title: mTAIL-seq exp #8 wt-actegg(0-2hr)

description: mTAIL-seq for activated egg(0-2hr) of wt, rep #1

value: activated egg 0-2hr


title: Sciatic nerve H3K4me3 Sham ChIP-seq 1

status: Public on Aug 01 2016

type: SRA

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

country: USA

institute: University of Wisconsin

description: Combined_Sham_H3K4me3_TagDirectory.ucsc.bedGraph.gz

library_source: genomic

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

molecule: genomic DNA

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.

tag: strain

value: Sprague Dawley

tag: passage

tag: antibody

tag: treatment

value: sham


title: total small RNAs (19-28nt) from WRR-1 aubergine 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: small RNAs (18-29nt), whole cells

library_source: transcriptomic

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.

molecule: total RNA

organism: Drosophila melanogaster

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 aubergine using Effectene (Qiagen); RNA was collected after 5 days.

tag: cell line

value: WRR-1 cells

value: dsRNA treated 5 days

tag: genotype

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


title: mTAIL-seq exp #4 wt-mature

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

country: South Korea

institute: Seoul National University

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

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: Drosophila mature oocyte

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

tag: developmental stage

value: oogenesis stage 14


title: total small RNAs (19-28nt) from WRR-1 zucchini knock-down cells, replicate 2

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

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


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

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

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


title: total small RNAs (19-28nt) from WRR-1 armitagei knock-down cells, replicate 2

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


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

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


title: total small RNAs (19-28nt) from WRR-1 GFP control knock-down cells, replicate 2

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

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


title: total small RNAs (19-28nt) from UAS-wts-RNAi, UAS-RasV12 adult ovaries

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

source_name: UAS-wts-RNAi, UAS-RasV12 adult ovary

growth_protocol: Ovaries from 3-6-day old flies were manually dissected in cold PBS to exclude contamination with other tissues, then quickly frozen in liquid nitrogen to preserve RNA integrity.

tag: tissue

value: Adult female ovary

value: no treatment, no GAL4 activation

value: w1118; UAS-Wts-RNAi,UAS- RasV12


title: piwi-bound small RNAs (19-28nt) from WRR-1 cells, replicate 1

description: small RNAs (18-29nt), piwi-bound

growth_protocol: WRR-1 cells were cultured in Schneider Drosophila Medium supplemented with 10% FBS and 1% Penicillin-Streptomycin (10,000 U/mL). See material and Methods (ADD REFERENCE and PMID)

extract_protocol:
Piwi-bound small RNAs were extracted with phenol-chloroform and precipitated. See material and methods in ADD REFERENCE and PMID.
Small RNA libraries were prepared according to Malone et al. Cold Spring Harb Protoc. 2012. In short, Piwi-bound sRNAs 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.

value: piwi immunoprecipitates


title: total small RNAs (19-28nt) from OSS cells

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

source_name: OSS cells

growth_protocol: OSS cells were cultured in Shields and Sang M3 Insect Medium supplemented with 10% FBS, 1% Penicillin-Streptomycin (10,000 U/mL), and 10% fly extract. See material and Methods (ADD REFERENCE and PMID)

value: w[1118]; P [w+ hsp-70 bam+] 11-d bam[D86] ry e/d bam[D86] P[ovo-lacZ) P[vas-egfp]


title: total small RNAs (19-28nt) from WRR-1 cells

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

value: no treatment


title: -rap-2

city: Cambridge

first: Geneveive

last: Gould

state: Massachusetts

address: 77 Massachusetts Ave. 68-253

department: Biology

institute: MIT

description: other (Ribo-Zero subtracted RNA)

data_processing:
Reads were trimmed to 60 X 60 to be consisten with our earlier data and mapped using TopHat2, giving TopHat no annotations and allowing novel junction discovery.
A custom Bowite index was created for all splice junctions found by Tophat by concatenating the 50nt of sequence immediately before and after the junction to ensure the reads had at least a 10nt overhang on each side of the junction. Bowtie1 was run with this custom index (genome + novel splice junctions) on each end of each sequencing library separately because parried end reads would be able to map to this custom index with many 100nt fragments. Bowtie read mapping to the custom splice index was used to calculate entropy of each splice junction (see manuscript)
MISO was run on the samples to caculate Percent Spliced In (PSI).
Genome_build: SacCer3
Supplementary_files_format_and_content: TableS9.xlsx Percent Spliced In (PSI)

organism: Saccharomyces cerevisiae

source_name: yeast

extract_protocol:
RNA isolation for RNA-seq was performed as follows. RNA was isolated similar to Clarkson, B. K., Gilbert, W. V. & Doudna, J. A. Functional overlap between eIF4G isoforms in Saccharomyces cerevisiae. PLoS ONE 5, e9114 (2010). Pellets were resuspended in 1mL Acid Phenol and an equal volume of AES buffer (50mM NaAcetate pH 5.2, 10mM EDTA, 1% SDS) was added. In 2mL eppendorf tubes, samples were incubated at 65°C for 10 min with vortexing every minute. Samples were incubated on ice for 5 min and then transferred to a phaselock tube and one volume Cholrofom was added. After spinning, the top aqueous layer was transferred to a fresh phaselock tube and one volume of phenol:choloform:iaa (25:24:1) was added, tubes were spun, one volume of choloform was added, tubes were spun, and the aqueous layer was transferred to a fresh tube to be precipitated with 50uL 3M NaOAc (pH 5.5) and 550uL isopropenol. Samples were spun at max speed for 25 minutes at 4°C. The pellet was washed twice with 70% ethanol and resuspended in water.
RNA was isolated using the hot acid phenol method and DNase treated with Turbo DNase. rRNA was subtracted using the Illumina Ribo-Zero Gold rRNA Removal Kit (Yeast). RNA was then fragmented and first strand cDNA was performed. Second strand synthesis was carried out using dUTP instead of dTTP to generate strand specific libraries. Subsequently adaptors ligation, uracil digestion, and PCR were performed. All libraries were barcoded and sequenced in one NextSeq lane.
RNA-seq (Ribo-Zero, strand specific)

tag: rna extraction method

value: hot acid phenol

value: S288c S.cer.


title: t=12-2

description: other (Ribo-Zero subtracted RNA)

value: SK1 S.cer.

tag: time (h in sporulation medium)


title: t=7.5-2

description: other (Ribo-Zero subtracted RNA)


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

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

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


title: t=6-2

description: other (Ribo-Zero subtracted RNA)


title: piwi-bound small RNAs (19-28nt) from WRR-1 cells, replicate 2

description: small RNAs (18-29nt), piwi-bound


title: t=3-2

description: other (Ribo-Zero subtracted RNA)


title: piwi-bound small RNAs (19-28nt) from OSS cells, replicate 2

description: small RNAs (18-29nt), piwi-bound

source_name: OSS cells; see Niki, Y., Yamaguchi, T., Mahowald, A.P. (2006). Establishment of stable cell lines of Drosophila germ-line stem cells.  Proc. Natl. Acad. Sci. U.S.A. 103(44): 16325--16330. PMID: 17056713.

value: ovarian somatic sheath cells (OSS)


title: t=0-2

description: other (Ribo-Zero subtracted RNA)


title: piwi-bound small RNAs (19-28nt) from OSS cells, replicate 1

description: small RNAs (18-29nt), piwi-bound


title: t=8.5-2

description: other (Ribo-Zero subtracted RNA)


title: t=0-1

description: other (Ribo-Zero subtracted RNA)


title: HBC

city: beijing

first: kong

last: weiwen

address: Qinghua East Rd 35

country: China

institute: Beijing forestry university

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: cucumber ChineseLong v2
Genome_build: ftp://www.icugi.org/pub/genome/cucumber/
Genome_build: Botryotinia fuckeliana B05.10 v2.23
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release-23/fungi/fasta/botryotinia_fuckeliana/dna
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample; For gene ids, please see "cucumber_Chineselong_v2.gff3"  in ftp://www.icugi.org/pub/genome/cucumber/
Supplementary_files_format_and_content: CSV and  HBC  are pure cultured sample. HGBC contain both cucumber and Botrytis cinerea RNA

organism: Botrytis cinerea

source_name: Mycelium

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mycelium

tag: age

tag: protocol

value: anti-infection Botrytis cinerea


title: sk1-1

description: other (Ribo-Zero subtracted RNA)


title: total small RNAs (19-28nt) from WRR-1 piwi knock-down cells, replicate 2

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


title: -rap-1

description: other (Ribo-Zero subtracted RNA)


title: +rap-2

description: other (Ribo-Zero subtracted RNA)


title: Cornea7

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

organism: Homo sapiens

source_name: cornea

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: African

tag: Sex

value: Female

tag: postmortem delay (hr)

tag: primary cause of death

value: CVA

value: cornea


title: t=8.5-1

description: other (Ribo-Zero subtracted RNA)

tag: strain


title: t=7.5-1

description: other (Ribo-Zero subtracted RNA)


title: t=6-1

description: other (Ribo-Zero subtracted RNA)


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

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

value: WRR-1 cells

value: dsRNA treated 5 days

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


title: t=3-1

description: other (Ribo-Zero subtracted RNA)


title: 4+3N_RibosomeProfiling_rep1

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:
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.

