K18ac


title: H3K27_202_wild_type_rep1_ChIPSeq


title: input_wild_type_rep2_241


title: 1.K18R-K79me3-K79me3


title: input_wild_type_rep1_201


title: 1.K36R-K18ac-K36me3


title: 1.K18R-K79me3-K36me3


title: AEBP2_FS2_wild_type_ChIPSeq

value: anti-FS2 (Gift from Prof.Rob Klose; reference:Elife. 2012 Dec 18;1:e00205. doi:10.7554/eLife.00205)


title: mRNA_DKO3b1

data_processing:
Fastq files were demultiplexed and generated using bcl2fastq version 1.8.4
Reads were mapped to mm9 genome using STAR version 2.4.0 with options --outSAMstrandField intronMotif
Genome_build: mm9
Supplementary_files_format_and_content: RPKM

molecule: polyA RNA

extract_protocol:
RNA was purified using RNeasy per manufacturer’s instructions.
PolyA-tailed RNA was purified from total RNA and libraries were constructed using the TruSeq RNA Library Prep Kit v2.0 following manufacturer’s recommendations.


title: SUZ12_243_wild_type_rep2_ChIPSeq


title: AEBP2_FS2_wild_type_input


title: 1.K18R-K4me3-K4me3


title: mRNA_DKO3a2


title: 1.K18R-K79me3-K18ac


title: 1.K36R-H3-H3


title: 1.K18R-K4me3-Input


title: 1.K18R-K79me3-H3


title: mRNA_DKO3a1


title: smRNA-seq of HT22 as control

city: Beijing

first: Xiaowei

last: Chen

address: 15 Datun Road, Chaoyang District

country: China

institute: Institute of Biophysics, CAS

data_processing:
[Trimming of adapters and mapping to genomes] First the 3’ end adapters of reads generated by Illumina Genome Analyzer IIx were trimmed using The Flexible Adapter Remover (FAR, http://sourceforge.net/projects/theflexibleadap/). The minimum overlap between adapter and read was set to 6 bases. Two mismatches were allowed. Reads with length less than 10 bases trimming adapters were removed from the data. The last 6 bases were trimmed if adapter sequence was not found at 3’ end. The trimmed reads were grouped into unique reads. Unique reads with read counts of 3 or more were mapped to the human (UCSC hg19) or mouse (UCSC mm9) genomes using bowtie (Langmead et al., 2009). Reads mapping to the respective genomes without mismatches were used to obtain expression profiles for the miRNAs. When obtaining expression levels of isomiRs with non-template additions at 3’ end, three mismatches were allowed.
[Sequences of non-coding RNAs] The sequences of annotated pre-miRNAs and mature miRNAs were obtained from the miRBase Release 18 (Kozomara and Griffiths-Jones, 2011). Ribosomal RNA sequences were extracted from the Silva database (http://www.arb-silva.de/), Ensembl (GRCh37 and NCBIM37) and Functional RNA database (fRNAdb), sequences of tRNA from the Genomic tRNA Database (http://gtrnadb.ucsc.edu/), snRNA sequences from Ensembl (GRCh37 and NCBIM37) and the fRNAdb, human snoRNA sequences from the snoRNABase and Ensembl GRCh37, mouse snoRNA sequences from Ensembl NCBIM37 and the fRNAdb, piRNA sequences from the RNAdb, and repeated elements from the Repbase (http://www.girinst.org/repbase/). We obtained the coordinates of exons and introns from UCSC Table Browser (http://genome.ucsc.edu), and subsequently extracted the sequences from the genomes using a Python script.
[miRNA and isomiR expression profiling] Genomic coordinates of mature miRNAs were extracted (in BED format) from the annotation file in miRBase. Genomic coordinates of reads mapping to genome without mismatch were obtained (in BED format) using a Python script from mapping results. Only reads with length from 17 to 26 bases were selected. BEDTools (Version 2.9.0) (Quinlan and Hall, 2010) was used to compare the genomic coordinates to find reads overlapping with mature miRNAs. We considered reads overlapping with mature miRNAs by at least 17 bases to contribute to the expression of miRNAs and their isomiRs. Apart from miRNAs matching the miRBase sequences, we also counted reads mapping to each type of isomiR. To obtain the expression of isomiRs with non-template extension at 3’ end, we first mapped reads to the respective miRNAs sequences with one mismatch, and then counted reads that were one nucleotide longer than the miRBase sequence but else matched the miRBases sequence perfectly.
[Differential expression analysis] The number of reads mapping to miRNAs and their isomiRs were used to estimate their expression levels in the 3 pairs of libraries (SNB-19_siCtrl VS SNB-19_siTDP, SY-5Y_siCtrl VS SY-5Y_siTDP and HT22_siCtrl VS HT22_siTDP). We applied a Bayesian method developed by Audic and Claverie (Audic and Claverie, 1997) to identify differentially expressed miRNAs (p-value<0.001). The fold change in miRNA expression between the 3 pairs of libraries was also calculated. The Chi-squared test was employed to calculate the statistical significance of changes in isomiR expression patterns after TDP-43 knockdown.
Genome_build: human (UCSC hg19) or mouse (UCSC mm9) genomes
Supplementary_files_format_and_content: The processed data files are in tab-delimited txt format. The first column in the processed data file is the accession number of miRNA, and the second column is the the expression level.

source_name: HT22 as control

growth_protocol: Human neuroblastoma cell (SH-SY-5Y), human glioma cell (SNB-19), and mouse HT22 cells were cultured in DMEM supplemented with 10% fetal bovine serum at 5% CO2 and 37°C.

extract_protocol:
Following two rounds of transfection with the control or TDP-43 siRNAs, cells were lysed in Trizol (Invitrogen) for total RNA extraction with DNAs removed by treating samples using RNase-free DNase I (Roche).
Small RNA libraries (16-52 nt) were constructed using the TruSeq Small RNA Sample Prep Kit (Illumina) and sequenced using an Illumina Genome Analyzer IIx platform.

treatment_protocol: The siRNA oligos were transfected into the cells by lipofectamine2000 (Invitrogen) for 48 hours followed by a second transfection for another 72 hours.

value: hippocampal neuronal cells

tag: genotype/variation

value: control


title: mRNA_TKO3b1

value: J1 ESC


title: mRNA_DKO


title: 1.K18R-K4me3-K36me3


title: WT2

city: Chicago

first: Bercin

middle: K

last: Cenik

state: IL

address: 303 E Superior St

department: Biochemistry and Molecular Genetics

institute: Northwestern University

description: WT replicate 2

data_processing:
Quality assessment of the RNA-Seq data was done using NGS-QC-Toolkit (Patel and Jain, 2012) with default setting
Quality filtered reads generated by the tool were then aligned to the mouse reference genome GRCm38 (mm10) using the Tophat2 (v 2.0.0 ) aligner (Kim et al., 2013) using default setting.
Differential gene expression analysis was done using the R package DESeq2 (v 1.6.3) (Anders and Huber, 2010).
Read counts were normalized by taking the median of each gene count across samples and dividing each sample gene count by the relative ratio of library sizes between the calculated median and sample size. The averaged normalized expressions values of the samples were used to calculate fold change and p-values.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: DESeq2 output in .txt format containing average baseMean, log2foldchange and lcfSE values and p values. Data present reflect change in averaged dKO samples (HSA2,HSA3,HSA4) with respect to WT (WT1,WT2,WT3) samples. Fdr = 0.01, p-value = 0.05 were used as cut-offs.

source_name: embryonic hindlimb muscle

extract_protocol:
E17.5 embryos were sacrificed, deskinned, and hindlimb muscle was removed from the leg and flash frozen. Total RNA was extracted using QIAGEN Rneasy mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skeletal muscle


title: smRNA-seq of HT22 after TDP-43 knockdown

source_name: HT22 after TDP-43 knockdown

value: TDP-43 knockdown


title: 1.K18R-K4me3-K18ac


title: WT3

description: WT replicate 3

value: WT


title: WT1

description: WT replicate 1


title: HSA4

description: dKO replicate 3

value: MRTF-A/B dKO


title: mRNA_TKO

value: TKO


title: mRNA_TKO3a2-r2


title: 1.K18R-K36me3-Input


title: 1.K18R-K4me3-K79me3


title: mRNA_TKO3a1


title: AEBP2_204_wild_type_rep1_ChIPSeq

value: 129/1 XY ES cell line


title: 1.K18R-K79me3-K4me3


title: HSA3

description: dKO replicate 2


title: mRNA_TKO3a1-r2


title: 1.K18R-K36me3-K79me3


title: HSA2

description: dKO replicate 1


title: mRNA_TKO3a2


title: H7_dreived_D2.25_Smtmrs_ATAC-seq

city: Stanford

first: Rahul

last: Sinha

address: 265 Campus Drive

department: ISCBRM

institute: Stanford University School of Medicine

description: This files contain peaks that were reproducible between the two replicates for each cell type, in standard narrowPeak format.

