title: mRNA-seq PP242 Replicate 2

city: Baltimore

first: Mallory

middle: Ann

last: Freeberg

state: MD

address: 3400 N Charles St

department: Department of Biology

institute: Johns Hopkins University

description: mRNA quantification

data_processing:
mRNA quantification (mRNA-seq): Transcript abundances in each library were normalized to the total number of mapped reads (up to 1 mismatch) in millions and to the length (in kilobases) of each transcript to generated RPKM values. Reads mapping to the same genomic locus but to more than 1 transcript were evenly divided across all transcripts.
Binding site generation (PAR-CLIP):Overlapping reads with 0-2 T-to-C mismatches were clustered into peaks. Peaks were smoothed with a Gaussian smoothing technique described in Freeberg et al. (2013). Peaks with at least 1 T-to-C conversion event were kept as LARP1 binding sites. Read counts were summed per binding site, normalized to the number of million mapped reads per library, normalized to the gene RPKM value, and multiplied by 1,000 to account for the kilobase normalization of gene RPKM values.

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured in DMEM with 10% fetal bovine serum and 100 units/ml penicillin/streptomycin.

extract_protocol:
Total RNAs were extracted with acid-phenol:chloroform, pH 4.5 with isoamyl alcohol, 25:24:1. Replicate, strand-specific total mRNA-seq libraries were prepared in parallel using the two-linker ligation protocol as described in Levin et al. Nat Methods 2010 (PMID: 20711195).
RNA pellets were air-dried briefly, resuspended in 10 µL of PNK mix (70mM Tris pH 7.6, 10mM MgCl2, 5mM DTT, 1mM ATP, 1U/µL T4 polynucleotide kinase, 1U/µL SUPERase·In), and incubated at 37°C for 30 min. The reaction was combined with 90µL H2O and 100µL Phenol:Chloroform:Isoamyl Alcohol 25:24:1, mixed well, and spun for 5 min at 20,000Xg. The liquid phase was mixed with 12.5µL of 3M NaOAc, 250µL of 100% ethanol, 1µL of 15mg/mL glycoblue and precipitated for 2 hr at -80°C. RNAs were collected by centrifugation for 20 min at 20,000Xg at room temperature, followed by 2 washes with cold 75% ethanol. RNA pellets were resuspended in 10µL of ligation mix (50mM Tris pH 7.5, 10mM MgCl2, 10mM DTT, 1mM ATP, 0.1mg/mL BSA, 2µM 5’RNA linker, 1U/µL T4 RNA ligase, 1U/µL SUPERase•In, 10% DMSO) and incubated at 15°C for 2 hr. Ligation reaction was terminated by adding 10µL of 2X formamide gel loading buffer, heated for 2 min at 70°C, and then quickly chilled on ice. Samples were loaded onto a 6% TBE UREA gel and run at 150 V for 45 min. After staining with 1X Sybr Gold Stain, a gel piece corresponding to 70-90nt RNA (80-100nt ssDNA) was excised, crushed, and soaked in 400µL of 0.3M NaOAc overnight at room temperature. After removing gel pieces, the solution was combined with 1mL of 100% EtOH and 1µL of 15mg/mL glycoblue and precipitated for 2 hr at -80°C. RNAs were collected by centrifugation for 20 min at 20,000Xg at room temperature, followed by two washes with cold 75% ethanol. After brief drying, RNAs were resuspended in 15µL of H2O. 10μL of ligated RNA was combined with 2μL of 5µM RT primer, heated at 65°C for 5 min, and then quickly chilled on ice, followed by the addition of 1µL 10mM dNTP, 1μL of 0.1 M DTT, 4μL of 5X First strand buffer, 1μL of SUPERase•In (20 U/µL) and 1 µL of SuperScript III Reverse transcriptase (200 U/µL). RT reaction was kept at 50°C for 45 min, 55°C for 15 min and 90°C for 5 min. A test PCR was performed with 2.5 µL of RT product in 50 µL PCR mix: 1X AccuPrime PCR buffer I, 0.5 µM P5 long primer, 0.5 µM P7 primer, 0.2 µL AccuPrime Taq High Fidelity (5 U/µL). PCR was carried out with an initial 3 min denaturation at 98°C, followed by 14-22 cycles of 80 sec denaturation at 98°C, 90 sec annealing and extension at 65°C, and termination with a final 5 min extension at 65°C. 15 µL PCR product was collected after 14, 18, and 22 cycles and analyzed on a 10% TBE gel at 150 V for 1 hr to determine the optimal amplification cycles (the lowest cycle number required to generate 96-116 bp amplicons detected by Sybr Gold staining). A 50 µL PCR reaction was carried out with the determined cycle number. Amplicons were purified using DNA clean and concentrator-5, run on 10% TBE gels at 150 V for 1 hr and stained with Sybr Gold. A gel piece corresponding to 96-116 bp DNA was excised, crushed, and soaked overnight in 400 µL 0.3 M NaOAc at room temperature. After removing gel pieces, the solution was combined with 1 mL of 100% EtOH and 1 µL of 15 mg/mL glycoblue and precipitated for 2 hr at -80°C. DNAs were collected by centrifugation for 20 min at 20,000Xg at room temperature, followed by two washes with cold 75% ethanol. After brief drying, amplicons were resuspended in 20 μl of H2O. Purified amplicons (5 μl) were used to seed a second round of PCR in 50 μl: 1× Accu- Prime PCR buffer I, 0.5 μM Illumina Primer A, 0.5 μM Illumina Primer B, 0.2 μl AccuPirme Taq High Fidelity for 6 to 12 cycles. Second PCR amplicons were purified with DNA clean and concentrator-5.

treatment_protocol: In order to inhibit kinases involved in the PI3K pathway we treated cells with 2.5 μM PP242 for indicated times.

value: GGCTAC

value: TCGTATGCCGTCTTCTGCTTG

tag: 4-thiouracil addition?

value: No

tag: mtor inhibitor treatment?

value: Yes

tag: flowcell info id


title: mRNA-seq PP242 Replicate 1

status: Public on Jul 31 2014

type: SRA

country: USA

description: mRNA quantification

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

value: TAGCTT


title: TIC RNA-seq

city: Stanford

first: Andrew

last: Gentles

state: CA

address: 1201 Welch Road

institute: Stanford University

description: Tumor initiating cells

data_processing:
Bases were called using RTA 1.13.48, and reads were de-multiplexed using Casava 1.8.2
Reads were trimmed by 9bp at 5' end to remove Nugen primers using fastx-trimmer from the FastX toolkit
Alignment was performed to the mouse genome (UCSC mm9 assembly) using Tophat 1.4.0 with default parameters
Expression values (FPKM) were generated using Cufflinks and Cuffdiff with igenomes GTF gene models
Genome_build: UCSC mm9 Mus musculus
Supplementary_files_format_and_content: tab-delimited text file with FPKM values for each gene

molecule: total RNA

organism: Mus musculus

source_name: breast tumor initiating cells (TICs)

growth_protocol: Cells dissociated from tumors and immediately purified by FACS

extract_protocol:
Total RNA was extracted using RNeasy kit according to manufacturer's instruction (Qiagen, cat# 74004)
15 ng total RNA was amplified using the Ovation RNA-Seq System V2 (Nugen). 1 mg of resulting cDNA was fragmented (average size of 150-200 bases) and used to construct DNA libraries for sequencing using NEBNext DNA sample Prep Master Mix Set 1 (New England Biolabs, #E6040S).