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: Nonrandom_RibosomeProfiling_rep2


title: +rap-1

description: other (Ribo-Zero subtracted RNA)


title: Nonrandom_RibosomeProfiling_rep1


title: Tiirats1

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

data_processing:
Color-space base calling
Mapping, alignment with Lifescope
Lifescope transcriptome workflow
Genome_build: hg19

source_name: blood

growth_protocol: blood sample

extract_protocol:
Tempus blood kit
RNA was amplified with Ovation RNA-Seq System V2 Kit (NuGen, Emeryville, CA, USA) and the output double stranded DNA was used to prepare SOLiD 5500 W System DNA fragment library according to manufacturer’s protocols (Thermo Fisher Scientific Inc, Waltham, MA, USA). The barcoding primers in library preparation and fragment sequencing chemistry was applied (75 bp in forward directions). In case of 12 samples per flowchip lane approximately 33 million mappable reads were expected per one sample, which would be enough for successful whole transcriptome expression pattern analysis.
fragment

treatment_protocol: case-control design

tag: hypotrophy

value: control

value: F

tag: relation

value: mother


title: Tiirats2

value: case

value: daughter


title: Tiirats3

value: M

value: farther


title: OcESF2

city: West Haven

first: Koryu

last: Kin

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.

molecule: polyA RNA

organism: Oryctolagus cuniculus

source_name: endometrial stromal fibroblasts from rabbit

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: primary rabbit endometrial stromal fibroblasts grown in culture

tag: cell type

value: endometrial stromal fibroblast


title: OcESF1


title: sk1-2

description: other (Ribo-Zero subtracted RNA)

tag: rna extraction method

value: hot acid phenol

value: SK1 S.cer.


title: dbr1-2

description: other (Ribo-Zero subtracted RNA)

value: S288c S.cer.


title: t=12-1

description: other (Ribo-Zero subtracted RNA)

tag: time (h in sporulation medium)


title: DualLigation_RibosomeProfiling_rep2


title: RNA-seq_dbr1_null_1

data_processing:
60 X 60 bp reads (WT, upf1 null, and dbr1 null samples) were initially mapped with TopHat251 (tophat-2.0.0.Linux_x86_64) giving TopHat no annotations and allowing it to discover novel splice junctions using the following parameters: tophat -i 20 -I 10000 -a 10 --segment-length 15 --bowtie1 SacCer3 end1.fastq end2.fastq Each barcoded sample was mapped on its own and additionally all samples were mapped together to find as many novel splice junctions as possible.
A custom Bowite index was created for all splice junctions found by Tophat by concatenating the 50nt of sequence immediately before and after the junction to ensure the reads had at least a 10nt overhang on each side of the junction. Bowtie1 was run with this custom index (genome + novel splice junctions) on each end of each sequencing library separately because parried end reads would be able to map to this custom index with many 100nt fragments. Bowtie was run as follows: bowtie -S -m 1 -SacCer3_custom_index one_end_reads.fastq outfile.sam. Bowtie read mapping to the custom splice index was used to calculate entropy of each splice junction (see manuscript)
Cufflinks (version 2.2.1) was used to calculate FPKMs for the RNA-seq data. cuffdiff -o . --library-type fr-firststrand -u -N -b SacCer3.fsa saccharomyces_cerevisiae_R64-1-1_20110208.gff wt1.bam,wt1.bam dbr1-1.bam,dbr1-2.bam upf1-1.bam,upf1-2.bam
genome_build: SacCer3
supplementary_files_format_and_content: genes.fpkm_tracking standard output file from cufffidff. q1=WT, q2 = dbr1 null, q3 = upf1 null (SacCer3)

organism: Saccharomyces cerevisiae S288C

extract_protocol:
RNA isolation for RNA-seq was performed as follows. Overnight yeast cultures were grown in 5mL YPD media and were diluted in the morning into 50mL YPD and grown to log phase (OD600 0.5 to 1), spun down, and the pellets were frozen in liquid nitrogen. RNA was isolated similar to Clarkson, B. K., Gilbert, W. V. & Doudna, J. A. Functional overlap between eIF4G isoforms in Saccharomyces cerevisiae. PLoS ONE 5, e9114 (2010). Pellets were resuspended in 1mL Acid Phenol and an equal volume of AES buffer (50mM NaAcetate pH 5.2, 10mM EDTA, 1% SDS) was added. In 2mL eppendorf tubes, samples were incubated at 65°C for 10 min with vortexing every minute. Samples were incubated on ice for 5 min and then transferred to a phaselock tube and one volume Cholrofom was added. After spinning, the top aqueous layer was transferred to a fresh phaselock tube and one volume of phenol:choloform:iaa (25:24:1) was added, tubes were spun, one volume of choloform was added, tubes were spun, and the aqueous layer was transferred to a fresh tube to be precipitated with 50uL 3M NaOAc (pH 5.5) and 550uL isopropenol. Samples were spun at max speed for 25 minutes at 4°C. The pellet was washed twice with 70% ethanol and resuspended in water.
RNA was isolated using the hot acid phenol method (see RNA isolation above) to ensure isolation of high quality RNA. All 6 samples, 2 WT, 2 dbr1Δ, 2 upf1Δ, had RQN (quality) values of 8.8 or higher as measured on the Advanced Analytical machine. Strand specific libraries were prepared by the MIT Bio Micro Center using the TruSeq™ RNA Sample Prep Kit v2 (RS-122-2101 kit) through cDNA after which LM-PCR was preformed using the Beckman Coulter SPRIte system with a 200-400bp size cutoff. Samples were barcoded and all sequenced in one HiSeq2000 lane.


title: DualLigation_RibosomeProfiling_rep1


title: RNA-seq_dbr1_null_2


title: HGBC

description: Interaction sample total RNA contain both cucumber and Botrytis cinerea RNA

organism: Cucumis sativus

source_name: Leaf

tag: tissue

value: leaf

tag: agent

value: inoculated with Botrytis cinerea 96h

value: interaction sample


title: CSV

tag: age

value: four weeks

tag: protocol

value: anti-infection cucumber


title: 4+3N_RibosomeProfiling_rep2

value: wild-type


title: RNA-seq_WT1

data_processing:
60 X 60 bp reads (WT, upf1 null, and dbr1 null samples) were initially mapped with TopHat2 (tophat-2.0.0.Linux_x86_64) giving TopHat no annotations and allowing it to discover novel splice junctions using the following parameters: tophat -i 20 -I 10000 -a 10 --segment-length 15 --bowtie1 SacCer3 end1.fastq end2.fastq Each barcoded sample was mapped on its own and additionally all samples were mapped together to find as many novel splice junctions as possible.
A custom Bowite index was created for all splice junctions found by Tophat by concatenating the 50nt of sequence immediately before and after the junction to ensure the reads had at least a 10nt overhang on each side of the junction. Bowtie1 was run with this custom index (genome + novel splice junctions) on each end of each sequencing library separately because parried end reads would be able to map to this custom index with many 100nt fragments. Bowtie was run as follows: bowtie -S -m 1 -SacCer3_custom_index one_end_reads.fastq outfile.sam. Bowtie read mapping to the custom splice index was used to calculate entropy of each splice junction (see manuscript)
Cufflinks (version 2.2.1) was used to calculate FPKMs for the RNA-seq data. cuffdiff -o . --library-type fr-firststrand -u -N -b SacCer3.fsa saccharomyces_cerevisiae_R64-1-1_20110208.gff wt1.bam,wt1.bam dbr1-1.bam,dbr1-2.bam upf1-1.bam,upf1-2.bam
genome_build: SacCer3
supplementary_files_format_and_content: genes.fpkm_tracking standard output file from cufffidff. q1=WT, q2 = dbr1 null, q3 = upf1 null (SacCer3)

value: WT


title: 4N_RibosomeProfiling_rep2


title: RNA-seq_upf1_null_2


title: Lariat-seq

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

data_processing:
Library strategy: Lariat-seq
Reads were attempted to be aligned to the S.Cer. genome using the Bowtie (version 1.0.0) read aligner and those aligning with fewer than 4 mismatches were omitted from further analysis
Each unalignable read was split into two fragments such that each fragment was at least 12 bases long and the hexamer beginning the second fragment had maximum probability of being sampled from the S.Cer. 5’ss position weight matrix. The fragments will be referred to by their position at the 3’ or 5’ end of the original read moving forwards.
The fragment pairs were mapped to the S.Cer. genome using the bowtie read aligner allowing no mismatches. The fragments were required to map in an inverted order (3’ fragment upstream of 5’ fragment). The final base of each 5’ fragment, the putative branchpoint nucleotide, was omitted from this alignment due to the prevalence of mismatches at this position.
For all fragment pairs with a valid alignment, the final base of each 5’ fragment was re-added. The aligned position of the 3’ end of the 5’ fragment was called as a branchpoint and the aligned position of the 5’ end of the 3’ fragment was called as the corresponding 5’ss.
genome_build: SacCer3
supplementary_files_format_and_content: summary of reads crossing 5'SS-BPS junction (as described in manuscript) (SacCer3)

source_name: Lariat-seq

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.
Reverse transcription was performed on 2D gel isolated lariat RNA using 1ul Random hexamer Primers (3ug/ul) (Invitrogen) and SuperScript III reverse transcriptase (Invitrogen). RNA and primer mix was heated at 70°C for 10 minutes and then put on ice. 12 uL of Mix A (mix A: 4uL 5x 1st strand buffer, 2uL 100mM DTT, 1uL dNTPs (10mM), 4uL Actinomycin D [1mg/1mL], 1uL SuperaseIn (20U/ul)) was added to the RNA and primer. Then 1 uL of SSIII was added and the RT program was run: 25⁰C 10 minutes, 42⁰C 50 minutes, 70⁰C 15 minutes, 4⁰C hold. Sample volume was brought up to 200uL with water and then samples were phenol choloroform extracted and ethanol precipitated. Second strand synthesis was performed with DNA pol I and dUTP to make strand specific libraries. Next sampled underwent SPRI-TE (end repair, adenlyation, adapter ligation, gel purification #1). Subsequently uracil digestion was performed with USER, samples underwent PCR (with a barcoded primer) and gel puficiation before sequencing (1/30 of a HiSeq 2000 lane).