data_processing:
Sequenced reads were trimmed for adaptor sequences using skewer 0.1.127 with parameters -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -y AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -t 16 -q 21 -l 21 -n -u -f sanger for bulk-population RNA-seq and parameters -x CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG -y CTGTCTCTTATACACATCTGACGCTGCCGACGANNNNNNNNGTGTAGATCTCGGTGGTCGCCGTATCATT -t 16 -q 21 -l 21 -n -u -f sanger for single-cell RNA-seq.
Trimmed reads were then mapped to hg38 using STAR 2.4 with parameters  --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD  --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04   --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000  --alignSJoverhangMin 8   --alignSJDBoverhangMin 1 --sjdbScore 1 --twopassMode Basic --twopass1readsN -1 --outWigStrand Stranded
Normalized expression values (TPM) and transcript counts were then calculated using RSEM 1.2.21 with parameters --bam --estimate-rspd --seed 12345 --paired-end --forward-prob 0
Genome_build: hg38

organism: Homo sapiens

source_name: H7 ESC

extract_protocol:
Total RNA or chromatin was extracted as described below
Bulk RNA-seq: Total RNA from flow-sorted or differentiated cell populations was isolated using Trizol (ThermoFisher) as per manufacturer’s recommendation and was facilitated by addition of linear polyacrylamide (Sigma) as a carrier during RNA precipitation. Purified total RNA was treated with 4 units of RQ1 RNase-free DNase (Promega) at 37 dgrees Celsius for 1 hour to remove trace amounts of genomic DNA. The DNase-treated total RNA was cleaned-up using RNeasy micro kit (QIAGEN). Subsequently, the integrity of extracted RNA was assayed by on-chip electrophoresis (Agilent Bioanalyzer) and only samples with a high RNA integrity (RIN) value were used for subsequent cDNA preparation. Purified total RNA (10-50 ng) was reverse-transcribed into cDNA and amplified using the Ovation  RNA-seq System V2 (NuGEN). Amplified cDNA was sheared using the Covaris S2 (Covaris) using the following settings: total volume 120 l, duty cycle 10%, intensity 5, cycle/burst 100, total time 2 min. The sheared cDNA was cleaned up using Agencourt Ampure XP (Beckman Coulter) to obtain cDNA fragments >= 400 base pairs (bp). 500 ng of sheared and size-selected cDNA were used as input for library preparation using NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs) as per manufacturer’s recommendations. Resulting libraries (fragment distribution: 300-700 bp; peak 500-550 bp) were pooled (multiplexing) and sequenced using HiSeq 4000 or NextSeq 500 (Illumina) at the Stanford Functional Genomics Facility to obtain 2x150 base pair paired-end reads. For each RNA-seq library, the effectiveness of adapter ligation and the effective library concentration was determined by qPCR and bioanalyzer (Agilent) prior to pooling and loading them onto the sequencers. The reads obtained were trimmed for base call quality (PHRED score >= 21) and the presence of adapter sequences at the 3' end using Skewer (version: 0.1.127; Jiang et al, BMC Bioinformatics, 2014). Single-cell RNA-seq: Cells were briefly washed (DMEM/F12), dissociated (TrypLE Express), strained (100 micron filter), pelleted and resuspended in DMEM/F12 for counting. Before single-cell capture, two quality control steps were implemented. Firstly, cell size was estimated in order to determine whether cells should be loaded onto C1 capture arrays of either 10-17 micron or 17-25 micron size. Arrays were chosen for each lineage by estimating the median cell size of each given population on a flow cytometer on the basis of the FSC-W signal and choosing an array with an appropriate pore size to accommodate such cells. Secondly, to ensure the high viability of in vitro-differentiated cells prior to commencing single-cell RNA-seq, for each population a separate aliquot of cells was stained with 1.1 micromolar DAPI and analyzed by flow cytometry; for all cell populations that were used for single-cell RNA-seq, 98% of cells were viable (i.e., DAPI negative). For single-cell capture, cells were diluted to a concentration of 1000 cells/microliter, diluted 3:2 in C1 Cell Suspension Reagent, and loaded onto a Fluidigm C1 single-cell capture array chip for automated capture on a Fluidigm C1 Machine (Stanford Stem Cell Institute single-cell Core). After loading, the efficiency of single-cell capture was verified using an automated microscope that imaged each catured cell on the chip. The subsequent cell lysis, cDNA synthesis, and aplification was carried on the array chip inside the microfuidic chamber in an automated fashion using C1 machine using the SMARTer Ultra Low RNA Kit (Clontech, 634833) reagents as per the manufacturers' instructions (Fluidigm, PN 100-7168 Rev. A2). The amplified cDNA from individual cells was harvested into a 96 well and diluted using the harvesting reagent (Fluidigm). The concentration and integrity of amplified cDNA were assessed using a Fragment Analyzer (Advanced Analytical) in a 96 well plate format. Amplified cDNAs form only thos wells that (1) were not degraded, and (2) originated from wells that were microscopically verified to contain a single cell, were carried forward for subsequent library construction. Using a single-channel liquid handeling robot, Mosquito (TTP Labtech), amplified cDNAs from single-cells from all the lineages were diluted to a concentration range of 0.05-0.16 ng/microliter using C1 Harvest Reagent (Fluidigm) as a diluent and consolidated into 384 well plates. The diluted single-cell cDNAs were tagmented and converted to sequencing libraries in the 384 well plates using the Nextera XT DNA Sample Prep Kit (Illumina, FC-131-1096) in an automated fashion using another 16-channel Moquito robot (TTP Labtech) and 384 distinct illumina compatiblr molecular barcodes. The resulting sequencing libraies from a single such 384 plate were then pooled and cleaned up using Agencourt AMPure XP beads (Beckman Coulter). The pooled libraries were then analyzed for quality and concentration using bioanalyzer (Agilent) and qPCR and loaded on a single lane of NextSeq 500 or two lanes of Hiseq 4000 to obtain 1-2 million 2x150 reads per cell. The reads obtained were trimmed for base call quality (PHRED score >= 21) and the presence of adapter sequences using Skewer (version: 0.1.127; Jiang et al, BMC Bioinformatics, 2014). ATAC-seq: For each replicate, 50,000 cells were lysed in lysis buffer containing 0.01% IGEPAL CA-630 (Sigma, I8896) to obtain nuclei, which were directly used in the Tn5 transposition reaction (reagents from Nextera DNA Sample Preparation Kit; Illumina, FC-121-1030). Immediately following transposition, DNA fragments were purified (MinElute Kit, Qiagen) and PCR amplified for a total of 12-13 cycles using previously-designed primer sequences that include illumina compatible adapters and barcodes. The resulting ATAC-seq libraries were purified (MinElute Kit, Qiagen), pooled and final library-pool concentrations were assessed (Bioanalyzer) prior to next-generation sequencing. The quality of ATAC-seq libraries was confirmed by a shallow sequencing run using a MiSeq v3 (Stanford Functional Genomics Facility, 2x75bp reads) before deep sequencing was performed on a NextSeq 500 (2x75bp reads).

treatment_protocol: H7-derived day 2 paraxial mesoderm was briefly washed (DMEM/F12) and further differentiated into day 2.25 somitomeres for 6 hours (1 μM A-83-01 + 250 nM LDN-193189 + 1 μM XAV939 + 500 nM PD0325901) in CDM2 basal medium.

tag: source

value: H7 ESC

tag: sample type

value: H7 human embryonic stem cells derived day 2.25 Somitomeres (Smtmrs) cells


title: 1.K18R-K36me3-K4me3


title: smRNA-seq of SNB19 after TDP-43 knockdown

source_name: SNB19 after TDP-43 knockdown

value: glioma cells


title: H7_D3GARPpCrdcM_ATAC-seq

treatment_protocol: H7-derived day 2 lateral mesoderm was differentiated into day 4 cardiac mesoderm by briefly washing (DMEM/F12), treatment with 1 μM A8301 + 30 ng/mL BMP4 + 20 ng/mL FGF2 for 24 hrs followed by brief washing (DMEM/F12) and then treatment with 25 ng/mL Activin + 30 ng/mL BMP4 + 1 μM C59 for the next 24 hrs. Subsequently, day 4 cardiac mesoderm-containing cultures were dissociated into single cells (TrypLE Express) and stained with an anti-GARP APC antibody (Biolegend) and DAPI (Biolegend). Then, viable GARP+ cardiac mesoderm cells were purified using a fluorescence-activated cell sorter (FACSAria II, BD Biosciences)

value: H7 human embryonic stem cells derived day 3 GARP-positive Cardiac Mesoderm (D3GARPpCrdcM) cells


title: smRNA-seq of SHSY5Y after TDP-43 knockdown

source_name: SHSY5Y after TDP-43 knockdown

value: neuroblastoma cells


title: 1.K18R-K4me3-H3

value: Histone mutation library


title: mRNA_J1


title: Panc1_pLV-IL35_mRNASeq

city: Tianjin

first: Chongbiao

last: Huang

address: Huanhu Xi Road

department: Senior Ward

institute: Tianjin Medical University Cancer Institute and Hospital

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Pancreatic ductal adenocarcinoma

growth_protocol: These cells were cultured in DMEM basic medium added with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere of 95% air and 5% CO2.

extract_protocol:
Total RNA of cells was extracted by Trizol (Invitrogen)
The RNA fragments were copied into first strand cDNA using reverse transcriptase and random hexamer primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. The short cDNA fragments were finally prepared for sequencing on the Illumina Genome Analyzer using reagents provided in the Illumina Genomic DNA Sequencing Sample Prep Kit. The cDNA fragments were end-repaired using T4 DNA polymerase and Klenow DNA polymerase and a single adenine nucleotide base was added to the cDNA fragments by using 3prime to 5prime exonuclease.

tag: stain

value: Pancreatic


title: smRNA-seq of SNB19 as control

source_name: SNB19 as control


title: H7_D2LtM_ATAC-seq

treatment_protocol: H7-derived day 1 mid primitive streak was briefly washed (DMEM/F12) and differentiated towards day 2 lateral mesoderm for 24 hours (1 μM A-83-01 + 30 ng/mL BMP4 + 1 μM C59) in CDM2 basal medium.

value: H7 human embryonic stem cells derived day 2 Lateral Mesoderm (D2LtM) cells


title: 1.K18R-K36me3-H3


title: H7_D5CntrlDrmmtm_ATAC-seq

treatment_protocol: H7-derived day 3 early somites were briefly washed (DMEM/F12), treated with 3 μM CHIR99021 + 150 nM Vismodegib + 50 ng/mL BMP4 for 24 hours, and then washed again (DMEM/F12) and subsequently treated with CHIR99021 (3 μM) + 21K (5 nM) for 24 hours to yield day 5 central dermomyotome.

value: H7 human embryonic stem cells derived day 5 Central Dermomyotome (D5CntrlDrmmtm) cells


title: 1.K18R-K18ac-Input

value: Input


title: 1.K18R-K18ac-K79me3


title: Panc1_control_mRNASeq

value: pLV-vector


title: 1.K18R-K36me3-K18ac


title: H7_derived_ESMT_ATAC-seq

treatment_protocol: H7-derived day 2 paraxial mesoderm was briefly washed (DMEM/F12) and further differentiated into day 3 early somites for 24 hours (1 μM A-83-01 + 250 nM LDN-193189 + 1 μM C59 + 500 nM PD0325901; sometimes with the use of 1 μM XAV939 in lieu of C59) in CDM2 basal medium.