tag: strain

value: FVB

tag: cell type

value: breast tumor initiating cells (TICs)


title: ESC.2

city: Boston

first: Robert

middle: E

last: Kingston

state: MA

address: 185 Cambridge Street

institute: Massachusetts General Hospital

description: protocol specific to mouse samples: Cells were pretreated with mild detergents (0.2% Tween-20 and 0.2% Triton X-100) for 5 minutes followed by crosslinking, mononucleosome sized DNA fragments were agarose gel extracted and pooled

library_source: genomic

data_processing:
50 bp reads aligned with Bowtie aligner v. 0.12.7
tag processing and filtering with the SPP workflow (Kharchenko 2008)
GC-correction coefficient for each read was computed in such a way that the resulting genome-wide distributions of GC-content become similar to the target 50%  GC-content distribution
Genome_build: mm9, hg19
Supplementary_files_format_and_content: space delimited text files containing locus and coverage

molecule: genomic DNA

source_name: cell line

extract_protocol:
Cells underwent a 1.1% formaldehyde treatment for 10 minutes to preserve chromatin structure. Nuclei were then prepared from the crosslinked cells and the chromatin treated with multiple micrococcal nuclease (MNase) concentrations for 15 minutes at room temperature. Nucleosome-sized fragments were isolated and sequenced
Illumina, limited rounds of PCR, as in PMID: 23837789

value: embryonic stem cells

tag: sample type

value: Mnase-digested DNA


title: mRNA-seq Basal Replicate 2

description: mRNA quantification

value: ACTTGA


title: mRNA-seq Basal Replicate 1

description: mRNA quantification

value: ATCACG


title: TZM-bl Uninfected Day 3 Small RNA Deep Sequencing

city: Durham

first: Adam

middle: Wesley

last: Whisnant

state: NC

address: 213 Research Drive 427 CARL Bldg

department: Molecular Genetics and Microbiology

institute: Duke University

description: Total size fractionated small RNA deep sequencing with the TruSeq kit

data_processing:
Casava1.8.2 software used for basecalling.
Reads <15nt were discarded, adaptors trimmed, and low quality reads discarded using the FastX tool kit and the following pipeline: fastq_quality_filter -Q33| fastq_to_fasta -Q33 | fastx_clipper -a TruSeq-Index#  -l 15 –c | fastx_collapser
Bowtie v.0.12.7, with the following options: –a --best --strata –m 25, was used to remove adapters and size-fractionation markers with no variant nucleotides for all libraries but the PAR-CLIP libraries.  The aforementioned parameters were kept throughout the pipline
Total small RNA and RISC RIP-Seq reads were sequentially filtered by aligning to the viral genome (1mismatch, negative sense alignments allowed), then human pre-miRNAs from miRbasev19 (1mismatch), EnsemblncRNAv70 Homo sapiens (1mismatch), fRNAdbv3.4 Homo sapiens (1mismatch), then human genome 19 (2mismatches, negative sense alignments allowed)
PAR-CLIP reads were aligned to a reference of the human genome combined with either the near-full length viral genome or the 3'LTR of each virus to avoid ambiguous alignments occuring with both annotated LTRs on the same sequence.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data are in a tab-delineated BED format presented as chromosome/gene, starting location for aligned read relative to the start of the gene beginning at 1, ending position of the aligned read, aligned reads per million of total library reads, and the strand (+ or -) that the read aligns to.  Processed data files include alignemnts to HIV,  miRbase human pre-miRNAs v19,  Ensembl human ncRNAs v70, fRNAdb human ncRNAs v3.4,  human genome 19 alignments,  human+viral genome PARCLIP alignments and human+viral genome Nef+U3 PARCLIP alignments.

source_name: TZM-bl Cell Line

growth_protocol: Dulbecco’s modified Eagle medium (DMEM) (Sigma) supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
TRI-zol, PAGE fractionation ~15-40nt
RNA libraries were prepared according to standard Illumina Truseq protocols

treatment_protocol: Total RNA was isolated using TRIzol. The RNA fraction containing ~15- to 30-nt-long RNAs was isolated by polyacrylamide gel electrophoresis (PAGE) purification on 15% Tris-borate-EDTA (TBE)-urea gels (Bio-Rad), electroeluted from the excised gel slice (gel eluter; Hoefer), and cloned with the Illumina small RNA Truseq kit. Adapter-ligated small RNAs were reverse transcribed using SuperScript III, amplified using GoTaq green PCR master mix (Promega) with the Tru-Seq 3′ indices (Illumina), and sequenced on an Illumina HiSeq 2000.

value: TZM-bl

value: Cervical Epithelial Cell Line, HeLa derivative

tag: length of infection (days)