value: trizol


title: 4N_RibosomeProfiling_rep1


title: DualLigation_RibosomeProfiling_rep3


title: RNA-seq_WT2


title: RNA-seq_upf1_null_1


title: LLC tumors in C57BL/6 mice, cyclophosphamide-treated (6 days after 3rd CPA at 140 mg/kg-BW/6d, i.p.)_pool 2

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description:
G101_M8
poly-A selected RNA, strand-specific RNA-seq library
DEseq_191_G101M5M6_G101M7M8_LLC_UT_LLC_CPA.xlsx
DEseq_196_G101M7M8_G101M3M4_LLC_CPA_GL261B6_CPA.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

organism: Mus musculus

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 6-day repeating schedule, by i.p. injection as detailed in Wu and Waxman (PMID: 25069038)

value: C57BL/BNTac (Taconic)

tag: Sex

value: male

value: 12 weeks old

tag: tumor cell line implanted in mouse

value: LLC

tag: treatment

value: cyclophosphamide-treated (6 days after 3rd CPA at 140mg/kg-BW/6d, i.p.)

tag: rna extracted from

value: 5 individual tumors


title: B16F10 tumors in C57BL/6 mice, untreated_pool 1

description:
G101_M9
poly-A selected RNA, strand-specific RNA-seq library
DEseq_192_G101M9M10_G101M11M12_B16F10_UT_B16F10_CPA.xlsx
DEseq_194_G101M9M10_G101M1M2_B16F10_UT_GL261B6_UT.xlsx

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

tag: strain

value: untreated


title: dbr1-1

description: other (Ribo-Zero subtracted RNA)

value: hot acid phenol


title: B16F10 tumors in C57BL/6 mice, cyclophosphamide-treated (6 days after 3rd CPA at 140 mg/kg-BW/6d, i.p.)_pool 2

description:
G101_M12
poly-A selected RNA, strand-specific RNA-seq library
DEseq_192_G101M9M10_G101M11M12_B16F10_UT_B16F10_CPA.xlsx
DEseq_197_G101M11M12_G101M3M4_B16F10_CPA_GL261B6_CPA.xlsx

value: 3 individual tumors


title: LLC tumors in C57BL/6 mice, untreated_pool 2

description:
G101_M6
poly-A selected RNA, strand-specific RNA-seq library
DEseq_191_G101M5M6_G101M7M8_LLC_UT_LLC_CPA.xlsx
DEseq_193_G101M5M6_G101M1M2_LLC_UT_GL261B6_UT.xlsx


title: B16F10 tumors in C57BL/6 mice, cyclophosphamide-treated (6 days after 3rd CPA at 140 mg/kg-BW/6d, i.p.)_pool 1

description:
G101_M11
poly-A selected RNA, strand-specific RNA-seq library
DEseq_192_G101M9M10_G101M11M12_B16F10_UT_B16F10_CPA.xlsx
DEseq_197_G101M11M12_G101M3M4_B16F10_CPA_GL261B6_CPA.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: 4 individual tumors


title: total small RNAs (19-28nt) from WRR-1 aubergine knock-down cells, replicate 2

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

tag: cell line

value: WRR-1 cells

value: dsRNA treated 5 days

tag: genotype

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


title: B16F10 tumors in C57BL/6 mice, untreated_pool 2

description:
G101_M10
poly-A selected RNA, strand-specific RNA-seq library
DEseq_192_G101M9M10_G101M11M12_B16F10_UT_B16F10_CPA.xlsx
DEseq_194_G101M9M10_G101M1M2_B16F10_UT_GL261B6_UT.xlsx


title: RNA-seq wisp immature oocyte (biological replicate #2)

description:
RNA-seq for Droshophila immature oocyte total RNA
RS_wisp-immautre-oocyte_2

data_processing:
Sequencing reads were proccessed by FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit). First, the 3′ adapter sequences (5′-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3′) were removed, and reads were filtered by Phred quality score (fastq_quality_filter -Q 33 -p 30 -q 90).
The sequence reads were then aligned to the ERCC RNA spike-in sequences (ref) by STAR version 2.4.2a (Dobin et al., 2013) using options “--alignIntronMin 99999 --alignEndsType EndToEnd”.
Reads mapped to each spike-in were counted using htseq-count (Anders et al., 2015) with default options.
The reads not aligned to any spike-in RNAs were aligned to UCSC dm6 genome assembly using RSEM version 1.2.25 (Li and Dewey, 2011) with STAR (Dobin et al., 2013) and splicing junction annotations generated from the NCBI RefSeq. The reduced RefSeq transcript set for non-overlapping representation was prepared as previously described (Chang et al., 2014b).
The expected read counts were scaled by RUVg (k=1) in R package RUVSeq (Risso et al., 2014). Transcripts not detected with enough reads (< 100 normalized reads in all libraries) were removed to reduce noise.
Genome_build: dm6
Supplementary_files_format_and_content: A spreadsheet file contain normalized read counts by spike-in scaling.

source_name: oocyte

growth_protocol: 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 by TRIzol (Invitrogen), and the quality was checked by  Bioanalyzer 2100 (Agilent).
The same amount of control ERCC spike-in (Ambion,  4456739) was mixed with each sample with the same amount of total RNA, and  subsequently rRNA was depleted by Ribo-Zero (Epicentre). RNA-seq libraries were  constructed using Illumina TruSeq RNA sample preparation kit v2.

value: oocyte

tag: genotype/variation

value: wispKG5287 (wispy knockout)

tag: developmental stage

value: oogenesis stage 9-10


title: LLC tumors in C57BL/6 mice, cyclophosphamide-treated (6 days after 3rd CPA at 140mg/kg-BW/6d, i.p.)_pool 1

description:
G101_M7
poly-A selected RNA, strand-specific RNA-seq library
DEseq_191_G101M5M6_G101M7M8_LLC_UT_LLC_CPA.xlsx
DEseq_196_G101M7M8_G101M3M4_LLC_CPA_GL261B6_CPA.xlsx


title: RNA-seq wisp activated egg (biological replicate #2)

description:
RNA-seq for Droshophila activated egg total RNA
RS_wisp-activated-egg_2

source_name: egg

value: egg

value: activated egg 0-1hr


title: RNA-seq wisp mature oocyte (biological replicate #2)

description:
RNA-seq for Droshophila mature oocyte total RNA
RS_wisp-mature-oocyte_2

value: oogenesis stage 14


title: LLC tumors in C57BL/6 mice, untreated_pool 1

description:
G101_M5
poly-A selected RNA, strand-specific RNA-seq library
DEseq_191_G101M5M6_G101M7M8_LLC_UT_LLC_CPA.xlsx
DEseq_193_G101M5M6_G101M1M2_LLC_UT_GL261B6_UT.xlsx

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

value: C57BL/BNTac (Taconic)

value: male

value: 12 weeks old


title: GL261 tumors in C57BL/6 mice, cyclophosphamide-treated (6 days after 2nd CPA at 140 mg/kg-BW/6d, i.p.) pool 2

description:
G101_M4
poly-A selected RNA, strand-specific RNA-seq library
DEseq_190_G101M1M2_G101M3M4_GL261B6_UT_GL261B6_CPA.xlsx
DEseq_196_G101M7M8_G101M3M4_LLC_CPA_GL261B6_CPA.xlsx
DEseq_197_G101M11M12_G101M3M4_B16F10_CPA_GL261B6_CPA.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: 10 individual tumors


title: RNA-seq WT activated egg (biological replicate #2)

description:
RNA-seq for Droshophila activated egg total RNA
RS_wt-activated-egg_2


title: GL261 tumors in C57BL/6 mice, untreated_pool 1

description:
G101_M1
poly-A selected RNA, strand-specific RNA-seq library
DEseq_190_G101M1M2_G101M3M4_GL261B6_UT_GL261B6_CPA.xlsx
DEseq_193_G101M5M6_G101M1M2_LLC_UT_GL261B6_UT.xlsx
DEseq_194_G101M9M10_G101M1M2_B16F10_UT_GL261B6_UT.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