value: H7 human embryonic stem cells derived day 3 Early Somite (ESMT) cells


title: smRNA-seq of SHSY5Y as control

source_name: SHSY5Y as control

value: control


title: 1.K18R-K18ac-K4me3


title: H7_derived_Sclrtm_ATAC-seq

treatment_protocol: H7-derived day 3 early somites were briefly washed (DMEM/F12) and further differentiated into day 5-6 ventral sclerotome for 48-72 hours (5 nM 21K + 1 μM C59) in CDM2 basal media.

value: H7 human embryonic stem cells derived Sclerotome (Sclrtm) cells


title: 1.K18R-K18ac-K36me3


title: MIHA HBx d14

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
To obtain high quality reads for downstream analysis, raw sequencing reads were firstly filtered for adapters sequences and low quality, in which more than 5% of the bases in a read contained unknown bases (‘N’) and more than 50% of the bases having a base quality value of ≤ 10, and were removed using cutadapt (Martin, 2011) and custom scripts. Subsequently, low complexity bases (more than 10bp of continuous bases of “A” and “T”) were trimmed from the 3’ end using prinseq (Schmieder and Edwards, 2011). Reads with length < 40bp were then discarded. Finally, sequencing reads were filtered for rRNA sequence and remaining high quality reads were used for downstream analysis.
The high quality reads were aligned against human transcriptome (hg19) using RSEM package v1.2.21 (Li and Dewey, 2011). Expression estimation and tests for differential expression were accomplished using EBSeq v1.6.0 (Leng at el, 2013) which is part of the RSEM package.
Genome_build: Human genome (hg19)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: Liver

growth_protocol: MIHA liver cells were routinely cultured in DMEM medium supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Mini Kit according to manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: pcDNA6b-3xFLAG plasmids carrying empty vector alone, C-terminal truncated HBx d14 or C-terminal truncated HBx d35 were stably transfected into MIHA cells by Lipofectamine 2000 with stable cells selected using blasticidin

value: MIHA

tag: transfection

value: C-terminal truncated HBx mutants (delta 14)


title: MIHA HBx d35

value: C-terminal truncated HBx mutants (delta 35)


title: H7_derived_DLL1pPXM_ATAC-seq

treatment_protocol: H7-derived day 1 anterior primitive streak was briefly washed (DMEM/F12) and differentiated towards day 2 paraxial mesoderm for 24 hours (1 μM A-83-01 + 3 μM CHIR99021 + 250 nM LDN-193189 + 20 ng/mL FGF2) in CDM2 basal medium. Subsequently, day 2 paraxial mesoderm-containing cultures were dissociated into single cells (TrypLE Express) and stained with an anti-DLL1 PE antibody (Biolegend) and DAPI (Biolegend). Then, viable DLL1+ paraxial mesoderm cells were purified using a fluorescence-activated cell sorter (FACSAria II, BD Biosciences).

value: H7 ESC

value: H7 human embryonic stem cells derived DLL1-positive paraxial mesoderm (DLL1pPXM) cells


title: 1.K18R-K36me3-K36me3


title: H7_derived_MPS_ATAC-seq

treatment_protocol: Partially confluent cultures of mTeSR1-maintained H7 human embryonic stem cells (WiCell) were dissociated into very fine clumps using Accutase (Gibco) and sparsely passaged ~1:12-1:20 onto new Geltrex-coated cell culture plates in mTeSR1 supplemented with 1 μM thiazovivin (Tocris; a ROCK inhibitor to prevent cell death after dissociation) overnight. The following morning, H7 human embryonic stem cells were briefly washed (in DMEM/F12) before treatment for 24 hours with 30 mg/mL Activin A + 40 ng/mL BMP4 + 6 μM CHIR99021 + 20 ng/mL FGF2 + 100 nM PIK90 in CDM2 basal media to induce differentiation into mid primitive streak.

value: H7 human embryonic stem cells derived Mid Primitive Streak (MPS) cells


title: 1.K18R-K18ac-K18ac


title: MIHA EV

value: empty vector control


title: 1.K18R-K18ac-H3


title: H7_derived_APS_ATAC-seq

treatment_protocol: Partially confluent cultures of mTeSR1-maintained H7 human embryonic stem cells (WiCell) were dissociated into very fine clumps using Accutase (Gibco) and sparsely passaged ~1:12-1:20 onto new Geltrex-coated cell culture plates in mTeSR1 supplemented with 1 μM thiazovivin (Tocris; a ROCK inhibitor to prevent cell death after dissociation) overnight. The following morning, H7 human embryonic stem cells were briefly washed (in DMEM/F12) before treatment for 24 hours with 30 ng/mL Activin A + 4 μM CHIR99021 + 20 ng/mL FGF2 + 100 nM PIK90 in CDM2 basal media to induce differentiation into anterior primitive streak.

value: H7 human embryonic stem cells derived Anterior Primitive Streak (APS) cells


title: P7 Cerebellum H3K27ac ChIP-seq Rep 1

value: Postnatal day 7 (P7)

value: H3K27Ac, Abcam Ab4729


title: H7_hESC_ATAC-seq

source_name: WiCell

treatment_protocol: H7 human embryonic stem cells (WiCell) were cultured feeder-free in mTeSR1 (StemCell Technologies; supplemented with 1% penicillin/streptomycin) on a Geltrex basement membrane (Gibco), with mTeSR1 media changed daily.

value: WiCell

value: H7 human embryonic stem cells


title: 1.K18R-H3-K79me3

value: Histone mutation library


title: YAP3

last: Cox

address: 77 Avenue Louis Pasteur

department: Brigham and Women's Hospital

data_processing:
Alignment: STAR (v2.3.0e_r291)
Read counting: htseq-count (v0.6.0, parameters –t exon), Ensembl transcriptome version v70
Genome_build: zv9
Supplementary_files_format_and_content: raw counts mapped to Ensembl transcriptome

organism: Danio rerio

source_name: Liver tissue isolated from adult lf:Yap fish

extract_protocol:
Livers were dissected out of adult fish and flash frozen in liquid nitrogen. RNA was harvested using Trizol reagent and purified using the Rnease Mini Kit. I
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: liver

value: adult


title: fve-4 rep1

city: Taipei

first: Keqiang

last: Wu

address: No.1, Sec.4, Roosevelt Rd.

department: Institute of Plant Biology

country: Taiwan

institute: National Taiwan University

data_processing:
Illumina's CASAVA pipeline (Version 1.8) to produces FASTQ files.
First step in the trim process is to convert the quality score (Q) to error probability. Next, for every base a new value is calculated: 0.05 − Error probability. This value will be negative for low quality bases, where the error probability is high.
For every base, we calculate the running sum of this value. If the sum drops below zero, it is set to zero. The part of the sequence to be retained is between the first positive value of the running sum and the highest value of the running sum.
Everything before and after this region is trimmed off. In addition, if the read length is shorter than 35bp, the read will be discarded.
Reads were mapped to the TAIR10 genome using Bowtie2, and only reads with a mapping  identity ≥98%.  Values for RPKM were computed based on these mapped reads using RackJ (http://rackj.sourceforge.net/), and Student’s t-tests were performed on RPKM values.
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample.

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Long day for 14-day

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: seedling

tag: age

value: fve -/-

tag: cultivar


title: 1.K18R-H3-K4me3

source_name: yeast cells

tag: strain

tag: library

tag: 1st ip


title: WT3

source_name: Liver tissue isolated from adult WT fish

value: WT

tag: developmental stage


title: YAP1


title: WT2


title: hda9-1 rep3


title: hda9-1 rep1


title: hda9-1 rep2


title: 1.K18R-H3-K36me3

tag: 2nd ip / input


title: 1.K18R-H3-H3


title: H3K27ac_TKO3a2-r2

source_name: Embryonic stem cell (ESC)

tag: cell type

value: ESC

tag: line

tag: antibody

value: H3K27ac (Active Motif 39133)


title: H3K27ac_DKO-r2

value: J1 ESC

tag: genotype

value: DKO


title: H3K27ac_TKO3a1-r2


title: fld-6 rep1

value: fld -/-


title: hda5-1 rep3


title: hda6-6 rep3


title: H3K27ac_TFX


title: hda6-6 rep2


title: hda5-1 rep1


title: hda6-6 rep1


title: YAP2


title: H3K4me1_TKO3a1

value: H3K4me1 (Abcam ab8895)


title: H3K4me1_TFX


title: Col rep3

value: wild type


title: H3K27ac_DKO


title: Col rep2


title: WT1


title: H3K27me3_TFX

value: H3K27me3 (Active Motif 39155)


title: 1.K18R-H3-K18ac


title: Col rep1


title: TRIzol+yeast tRNA_pooled3

status: Public on Aug 01 2016

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were processed further for quality assessment, quality filtering, and adaptor trimming, and quality filtered again using a Phred quality score threshold of 20
The ligated adaptor sequences were trimmed, leaving a minimum overlap of five bases while allowing an error rate of 0.1 using CutAdapt 1.2.1
Using the short read aligner Bowtie 1.0.0 [27], filtered sequence reads were aligned to the Human reference genome assembly humanv37 from Ensembl and the best hits to the genome were identified using BEDtools 2.17
Small RNA species were annotated by mapping with the reference gene feature annotation table from the Ensembl database
Quantification/enrichment reads for miRNAs were first aligned to the Rfam RNA families database to filter other small RNA species, and then reads were mapped for small RNA annotation against reference.mature/precursor hg19_mature RNA sequences from the miRBase (miRbase 19)database .The miRNA read count matrix for each sample was generated using open source tools Picard 1.84
Genome_build: mirBASE19
Supplementary_files_format_and_content: miRNA count file

source_name: TRIzol+yeast tRNA_pooled_serum

extract_protocol:
Different extraction procedures such as TRIzol with and without carrier glycogen/yeast tRNA/bacteriophage MS2), miRNAeasy ,mirVANA and TRIzol with exosome precipitation using exoquick buffer.
Illumina  Trueseq small RNA kit