tag: illumina truseq index number


title: LARP1 PAR-CLIP PP242

description: LARP1-bound RNA fragments

extract_protocol:
Crosslinked cell pellets were collected by scrapping and lysed with 600μl PAR-CLIP lysis buffer (0.1% SDS, 0.5% deoxycholate, 0.5% NP-40 in PBS without Mg2+, Ca2+) on ice for 10 minutes. To remove DNA, 10μl of RQ1 DNAse was added to each tube. Tubes were incubated at 37°C for 10 min with gentle rocking. Afterwards, 1U/µl of RNase T1 was supplemented, and the lysates were incubated at room temperature for 15 min with gentle rocking. Lysates were spun at 4°C for 10 min at 14,000 rpm. The soluble fractions were incubated with LARP1 antibody-Dynabeads Protein A for 1 hr at 4°C. Immunoprecipitates were collected on the magnetic stand and were washed three times with IP-wash buffer (50mM HEPES-KOH [pH 7.5], 300mM KCl, 0.05% NP-40, 0.5mM DTT, and EDTA-free protease inhibitor). Immunoprecipitates were resuspended in 40μl of IP-wash buffer containing 50U/μl RNase T1 and incubated at room temperature with gentle rocking for 15 min followed by incubation on ice for 5 min. Immunoprecipitates were washed with high-salt wash buffer (50mM HEPES-KOH [pH 7.5], 500mM KCl, 0.05% NP-40, 0.5mM DTT, EDTA-free protease inhibitor), three times with the PAR-CLIP lysis buffer, twice with high-salt wash buffer (0.1% SDS, 0.5% deoxycholate, 0.5% NP-40 in 5x PBS without Mg2+, Ca2+), and twice with PNK (polynucleotide kinase) buffer (50mM Tris-Cl pH 7.4, 10mM MgCl2, 0.5% NP-40). For visualization of crosslinked RNAs, immunoprecipitates were incubated in 40μl of PNK mixture (1μl P32γATP, 4μl 10x PNK buffer [NEB], 2μl T4 PNK enzyme [NEB], 33μl water) for 30 min at 37°C. Labeled immunoprecipitates were washed three times with PNK buffer and resuspended with 30μl of 2x NUPAGE LDS sample buffer (15μl 1x PNK with 15μl Novex LDS sample buffer). Denatured samples were resolved in 4-12% NUPAGE Bis-Tris gel and transferred to nitrocellulose membrane at 30 V for 1 hr using NuPAGE transfer buffer. The membrane was expose to X-ray film at -80°C for 4 hr to visualize crosslinked RNAs.
RNA pellets were air-dried briefly, resuspended in 10 µL of PNK mix (70mM Tris pH 7.6, 10mM MgCl2, 5mM DTT, 1mM ATP, 1U/µL T4 polynucleotide kinase, 1U/µL SUPERase·In), and incubated at 37°C for 30 min. The reaction was combined with 90µL H2O and 100µL Phenol:Chloroform:Isoamyl Alcohol 25:24:1, mixed well, and spun for 5 min at 20,000Xg. The liquid phase was mixed with 12.5µL of 3M NaOAc, 250µL of 100% ethanol, 1µL of 15mg/mL glycoblue and precipitated for 2 hr at -80°C. RNAs were collected by centrifugation for 20 min at 20,000Xg at room temperature, followed by 2 washes with cold 75% ethanol. RNA pellets were resuspended in 10µL of ligation mix (50mM Tris pH 7.5, 10mM MgCl2, 10mM DTT, 1mM ATP, 0.1mg/mL BSA, 2µM 5’RNA linker, 1U/µL T4 RNA ligase, 1U/µL SUPERase•In, 10% DMSO) and incubated at 15°C for 2 hr. Ligation reaction was terminated by adding 10µL of 2X formamide gel loading buffer, heated for 2 min at 70°C, and then quickly chilled on ice. Samples were loaded onto a 6% TBE UREA gel and run at 150 V for 45 min. After staining with 1X Sybr Gold Stain, a gel piece corresponding to 70-90nt RNA (80-100nt ssDNA) was excised, crushed, and soaked in 400µL of 0.3M NaOAc overnight at room temperature. After removing gel pieces, the solution was combined with 1mL of 100% EtOH and 1µL of 15mg/mL glycoblue and precipitated for 2 hr at -80°C. RNAs were collected by centrifugation for 20 min at 20,000Xg at room temperature, followed by two washes with cold 75% ethanol. After brief drying, RNAs were resuspended in 15µL of H2O. 10μL of ligated RNA was combined with 2μL of 5µM RT primer, heated at 65°C for 5 min, and then quickly chilled on ice, followed by the addition of 1µL 10mM dNTP, 1μL of 0.1 M DTT, 4μL of 5X First strand buffer, 1μL of SUPERase•In (20 U/µL) and 1 µL of SuperScript III Reverse transcriptase (200 U/µL). RT reaction was kept at 50°C for 45 min, 55°C for 15 min and 90°C for 5 min. A test PCR was performed with 2.5 µL of RT product in 50 µL PCR mix: 1X AccuPrime PCR buffer I, 0.5 µM P5 long primer, 0.5 µM P7 primer, 0.2 µL AccuPrime Taq High Fidelity (5 U/µL). PCR was carried out with an initial 3 min denaturation at 98°C, followed by 14-22 cycles of 80 sec denaturation at 98°C, 90 sec annealing and extension at 65°C, and termination with a final 5 min extension at 65°C. 15 µL PCR product was collected after 14, 18, and 22 cycles and analyzed on a 10% TBE gel at 150 V for 1 hr to determine the optimal amplification cycles (the lowest cycle number required to generate 96-116 bp amplicons detected by Sybr Gold staining). A 50 µL PCR reaction was carried out with the determined cycle number. Amplicons were purified using DNA clean and concentrator-5, run on 10% TBE gels at 150 V for 1 hr and stained with Sybr Gold. A gel piece corresponding to 96-116 bp DNA was excised, crushed, and soaked overnight in 400 µL 0.3 M NaOAc at room temperature. After removing gel pieces, the solution was combined with 1 mL of 100% EtOH and 1 µL of 15 mg/mL glycoblue and precipitated for 2 hr at -80°C. DNAs were collected by centrifugation for 20 min at 20,000Xg at room temperature, followed by two washes with cold 75% ethanol. After brief drying, amplicons were resuspended in 20 μl of H2O. Purified amplicons (5 μl) were used to seed a second round of PCR in 50 μl: 1× Accu- Prime PCR buffer I, 0.5 μM Illumina Primer A, 0.5 μM Illumina Primer B, 0.2 μl AccuPirme Taq High Fidelity for 6 to 12 cycles. Second PCR amplicons were purified with DNA clean and concentrator-5.

treatment_protocol: To label cells with 4-thiouridine (4sU), cells were seeded in two 15 cm plates to grow overnight to reach 70 % confluency, and on the next day, cells were incubated with 100 μM 4sU for 14 hours. After washing with cold PBS, cells were irradiated in the CL-1000 Ultraviolet Crosslinker on ice with 150 mJ/cm2. In order to inhibit kinases involved in the PI3K pathway we treated cells with 2.5 μM PP242 for indicated times.

value: TTAGGC

tag: mapped reference genome


title: ESC.1


title: LARP1 PAR-CLIP Basal

description: LARP1-bound RNA fragments

treatment_protocol: To label cells with 4-thiouridine (4sU), cells were seeded in two 15 cm plates to grow overnight to reach 70 % confluency, and on the next day, cells were incubated with 100 μM 4sU for 14 hours. After washing with cold PBS, cells were irradiated in the CL-1000 Ultraviolet Crosslinker on ice with 150 mJ/cm2.


title: hFib.4

description: protocol specific to human samples: mono nucleosome sized fragments were isolated using SPRI beads, each MNase concentration barcoded separately

value: fibroblasts differentiated from hESC


title: hFib.3


title: hFib.1


title: hiPSC.2

value: induced pluripotent stem cells


title: hiPSC.1


title: hESC.3


title: hESC.2


title: hESC.1


title: Sample 1367 phase G2 HT-1080

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

description: Library strategy: RepliSeq

data_processing:
Basecalls performed with Illumina RTA version 1.12.4.2
Uniquely mapping high-quality reads were mapped to the genome minus the Y chromosome. Replication signals within each six cell cycle fraction were derived from the density of sequence tags mapping within a 50 kb sliding window (stepped 1 kb across the genome); these densities were normalized to 4 million tags per genome. To avoid variation due to copy number or sequence bias, cell cycle-specific replication signals at each location were determined as a percentage of the sum of the six normalized tag density signals (Percentage-normalized Signal).
To transform the six fraction replication signals into one track (Wavelet-smoothed Signal), the percentage-normalized signals at each location were used to calculate a weighted average value based on the average DNA content of each fraction according to flow cytometry [higher values correspond to earlier replication; formula=(0.917*G1b)+(0.750*S1)+(0.583*S2)+(0.417*S3)+(0.250*S4)+(0*G2)]. These weighted average data were smoothed by wavelet transformation [J7 level, corresponding to a scale of 128 kb; see Thurman et al.(2007)].
Replication initiation zones were flagged by determining local maxima in the wavelet-smoothed data (Peaks) and, similarly, replication termination zones were flagged by local minima (Valleys).
Genome_build: hg19
Supplementary_files_format_and_content: normalized signal, bed, per fraction signal; wavelet smoothed signal, bigWig, scores represent an entire signal profile of all six fractions of the cycle; peaks/valleys, bed, scores replication initiation and termination zones.