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

value: untreated

value: 9 individual tumors


title: RNA-seq wisp mature oocyte (biological replicate #1)

description:
RNA-seq for Droshophila mature oocyte total RNA
RS_wisp-mature-oocyte_1


title: GL261 tumors in C57BL/6 mice, untreated_pool 2

description:
G101_M2
poly-A selected RNA, strand-specific RNA-seq library
DEseq_190_G101M1M2_G101M3M4_GL261B6_UT_GL261B6_CPA.xlsx
DEseq_193_G101M5M6_G101M1M2_LLC_UT_GL261B6_UT.xlsx
DEseq_194_G101M9M10_G101M1M2_B16F10_UT_GL261B6_UT.xlsx


title: RNA-seq WT immature oocyte (biological replicate #2)

description:
RNA-seq for Droshophila immature oocyte total RNA
RS_wt-immautre-oocyte_2


title: GL261 tumors in C57BL/6 mice, cyclophosphamide-treated (6 days after 2nd CPA at 140mg/kg-BW/6d, i.p.)_pool 1

description:
G101_M3
poly-A selected RNA, strand-specific RNA-seq library
DEseq_190_G101M1M2_G101M3M4_GL261B6_UT_GL261B6_CPA.xlsx
DEseq_196_G101M7M8_G101M3M4_LLC_CPA_GL261B6_CPA.xlsx
DEseq_197_G101M11M12_G101M3M4_B16F10_CPA_GL261B6_CPA.xlsx


title: Mouse set 3 36S H3K9Ac

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

country: Canada

institute: Insititut de Recherches Cliniques

description:
Homer_mouse_set3_pos.txt
Homer_mouse_set3_neg.txt

data_processing:
ChIP-Seq reads were aligned to mm10 or hg19 using Bowtie2 v2.10
.bam files were converted into .sam files using samtools
The annotatePeaks.pl function of the Homer software was used to quantify read densities around gene Transcription Start Sites.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: Each processed data file is the result of a call to annotatepeaks.pl in the Homer software and covers an entire set of samples. Each line in the file represents one ensembl transcript with each column representing a sinble bin of 25bp. The first column is the Ensembl Transcript ID, the next 101 match the 36S H3 sample, the next 101 match the 36 H3K9Ac, then 36N H3, then 36N H3K9Ac. There is one output file for transcripts on the positive strand and one for transcripts on the negative strand. In the positive file, the genomic area covered is -500bp to +200bp relative to the TSS. In the negative file, the genomic area covered is -2000bp to +500bp relative to the TSS.

source_name: AML cells

extract_protocol:
Cells were fixed with 1% formaldehyde. Cell lysis was performed using the following buffers: total cell lysis - 5mM PIPES pH 8, 85mM KCl, 0.5% NP-40, 1X protease inhibitor cocktail, 1mM PMSF, and nuclear lysis – 50mM Tris, 10mM EDTA, 1% SDS, 1X protease inhibitor cocktail, 1mM PMSF. After sonication (Covaris E220 sonicator), immunoprecipitation was performed using Protein A/G Dynabeads (Life Technologies)
Sequencing libraries were prepared from immunoprecipitated chromatin using the TruSeq DNA kit from Illumina according to the manufacturer’s instructions and sequenced using the TruSeq PE Clusterkit v3-cBot-HS

value: Gfi1 36S/wt

tag: mouse strain

tag: antibody

value: H3K9Ac (ab4441; Abcam)


title: Mouse set 3 36N H3

value: Gfi1 36N/wt

value: H3 (ab1791; Abcam)


title: RNA-seq WT immature oocyte (biological replicate #1)

description:
RNA-seq for Droshophila immature oocyte total RNA
RS_wt-immautre-oocyte_1


title: RNA-seq wisp immature oocyte (biological replicate #1)

description:
RNA-seq for Droshophila immature oocyte total RNA
RS_wisp-immautre-oocyte_1


title: Mouse set 3 36N H3K9Ac


title: RNA-seq WT activated egg (biological replicate #1)

description:
RNA-seq for Droshophila activated egg total RNA
RS_wt-activated-egg_1


title: Mouse set 2 36N H3K9Ac

description:
Homer_mouse_set2_pos.txt
Homer_mouse_set2_neg.txt


title: Mouse set 2 36S H3K9Ac


title: RNA-seq WT mature oocyte (biological replicate #2)

description:
RNA-seq for Droshophila mature oocyte total RNA
RS_wt-mature-oocyte_2


title: Mouse set 3 36S H3


title: RNA-seq WT mature oocyte (biological replicate #1)

description:
RNA-seq for Droshophila mature oocyte total RNA
RS_wt-mature-oocyte_1


title: Mouse set 1 36N H3K9Ac

description:
Homer_mouse_set1_pos.txt
Homer_mouse_set1_neg.txt


title: Mouse set 1 36S H3


title: RNA-seq wisp activated egg (biological replicate #1)

description:
RNA-seq for Droshophila activated egg total RNA
RS_wisp-activated-egg_1


title: Mouse set 0 36N H3K9Ac

description:
Homer_mouse_set0_pos.txt
Homer_mouse_set0_neg.txt

data_processing:
ChIP-Seq reads were aligned to mm10 using Bowtie2 v2.10
.bam files were converted into .sam files using samtools
The annotatePeaks.pl function of the Homer software was used to quantify read densities around gene Transcription Start Sites.
Genome_build: mm10
Supplementary_files_format_and_content: Each processed data file is the result of a call to annotatepeaks.pl in the Homer software and covers an entire set of samples. Each line in the file represents one ensembl transcript with each column representing a sinble bin of 25bp. The first column is the Ensembl Transcript ID, the next 101 match the 36S H3 sample, the next 101 match the 36 H3K9Ac, then 36N H3, then 36N H3K9Ac. There is one output file for transcripts on the positive strand and one for transcripts on the negative strand. In the positive file, the genomic area covered is -500bp to +200bp relative to the TSS. In the negative file, the genomic area covered is -2000bp to +500bp relative to the TSS.

source_name: Lin-Sca1-cKit+ cells

tag: antibodies


title: Mouse set 1 36S H3K9Ac


title: HsESF2

source_name: endometrial stromal fibroblasts from human

tag: culture type

value: primary human endometrial stromal fibroblasts grown in culture

tag: cell type

value: endometrial stromal fibroblast


title: Mouse set 0 36N Input


title: SiBASP1_plusTAM_260315

city: Bristol

first: Andrew

middle: D.

last: Davidson

address: Faculty of Biomedical Sciences, University Walk

department: School of Cellular and Molecular Medicine

country: United Kingdom

institute: University of Bristol

data_processing:
Reads were processed using RTA version 1.18.64, with default filter and quality settings. The reads were demultiplexed with CASAVA 1.8.4 (allowing no mismatches)
Sequenced reads were groomed using FASTQ Groomer and checked for quality using FastQC (Galaxy https://usegalaxy.org/).
Sequenced reads were  mapped to the Homo sapiens hg38 canonical female  genome using TopHat  (Galaxy version 0.9) using 158 bp as a mean inner distance between mate pairs, a Std.Dev for distance between mate pairs of 20 and the remaining settings left as the default settings.
The Tophat : accepted hits BAM files were used for Cufflinks (Galaxy v2.2.10) analysis using the default settings with bias correction and the UCSC Main on human: knownGene (genome) for reference annotation.  The Cufflinks assembled transcript files were analysed by Cuffmerge (Galaxy v2.2.1.0) using the default settings and the reference annotation UCSC Main on Human: refFlat (genome). Cuffdiff (Galaxy v2.2.1.2) analysis was done using the default conditions (FDR of 0.05, min. alignment count of 10; geometric library normalization, poole dispersion estimation method, no bias correction).
All processing steps described above were done using the described applications on Galaxy (https://usegalaxy.org)
Genome_build: hg38 canonical female  genome
Supplementary_files_format_and_content: Cuffdiff tab-delimited text files include the FPKM tracking file and Cuffdiff gene expression values

growth_protocol: MCF7 cells were seeded in DMEM to 10cm plates and grown for 24 hours.

extract_protocol:
MCF7 cells were harvested 48 hours after initial transfection. RNA was extracted from cells using Qiagen Qiashredder columns and a Qiagen RNAeasy Mini Kit.
RNA libraries were prepared for sequencing using standard TruSeq® Illumina protocols

treatment_protocol: MCF7 cells were transfected with siRNAs against BASP1 or negative control siRNAs using Lipofectamine in OptiMEM. After 24 hours, media was changed to DMEM and cells treated with or without 100nM Tamoxifen.

value: MCF7 cells

value: invasive breast ductal carcinoma

tag: transfected with

value: siRNA against BASP1

tag: treated with

value: 100nM Tamoxifen

tag: experiment date


title: HsESF1


title: Mouse set 0 36S H3K9Ac


title: SiNeg_plusTAM_260315

value: negative control siRNA


title: SiNeg_minusTAM_260315


title: Mouse set 2 36N H3


title: BASPSi_plusTAM_190315


title: BASPSi_minusTAM_190315


title: SiBASP1_minusTAM_260315


title: Mouse set 1 36N H3


title: NegSi_plusTAM_190315


title: Neg_minusTAM_120315


title: BASP_plusTAM_120315


title: NegSi_minusTAM_190315


title: Neg_plusTAM_120315


title: LNCaP_SMARCA2_Vehicle_ChIPSeq

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie-1.0.0 with the following parameters -v 3 -k 3 -m 2. And only those reads with unique or two mapped locations are remained for further analysis.
Each mapped reads has been extended into a 300 bp fragment (presumably coinciding with library size) in a direction from 5'-3' along with chromosome axis. And the bigwig files would be made on these processed alignments.
Genome_build: hg19

source_name: prostate

growth_protocol: LNCaP cells were cultured in RPMI 1640 (Invitrogen) supplemented with 10% charcoal-stripped FBS (Omega Scientific) and 1mM L-glutamine.