value: Serum

value: Orphan samples

value: DoD Serum Repository

value: small RNA

value: pooled serum samples

tag: rna extraction method

value: TRIzol+yeast tRNA


title: miRNeasy_pooled 2

value: miRNeasy


title: TRIzol+MS2_pooled 2


title: TRIzol+yeast tRNA_pooled1


title: miRNeasy_pooled 3


title: TRIzol+MS2_pooled 3


title: TRIzol+yeast tRNA_pooled4


title: miRNeasy_pooled 1


title: TRIzol LS+glycogen_pooled 3

source_name: TRIzol LS+glycogen_pooled_serum

value: TRIzol LS+glycogen


title: TRIzol_pooled 3

value: TRIzol


title: TRIzol+MS2_pooled 1


title: TRIzol LS+glycogen_pooled 2


title: TRIzol_pooled 1


title: TRIzol_pooled 2


title: TRIzol LS+glycogen_pooled 1


title: TRIzol+yeast tRNA_pooled2


title: Exosome+TRIzol_unpooled 2

value: unpooled serum samples

value: Exosome+TRIzol


title: Exosome+TRIzol_unpooled 3


title: Exosome+TRIzol_unpooled 1


title: miRNeasy_unpooled 1


title: miRVANA_unpooled 2

value: miRVANA


title: miRVANA_unpooled 1


title: TRIzol+yeast tRNA_unpooled 3

source_name: TRIzol+yeast tRNA_unpooled_serum


title: miRNeasy_unpooled 3


title: miRNeasy_unpooled 2


title: TRIzol+MS2_unpooled 1


title: TRIzol LS+glycogen_unpooled 2

source_name: TRIzol LS+glycogen_unpooled_serum


title: TRIzol LS+glycogen_unpooled 3


title: TRIzol_unpooled 2


title: TRIzol_unpooled 3


title: TRIzol LS+glycogen_unpooled 1


title: TRIzol_unpooled 1


title: TRIzol+MS2_unpooled 3


title: Waite population 4

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

country: Australia

institute: The University of Queensland

data_processing:
The quality of raw data from each library was controlled by CLC Genomic Workbench version 7.5.1.  Raw data were stripped of adapters and reads with quality score above 0.05 and less than 2 ambiguous nucleotides were retained. Reads without 3’ adapters and also reads with less than 16 nt were discarded from the libraries. Clean data considered as mappable reads for further analysis.
Tab separated files with the read sequences and their counts were used as input file for novel and homologous miRNA analysis using sRNAtoolbox. Although sRNAtoolbox is a powerful tool for novel miRNA identification, all predicted miRNAs were then individually inspected for their pre-miRNA secondary structure, mature miRNA position on the stem loop, and their abundance in our libraries. We also double-checked their possible similarity with other RNA sequences (such as tRNA and rRNA) in Rfam
We also Used CLC genomic workbench to produce pxy-miRNA profile
Genome_build: The first assembly of P. xylostella genome (GCA_000330985.1) was used
Supplementary_files_format_and_content: text file, miRNA copy number

organism: Plutella xylostella

source_name: Waite population_Larvae

extract_protocol:
Total RNA was extracted from fifteen 3rd instar larval samples using Triazol® following the manufacturer’s protocol (Life Technologies).
The small RNA libraries were generated from both populations with three biological replicates using the Illumina Truseq small RNA preparation kit at the Australian Genome Research Facility (AGRF-Melbourne, Australia). The purified cDNA libraries were sequenced on Illumina HiSeq and raw sequencing reads (50 nt) were obtained using Illumina’s Sequencing Control Studio software.

treatment_protocol: No Treatment

tag: population

value: South Australia (Waite)

value: whole larval body

tag: developemental stage

value: 3rd instar Larvae


title: Waite population 3


title: TRIzol+yeast tRNA_unpooled 2

tag: sample type


title: Queensland Population 3

source_name: Queensland Population_Larvae

value: Queensland (Gatton)


title: Waite population 1


title: Queensland Population 2


title: Degradome of Os02g12290iL1 (RNAi line) at high temperature

city: Guangzhou

first: Hai

last: Zhou

state: Guangdong

address: Wushan

department: College of Life Sciences

institute: South China Agricultural University

description: Degradome sequence

data_processing:
The degradome tags were aligned to TIGR6.1 genome and cDNA sequences using bowtie (Langmead et al., 2009) allowing up to two mismatches. All the plot figure is generated with R (http://www.R-project.org) using degradome data which obtained with the tag count at each cleavage site that were normalized to tag perl 20 million.
Genome_build: Orazy TIGR6.1
Supplementary_files_format_and_content: Wig files were generated using MACS program, fasta files contain sequence and counts

organism: Oryza sativa Japonica Group

source_name: Young panicles from microspore mother cell to meiosis of Os02g12290iL1 plants grown at high temperature.

growth_protocol: ZH11 and Os02g12290iL1 were grown in the cabinet at day average temperatures (DAT) of 28°C.

extract_protocol:
Total RNAs were extracted using TRIzol Reagent (Invitrogen).
Approximately 150 μg of total RNA was then selected for polyadenylated RNA using the Oligotex mRNA mini kit (Qiagen). The degradome library was constructed as previously described (German et al., 2008; German et al., 2009). PCR products were gel purified and subjected to SBS sequencing.

value: young panicles


title: Waite population 2


title: Queensland Population 1


title: TRIzol+yeast tRNA_unpooled 1

value: Serum


title: miRVANA_unpooled 3

value: Orphan samples


title: 4+3N_mRNA-seq_rep2

city: Muenster

first: Benedikt

middle: Sebastian

last: Nilges

address: Von-Esmarch-Straße 54

department: RNA Biology Group

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

data_processing:
Basecalls were performed with Illumina Casava 1.8.
3' adapter and/or 5' adapter sequences were removed with FastX-toolkit
Reads (RibosomeProfiling only) were aligned to rRNA genes with Bowtie 1.0.0. Non-rRNA reads were mapped with Bowtie to reference sets consisting of CDS sequences containing 18 nt of genomic flanking regions.
Raw read counts were determined using custom scripts.
Genome_build: sacCer3
Supplementary_files_format_and_content: Comma-delimited text files containing gene annotations and raw read count data.

growth_protocol: Cells were grown from OD600 of 0.02 to OD600=0.4, collected by rapid vacuum filtration, and immediately frozen in liquid nitrogen.

extract_protocol:
Frozen yeast cells for ribosome profiling were pulverized under cryogenic conditions in 50 mM Tris-HCl pH=7.5, 50 mM NH4Cl, 12 mM MgCl2, 0.5 mM DTT and 100 μg/ml CHX. Extracts were treated with RNAse I and resolved on sucrose gradients. RNA from monosome fractions was extracted by hot phenol and ribosome footprints of 28-32 nt were purified by size selection and gel extraction.
Footprints were dephosphorylated and ligated to one of three preadenylated 3' linkers. Footprints were reverse transcribed using the specified RT primer and cDNA was circularized and PCR-amplified.

treatment_protocol: YPD medium; cycloheximide (1 min)

tag: strain background

tag: genotype/variation

value: wild-type

tag: replicate


title: 4N_mRNA-seq_rep2


title: 4+3N_mRNA-seq_rep1


title: Nonrandom_mRNA-seq_rep1


title: Nonrandom_mRNA-seq_rep2


title: 4N_mRNA-seq_rep1


title: Degradome of ZH11 (WT) at high temperature

description: Degradome sequence

source_name: Young panicles from microspore mother cell to meiosis of ZH11 plants grown at high temperature.

treatment_protocol: ZH11 and Os02g12290iL1 were grown in the cabinet at day average temperatures (DAT) of 28°C.

tag: tissue

value: wild type (ZH11)


title: TRIzol+MS2_unpooled 2

value: DoD Serum Repository

value: small RNA


title: 4+3N_RibosomeProfiling+3_rep2_low

data_processing:
Library strategy: Ribosome profiling
Basecalls were performed with Illumina Casava 1.8.
3' adapter and/or 5' adapter sequences were removed with FastX-toolkit
Reads (RibosomeProfiling only) were aligned to rRNA genes with Bowtie 1.0.0. Non-rRNA reads were mapped with Bowtie to reference sets consisting of CDS sequences containing 18 nt of genomic flanking regions.
Raw read counts were determined using custom scripts.
Genome_build: sacCer3
Supplementary_files_format_and_content: Comma-delimited text files containing gene annotations and raw read count data.


title: 4+3N_RibosomeProfiling_rep1_low


title: Macrophage Amastigote (intracellular) stage cells with no arginine treatment rep2

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.7
Quality of the reads in fastq files were determined using fastqc and internal tools
SL RNA-Seq reads were aligned against Leishmania donovani BPK282A1 genome Version 8.1 downloaded from www.TriTrypDB.org
Samtools v0.1.19 was used to convert alignment files from one format to another
HTseq package was used to estimate read counts against each CDS
Genome_build: LdoBPK282A1 TriTrypDB Version 8.1
Supplementary_files_format_and_content: CDS level raw read count data were then normalized using edgeR package.

organism: Leishmania donovani

source_name: laboratory culture, whole cell lysate

growth_protocol: L. donovani, MHOM/SD/00/1S cell line was used. Promastigotes and amastigotes were grown and maintained in axenic cultures. Promastigotes were grown in medium 199 and supplemented with 10% fetal calf serum at 26 ◦C. Promastigote to amastigote differentiation in a host-free culture and the maintenance of axenic amastigotes were performed by inoculating late log phase promastigotes in medium 199 at pH 5.5 containing 25% fetal calf serum. The axenic amastigotes remained stable in culture for a long time. They were recycled routinely every 10 weeks by differentiating them back to promastigotes, in parallel initiating a new line of amastigotes.