growth_protocol: http://www.atcc.org/products/all/CCL-121.aspx#culturemethod Generally followed ATCC growth protocol, with a targeted HPRT knockout to avoid a contaminating tetraploid population (CL12)

extract_protocol:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwRepliSeq
Sequencing libraries were generated with Illumina RNA-Seq library kit, Illumina  TruSeq v2.

tag: tissue

value: connective tissue


title: Sample 1366 phase S4 HT-1080

description: Library strategy: RepliSeq


title: Sample 1364 phase S2 HT-1080

description: Library strategy: RepliSeq


title: Sample 1365 phase S3 HT-1080

description: Library strategy: RepliSeq


title: J1

status: Public on Jul 30 2014

city: HangZhou

first: Boxiong

last: Zhong

state: Zhejiang province

address: Yuhangtang Road 866

country: China

institute: Zhejiang University

data_processing:
Run Solexa pipeline [*fq]
Remove low qulity reads strictly
Trim 3' adaptor sequenceclean.txt].
Remove 5' adaptor contaminants
Plot data distribution

organism: Bombyx mori

source_name: Posterior silk gland

growth_protocol: Domesticated silkworms (Bombyx mori), was reared at 25°C on a natural diet of clean mulberry leaves.

extract_protocol:
total RNA
Total RNA of each sample was immediately isolated from posterior silk gland of silkworm using Trizol reagent for RNA isolation. Following purification, total RNA samples were immediately preserved in ethanol and stored at -80℃ until further use. For deep sequencing, the total RNA samples were prepared as follows: total RNA of each sample was size-fractionated on a 15% PAGE gel, and a 16–30 nt fraction collected. The 5′ RNA adapter (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’) was ligated to the RNA pool with T4 RNA ligase. Ligated RNA was size-fractionated on a 15% agarose gel, and a 40–60 nt fraction excised. The 3′RNA adapter (5’-pUCGUAUGCCGUCUUCUGCUUGidT-3’; p, phosphate; idT, inverted deoxythymidine) was subsequently ligated to precipitated RNA using T4 RNA ligase. Ligated RNA was size-fractionated on a 10% agarose gel, and the 70-90 nt fraction (total RNA + adaptors) excised. Small RNAs ligated with adaptors were subjected to RT-PCR (Superscript II reverse transcriptase, 15 cycles of amplification) to produce sequencing libraries. PCR products were purified and total RNA libraries sequenced using Solexa sequencing technology.

treatment_protocol: Posterior silk glands were manually dissected and collected day by day from the fourth instar molting to day 8 of the fifth instar that before spinning at low temperature in 0.7% NaCl solution, rinsed and stored in liquid nitrogen immediately.

tag: Stage

value: fourth instar molting to day 8 before spinning

value: Posterior silk gland


title: Sample 1362 phase G1b HT-1080

description: Library strategy: RepliSeq


title: R1


title: B2

value: Baiyu

value: fifth instar day 3 to day 8 before spinning


title: QB2

value: Qiufeng×Baiyu


title: B1

value: fourth instar molting to day 2 of fifth instar


title: CD4+ NL4-3 Day 3 Small RNA Deep Sequencing

description: Total size fractionated small RNA deep sequencing with protocol from Umbach et al J Virol 84:695-703

source_name: Primary cells isolated from peripheral blood

growth_protocol: Isolated from total blood by density gradient centrifugation (lymphocyte separation medium; Cellgro number 25-072-CV), and CD4+ T cells were then isolated using the Dynabead CD4 positive isolation kit from Invitrogen (number 1131 D). Cells were activated by incubation in phytohemagglutinin (PHA) and mouse monoclonal antibodies specific for human CD28 and CD49d (BD Biosciences number 347690) for three days. Activation of the CD4+ T cells was confirmed by fluorescence-activated cell sorting (FACS) by using an anti-CD69 antibody, and the cells were then cultured in RPMI supplemented with 10% FBS and interleukin-2

treatment_protocol: otal RNA was isolated using TRIzol. The RNA fraction containing ~15- to 30-nt-long RNAs was isolated by polyacrylamide gel electrophoresis (PAGE) purification on 15% Tris-borate-EDTA (TBE)-urea gels (Bio-Rad), electroeluted from the excised gel slice (gel eluter; Hoefer), and cloned as previously described (Umbach & Cullen, 2010.  J. Virol. 84:695-703). Adapter-ligated small RNAs were reverse transcribed using SuperScript III, amplified using GoTaq green PCR master mix (Promega) with the Tru-Seq 3′ indices (Illumina), and sequenced on an Illumina HiSeq 2000.

tag: hiv-1 strain

value: CD4+ T-cells


title: CHG101

city: Singapore

first: Niantao

last: Deng

state: Singapore

address: Center for Computational Biology, level 6, 8 College Road

country: Singapore

institute: Duke NUS Graduate Medical School

data_processing:
Sequencing tags were mapped against the human  reference genome (hg19) using Burrows-Wheeler Aligner (BWA)
101-base reads were trimmed by the first and last 10-base to increase SNP call performance.
Uniquely mapped tags were used for peak calling by CCAT version 3.0.
Peak regions were filtered by a p-value cut-off of 0.05 for all marks except for H3K27me3 for which 1.5-fold above input was used to filter peak regions. For each histone modification, peak regions from all tissue samples  were pooled, and overlapping peak regions were merged to create a total set of peak regions for that modification.
Genome_build: hg19
Supplementary_files_format_and_content: interval format for ucsc genome browser, including 8 columns: "chromosome" "position of the peak" "start of region" "end of region" "read counts in ChIP library" "read counts in control library" "fold-change score" "local FDR"

source_name: Gastric Primary Sample

extract_protocol:
Fresh-frozen cancer and normal tissues were dissected using a razor blade in liquid nitrogen to obtain ~5mg sized pieces (~ 5 ml by apparent volume). Tissue pieces were fixed in 1% formaldehyde/TBSE buffer for 10 minutes (min) at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Tissue pieces were washed 3 times with TBSE buffer, and transferred into Lysonator cartridges (SG Microlab Devices, Singapore). Tissues were dissociated following the manufacturer’s guidelines (4K Hz for 3 min), and taken directly to the lysis step in the Nano ChIP assay. Dissociated tissues were lysed in 200 ml of lysis buffer and divided into two 1.5 ml tubes for sonication (6 min) using  a Bioruptor (Diagenode). 5 CHiPs were performed on individual chromatin preparations using the following antibodies: H3K4me3 (07-473, Millipore); H3K4me1 (ab8895, Abcam); H3K27ac (ab4729, Abcam); H3K36me3 (ab9050, Abcam); H3K27me3 (07-449, Millipore).
Amplified DNA was digested with BpmI (New EngliandBiolabs), ligated to a 2ndBpmI adaptor and digested again to trim the WGA primer regions and semi-random priming ends. 15 ng of amplified DNA was used for each Illumina sequencing library using the ChIPseq kit (Illumina). Each library was sequenced on one lane of HiSeq2000 to obtain either 36- or 101-base single reads.