extract_protocol:
Cells were grown to 70%-80% confluence, and crosslinked with 1% formaldehyde for 10 min at room temperature. After washing twice with cold PBS, cells were collected and resuspended in lysis buffer (1% SDS, 5 mM EDTA, 50 mM Tris (pH 8.0), 1x protease and phosphatase inhibitors). After sonication, the soluble chromatin was diluted in 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris (pH 8.0), 1x protease and phosphatase inhibitors). Then samples were precleared and immunoprecipitated with the appropriate antibodies overnight at 4°C. The next day, protein A or G beads blocked with BSA were added for 2 h at 4°C, and then washed sequentially for 10 min with TSE I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris (pH 8.0), 150 mM NaCl), TSE II (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris (pH 8.0), 500 mM NaCl), buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris (pH 8.0), and TE buffer (10 mM Tris (pH 8.0), 1mM EDTA (pH 8.0)). DNA was eluted in Elution buffer (1% SDS, 0.1M NaHCO3) at room temperatue for 30 min. The crosslinking was reversed by incubation for 16 h at 65°C. During the purification, ChIP DNA was treated with DNase-free RNase for 30 min at 37°C.
Libraries were prepared according to NEBNext ChIP-Seq Library Prep Master Mix Set (E6240L). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10 or 14 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an E-gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq5000 following the manufacturer's protocols.

treatment_protocol: No treatment.

value: prostate cancer cells

tag: passages

value: LNCaP

tag: chip antibody

value: SMARCA2 (Abcam, ab15597)


title: LNCaP_SMARCA1_Vehicle_ChIPSeq

value: SMARCA1 (Abcam, ab37003)


title: LNCaP_CHD4_Vehicle_ChIPSeq

value: CHD4 (Abcam, ab72418)


title: LNCaP_CHD1_Vehicle_ChIPSeq

value: CHD1 (Santa Cruz, H-210)


title: LNCaP_MI2_Vehicle_ChIPSeq

value: Mi2-α (Santa Cruz, C-16)


title: BASP_minusTAM_120315


title: LNCaP_INOC1_Vehicle_ChIPSeq

value: INOC1 (Santa Cruz, H-300)


title: Mouse set 0 36S Input

value: Gfi1 36S/wt


title: LNCaP_SNF2H_Vehicle_ChIPSeq

value: SNF2H (Abcam, ab72499)


title: RnESF2

source_name: endometrial stromal fibroblasts from rat

value: primary rat endometrial stromal fibroblasts grown in culture


title: Sciatic nerve H3K27me3 ChIP-seq 1

description: H3K27me3  sciatic nerve

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 relative to sequencing of an input chromatin sample.
input samples have been deposited as: GSM1541282and GSM1541283
Genome_build: Rn5

source_name: sciatic nerve

extract_protocol:
Rats were sacrificed and freshly dissected rat sciatic nerve was minced in 1% formaldehyde for 10min and then quenched for 10min with glycine to a final concentration of 0.125M. Samples were sequentially lysed in buffers LB1, LB2, and LB3 + 0.03% SDS (Schmidt et. al., 2009). DNA was fragmented to an average size of 0.5-2kb using 4x10min Bioruptor (Diagenode) cycles on the medium setting. Each aliquot of sonicated chromatin (300ug) was incubated overnight at 4°C with 5ug of antibody. A 10% aliquot was saved for input analysis. An 80ul aliquot of Protein G Dynabead (Invitrogen) slurry was added to each ChIP sample for 4hrs at 4°C. IPs were washed 5x in RIPA buffer than eluted at 65°C with reverse crosslinking buffer (50mM Tris, 10mM EDTA, 1% SDS). ChIP DNA was purified by phenol chloroform extraction and resuspended in 10mM Tris pH 8.0. Antibody used in the study: H3K27me3 Active Motif, catalog no. 39155
Libraries were prepared from ChIP DNA, and respective inputs, using the Illumina TruSeq ChIP Sample Preparation Kit.

value: Sprague Dawley

tag: antiboy

value: H3K27me3 (Active Motif, catalog no. 39155)

tag: passage


title: RnESF1

value: endometrial stromal fibroblast


title: Sciatic nerve H3K27me3 ChIP-seq 2

description: H3K27me3  sciatic nerve

tag: strain


title: Mouse set 2 36S H3

value: H3 (ab1791; Abcam)


title: LNCaP_BRG1_Vehicle_ChIPSeq

tag: cell line

value: BRG1 (Santa Cruz, H-88)


title: Xins fraction from Mbnl knocked down worms, rep 1

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

data_processing:
We used the transcriptome from downloaded from http://planmine.mpi-cbg.de/.
To calculate the effective number of unique mappable positions in each transcript (i.e. the effective length) we performed the following steps. For each read length k, we extracted the L-k+1 (L being the transcript length) k-mer sequences from each canonical transcript and then aligned the full set of k-mers against the respective genome using Bowtie, allowing for a maximum of two mismatches. k-mers with no or one unique genomic alignment were then likewise aligned back to the canonical transcriptome. For each transcript, the number of such k-mers having a unique transcriptomic alignment was determined. This corresponds to the transcript’s effective number of unique mappable positions for k-mer mRNA-Seq reads. For each sample, the corresponding mRNA-Seq data were aligned against the respective genome using Bowtie, allowing for a maximum of two mismatches. Reads with one unique genomic alignment were then aligned against the canonical transcriptome and, for each transcript, the number of reads with one unique transcriptomic alignment were counted. Gene expression levels were determined as reads per thousand mappable positions of target transcript sequence per million of reads, where the reads uniquely align to the analyzed transcriptome. This procedure for estimating gene expression levels is a corrected version of the widely used RPKM (reads per kilobase of target transcript sequence per million of total reads) metric, and is referred to as “cRPKM” [Labbe RM et al. Stem Cells (2012)].
Genome_build: smed v3.1
Supplementary_files_format_and_content: Tab-delimited text files include cRPKM values (as defined above), as well as the total read count for each gene's canonical transcript

organism: Schmidtea mediterranea

source_name: Xins cell fraction

extract_protocol:
Trizol LS (Ambion) following manufacturer instructions
TruSeq RNA v2 (Illumina)

treatment_protocol: Animals were injected with dsRNA against the coding region of the gene of interest (control(RNAi) planarians were injected with dsRNA coding for GFP) for 3 consecutive days (days 1, 2 and 3 after RNAi) and kept at 20ºC. dsRNAs were delivered at a concentration of 1µg/µl. When multiple dsRNAs were used simultaneously, each dsRNA was injected at a concentration of 1µg/µl in the same solution

tag: experiment

value: Mbnl siRNA

tag: cellular fraction

value: Xins cell fraction

value: Berlin-1 strain asexual type


title: Xins fraction from control worms, rep 2

value: Control (GFP siRNA)


title: Xins fraction from bruli knocked down worms, rep 1

value: Bruli siRNA


title: Xins fraction from Mbnl knocked down worms, rep 2


title: Xins fraction from control worms, rep 1


title: Xins fraction from bruli knocked down worms, rep 2


title: X2 fraction from Mbnl knocked down worms, rep 1

source_name: X2 cell fraction

value: X2 cell fraction


title: X1 fraction from wild type worms

source_name: X1 cell fraction

value: Wild type

value: X1 cell fraction


title: X1 fraction from Mbnl knocked down worms, rep 1


title: X1 fraction from Mbnl knocked down worms, rep 2


title: Whole worm treated with dsRNA against Rbfox1

source_name: Whole worm

value: Rbfox1 siRNA

value: Whole worm


title: Whole worm treated with dsRNA against Ptbp genes

value: Ptbp siRNA


title: X1 fraction from control worms, rep 1


title: Whole worm treated with dsRNA against Esrp genes

value: Esrp siRNA


title: X1 fraction from bruli knocked down worms, rep 1


title: Whole worm treated with dsRNA against GFP


title: X1 fraction from control worms, rep 2


title: Xins fraction from wild type worms, rep 2


title: Whole worm treated with dsRNA against Rbfox genes

value: RbfoxS siRNA


title: Whole worm treated with dsRNA against Mbnl genes


title: Whole worm treated with dsRNA against Nova genes

value: Nova siRNA


title: Whole worm treated with dsRNA against bruli


title: smedwi2

city: Berlin

first: Marta

last: Rodriguez Orejuela

address: Robert-Roessle str. 10 (H. 87)

department: Berlin Institute for Medical Systems Biology

institute: Max Delbruck Centrum

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion with CASAVA-1.8.2
Adapter removal with Flexbar v2.5
Alignment to platyhelminthes rRNA reference using bowtie2 v2.1.0
Map non-rRNA reads to planarian transcriptome (see Suppl. Methods) with bowtie2 v2.1.0
Count aligned reads per transcript with htseq-count v0.6.1p1.
Transcript per million calculation using a custom python script
Genome_build: Schmidtea mediterranea transcriptome (“dresden”)
Supplementary_files_format_and_content: tab-delimited text file with TPM values for each Sample

extract_protocol:
Trizol (see Suppl. Methods)
TruSeq RNA v2 (Illumina)

treatment_protocol: RNAi (see Suppl. Methods)

tag: developmental stage

value: Adult

tag: RNAi

tag: tissue


title: smedH2B


title: X2 fraction from wild type worms


title: gfp_d30

description: gfp(RNAi)

source_name: control(RNAi) Day 30

value: gfp(RNAi)


title: X2 fraction from control worms, rep 1


title: mbnl_d30

description: Smed-mbnl-1;Smed-mbnl-like-1, -2, -3(RNAi)

source_name: mbnl(RNAi) Day 30


title: gfp_d20

description: gfp(RNAi)

source_name: control(RNAi) Day 20


title: VCaP-LTAD vehicle

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
The illumina hiseq2000-generated RNA-Seq reads was in 50 bp length and an initial filtering process was taken to remove any non-desirable contamination sequences.
The reads were mapped to the human Noncode v4 or GENCODE v19 lncRNA database.
The expression levels of mapped transcripts were normalized into transcript parts per kilobase of exon model per million mapped reads (PRKM) to faciliate comparison among different samples.
Genome_build: hg19

source_name: VCaP-LTAD vehicle 24 h treatment

growth_protocol: LNCaP cells were cultured in RPMI 1640 containing 10% FBS.  Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days. VCaP cells were cultured in DMEM containing 10% FBS.  Before hormone treatment, cells were incubated in DMEM containing 2.5% charcoal/dextran treated FBS for three days. LTAD and VCaP -LTAD cells were cultured in phenol red free medium supplemented with 10 % charcol dextran treated FBS.