extract_protocol:
Extraction of intracellular parasites from macrophage cells: THP1 macrophages were grown in 8 plates in 37°C at a density of 1x107 cells per plate. Mid log-phase L. donovani promastigotes were added to THP1 culture for 4 hours at a ratio of 1:10 macrophage to parasite. Subsequently, plates were washed three times with room temperature PBS and the incubated for 48 hours in RPMI 1640 growth medium. Macrophages, infected or not, were collected with a scraper and washed with ice-cold PBS for 4 minutes at 48 X g. The pellets were then resuspended in 1 mL PBS and transferred to Eppendorf tubes. Separation of amastigotes was facilitated initially by passing the pellet repeatedly through a 1 mL syringe with 27G needle. Lysates were then centrifuge 15 minutes at 2369Xg at 4˚C. Pellet was then resuspemded in PBS and overlayed on1 ml Percoll (****). Cells were then centrifuged
Logarithmically-growing cells were collected and resuspended at a concentration of 5x108 cells/mL in TriZOL (Invitrogen). The aqueous phase was isolated by adding 0.2 mL chloroform (Fisher Scientific) and centrifugation at 12,000 x g for 15 minutes at 4°C. The aqueous phase was isolated and RNA was precipitated by adding 1 volume of 100% isopropanol (Fisher Scientific) and centrifugation at 12,000 x g for 10 minutes at 4°C. The RNA pellet was washed with 75% ethanol (Pharmco) and was resuspended in nuclease-free water (Ambion). Purified RNA was treated with 20 units of DNAse I (Ambion) and was precipitated using 1/10 volumes 3M sodium acetate (Sigma) and 3 volumes 100% ethanol. RNA was pelleted by centrifugation at 15,000 g-1 and the resulting pellet was washed with cold 75% ethanol and resuspended in RNAse-free water (Ambion).
TruSeq Stranded Total RNA Library Prep Kit from illumina and its standared protocol was used to prepare RNAseq libraries from total RNA.

treatment_protocol: Mid-exponential phase promastigotes or amastigotes (1 x 107 cells/ml) were washed twice in Earl’s salt solution and then resuspended to a final density of 1 x 107 cells/ml in M199 Earl's salt base (from Biological Industries), lacking all amino acids and glucose. This medium was supplemented with 5 mM glucose and 10% heat-inactivated and dialyzed fetal calf serum as well as all amino acids except arginine. Starvation was carried out at 26°C for the wanted amount of time and terminated by moving the cells to ice. The starved cells were used for assays after two additional washes in ice cold Earl's salt solution.

tag: strain

tag: lifestage

value: Intracellular (Macrophage) Amastigote

value: Wildtype

tag: treatment

value: No Treatment


title: Macrophage Amastigote (intracellular) stage cells with no arginine treatment rep1


title: Nonrandom_RibosomeProfiling_rep2_low


title: Axenic Amastigote stage cells in arginine depleted medium rep2

extract_protocol:
NA
Logarithmically-growing cells were collected and resuspended at a concentration of 5x108 cells/mL in TriZOL (Invitrogen). The aqueous phase was isolated by adding 0.2 mL chloroform (Fisher Scientific) and centrifugation at 12,000 x g for 15 minutes at 4°C. The aqueous phase was isolated and RNA was precipitated by adding 1 volume of 100% isopropanol (Fisher Scientific) and centrifugation at 12,000 x g for 10 minutes at 4°C. The RNA pellet was washed with 75% ethanol (Pharmco) and was resuspended in nuclease-free water (Ambion). Purified RNA was treated with 20 units of DNAse I (Ambion) and was precipitated using 1/10 volumes 3M sodium acetate (Sigma) and 3 volumes 100% ethanol. RNA was pelleted by centrifugation at 15,000 g-1 and the resulting pellet was washed with cold 75% ethanol and resuspended in RNAse-free water (Ambion).
TruSeq Stranded Total RNA Library Prep Kit from illumina and its standared protocol was used to prepare RNAseq libraries from total RNA.

value: Axenic Amastigote

value: Arginine depleted medium


title: Nonrandom_RibosomeProfiling_rep1_low


title: Procyclic Promastigote stage cells in arginine repleted medium rep1

value: Procyclic Promastigote

value: Arginine repleted medium


title: Axenic Amastigote stage cells in arginine repleted medium rep1


title: Procyclic Promastigote stage cells in arginine depleted medium rep2


title: Procyclic Promastigote stage cells in arginine depleted medium rep1


title: Axenic Amastigote stage cells in arginine depleted medium rep1


title: ribosomal RNA depleted total RNA from WRR-1 dsRED control knock-down cells, replicate 1

city: Cold Spring Harbor

first: Delphine

last: Fagegaltier

state: NY

address: One Bungtown Rd

department: Genomics Division

institute: Cold Spring Harbor Lab

description:
rRNA depleted
average insert size: ~350bp
dsREDKD_vs_control_RNAseq.xlsx

data_processing:
Reads were aligned to the drosophila transcriptome using tophat2 and options  -G dmel-r5.43.gff --no-novel-juncs -g 10.
Uniquely mapping reads were assigned to features (genes or genes and piRNA clusters) using HTSeq; counts matching ribosomal RNAs and transposons insertions were excluded.
Normalized counts and differential gene expression were estimated with DESeq2.
Genome_build: dm3 BDGP release 5
Supplementary_files_format_and_content: Processed files contain HTSeq counts,or DESeq2 standard processing results for knock downs compared to non transfected WRR-1 control cells;  the mean of the normalized counts in replicates, and DESeq2 outputs are reported.

organism: Drosophila melanogaster

source_name: WRR-1 cells

extract_protocol:
Total RNAs were prepared with Trizol reagent (Invitrogen).
Following ribo-zero rRNA depletion, libraries were prepared from 200ng RNAs with ScriptSeq v2 (Epicentre).

treatment_protocol: WRR-1 cells were transfected with 10ug of dsRNA against dsRED using Effectene (Qiagen); RNA was collected after 5 days.

tag: cell line

value: WRR-1 cells

value: dsRNA treated 5 days

value: w1118; Act-5C-GAL4,UAS-Wts-RNAi,UAS- RasV12 (WRR-1)


title: Procyclic Promastigote stage cells in arginine repleted medium rep2


title: MvESF2

city: West Haven

first: Koryu

last: Kin

state: CT

address: 840 West Campus Drive

department: EEB

institute: Yale University

data_processing:
Basecalls performed using CASAVA version 1.4
mRNA-seq reads were aligned to the human (GRCh37.69), rabbit (OryCun2.0.75), cow (UMD3.1.75), ferret (MusPutFur1.0.75), opossum (MonDom5.75) and rat (Rnor_5.0.75) cDNA builds using Tophat2 version 2.0.5
Number of times reads overlapped with known features (gene counts) was counted using HTSeq
transcripts per million (TPM) values were calculated according to Wagner et al (2012) Theor. Biosci.
Genome_build: Human (GRCh37.69), Rabbit (OryCun2.0.75), Cow (UMD3.1.75), Ferret (MusPutFur1.0.75), Opossum (MonDom5.75), Rat (Rnor_5.0.75)
Supplementary_files_format_and_content: Comma-delimited csv files include read counts for each Sample as well as a comma-delimited csv file which contains TPM values corrected by using only genes which have 1-to-1 orthologues in all species.  All csv files can be found in the tar archive on the series record.

organism: Neogale vison

source_name: endometrial stromal fibroblasts from opossum

extract_protocol:
Cells grown in cluture were treated with trypsin and detached from flasks, and RNA was isolated using the RNeasy  Micro RNA extraction kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: culture type

value: mink endometrial stromal fibroblast line (ATCC:CLR-2675) grown in culture

value: endometrial stromal fibroblast


title: Branch-seq_bottom

city: Cambridge

first: Geneveive

last: Gould

state: Massachusetts

address: 77 Massachusetts Ave. 68-253

department: Biology

institute: MIT

description:
other (2D arc RNA)
Branch_seq_CPMs.xlsx

data_processing:
Library strategy: Branch-seq
Reads were trimmed to 30 by 30nt and mapped with Bowtie1 (bowtie-1.0.0) using the following parameters: bowtie -S -m 1 -1 end1reads.fastq -2 end2reads.fastq.
Branch-seq reads for each gel slice were mapped to the genome and then combined using samtools merge (samtools-0.1.7a).
winBPS and GEM-BPS were used to call peaks on the merged data (see manuscript for details)
genome_build: SacCer2
supplementary_files_format_and_content: tabs (in excel) for 198 annotated and 268 novel BPS counts per million (CPM) (SacCer2)

organism: Saccharomyces cerevisiae S288C

extract_protocol:
Yeast were grown to OD600 0.94-0.98 and were collected by centrifugation at 7000 RPM for 5 min at 4°C. Media was poured off and yeast were washed twice in water and frozen at -80°C. Cells were thawed and transferred to tubes containing 2.8mm ceramic beads and 1mL Trizol (Life Technologies) was added to 1/10 cell pellet. An Omni Bead Ruptor was used to lyse the cells, twice for 20 seconds on ½ max speed and once for 10 seconds on max speed. Samples were incubated at room temp for 5 min, 1/5 volume of chloroform was added and mixed, samples incubated at room temp 2-3 min and were spun at max speed for 15 min at 4°C. The upper aqueous layer was transferred to a new tube and precipitated with ½ volume isopropenol. After 5min on ice, samples were spun at max speed, 4°C for 25 min. The RNA pellet was washed with 70% ethanol before storage at -80°C.
Briefly, lariat RNA was isolated from a 2D PAGE gel, lariats were debranched using DBR1 (debranching enzyme), and adaptors are added to the ends of the linearized lariat RNA by poly(A) tailing the RNA, performing RT with an anchored oligo-dT primer with Illumina adaptors attached, circularization, and PCR, similar to the original ribosome footprint profiling method (Ingolia et al., Science, 2009). Paired end sequencing was used to sequence the 5'SS (end1) and BPS (end2) of individual lariat RNAs using a custom 2nd end sequencing primer. See paper (Gould et al. 2015, in preparation) for more information. Samples were barcoded and all sequenced in one MiSeq lane.