tag: tissuetype

value: Tumor

tag: chip antibody

tag: reads length


title: CHG099


title: CHG097

value: Normal


title: CHG095


title: CHG092


title: CHG093


title: BQ2

value: Baiyu×Qiufeng


title: QB1


title: BQ1


title: Q2

value: Qiufeng


title: CHG096


title: Sample 1363 phase S1 HT-1080

description: Library strategy: RepliSeq


title: CHG100


title: Q1


title: CHG098

value: Input


title: CHG087


title: CHG083

value: 101 (then trimmed first and last 10 bases to improve SNP call performance)


title: CHG081


title: CHG089


title: CHG080


title: CHG079


title: CHG082


title: CHG086


title: CHG051


title: CHG052


title: CHG078


title: CHG049


title: CHG050


title: CHG091


title: CHG094


title: CHG090


title: CHG048


title: CHG047


title: CHG088


title: CHG037


title: CHG040


title: CHG039


title: CHG036


title: CHG034


title: CHG035


title: CHG031


title: CHG028


title: CHG026


title: CHG033


title: CHG024


title: CHG023


title: CHG025


title: CHG022


title: CHG019


title: CHG020


title: CHG018


title: CHG017


title: CHG038


title: mESC_WCE

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
mESC_WCE
barcode: ATCACG

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files: For all samples, reads were aligned with bowtie 0.12.9 to the mm9 genome.  Aligned sequences were processed with MACS 1.4.2 with parameters -w -S --space=50 --keep-dup=auto -p 1e-9. Counts were normalized to reads per million.

source_name: Embryonic stem cells

growth_protocol: V6.5 (C57BL/6-129) and SHBcT4 murine ES cell lines and Nanog-GFP OSKM#2  iPSCs were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates. Colonies 23 and 44 were grown under typical ES conditions plus 2ug/ml doxycycline. Oct4-GFP OSKM#2 and #4 and Oct4-GFP SNEL#3 and #4 were grown under ESC naive 2i condition without feeder. MEFs were grown in DMEM supplemented with 10%FBS, Glutamine and P/S.

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

tag: antibody catalog number

value: V6.5 embryonic stem cells


title: CHG021


title: Oct4-GFP SNEL#1

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
MethylC-seq data was processed as previously described (Lister et al., 2011, PMID: 21289626).
Genome_build: mm10
Supplementary_files_format_and_content: The processed data for the allc_<sample>_<chr>.tsv files contain a row of headers indicating the chromosome, position, strand, methylation class, methylation count, total coverage, and methylation call. This is a tab delimited file.

source_name: Oct4-GFP SNEL

extract_protocol: Bisulphite treatment and sequencing library preparation were performed as previously described (Lister et al., 2011). Briefly, genomic DNA from each iPSC and ESC was fragmented by sonication prior to ligation of methylated sequencing adaptors. Fragments were size-selected by gel electrophoresis and purification, treated with sodium-bisulphite and amplified with 4 cycles of PCR to generate libraries that were sequenced on the Illumina HiSeq platform.

tag: strain background

value: mixed; 129Sv/Jae and C57/Bl6

value: Induced pluripotent stem cells

tag: echotype

value: pluripotent


title: mESC_Med1_sc5334_ChipSeq

description:
mESC_Med1_sc5334
barcode: TTAGGC

value: Santa Cruz SC-5334


title: CHG029


title: Oct4-GFP ESCs

source_name: Oct4-GFP ESCs

value: Embryonic stem cells


title: Oct4-GFP OKSM#2

source_name: Oct4-GFP OKSM


title: CHG030


title: Nanog-GFP SNEL#3

source_name: Nanog-GFP SNEL


title: SNEL4_WCE

description:
SNEL4_WCE
barcode: TGACCA

source_name: iPSC

value: SNEL #4


title: CHG032


title: mESC_Med1_Bethyl_ChipSeq

description:
mESC_Med1_Bethyl
barcode: CGATGT

value: Bethyl A300-793A


title: Nanog-GFP ESCs

source_name: Nanog-GFP ESCs


title: CHG027


title: SNEL4_MED1

description:
SNEL4_MED1
barcode: ACTTGA


title: SNEL3_MED1

description:
SNEL3_MED1
barcode: CAGATC

value: SNEL #3


title: Nanog-GFP SNEL#2


title: SNEL3_WCE

description:
SNEL3_WCE
barcode: TTAGGC


title: Nanog-GFP OKSM#2

source_name: Nanog-GFP OKSM


title: OSKM4_WCE

description:
OSKM4_WCE
barcode: ATCACG

value: OSKM #4


title: KH2 ESC

source_name: KH2 ESC


title: MEF_MED1_ChipSeq

description:
Chromatin IP against MEF_MED1
barcode: ACAGTG

source_name: Mouse embryonic fibroblasts


title: MEF_WCE_ChipSeq

description:
Chromatin IP against MEF_WCE
barcode: ATCACG


title: KH2 OKSM

source_name: KH2 OKSM


title: iPSC_WCE_ChipSeq

description:
Chromatin IP against iPSC_WCE
barcode: CGATGT

value: NGFP iPSC


title: BC_2 OKSM

source_name: BC_2 OKSM


title: 44_WCE_ChipSeq

description:
Chromatin IP against 44_WCE
barcode: TGACCA

value: partially reprogrammed colony 44


title: iPSC_MED1_ChipSeq

description:
Chromatin IP against iPSC_MED1
barcode: GCCAAT


title: 44_MED1_ChipSeq

description:
Chromatin IP against 44_MED1
barcode: ACTTGA


title: 23_WCE_ChipSeq

description:
Chromatin IP against 23_WCE
barcode: TTAGGC

value: partially reprogrammed colony 23


title: 23_MED1_ChipSeq

description:
Chromatin IP against 23_MED1
barcode: CAGATC


title: FC2_soma_SN_PE

first: Leon

last: Reijmers

state: MASSACHUSETTS

address: 136 Harrison Ave

department: Neuroscience

institute: Tufts University

data_processing:
Basecalling with Illumina CASAVA 1.9.
Indexed mm9 genome generated with STAR(v2.1.1d) using the UCSC NCBI37 annotation and these options: --sjdbFileChrStartEnd -sjdbOverhang 201
Reads aligned to indexed genome with STAR(v2.1.1d) using these options: --outSAMstrandField intronMotif
R/FPKM calculations with Cufflinks(v2.0.2) using these options:  -u -F 0 -A 0.01 -G <custom.gtf> -M <ribosomal RNA>
Genome_build: mm9
Supplementary_files_format_and_content: FPKM.csv : abundance measurements
Supplementary_files_format_and_content: gtf: custom GTF

source_name: hippocampal CA1 dissection

extract_protocol:
Immunoprecipitation of GFP-tagged ribosomes from in vivo micro dissections of dendrites and soma of CA1 hippocampal neurons.
Library preparation included these steps: 1) Nugen Ovation RNA-Seq System V2 2) Treatment with Single Strand Nuclease (Promega) for 30 minutes at room temperature. 3) Library preparation with Illumina TruSeq DNA Kit v2. 4) Size selection with Invitrogen E-Gel SizeSelect 2%.