extract_protocol:
Total RNA was extracted using ISOGEN reagent.
RNA sequencing (RNA-seq) library construction and sequencing was performed according to the manufacturer’s protocol (OP-Hiseq2000-sequencing-cBot-v3.0.) for hiseq2000.

treatment_protocol: Cells were treated with siControl or siAR (10 nM) for 48 h and then treated with Et or 10 nM dihydrotestosterone (DHT) for 24 h.

value: VCaP-LTAD cells

value: prostate cancer


title: VCaP-LTAD DHT

source_name: VCaP-LTAD DHT 24 h treatment


title: VCaP DHT + Bicalutamide treated

source_name: VCaP DHT + Bicalutamide 24 h treatment

value: VCaP cells


title: VCaP vehicle + siAR

source_name: VCaP vehicle + siAR 24 h treatment


title: mbnl_d25

source_name: mbnl(RNAi) Day 25


title: Whole worm treated with dsRNA against Celf genes

value: Celf siRNA

value: Berlin-1 strain asexual type


title: Xins fraction from wild type worms, rep 1

value: Xins cell fraction


title: VCaP DHT + siAR

source_name: VCaP DHT + siAR 24 h treatment


title: LTAD DHT

source_name: LTAD DHT 24 h treatment

value: LTAD cells


title: bruli_d25

description: Smed-bruno-like(RNAi)

source_name: bruli(RNAi) Day 25

value: Smed-bruno-like(RNAi)


title: VCaP vehicle treatment

source_name: VCaP vehicle 24 h treatment


title: bruli_d30

description: Smed-bruno-like(RNAi)

source_name: bruli(RNAi) Day 30


title: mbnl_d20

source_name: mbnl(RNAi) Day 20


title: LTAD vehicle

source_name: LTAD vehicle  24 h treatment


title: LNCaP vehicle + siAR

source_name: LNCaP vehicle + siAR 24h treatment

value: LNCaP cells


title: bruli_d20

description: Smed-bruno-like(RNAi)

source_name: bruli(RNAi) Day 20


title: VCaP DHT treated

source_name: VCaP DHT treated for 24 h


title: LNCaP DHT + siAR

source_name: LNCaP DHT + siAR 24 h treatment


title: X1 fraction from bruli knocked down worms, rep 2

source_name: X1 cell fraction

value: Bruli siRNA

value: X1 cell fraction


title: LNCaP DHT treated

source_name: LNCaP DHT treated for 24 h


title: X2 fraction from bruli knocked down worms, rep 1

source_name: X2 cell fraction

value: X2 cell fraction


title: LNCaP DHT + Bicalutamide treated

source_name: LNCaP DHT + Bicalutamide 24 h treatment


title: gfp_d25

description: gfp(RNAi)

source_name: control(RNAi) Day 25

value: Whole worm


title: LNCaP vehicle treatment

source_name: LNCaP vehicle 24h treatment


title: S3

city: Guangzhou

first: Zhaofeng

last: Huang

state: Guangdong

address: 74# zhongshan 2nd Road

department: Zhongshan School of Medicine

institute: Sun Yat-sen University

description: DNA isolated from human sperm without selection

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the hg18 genome assembly using Rsubread R package
peaks were called using MACS  version 2. 0. 9 with the  setting  pvalue < 0.05. different peaks were compared between sample with or without selection
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files with significant different peak

source_name: nucleasome DNA from subject 3 sperm cell

extract_protocol:
Sperm is washed with PBS for twice and resuspended in a lysis buffer contaning NP-40 and sodium deoxycholate. Mnase was added to digest genomic DNA without the protection of histone. Sooluble chromatin fraction can be isolated upon centrifugation. DNA is obtained by phenol/chroloform extraction after treatment with RnaseA and proteinase K. DNA is size-selected by 5% agrose-gel electrophoresis to ensure the use of mononuclesomal DNA(150bp) in the preparation of sequecing libraries.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~150 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: sample type

value: nucleosome DNA

value: sperm


title: PS2

description: DNA isolated from human sperm after density selection

source_name: nucleasome DNA from subject 2 sperm cell after density selection


title: S1

source_name: nucleasome DNA from subject 1 sperm cell


title: Human set 5 36S H3

description:
Homer_human_set5_pos.txt
Homer_human_set5_neg.txt

source_name: AML cells

tag: genotype

tag: antibody

value: H3 (ab1791; Abcam)


title: PS1

source_name: nucleasome DNA from subject 1 sperm cell after density selection

tag: cell type


title: Human set 5 36N H3


title: Human set 4 36N H3

description:
Homer_human_set4_pos.txt
Homer_human_set4_neg.txt


title: Human set 4 36S H3K9Ac

value: H3K9Ac (ab4441; Abcam)


title: Human set 5 36S H3K9Ac


title: ribosomal RNA depleted total RNA from WRR-1 argonaute-3 knock-down cells, replicate 2

description:
rRNA depleted
average insert size: ~350bp
ago3KD_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.

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 argonaute 3 using Effectene (Qiagen); RNA was collected after 5 days.

value: WRR-1 cells

tag: treatment

value: dsRNA treated 5 days

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


title: Human set 5 36N H3K9Ac


title: ribosomal RNA depleted total RNA from WRR-1 argonaute 3 knock-down cells, replicate 2

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


title: Human set 4 36S H3


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

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

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


title: ribosomal RNA depleted total RNA from WRR-1 argonaute 3 knock-down cells, replicate 1


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

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

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


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

description:
rRNA depleted
average insert size: ~350bp

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


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

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

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


title: ribosomal RNA depleted total RNA from WRR-1 cells P154, replicate 1

value: Passage 154


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


title: PS3

source_name: nucleasome DNA from subject 3 sperm cell after density selection


title: ribosomal RNA depleted total RNA from RasV12 (R7) cells

source_name: RasV12 (R7) cells

value: RasV12 cells (R7)

value: Passage 68

value: w1118; Act5C-GAL4,UAS-RasV12 cells (R7)


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


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


title: ribosomal RNA depleted total RNA from WRR-1 argonaute-3 knock-down cells, replicate 1


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


title: ribosomal RNA depleted total RNA from WRR-1 cells P154, replicate 2


title: ribosomal RNA depleted total RNA from Wts-RNAi, RasV12 whole ovaries

source_name: UAS-wts-RNAi, UAS-RasV12 adult ovary

growth_protocol: Ovaries were collected from 3-5 day-old females reared at 25oC in standard conditions.

value: Adult female ovary, no treatment, no GAL4 activation

value: w1118; UAS-Wts-RNAi,UAS- RasV12


title: ribosomal RNA depleted total RNA from OSS cells

source_name: OSS cells

value: ovarian somatic sheath cells (OSS)

value: no treatment

value: w[1118]; P [w+ hsp-70 bam+] 11-d bam[D86] ry e/d bam[D86] P[ovo-lacZ) P[vas-egfp]


title: ribosomal RNA depleted total RNA from RasV12 (R3) cells

source_name: RasV12 (R3) cells

value: RasV12 cells (R3)

value: Passage 77

value: w1118; Act5C-GAL4,UAS-RasV12 cells (R3)


title: S2

source_name: nucleasome DNA from subject 2 sperm cell

value: nucleosome DNA

value: sperm


title: CXCR5-P14 #2

status: Public on Jul 31 2016

city: Clayton

first: Yew Ann

last: Leong

state: Victoria

address: Wellington Road

department: BIochemistry

institute: Monash University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed with Trimmomatic-0.32 using a leading and trailling quality cutoff of 24.
Trim_galore using a stringency of 3 to trim illumina adaptors.
The reads were mapped to the mm10 reference genome using STAR.
Reads were assigned to transcripts using HTSeq version 0.6.0 using the default setting.
Genome_build: Mus Musculus.GRCm38.75.
Supplementary_files_format_and_content: dyu_counts.txt

source_name: splenic CD8+ T cells

extract_protocol:
Spleens were collected from infected mice to prepare single cell suspension. Target cells of interest were then sorted using flow cytometry and RNA was extracted using RNAeasy Kit from Qiagen.
PolyA RNA seq libraries prepared using Ilumina Stranded Sample prep, Protocol 15031047 RevD Sept 2012.
c-bot clustering using 12pM of library pool. Illumina Protocol 15006165 Rev K Oct 2012.

tag: infection

value: Infected

tag: cxcr5 expression

tag: activation

value: Activated CD44+


title: siProxSC_III.bam

city: Warsaw

first: Katarzyna

last: Paczkowska

address: Roentgena 5

department: Department of Genetics

country: Poland

institute: Cancer Center - Institute

data_processing:
Raw reads were processed by Torrent Suite analysis pipeline and mapped to human genome assembly hg19 AmpliSeqTranscriptome version by TMAP.
Reads corresponding to each gene were counted with htseq-count (PMID:25260700).
Normalization and differential expression were conducted by DESeq2 (PMID:25516281), using default parameters and options.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated values file with DESeq2 output for each gene comparing expression in two groups

source_name: CGTH-W-1_PROX1 siRNA (Scruz)

growth_protocol: CGTH-W-1 cell line (German Collection of Microorganisms and Cell Cultures, DSMZ no. ACC 360) was cultured in RPMI-1640 supplemented with 10% FBS (Gibco).