value: trizol


title: MvESF1

source_name: endometrial stromal fibroblasts from mink

tag: cell type


title: S2_CM37_10minC

city: Ithaca

first: Dig

middle: Bijay

last: Mahat

address: 526 campus Rd

department: Molecular Biology & Genetics

institute: Cornell University

description: nascent RNA

data_processing:
PRO-seq: adapters were removed and the reads were trimmed to 36bp. Reverse complement of reads were generated.
PRO-seq: reads were first mapped to ribosomal genome and anything that did not map to ribosomal genome were mapped to rest of the genome using mm10. The bedgraph files were normalized with the custom normalization approach as discribed in the paper and the bigWig files were generated from the normalized bedgraph files.
Genome_build: dm3
Supplementary_files_format_and_content: bigWig for PRO-seq

molecule: other

source_name: S2 cells

extract_protocol:
Nuclei were isolated for PRO-seq and run-on reactions were performed with biotinylated nucleotides.
PRO-seq libraries were performed according to the paper: Kwak H, Fuda NJ, Core LJ, Lis JT. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 2013 Feb 22;339(6122):950-3. PMID: 23430654.
OTHER (PRO-seq)

value: cell culture

tag: assay

value: PRO-seq

tag: chip antibody


title: ribosomal RNA depleted total RNA from WRR-1 cells, replicate 2

value: no treatment, Passage 112

tag: genotype


title: Branch-seq_middle

description:
other (2D arc RNA)
Branch_seq_CPMs.xlsx

tag: rna extraction method


title: ribosomal RNA depleted total RNA from WRR-1 cells, replicate 1

value: no treatment, Passage 111


title: 1.K18R-H3-Input

city: Jerusalem

first: Nir

last: Friedman

address: Givat Ram

department: School of Engineering

institute: The Hebrew University of Jerusalem

data_processing:
Pair-end reads were mapped to the yeast genome (sacCer3) using bowtie2 with maximal fragment size of 1000bp.
We treated duplicate fragments as potential PCR artifacts. We thus treated the set of unique fragments found as the read-set. We defined mononucleosome fragments as these shorter than 220bp.
We used the nucleosome location atlas defined by Weiner et al(Weiner et al., 2015). We measured nucleosome coverage by counting the number of fragments overlapping a window of size 50bp around the center of the nucleosome.
Genome_build: sacCer3
Supplementary_files_format_and_content: csv file containing read counts for each nucleosome location in each combinatorial ChIP sample

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes at room temperature with occasional shaking, quenched with 0.125 M glycine for 5 minutes at room temperature with occasional shaking, collected by centrifugation, (4000 g, 5 minutes), washed with cold ddH2O supplemented with EDTA-free protease inhibitors cocktail (Roche) and the pellet was resuspended in buffer Z (1 M sorbitol, 50 mM Tris 7.4, 10 mM β-mercaptoethanol) with zymolyase (Seikagaku) at 0.3 - 1 units per 1 ml of original cell volume. Cells were gently rotated at 30ºC for 25 minutes until > 95% of cells were spheroplasted. Spheroplasts were pelleted (6500 g, 10 minutes) and resuspended in NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail) at final concentration of 200 OD/ml. Chromatin was digested with 12.5 units/ml MNase (Worthington) for 20 minutes at 37ºC, and digestion was stopped by removing the tubes into ice and addition of 1 volume of ice cold MNase stop buffer ( 220 mM NaCl, 0.2% SDS, 0.2% DOX, 10 mM EDTA, 2%,Triton X-100, EDTA-free protease inhibitor cocktail). Tubes were kept on ice for 10 minutes, vortexed 3 x 10 seconds, centrifuged (16,000 g, 10 minutes, 4ºC), and the supernatant containing the nucleosomes was removed to a fresh tube.
See attached paper - http://biorxiv.org/content/early/2016/06/27/060962

tag: library

value: Histone mutation library

tag: 1st ip

tag: 2nd ip / input

value: Input


title: S2_C646_10minCBPIn

description: nascent RNA


title: Branch-seq_top

description:
other (2D arc RNA)
Branch_seq_CPMs.xlsx


title: mTAIL-seq exp #1 1ug

city: Seoul

first: Jaechul

last: Lim

address: 1 Gwanak-ro, 1 Gwanak-gu

country: South Korea

institute: Seoul National University

description: mTAIL-seq by 1 ug of total RNA from HeLa cells

data_processing:
The base calls and signal intensities were processed by Illumina RTA 1.17.28 for MiSeq. The read 1 sequences were reanalyzed for more sensitive basecalling using AYB 2. The read 1 sequences were aligned to the common contaminants set, which is composed of rDNA repeat units (GenBank accession U13369.1), PhiX genome (GenBank accession J02482.1), Illumina TruSeq primer sequences, and all sequences for 5S and 5.8S rRNAs of respective species (retrieved from Rfam 11.0 of the Wellcome Trust Sanger Institute) using GSNAP 2013-03-31 with maximum 5% mismatches allowed. Clusters with any match to the contaminants were removed from the subsequent analyses. The sequences having completely identical nucleotides in the 21st to 35th cycle in read 1 (representative region of the insert) and the 1st to 15th cycle in read 2 (degenerate bases in 3′ adapter) are deduplicated by leaving only a cluster with the maximum PHRED quality sum of read 1. The degenerate and fixed delimiter sequence in 3′ adapter was clipped out from read 2 by searching perfect match of delimiter sequence (‘GTCAG’ as in the direction of read 2) between the 14th and 16th cycles in read 2. The clusters missing a delimiter sequence or having low diversity in degenerate region (at least two occurrences for all of A, C, G and T) were removed from further analyses.
The fluorescence signal intensities were processed into “Relative T signal” as described in our previous paper (Chang et al, 2014). The signals from a spike-in sample were purified with an outlier filter based on robust Mahalanobis distance (mvoutlier package 1.9.9; quan=0.5, alpha=0.025). Random 500 clusters per each spike-in were chosen for parameter calculation of a Gaussian mixture hidden Markov model (GMHMM). We trained the model using Baum-Welch algorithm implemented in the GHMM library (http://ghmm.org) with topology and initial parameters shown in fig. S1A and table S7 and S8 (1,000 iterations). The procedure was iterated to maximize likelihood, not using any property (eg. designed length of poly(A) tail) of spike-ins. Relative T signals outside the range of [-5, 5] were clipped into the range for both training and later calculations.
The length of poly(A) tails were first measured with base call-based “Strategy II” described in fig. S1A. For clusters with the measured length is shorter than 8 nt, the length is called as the final poly(A) tail length. For the others, normalized T signals starting from the first position in T-stretch detected by Strategy II were analyzed with the GMHMM. The hidden states were decoded with the standard Viterbi algorithm implemented in the GHMM library. The number of cycles with state 1 and 2 was called as the length of poly(A) tail. For the estimation of performance, we applied the process to all spike-in samples except the clusters used for the parameter fitting of the model.
The remaining reads after contaminant filter and the first duplication filters were then aligned to the genome sequences (UCSC hg19, positions of splicing junctions were processed from the UCSC Genome Browser database for version of Jan 24, 2013) using GSNAP 2013-03-31. Three different versions of alignments to genome were used in this study. (1) R1 alignment: using only the full read 1 sequences which are 51 nt long. This was used for identification of a cluster. (2) R2 short alignment: using only 40 nt right next to the 3′ adapter of read 2. This was used in searching for the poly(A)-free 3′ hydroxyl ends. (3) paired alignment: using the full read 1 sequences and part of read 2 sequences trimmed of degenerate bases and delimiter. We filtered out poly(A) stretches encoded from genome using this alignment set. All the alignments were performed with maximum mismatches of 5%, minimum mapping quality of 3. All multi-mapped reads were removed. The remaining PCR artifacts with few mismatches were removed again using the R1 alignment with 15 degenerate bases inside the 3′ adapter region. To detect that kind of artifacts, we clustered the R1 alignments with maximum distance between mapped positions of 10 bp, they were then clustered again within the first cluster using degenerate bases from read 2 of respective reads with CD-HIT-EST 4.5.4 (word size=6, sequence identity=0.85). For a set of detected duplicates, we chose a read with maximum sum of PHRED quality in read 1 to leave.
For classification and transcript-level analyses, we compiled reference annotations for human and mouse using NCBI RefSeq, RepeatMasker, gtRNAdb, Rfam and miRBase databases (the first three were downloaded from the UCSC Genome Browser on Apr 25, 2013; Rfam version 11; miRBase version 19). The R1 alignments were annotated with intersection with the compiled annotations using BEDTools {Quinlan, 2010 #66}. When multiple annotations were overlapped to an alignment, we chose a class for the statistics requiring exclusive assignment of a genomic source type by the following priority: miRNA, rRNA, tRNA, Mt-tRNA, snoRNA, scRNA, srpRNA, snRNA, lncRNA, RNA, ncRNA, misc_RNA, Cis-reg, ribozyme, RC, IRES, frameshift_element, LINE, SINE, Simple_repeat, Low_complexity, Satellite, DNA, LTR, CDS, 3′ UTR, 5′ UTR, intron, Other, Unknown (higher priority first). The transcript-level analyses were performed using our custom non-redundant RefSeq (nrRefSeq) transcript set, which is a reduced set retaining only the longest isoform or transcript when regions overlap with each other. The positions of read 1 in nrRefSeq transcripts were positioned with BEDTools intersection between alignments to genome sequences and nrRefSeq annotation set, and then translated to the transcript-level coordination with in-house software.
As poly(A) tails were initially detected with a constraint that it must begin within the first 30 cycles, so the maximum detectable 3′ end modification of poly(A) tails was limited to the last 30 nucleotides of insert. To exclude A stretches obviously encoded from genomic sequence (with or without 3′ end modifications), we masked detected poly(A) tail ranges with read 2 alignments so that the 3′-most position of alignable (not clipped) is eliminated from poly(A) tail or its 3′ end modifications. All statistics regarding transcript-level modification rates were calculated for transcripts having more than 200 tags with poly(A) tails longer than 8 nt.
Genome_build: hg38, dm6
Supplementary_files_format_and_content: The spreadsheet files contain the poly(A) tail length distribution and 3' end modification frequencies next to poly(A) tails for all detected transcripts

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM (Welgene) supplemented with 10% fetal bovine serum (Welgene).   All the fly strains were obtained from Bloomington stock center. w1118 was used as wild type control. wispKG5287 was previously described as a null allele of wisp (Benoit et al., 2008). Immature oocytes and mature oocytes were collected by hand dissection in Grace′s Unsupplemented Insect Media (Gibco, 11595-030) from 3 or 4 day old female flies. Unfertilized activated eggs were produced from w1118 virgin females mated to sterile males (son of tud1 mothers) . Fly eggs and embryos were collected on grape juice plates for the designated time frame at 25°C.