tag: genotype

tag: background strain

tag: behavior

value: fear conditioned

tag: location

value: soma

tag: fraction

value: supernatant


title: FC2_soma_SN_SE


title: FC2_soma_IP_PE

value: immunoprecipitate

tag: antibody

value: HtzGFP-19C8 (Monoclonal Antibody Core Facility at Memorial Sloan Kettering Cancer Center)


title: FC2_dend_SN_PE

value: dendrite


title: FC2_soma_IP_SE


title: FC2_dend_IP_PE


title: FC2_dend_SN_SE


title: OSKM8_WCE

description:
OSKM8_WCE
barcode: CGATGT

tag: cell type

value: OSKM #8


title: FC2_dend_IP_SE


title: FC1_soma_IP_PE


title: OSKM8_MED1

description:
OSKM8_MED1
barcode: GCCAAT


title: HC2_soma_IP_PE

value: home cage


title: FC1_soma_IP_SE


title: OSKM4_MED1

description:
OSKM4_MED1
barcode: ACAGTG


title: HC2_dend_SN_PE


title: FC1_dend_IP_PE


title: FC1_dend_IP_SE


title: HC2_dend_IP_PE


title: HC2_dend_IP_SE


title: HC2_dend_SN_SE


title: HC1_soma_IP_PE


title: HC1_dend_IP_PE


title: HC1_soma_IP_SE


title: HC1_dend_IP_SE


title: het5450

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

description:
Sample 13
library strategy: ERRBS and RRBS

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were filtered from the adapter sequences using FAR software and aligned to genome using the bismark alignment software, retaining uniquely aligning reads with maximum of 2 directional mismatches
methylCall files were generated using methylKit
Genome_build: mm10
Supplementary_files_format_and_content: The methylCall files are tab-delimited file with colums chrBase, chr, base, strand, coverage (Number of reads that map to genomic region containing base), freqC (Percentage of reads sequencing base as cytosine after bisulfite conversion), freqT (Percentage of reads sequencing base as thymine after bisulfite conversion).

source_name: het, mouse lung tissue

growth_protocol: not applicable

extract_protocol: DNA was extracted using Qiagen Puregene kit protocol; Libraries were prepared using RRBS and ERRBS as described in manuscript

tag: genotype/variation

value: Ctcf heterozygous

tag: treatment

value: treated at 14 days with single dose of 1mg/g body weight urethane

tag: age

value: 50 weeks

tag: gender

value: F

value: whole lung


title: het5433

description:
Sample 12
library strategy: ERRBS and RRBS

value: 54 weeks

tag: tissue


title: WT5491

description:
Sample 7
library strategy: ERRBS and RRBS

source_name: WT, mouse lung tissue

value: wild-type

value: 49 weeks


title: het5464

description:
Sample 8
library strategy: ERRBS and RRBS

value: M


title: het5466

description:
Sample 10
library strategy: ERRBS and RRBS


title: het5504

description:
Sample 11
library strategy: ERRBS and RRBS

value: 48 weeks


title: het5480

description:
Sample 15
library strategy: ERRBS and RRBS


title: het5471

description:
Sample 14
library strategy: ERRBS and RRBS

value: 51 weeks


title: WT5474

description:
Sample 5
library strategy: ERRBS and RRBS


title: het5498

description:
Sample 9
library strategy: ERRBS and RRBS

value: 46 weeks


title: WT5489

description:
Sample 6
library strategy: ERRBS and RRBS


title: WT5512

description:
Sample 4
library strategy: ERRBS and RRBS


title: WT5443

description:
Sample 3
library strategy: ERRBS and RRBS

value: 53 weeks


title: WT5434

description:
Sample 2
library strategy: ERRBS and RRBS

value: 55 weeks


title: WT5347

description:
Sample 1
library strategy: ERRBS and RRBS

value: 52 weeks


title: S7

city: Hangzhou

first: Xin

last: Tao

address: Shiqiao Road 145

institute: Zhejiang Academy of Agricultural Sciences

description: Sample 5

data_processing:
Illumina Casava1.8 software used for basecalling.
Data obtained from the high-throughput sequencing were processed by removing low-quality data, clipping 3ʹ adapters and 5ʹ adapters, discarding poly-A/T-containing sequences and fragments <15 nt and >32 nt. All clean sequences were used for ncRNA and to remove non-miRNAs (rRNA, tRNA and snRNA, among others) using BLASTN and Rfam10.1.
The processed data were mapped to the Sus scrofa draft genome assemblywith no mismatches, using the Bowtie v0.12.2.
Unique sequences were aligned with swine miRNA sequences from miRBase 19.0 to identify known swine miRNAs.
Novel miRNA candidate precursors were identified using the miRDeep2.
Genome_build: SGSC Sscrofa 9.2, NCBI project 10718, GCA_000003025.2
Supplementary_files_format_and_content: xls files include read counts and sequence of each Sample

organism: Sus scrofa

source_name: suckling piglets_jejunum

extract_protocol:
To obtain representative measurements from the 2-cm jejunal samples, three cross-sections of approximately 2 mm were pooled and lysed using PRO 200 Post-Mounted Laboratory Homogenizer (PRO Scientific, Oxford, USA). Total RNA was extracted using an E.Z.N.A. HP Total RNA kit (Omega Bio-Tek, Norcross, USA).
For small RNA library construction, 4 jejunal total RNA samples isolated from each treatment and control were separately pooled with equal contribution.Solexa sequencing was performed as follows: about 10μg total RNA was size-fractionated by Novex 15% TBE-Urea gel (Invitrogen, Karlsruhe, Germany) and RNA fragments of length between 15 and 32 bases were isolated. The purified small RNAs were ligated with 5’ adapter (Illumina, CA, USA) and 3’ adapter (Illumina) with T4 RNA ligase (Ambion, Austin,USA). Subsequently, RNA fragments with the adapters at both ends were reverse transcribed to single-stranded cDNA using Superscript Ⅱ reverse transcriptase (Invitrogen, Carlsbad, USA), and the resulting cDNA was subjected to 15 PCR cycles using Illumina’s small RNA primer sets. The amplification products were quantified on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies,Palo Alto,USA) and sequenced on the HiSeq2000 (Ilumina)

tag: breed

value: Duroc x Yorkshire x Landrace

tag: gender type

value: Barrows

tag: sample group

value: suckling piglets

value: Small intestine; Jejunum

tag: molecule subtype

value: microRNA


title: Asf1_ChIPseq1

city: Hyderabad

first: Pooran

middle: Singh

last: Dewari

state: Andhra Pradesh

address: Uppal Road

department: Transcription Lab

country: India

institute: Centre for Cellular and Molecular Biology

data_processing:
Reads with phred score < 20 on 80% of the bases were filtered out with FASTX toolkit V0.0.13.
Reads were aligned to the yeast genome using Bowtie 0.12.8 allowing unique alignments with 3 mismatches and taking the best stratum.
Reads were extended to ChIP fragment size (160 bp).
Read coverage at each position in the genome is scaled to 1 million and normalized to the total number of reads in the library.
Genome_build: sacCer3
Supplementary_files_format_and_content: Coverage at each base is bundled as .bedGraph files.