extract_protocol:
RNA was isolated with GeneMATRIX Universal RNA Purification Kit, (cat. no. E3598, EURx), and RNA integrity was assessed using Agilent RNA 6000 Nano Kit on Agilent 2100 Bioanalyzer. All transfections were performed in three independent replicates, numbered I, II and III. Efficacy of PROX1 knockdown was measured with RT-qPCR using specific primers (forward 5'-CCAGCTCCAATATGCTGAAGACCTA-3'; reverse 5'-CATCGTTGATGGCTTGACGTG-3') and Sybr Green chemistry.
RNA was subjected to library preparation using Ion AmpliSeq Transcriptome Human Gene Expression Panel, according to manufacturer's protocol. Briefly, RNA was reverse transcribed and cDNA subjected to multiplex PCR reaction to amplify parts of targeted transcripts. Amplicons were then partially digested at primer sequences followed by adapters ligation to amplicons and purification on AMPure® XP beads. Resulting library was  quantified on Bioanalyzer 2100 and diluted to ~100 pM prior to template preparation. Up to eight barcoded libraries were subjected to automated template preparation with Ion PI IC 200 Kit on the Ion Chef Instrument, which performs emulsion PCR on Ion Sphere particles (ISPs), followed by ISPs recovery and template loading on a PI chip. Barcoded RNA-Seq libraries samples were sequenced on a PI chip using the sequencing reagents provided as part of the Ion PI IC 200 Kit, according to the manufacturer’s instructions.

treatment_protocol: Cells were transfected either with non-targeting MISSION® siRNA Universal Negative Control (Sigma Aldrich, cat. no. SIC001) [siNEG-samples] or two PROX1 specific siRNA: 1) Sigma-Aldrich - cat. no. EHU053851 [siProxSig-samples] and 2)  Santa Cruz - cat. no. sc-106451 [siProxSC-samples] in a presence of Lipofectamine 2000 (LifeTechnologies, cat. no.11668-019). Treatment of cells with Lipofectamine 2000 alone was also performed [lipo-samples]. 48 hours later cells were harvested.

value: follicular thyroid carcinoma cells

tag: treated with

value: PROX1 siRNA (Scruz)


title: Naïve P14 #2

value: Uninfected

value: Naïve CD44-CD62L+


title: CXCR5+P14 #2


title: CXCR5-P14 #3


title: Naïve P14 #1


title: Human set 4 36N H3K9Ac

value: H3K9Ac (ab4441; Abcam)


title: siProxSC_II.bam


title: siProxSC_I.bam


title: CXCR5+P14 #3


title: CXCR5+P14 #1


title: siProxSig_I.bam

source_name: CGTH-W-1_PROX1 siRNA (Sigma)

value: PROX1 siRNA (Sigma)


title: CXCR5-P14 #1


title: siProxSig_III.bam


title: siNeg_III.bam

source_name: CGTH-W-1_non-targeting siRNA

value: non-targeting siRNA


title: siNeg_I.bam


title: lipo_I.bam

value: Lipofecatmine


title: siProxSig_II.bam


title: singles-PB1022-mono-160128-94

status: Public on Jul 30 2016

first: Jason

middle: Daniel

last: Buenrostro

address: 415 Main Street

institute: Broad Institute

description: Sample 382

data_processing:
library strategy: scATAC-seq
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 or mm10 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools. Reads were subsequently filtered for alignment quality of >Q30 and were required to be properly paired. Reads mapping to the mitochondria, unmapped contigs and chromosome Y were removed and not considered.
Genome_build: hg19
Supplementary_files_format_and_content: All samples supplied as a count table for all called regulatory elements.

source_name: Monocyte

extract_protocol:
Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips. Cells were permeabilized and accessible fragments were captured using 20 µL of Tn5 transposition mix (1.5x TD buffer, 1.5 µL transposease (Nextera DNA Sample Prep Kit, Illumina), 1x C1 Loading Reagent with low salt (Fluidigm), and 0.15% NP40) at 30 minutes at 37°C.
In a 96-well plate, 10 µL of harvested libraries were amplified in 50 µL PCR for an additional 14 cycles (1.25 µM custom Nextera dual-index PCR primers (Supplementary Table 1) in 1x NEBnext High-Fidelity PCR Master Mix) using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. The PCR products were pooled creating a final volume of ~4.8 mL. The pooled library was purified on a single MinElute PCR purification column (Qiagen) yielding libraries at an approximate concentration of ~1 µM. Libraries were quantified using qPCR prior to sequencing.