extract_protocol:
Total RNAs were extracted from HeLa cells or Drosophila samples by TRIzol reagent (Invitrogen, 15596-018).
Total RNA (~1–5 ug) was ligated to 3′ hairpin adaptor using T4 RNA ligase 2 (NEB, M0239) for overnight. 3′ ligated RNA was partially digested by RNase T1 (Ambion, AM2283) and subject to streptavidin beads (Invitrogen, 11206D). 5′ phosphorylation by PNK reaction (Takara, 2021B) and endonucleolytic cleavage by APE1 reaction (NEB, M0282) were performed on beads. Subsequently, RNA was eluted by 2X RNA loading dye and gel purified by 6% Urea-PAGE gel in the range of 300–750 nucleotides. The purified RNAs were ligated to 5′ adaptor, subjected to reverse-transcription (Invitrogen, 18080-085) and amplified by PCR using Phusion DNA polymerase (Thermo, F-530L). PCR products were purified by AMPure XP beads (Beckman, A63881).

treatment_protocol: No treatment

value: HeLa


title: mTAIL-seq exp #2 100ng

description: mTAIL-seq by 100 ng of total RNA from HeLa cells


title: Axenic Amastigote stage cells in arginine repleted medium rep2

value: Axenic Amastigote

value: Wildtype


title: hda5-1 rep2

source_name: seedling

value: seedling

tag: age

tag: cultivar


title: ribosomal RNA depleted total RNA from WRR-1 dsRED control knock-down cells, replicate 2


title: TM6

city: Augusta

first: Yutao

last: Liu

state: GA

address: 1120 15th Street

department: Cell Biology and Anatomy

institute: Medical College of Georgia

data_processing:
Sequencing data were trimmed to remove adapter sequences
Alignment was done against the human reference database using the Bowtie software
Only exact matches to known mature miRNA sequences in miRBase were counted
Read counts were normalized with the Trimmed mean of M (TMM) method using the edgeR package in R, with the data being trimmed using an M value of 30% and an A value of 5%
Only miRNAs with a mean number of normalized reads greater than 1 and with expression in 3 or more of the individual tissues were included in the analysis
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text containing 1.) the raw number of reads per miRNA per sample and 2.) the normalized number of reads per miRNA per sample

source_name: trabecular meshwork

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit from ThermoFisher Scientific Inc. (Waltham, MA, USA) according to the recommended procedure. The quantity of RNA yield was determined with NanoDrop from ThermoFisher Scientific Inc. (Waltham, MA, USA), and the quality was assessed using the RNA 6000 Nano Kit with Bioanalyzer 2100 from Agilent Technologies (Santa Clara, CA, USA).
The TruSeq Small RNA Sample Prep kit from Illumina (San Diego, CA, USA) was used to generate the small RNA sequencing library. Briefly, 1 µg of total RNA was ligated using the manufacturer supplied RNA 3’ and RNA 5’ adapters. To produce cDNA constructs, the ligated small RNA was subjected to RT-PCR with a sample specific index sequence followed by gel purification. Amplified miRNAs were enriched and validated with the Agilent Bioanalyzer 2100 using High Sensitivity DNA chips. Using a MiSeq Reagent Kit v2 with 50 cycles, the validated small RNA sequencing libraries were normalized, denatured, and loaded to the Illumina MiSeq sequencer.

treatment_protocol: The ocular tissues were dissected out by the surgeon (RRA) and immersed in RNALater (Ambion, Inc.), to preserve the RNA at 4˚C overnight, and then stored at -80˚C until RNA extraction.

tag: age (years)

tag: race

value: Caucasian

tag: Sex

value: Male

tag: postmortem delay (hr)

tag: primary cause of death

value: Sepsis

value: trabecular meshwork


title: TM1

value: IC Bleed

tag: tissue


title: TM5

value: MI


title: TM4

value: African

value: Female

value: CVA


title: mTAIL-seq exp #2 33ng

description: mTAIL-seq by 33 ng of total RNA from HeLa cells

tag: cell line


title: mTAIL-seq exp #1 10ug

description: mTAIL-seq by 10 ug of total RNA from HeLa cells


title: Cornea3

source_name: cornea

value: cornea


title: Cornea2

value: African-American

value: Renal Cancer


title: Cornea4


title: TM7


title: TM3

value: ARDS


title: CB7

source_name: ciliary body

value: ciliary body


title: Cornea1

value: Breast Cancer


title: hho2-1

city: Newark

first: Vinay

last: Nagarajan

state: DE

address: 15 Innovation Way

institute: University of Delaware

data_processing:
Trimmed 1 nt to remove N; FastX toolkit
Tophat v2.0.11
Cuffdiff v2.2.1
Genome_build: Arabidopsis TAIR 10

source_name: SALK-T-DNA; Single mutant

growth_protocol: Agar-solidified MS medium -Pi described in Jain et al., 2007

extract_protocol: Script Seq v2.0

treatment_protocol: P- for 7d grown vertically

tag: ecotype

tag: genotype/variation


title: phr1

source_name: SALK-T-DNA; Single mutant Nilsson et al., 2007


title: hho2phr1

source_name: Double mutant


title: CB5


title: Col-0

source_name: WT


title: TM2

value: Lymphoma


title: CB3


title: CB4


title: Cornea6


title: CB1

value: Lung Cancer


title: mTAIL-seq exp #10 e30

description: mTAIL-seq for activated egg of wisp, rep #1

source_name: Drosophila embryo

tag: developmental stage

value: 3.0-4.5hr after egg laying (AEL)


title: mTAIL-seq exp #10 e15

tag: genotype

value: 1.5-2.0hr after egg laying (AEL)


title: Trex1fl/fl CD19-Cre+ repl2

city: Heidelberg

first: Axel

last: Roers

address: Im Neuenheimer Feld 305

department: Institute of Immunology

institute: Heidelberg University Hospital

data_processing:
Basecalling was performed with bcl2fastq 1.8.4
alignment of single-end data against mm10 with gsnap version 2014-12-17; splice sites were supported by using Ensembl version 75 (gsnap -d mm10 --gunzip --use-sarray=1 -B 4 -t 16 -N 1 -s EnsemblGene-75.ss.mm10.iit -n 1 -A sam)
read counting was done with featureCounts version 1.4.6 (-a EnsemblGene-75.mm10.TR.gtf -s 2 -Q 1) and the Ensembl version 75 gtf file
[gene expression] DESeq2 version 1.8.1 and the count file from featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file from featureCounts (featureCounts.mm10.e75.csv.gz); columns are in the following order: Ensembl Gene ID, Chromosom, Exon Start Coordinates, Exon End Coordinates, Gene Length; Fragment counts from the six samples
Supplementary_files_format_and_content: tab delimited file (deseq.comparison.csv) of one comparison which was done with DESeq2; columns 1-7 are standard output from DESeq2; columns 8-13 normalized counts for the samples; columns 14-15 normalized mean counts for the two conditions, columns 16-22 gene information from Ensembl (gene name, chromosome, start, end, strand, biotype, description)

source_name: Trex1fl/fl CD19-Cre+

extract_protocol:
RNA was isolated using Rneasy Mini Kit (Qiagen)
Samples were subjected the standard workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB)

tag: cell type

value: CD19+ B cells

value: Trex1 loss


title: Trex1fl/fl CD19-Cre+ repl1


title: Trex1fl/fl CD19-Cre- repl2

source_name: Trex1fl/fl CD19-Cre-

value: control


title: Trex1fl/fl CD19-Cre+ repl4


title: Trex1fl/fl CD19-Cre- repl4


title: mTAIL-seq exp #10 e20

description: mTAIL-seq for activated egg of wt, rep #1

value: 2.0-3.0hr after egg laying (AEL)


title: Trex1fl/fl CD19-Cre- repl1


title: mTAIL-seq exp #10 e10

value: 1.0-1.5hr after egg laying (AEL)


title: GL261 tumors in scid mice, 9 day schedule cyclophosphamide (6 days after 2nd CPA at 140 mg/kg-BW/9d, i.p.)_pool 2

city: Boston

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description:
G94_M4
poly-A selected RNA, unstranded RNA-seq library
DEseq_164_G94_M5M6_G94_M3M4_GL261scid_UT_vs_D15.xlsx
DEseq_165_G94_M1M2_G94_M3M4_GL261scid_D12_vs_D15.xlsx

data_processing:
Sequence reads were mapped to the mouse genome, release mm9 (NCBI 37) using TopHat (version 2.0.13) (Trapnell et al, Nat. Biotechnol, 2010)
DESeq (Anders et  al, Genome Biol, 2010) was used to compute differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: A Microsoft Excel file provides normalized read counts of gene expression across all samples, and differential expression results comparing: (1)cyclophosphamide-treated tumors vs. untreated tumors; (2) untreated or treated tumors from different mouse tumor cell lines; (3) tumors treated with cyclophosphamide given on different drug schedules; (4) untreated or cyclophosphamide-treated tumors implanted and grown in C57Bl6 mice vs. ICR-scid mce.
Supplementary_files_format_and_content: Bigwig files

source_name: tumor tissue

growth_protocol: Tumor cells were expanded in cell culture and then implanted by s.c. injection on the posterior flanks of mice. Tumor growth was monitored twice a week.

extract_protocol: Trizol reagent was used to prepare total tumor RNA samples from each individual tumor using standard protocols. Poly-A-enriched RNA-seq libraries were prepared for Illumina sequencing using a strand-specific sample preparation protocol

treatment_protocol: Cyclophosphamide (CPA) was administered at a dose of 140 mg/kg body weight on an every 9-day repeating schedule, by i.p. injection as detailed in Wu and Waxman (PMID: 25069038)

tag: strain

value: ICR scid (Taconic)

value: male

value: 12 weeks old

tag: tumor cell line implanted in mouse

tag: treatment

value: cyclophosphamide-treated (6 days after 2nd CPA at 140 mg/kg-BW/9d, i.p.)