organism: Saccharomyces cerevisiae

source_name: mid-log phase ASF1-18myc cells, ChIP

growth_protocol: The ASF1-18myc strain was grown to A600 = 0.7 in YEP + 2% glucose medium at 30 degrees Celsius.

extract_protocol: The ChIP protocol is essentially as described in Liu et al., 2005 (PMID 16122352). Immunoprecipitated chromatin was reverse cross-linked at 65 degrees for 10 hours. After one hour of RNase A treatment, DNA was extracted with phenol-chloroform-isoamyl alcohol (PCI) twice and precipitated using ethanol. Anti-Myc tag antibody, clone A46 (Upstate (Millipore), catalog number: 05-724, lot: JBC1868960) and Protein A and G Sepharose 4 Fast Flow (GE Healthcare) beads were used. IP and Mock DNA samples were processed according to the Illumina standard protocol for ChIP-seq.

treatment_protocol: Cells were fixed with formaldehyde (final conc. 1%) for six hours and quenched with glycine (final conc. 0.125M) for 10 minutes.

tag: strain

tag: genetic background

tag: growth phase

tag: chip antibody

value: anti-Myc tag antibody, clone A46


title: Asf1_ChIPseq2


title: W7

description: Sample 6

source_name: weaning piglets_jejunum

value: weaning piglets

tag: time point

value: 7d after weaning


title: S4

description: Sample 3


title: W1

description: Sample 2

value: 1d after weaning


title: kc_suhw-gp60_1_ga2

status: Public on Jul 29 2014

city: Bethesda

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description: nuclear RNA

data_processing:
trim adapters with cutadapt v1.2.1; --quality-cutoff=20 –minimum-length=36 –quality-base was adjusted as appropriate for each library
map to UCSC's dm3 using TopHat2/Bowtie2, using –phred64-quals where appropriate
count reads with htseq-count, using annotations from FlyBase r5.54
sum read counts for technical replicates (same biological sample on different sequencing machine)
RIP-enrichment calculated with DESeq, with method=”per-condition” and fitType=”local”
Genome_build: UCSC dm3
Supplementary_files_format_and_content: Tab-delimited text files of read counts from htseq-count, one file per biological replicate. Column 1 is FlyBase r5.54 accession; column 2 is sum of read counts across technical replicates.

organism: Drosophila melanogaster

source_name: Kc167 cells

extract_protocol:
BG3 and Kc nuclear extracts were prepared from 3.0 x 108 to 6.3 x 109 cells per IP essentially as described in PMID: 16862159 with the following modifications: cell extracts were immediately cleared by centrifugation after dounce homogenization and purified nuclei were lysed by dounce homogenization with the B pestle in HBSMT (50 mM HEPES, pH 6.7; 150 mM NaCl; 5 mM KCl; 2.5 mM MgCl2; 0.3% Triton X-100) supplemented with 1 mM PMSF, Complete EDTA-free protease inhibitor (Roche), and 1 U/uL RNasin (Promega).
Nuclear extracts were incubated rotating for 1 h at 4˚C with Protein A conjugated sepharose (GE Healthcare) prebound to preimmune serum. Precleared extracts were then transferred to Protein A sepharose prebound to Shep or Su(Hw) antisera [PMID: 23209434] for 1 h at 4˚C, rotating. Beads and bound complexes were washed in HBSMT three times and HBSM twice. RNA was isolated directly from Protein A beads by acid:phenol extraction, and EtOH precipitated with NaOAc. RNA was DNase I treated, poly(A)+ RNA was selected using a MicroPoly(A)Purist column (Ambion), and 100 ng was cloned using the standard Illumina mRNA-seq v2.2 cloning protocol. Libraries were sequenced using commercial sequencing primers. Highly similar profiles were obtained using two independent Shep antibodies; therefore, the antibody displaying the highest signal to noise ratio was utilized for subsequent analyses.

tag: cell line

value: Kc167 cells

tag: machine

value: GA II

value: Su(Hw) Gp60

tag: quality score

tag: biological replicate


title: kc_shep-rb5_2_ga2

description: nuclear RNA

tag: antibody

value: Shep Rb5


title: kc_shep-rb5_3_ga2

description: nuclear RNA


title: kc_input_2_ga2

description: nuclear RNA

value: input


title: kc_input_1_ga2

description: nuclear RNA


title: S1

description: Sample 1


title: kc_suhw-gp60_2_ga2

description: nuclear RNA


title: Mock

source_name: mid-log phase ASF1-18myc cells, mock

value: normal rabbit IgG


title: SABG1242-CC30

city: Rochester

first: Steven

last: Gill

address: Box 672, Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester School of Medicine and Dentistry

data_processing:
Sequences were cleaned using Seqclean-"-c 5 -I 25 -v vectors.fasta
Alignment using SHRiMP2.2.3 - "-N 8 --qv-offset 33 --all-contigs"
Differential expression using cuffdiff(cufflinks-2.0.2) - "--FDR 0.05 -u -p 12"
Genome_build: All sequences were aligned to MRSA252 (GenBank ID = NC_002952.2).
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample in "frm_gene_exp.diff.txt"

organism: Staphylococcus aureus

source_name: SABG 1242

growth_protocol: Individual S. aureus colonies for each strain were grown O/N in TSB, diluted to an OD600 ~0.05, incubated with shaking at 37C to an OD600~0.6 and collected for RNA extraction.