value: Monocyte

tag: doner id


title: singles-PB1022-mono-160128-96

description: Sample 384


title: singles-PB1022-mono-160128-95

description: Sample 383


title: lipo_III.bam


title: singles-PB1022-mono-160128-93

description: Sample 381


title: singles-PB1022-mono-160128-92

description: Sample 380


title: singles-PB1022-mono-160128-89

description: Sample 377


title: singles-PB1022-mono-160128-87

description: Sample 375


title: singles-PB1022-mono-160128-88

description: Sample 376


title: singles-PB1022-mono-160128-84

description: Sample 372


title: singles-PB1022-mono-160128-83

description: Sample 371


title: singles-PB1022-mono-160128-90

description: Sample 378


title: singles-PB1022-mono-160128-91

description: Sample 379


title: singles-PB1022-mono-160128-82

description: Sample 370


title: singles-PB1022-mono-160128-81

description: Sample 369


title: singles-PB1022-mono-160128-80

description: Sample 368


title: siNeg_II.bam


title: singles-PB1022-mono-160128-75

description: Sample 363


title: singles-PB1022-mono-160128-76

description: Sample 364


title: singles-PB1022-mono-160128-78

description: Sample 366


title: singles-PB1022-mono-160128-77

description: Sample 365


title: singles-PB1022-mono-160128-79

description: Sample 367


title: lipo_II.bam


title: singles-PB1022-mono-160128-74

description: Sample 362


title: singles-PB1022-mono-160128-71

description: Sample 359


title: singles-PB1022-mono-160128-70

description: Sample 358


title: singles-PB1022-mono-160128-69

description: Sample 357


title: singles-PB1022-mono-160128-68

description: Sample 356


title: singles-PB1022-mono-160128-67

description: Sample 355


title: singles-PB1022-mono-160128-64

description: Sample 352


title: singles-PB1022-mono-160128-63

description: Sample 351


title: singles-PB1022-mono-160128-86

description: Sample 374


title: singles-PB1022-mono-160128-85

description: Sample 373


title: singles-PB1022-mono-160128-62

description: Sample 350


title: singles-PB1022-mono-160128-60

description: Sample 348


title: singles-PB1022-mono-160128-61

description: Sample 349


title: singles-PB1022-mono-160128-58

description: Sample 346


title: singles-PB1022-mono-160128-57

description: Sample 345


title: singles-PB1022-mono-160128-65

description: Sample 353


title: singles-PB1022-mono-160128-55

description: Sample 343


title: singles-PB1022-mono-160128-51

description: Sample 339


title: singles-PB1022-mono-160128-73

description: Sample 361


title: singles-PB1022-mono-160128-48

description: Sample 336


title: singles-PB1022-mono-160128-52

description: Sample 340


title: singles-PB1022-mono-160128-72

description: Sample 360


title: singles-PB1022-mono-160128-49

description: Sample 337


title: singles-PB1022-mono-160128-50

description: Sample 338


title: singles-PB1022-mono-160128-47

description: Sample 335


title: singles-PB1022-mono-160128-53

description: Sample 341


title: singles-PB1022-mono-160128-46

description: Sample 334


title: singles-PB1022-mono-160128-42

description: Sample 330


title: singles-PB1022-mono-160128-45

description: Sample 333


title: singles-PB1022-mono-160128-44

description: Sample 332


title: singles-PB1022-mono-160128-43

description: Sample 331


title: singles-PB1022-mono-160128-40

description: Sample 328


title: singles-PB1022-mono-160128-39

description: Sample 327


title: singles-PB1022-mono-160128-59

description: Sample 347


title: singles-PB1022-mono-160128-38

description: Sample 326


title: singles-PB1022-mono-160128-37

description: Sample 325


title: singles-PB1022-mono-160128-36

description: Sample 324


title: singles-PB1022-mono-160128-54

description: Sample 342


title: singles-PB1022-mono-160128-33

description: Sample 321


title: singles-PB1022-mono-160128-32

description: Sample 320


title: singles-PB1022-mono-160128-30

description: Sample 318


title: singles-PB1022-mono-160128-66

description: Sample 354


title: singles-PB1022-mono-160128-31

description: Sample 319


title: singles-PB1022-mono-160128-34

description: Sample 322


title: singles-PB1022-mono-160128-28

description: Sample 316


title: singles-PB1022-mono-160128-25

description: Sample 313


title: singles-PB1022-mono-160128-26

description: Sample 314


title: singles-PB1022-mono-160128-24

description: Sample 312


title: singles-PB1022-mono-160128-29

description: Sample 317


title: singles-PB1022-mono-160128-23

description: Sample 311


title: singles-PB1022-mono-160128-27

description: Sample 315


title: singles-PB1022-mono-160128-41

description: Sample 329


title: singles-PB1022-mono-160128-22

description: Sample 310


title: singles-PB1022-mono-160128-21

description: Sample 309


title: singles-PB1022-mono-160128-20

description: Sample 308


title: singles-PB1022-mono-160128-18

description: Sample 306


title: singles-PB1022-mono-160128-16

description: Sample 304


title: singles-PB1022-mono-160128-17

description: Sample 305


title: singles-PB1022-mono-160128-19

description: Sample 307


title: singles-PB1022-mono-160128-15

description: Sample 303


title: singles-PB1022-mono-160128-35

description: Sample 323


title: singles-PB1022-mono-160128-13

description: Sample 301


title: singles-PB1022-mono-160128-12

description: Sample 300


title: singles-PB1022-mono-160128-11

description: Sample 299


title: singles-PB1022-mono-160128-56

description: Sample 344


title: singles-PB1022-mono-160128-10

description: Sample 298


title: singles-PB1022-mono-160128-14

description: Sample 302


title: singles-PB1022-mono-160128-9

description: Sample 297


title: singles-PB1022-mono-160128-7

description: Sample 295


title: singles-PB1022-mono-160128-3

description: Sample 291


title: singles-PB1022-mono-160128-6

description: Sample 294


title: singles-PB1022-mono-160128-2

description: Sample 290


title: singles-PB1022-mono-160128-8

description: Sample 296


title: singles-PB1022-mono-160128-5

description: Sample 293


title: singles-PB1022-mono-160128-1

description: Sample 289


title: BM1077-LMPP-Frozen-160107-96

description: Sample 288

source_name: LMPP

value: lymphoid primed multipotent progenitor


title: BM1077-LMPP-Frozen-160107-94

description: Sample 286


title: BM1077-LMPP-Frozen-160107-92

description: Sample 284


title: BM1077-LMPP-Frozen-160107-91

description: Sample 283


title: singles-PB1022-mono-160128-4

description: Sample 292


title: BM1077-LMPP-Frozen-160107-89

description: Sample 281


title: BM1077-LMPP-Frozen-160107-93

description: Sample 285


title: BM1077-LMPP-Frozen-160107-86

description: Sample 278


title: BM1077-LMPP-Frozen-160107-87

description: Sample 279


title: BM1077-LMPP-Frozen-160107-85

description: Sample 277


title: BM1077-LMPP-Frozen-160107-90

description: Sample 282


title: BM1077-LMPP-Frozen-160107-83

description: Sample 275


title: BM1077-LMPP-Frozen-160107-80

description: Sample 272


title: BM1077-LMPP-Frozen-160107-82

description: Sample 274


title: BM1077-LMPP-Frozen-160107-81

description: Sample 273


title: BM1077-LMPP-Frozen-160107-79

description: Sample 271


title: BM1077-LMPP-Frozen-160107-78

description: Sample 270


title: BM1077-LMPP-Frozen-160107-77

description: Sample 269


title: BM1077-LMPP-Frozen-160107-75

description: Sample 267


title: BM1077-LMPP-Frozen-160107-95

description: Sample 287


title: BM1077-LMPP-Frozen-160107-74

description: Sample 266


title: BM1077-LMPP-Frozen-160107-76

description: Sample 268


title: BM1077-LMPP-Frozen-160107-72

description: Sample 264


title: BM1077-LMPP-Frozen-160107-73

description: Sample 265


title: BM1077-LMPP-Frozen-160107-66

description: Sample 258


title: BM1077-LMPP-Frozen-160107-67

description: Sample 259


title: BM1077-LMPP-Frozen-160107-70

description: Sample 262


title: BM1077-LMPP-Frozen-160107-59

description: Sample 251


title: BM1077-LMPP-Frozen-160107-71

description: Sample 263


title: BM1077-LMPP-Frozen-160107-88

description: Sample 280


title: BM1077-LMPP-Frozen-160107-63

description: Sample 255


title: BM1077-LMPP-Frozen-160107-64

description: Sample 256


title: BM1077-LMPP-Frozen-160107-55

description: Sample 247


title: BM1077-LMPP-Frozen-160107-61

description: Sample 253


title: BM1077-LMPP-Frozen-160107-84

description: Sample 276


title: BM1077-LMPP-Frozen-160107-62

description: Sample 254


title: BM1077-LMPP-Frozen-160107-57

description: Sample 249


title: BM1077-LMPP-Frozen-160107-58

description: Sample 250


title: BM1077-LMPP-Frozen-160107-54

description: Sample 246


title: BM1077-LMPP-Frozen-160107-49

description: Sample 241


title: BM1077-LMPP-Frozen-160107-53

description: Sample 245


title: BM1077-LMPP-Frozen-160107-69

description: Sample 261


title: BM1077-LMPP-Frozen-160107-52

description: Sample 244


title: BM1077-LMPP-Frozen-160107-51

description: Sample 243


title: BM1077-LMPP-Frozen-160107-50

description: Sample 242


title: BM1077-LMPP-Frozen-160107-47

description: Sample 239


title: BM1077-LMPP-Frozen-160107-48

description: Sample 240


title: BM1077-LMPP-Frozen-160107-41

description: Sample 233


title: BM1077-LMPP-Frozen-160107-56

description: Sample 248


title: BM1077-LMPP-Frozen-160107-45

description: Sample 237


title: BM1077-LMPP-Frozen-160107-46

description: Sample 238


title: BM1077-LMPP-Frozen-160107-39

description: Sample 231


title: BM1077-LMPP-Frozen-160107-40

description: Sample 232


title: BM1077-LMPP-Frozen-160107-38

description: Sample 230


title: BM1077-LMPP-Frozen-160107-65

description: Sample 257


title: BM1077-LMPP-Frozen-160107-36

description: Sample 228


title: BM1077-LMPP-Frozen-160107-60

description: Sample 252


title: BM1077-LMPP-Frozen-160107-68

description: Sample 260


title: BM1077-LMPP-Frozen-160107-33

description: Sample 225


title: BM1077-LMPP-Frozen-160107-34

description: Sample 226


title: BM1077-LMPP-Frozen-160107-37

description: Sample 229


title: BM1077-LMPP-Frozen-160107-35

description: Sample 227


title: BM1077-LMPP-Frozen-160107-31

description: Sample 223


title: BM1077-LMPP-Frozen-160107-32

description: Sample 224


title: BM1077-LMPP-Frozen-160107-28

description: Sample 220


title: BM1077-LMPP-Frozen-160107-26

description: Sample 218


title: BM1077-LMPP-Frozen-160107-25

description: Sample 217


title: BM1077-LMPP-Frozen-160107-29

description: Sample 221


title: BM1077-LMPP-Frozen-160107-23

description: Sample 215


title: BM1077-LMPP-Frozen-160107-43

description: Sample 235


title: BM1077-LMPP-Frozen-160107-42

description: Sample 234


title: BM1077-LMPP-Frozen-160107-22

description: Sample 214


title: BM1077-LMPP-Frozen-160107-21

description: Sample 213


title: BM1077-LMPP-Frozen-160107-20

description: Sample 212


title: BM1077-LMPP-Frozen-160107-44

description: Sample 236


title: BM1077-LMPP-Frozen-160107-19

description: Sample 211


title: BM1077-LMPP-Frozen-160107-17

description: Sample 209


title: BM1077-LMPP-Frozen-160107-15

description: Sample 207


title: BM1077-LMPP-Frozen-160107-18

description: Sample 210


title: BM1077-LMPP-Frozen-160107-13

description: Sample 205


title: BM1077-LMPP-Frozen-160107-27

description: Sample 219


title: BM1077-LMPP-Frozen-160107-14

description: Sample 206


title: BM1077-LMPP-Frozen-160107-30

description: Sample 222


title: BM1077-LMPP-Frozen-160107-6

description: Sample 198


title: BM1077-LMPP-Frozen-160107-9

description: Sample 201


title: BM1077-LMPP-Frozen-160107-12

description: Sample 204


title: BM1077-LMPP-Frozen-160107-7

description: Sample 199


title: BM1077-LMPP-Frozen-160107-10

description: Sample 202


title: BM1077-LMPP-Frozen-160107-5

description: Sample 197


title: BM1077-LMPP-Frozen-160107-2

description: Sample 194


title: BM1077-LMPP-Frozen-160107-24

description: Sample 216


title: BM1077-LMPP-Frozen-160107-1

description: Sample 193


title: singles-SU353-LSC-160209-96

description: Sample 192

source_name: LSC

value: acute myeloid leukemia, leukmeia stem cell


title: BM1077-LMPP-Frozen-160107-3

description: Sample 195


title: BM1077-LMPP-Frozen-160107-16

description: Sample 208


title: singles-SU353-LSC-160209-95

description: Sample 191


title: singles-SU353-LSC-160209-93

description: Sample 189


title: singles-SU353-LSC-160209-92

description: Sample 188


title: singles-SU353-LSC-160209-91

description: Sample 187


title: singles-SU353-LSC-160209-90

description: Sample 186


title: BM1077-LMPP-Frozen-160107-4

description: Sample 196


title: singles-SU353-LSC-160209-88

description: Sample 184


title: singles-SU353-LSC-160209-89

description: Sample 185


title: BM1077-LMPP-Frozen-160107-11

description: Sample 203


title: singles-SU353-LSC-160209-86

description: Sample 182


title: BM1077-LMPP-Frozen-160107-8

description: Sample 200


title: singles-SU353-LSC-160209-94

description: Sample 190


title: singles-SU353-LSC-160209-76

description: Sample 172