tag: rna extracted from

value: 12 individual tumors


title: GL261 tumors in scid mice, untreated_pool 1

description:
G94_M5
poly-A selected RNA, unstranded RNA-seq library
DEseq_163_G94_M5M6_G94_M1M2_GL261scid_UT_vs_D12.xlsx
DEseq_164_G94_M5M6_G94_M3M4_GL261scid_UT_vs_D15.xlsx

treatment_protocol: No drug treatment. Other methods as detailed in Wu and Waxman (PMID: 25069038)

tag: age

value: untreated

value: 6 individual tumors


title: CB2

tag: age (years)

value: Caucasian

value: Female

value: Pancreatic Cancer

value: ciliary body


title: mTAIL-seq exp #10 e05

description: mTAIL-seq for mature oocyte of wisp, rep #1

value: 0.5-1.0hr after egg laying (AEL)


title: mTAIL-seq exp #9 S2cell

description: mTAIL-seq for activated egg(0-2hr) of wt, rep #2

source_name: Drosophila S2 cell


title: GL261 tumors in scid mice, untreated_pool 2

description:
G94_M6
poly-A selected RNA, unstranded RNA-seq library
DEseq_163_G94_M5M6_G94_M1M2_GL261scid_UT_vs_D12.xlsx
DEseq_164_G94_M5M6_G94_M3M4_GL261scid_UT_vs_D15.xlsx

treatment_protocol: No drug treatment. Other methods as detailed in Wu and Waxman (PMID: 25069038).


title: GL261 tumors in scid mice, cyclophosphamide-treated (6 days after 2nd CPA at 140 mg/kg-BW/6d, i.p.)_pool 1

description:
G94_M1
poly-A selected RNA, unstranded RNA-seq library
DEseq_163_G94_M5M6_G94_M1M2_GL261scid_UT_vs_D12.xlsx
DEseq_165_G94_M1M2_G94_M3M4_GL261scid_D12_vs_D15.xlsx

treatment_protocol: Cyclophosphamide (CPA) was administered at a dose of 140 mg/kg body weight on an every 6-day repeating schedule, by i.p. injection as detailed in Wu and Waxman (PMID: 25069038)

value: 9 individual tumors


title: GL261 tumors in scid mice, 9 day schedule cyclophosphamide (6 days after 2nd CPA at 140 mg/kg-BW/9d, i.p.)_pool 1

description:
G94_M3
poly-A selected RNA, unstranded RNA-seq library
DEseq_164_G94_M5M6_G94_M3M4_GL261scid_UT_vs_D15.xlsx
DEseq_165_G94_M1M2_G94_M3M4_GL261scid_D12_vs_D15.xlsx


title: mTAIL-seq exp #9 wt-actegg(0-2hr)2

source_name: Drosophila activated egg

value: activated egg 0-2hr


title: mTAIL-seq exp #7 wisp-actegg2

description: mTAIL-seq for activated egg of wisp, set #2

value: wispKG5287 (wispy knockout)

value: activated egg 0-1hr


title: MdESF2

organism: Monodelphis domestica

source_name: endometrial stromal fibroblasts from opossum

tag: culture type

value: primary opossum endometrial stromal fibroblasts grown in culture

value: endometrial stromal fibroblast


title: mTAIL-seq exp #10 e00

description: mTAIL-seq for mature oocyte of wt, rep #1

value: 0-0.5hr after egg laying (AEL)


title: CB6

tag: race

tag: Sex

value: MI


title: E2A ChIP-Seq total thymocytes

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
Sequence reads that passed the Illumina quality filtering were considered for alignment. Reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using bowtie version 1.0.0.
Genome coverage and subsequent data conversion was done with 'bedtools' (version 2.16.2) and 'Kent source utilities' (version 2.79) using 'bedtools genomecov' and 'bedGraphToBigWig' , respectively.
Supplementary_files_format_and_content
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read density coverage in reads per million after extension to 150 base pairs

source_name: Total Thymocytes

extract_protocol:
E2A-Bio bound DNA was isolated with Streptavidin coupled beads and purified through phenol-chloroform extraction.
About 5 ng of ChIP-precipitated DNA was 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 200–350 bp were selected. Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS library quantification kit. Cluster generation and sequencing was performed by using the Illumina/Solexa Genome Analyzer II and IIx systems according to the manufacturer’s guidelines.

tag: strain background

value: Tcf3(Bio/Bio) Rosa26(BirA/BirA)

value: total thymocytes

tag: chip antibody

value: Streptavidin (BioChIP using a Streptavidin pulldown; PMID:21552207)


title: MdESF1


title: mTAIL-seq exp #6 wt-mature2

description: mTAIL-seq for mature oocyte of wt, rep #2

source_name: Drosophila mature oocyte

value: oogenesis stage 14


title: mTAIL-seq exp #5 wisp-immature2

description: mTAIL-seq for immature oocyte of wisp, rep #2

source_name: Drosophila immature oocyte

value: oogenesis stage 9-10


title: mTAIL-seq exp #4 wt-actegg


title: mTAIL-seq exp #5 wt-immature2

description: mTAIL-seq for immature oocyte of wt, rep #2


title: mTAIL-seq exp #6 wisp-mature2

description: mTAIL-seq for mature oocyte of wisp, rep #2


title: mTAIL-seq exp #4 wisp-actegg


title: Sciatic nerve H3K4me3 ChIP-seq 1 d post-transection 2

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

data_processing:
Illumina Pipeline Casava 1.8.2
Reads were mapped to the Rattus norvegicus genome Rn5 using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) to produce SAM files for further analysis.
Hypergeometric optimization of motif enrichment (HOMER) (Heinz et al., 2010) was used to determine enriched binding regions for H3K27me3-ChIP
Genome_build: Rn5

organism: Rattus norvegicus

source_name: sciatic nerve

growth_protocol: Male Sprague Dawley rats (Harlan Laboratory) were housed with a normal light/dark cycles and ad libitum access to rat chow and water.

extract_protocol:
Sciatic nerves were subjected to MNase-ChIP with anti-H3K4me3 antibody as described previously with minor modification (Ma et al., 2015). After incubation with Dynabeads Protein G (Invitrogen, 10004D), ChIP samples were washed with washing buffer 1 (WB1, 50 mM Tris-HCl, pH7.5; 10 mM EDTA; 125 mM NaCl) once, WB2 (50 mM Tris-HCl, pH7.5; 10 mM EDTA; 250 mM NaCl) once, and WB3 (50 mM Tris-HCl, pH7.5; 10 mM EDTA; 500 mM NaCl) twice. The samples then eluted at 65°C with elution buffer (50 mM NaCl; 50 mM Tris-HCl, pH 7.5; 5mM EDTA; 1% SDS) for 15 min.
Libraries were prepared from ChIP DNA, and respective inputs, using the Illumina TruSeq ChIP Sample Preparation Kit.

treatment_protocol: Sciatic nerves of adult Sprague-Dawley rats were cut by following the surgery protocol described previously (Hung et al., 2015).  As a control, the contralateral limb also received a sham operation consisting of only a skin incision. The nerve tissue distal to the transection and contralateral (sham) nerves were isolated at 1 d post-transection.

value: Sprague Dawley

tag: passage

tag: antibody

value: post-transection


title: GL261 tumors in scid mice, cyclophosphamide-treated (6 days after 2nd CPA at 140 mg/kg-BW/6d, i.p.)_pool 2

description:
G94_M2
poly-A selected RNA, unstranded RNA-seq library
DEseq_163_G94_M5M6_G94_M1M2_GL261scid_UT_vs_D12.xlsx
DEseq_165_G94_M1M2_G94_M3M4_GL261scid_D12_vs_D15.xlsx

value: ICR scid (Taconic)

value: male

value: 12 weeks old


title: mTAIL-seq exp #4 wisp-mature


title: mTAIL-seq exp #3 wt-immature

description: mTAIL-seq for immature oocyte of wt, rep #1


title: total small RNAs (19-28nt) from WRR-1 argonaute3 knock-down cells, replicate 1

description: small RNAs (18-29nt), whole cells

data_processing:
The 3' linker (CTGTAGGCACCATCAATCGTATGCCGTCTTCTGCTTG) sequence is clipped from the sequenced reads with fastx-clipper.
Only reads with a minimum length of 16nt are kept for further processing.
Identical reads are collapsed with fastq_collapser.
Reads were mapped with bowtie to the Drosophila melanigaster genome (dm3), iteratively with up to 2 mismatches. Bedtools were used to intersect mapped reads to cluster coordinates.
Genome_build: dm3 BDGP release 5
Supplementary_files_format_and_content: Processed data file contains read counts at piRNA clusters normalized to the total number of reads mapped to the genome.

source_name: WRR-1 cells

extract_protocol:
Total RNAs were prepared with Trizol reagent (Invitrogen). 19-28nt small RNAs were size selected on a 15% polyacrylamide, 7M urea gel.
Small RNA libraries were prepared according to Malone et al. Cold Spring Harb Protoc. 2012. In short, size selected RNAs are ligated with a 3' adaptor (Modban) with mutant T4 RNA ligase 2, truncated (home made) and ligated products extracted from a 15%  polyacrylamide, 7M urea gel. A 5’ adaptor is then added with T4 RNA ligase (Ambion) and selected ligated products reverse transcribed with Superscript lll reverse transcriptase (Invitrogen). Amplification of the cDNA using Illumina primers results in a final library sequenced on an Illumina GAIIX platform.

treatment_protocol: WRR-1 cells were transfected with 10ug of dsRNA against argonaute 3 using Effectene (Qiagen); RNA was collected after 5 days.

tag: cell line

value: WRR-1 cells

value: dsRNA treated 5 days

value: w1118; Act-5C-GAL4,UAS-Wts-RNAi,UAS- RasV12 (WRR-1)


title: BtESF2

organism: Bos taurus

source_name: endometrial stromal fibroblasts from cow

value: primary cow endometrial stromal fibroblasts grown in culture


title: BtESF1

value: endometrial stromal fibroblast


title: mTAIL-seq exp #3 wisp-immature

description: mTAIL-seq for immature oocyte of wisp, rep #1

value: wispKG5287 (wispy knockout)

tag: developmental stage


title: Sciatic nerve H3K4me3 ChIP-seq 1 d post-transection 1

description: Combined_Cut_H3K4me3_TagDirectory.ucsc.bedGraph.gz


title: Cornea5

source_name: cornea

value: Caucasian

value: Male

tag: postmortem delay (hr)

tag: primary cause of death

value: Lung Cancer

tag: tissue

value: cornea


title: mTAIL-seq exp #7 wt-actegg2

description: mTAIL-seq for activated egg of wt, rep #2

tag: genotype

value: activated egg 0-1hr


title: Sciatic nerve H3K4me3 Sham ChIP-seq 2

tag: strain

tag: treatment

value: sham