extract_protocol:
Three ml aliquots from each culture were transferred to RNAProtect and then RNA extracted by acid phenol/mechanical lysis.
Illumina TruSeq library preparation from RiboZero depleted total RNA

value: exponential in TSB (OD600=~0.6)

tag: clonal complex

value: SABG 1242


title: SABG290-CC45

source_name: SABG 290

value: SABG 290


title: kc_input_3_ga2

description: nuclear RNA


title: SABG1267-CC30

source_name: SABG 1267

value: SABG 1267


title: SABG1605-CC30

source_name: SABG 1605

value: SABG 1605


title: SABG1524-CC45

source_name: SABG 1524

value: SABG 1524


title: SABG1214-CC30

source_name: SABG 1214

value: SABG 1214


title: SABG149-CC30

source_name: SABG 149

value: SABG 149


title: SABG1233-CC30

source_name: SABG 1233

value: SABG 1233


title: W4

description: Sample 4

value: Duroc x Yorkshire x Landrace

value: Barrows

value: weaning piglets

value: 4d after weaning

value: Small intestine; Jejunum

value: microRNA


title: SABG1176-CC30

source_name: SABG 1176

value: SABG 1176


title: C341D-CC30

source_name: SABG C341D

value: SABG C341D


title: MRSA252

value: exponential in TSB (OD600=~0.6)


title: SABG1770-CC8

source_name: SABG 1770

value: SABG 1770


title: SABG2018-CC8

source_name: SABG 2018

value: SABG 2018


title: SABG1500-CC30

source_name: SABG 1500

value: SABG 1500


title: hFib.2

description: protocol specific to human samples: mono nucleosome sized fragments were isolated using SPRI beads, each MNase concentration barcoded separately

source_name: cell line

tag: cell type

value: fibroblasts differentiated from hESC

tag: sample type

value: Mnase-digested DNA


title: UAMS-1


title: SABG1612-CC8

source_name: SABG 1612

value: SABG 1612


title: HC2_soma_IP_SE

source_name: hippocampal CA1 dissection

tag: genotype

tag: background strain

tag: behavior

value: home cage

tag: location

value: soma

tag: fraction

value: immunoprecipitate

value: HtzGFP-19C8 (Monoclonal Antibody Core Facility at Memorial Sloan Kettering Cancer Center)


title: SABG1114-CC8

source_name: SABG 1114

tag: strain

value: SABG 1114


title: SABG1769-CC5

source_name: SABG 1769

tag: growth phase

value: SABG 1769


title: SABG1750-CC5

source_name: SABG 1750

value: SABG 1750


title: SABG547-CC8

source_name: SABG 547

value: SABG 547


title: SABG1057-CC5

source_name: SABG 1057

value: SABG 1057


title: C128-CC1

source_name: SABG C128

value: SABG C128


title: C345D-CC8

source_name: SABG C345D

value: exponential in TSB (OD600=~0.6)

value: SABG C345D


title: kc_shep-rb5_1_ga2

description: nuclear RNA

source_name: Kc167 cells

value: Kc167 cells

value: GA II

value: Shep Rb5


title: N315


title: C348-CC5

source_name: SABG C348

value: SABG C348


title: SABG1150-CC5

source_name: SABG 1150

value: SABG 1150


title: SABG1213-CC5

source_name: SABG 1213

value: SABG 1213


title: C340D-CC5

source_name: SABG 340D

value: SABG 340D


title: SABG1096-CC5

source_name: SABG 1096

value: SABG 1096


title: S3

city: Guangzhou

first: Gong

last: Zhang

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

institute: Jinan University

description:
total tRNA
s_7

data_processing:
Reads that aligned to rRNA sequences (X68434, X64887) with less than 3 mismatches were considered as rRNA reads and were thus removed
The remaining reads were aligned to the tRNA reference sequences using modified Smith-Waterman algorithm that considers modified nucleotides. Zero to three errors (including mismatches, insertions and deletions) was allowed in the alignment.
MS experiments to determine tRNA reference sequences including modifications (see Lactis_tRNA_only_mod.txt).
For the information of the non-modified sequence, the link is here: http://gtrnadb.ucsc.edu/Lact_lact_cremoris_MG1363/lactLact_CREMORIS_MG1-tRNAs.fa
Genome_build: MS-derived 'Lactis_tRNA_only_mod.txt' (linked as supplementary file on Series record)
Supplementary_files_format_and_content: Tab-delimited .txt file (Lactis_tRNA_exp.txt) containing the mapped tRNA read count of the three datasets when allowing 0~3 mismatches

organism: Lactococcus cremoris subsp. cremoris MG1363

source_name: total tRNA isolate from exponential phase

growth_protocol: L. lactis cells were grown in batch fermentors in GM17 media supplemented with 0.5 % glucose.

extract_protocol:
Cells were lysed and total tRNA was isolated with phenol chloroform method
tRNA library for NGS was prepared using the Small RNA sample Prep Kit FC-102-1009 from Illumina. The barcoded adapters were ligated to both ends of the resulting fragments, according the standard New England Biolabs protocol. Fragments with an insert size of 220 bp on average were excised using the Caliper XT gel system and the extracted DNA was amplified with PCR. The quality of the product was verified on BioRad Experion instrument. If the quality of the product met the criteria, the product was multiplexed in an equimolar pool of four similar products. This pool is hybridized to the Agilent SureSelect All exon V2, according to the provided protocol. After amplification of the enriched products with PCR the quality of the products was verified on the BioRad Experion instrument and sequenced on the HiSeq2000 with 100 bp single reads. Image Files were processed using standard Illumina base calling software and the generated reads were ready for downstream processing after demultiplexing.

tag: spiking of exogenous trna

value: spiked with Phe-tRNAGAA from yeast and Lys-tRNAUUU from E. coli

tag: stage at which the spiking in of exogenous trna was performed

value: after isolation of total tRNA from L. lactis  and before prepartion of NGS library


title: Flower

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

institute: Jawaharlal Nehru University

data_processing:
Illumina 1.8 pipeline used for basecalling
Low-quality reads and reads containg adaptor/primer contamination were filtered using NGS QC Toolkit v2.3
Base mean value was calculated for all the genes in each tissue sample using DESeq
Genome_build: Catharanthus Transcriptome v1.0 (http://nipgr.res.in/mjain.html?page=catharanthus)
Supplementary_files_format_and_content: tab delimited text files include base mean values for each sample

organism: Catharanthus roseus

source_name: Mature plant

growth_protocol: Plants were grown in field

extract_protocol:
Tissue samples were collected and frozen in liquid nitrogen. Total RNA was isolated using TRI reagent from Sigma
Libraries were prepared using mRNA-Seq Sample Prep kit (Illumina) according to the manufacturer’s protocol

tag: variety

value: Prabal

tag: tissue

value: Flower


title: Leaf

value: Leaf


title: Root

value: Root


title: S2

description:
total tRNA
s_8

value: after harvesting of L. lactis and before cell lysis

tag: repetition

value: Biological repetition of Sample 1


title: S1

description:
total tRNA
s_6


title: C93-CC15

source_name: SABG C93

value: exponential in TSB (OD600=~0.6)

value: SABG C93


title: Trophectoderm sample 2

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

data_processing:
The 100 base long single end reads were aligned to the mouse genome (mm10, Ensembl (Flicek et al., 2013)), using the STAR aligner (STAR_2.3.0e.Linux_x86_64) (Dobin et al., 2013), allowing for up to 4 mismatches.
Only the reads aligned uniquely to one genomic location, and with alignment quality above 10 were retained for following analyses. The duplicate reads were eliminated with Picard tools (v. 1.86) (http://picard.sourceforge.net).
Reads were converted into bigWig format via UCSC genome tools.
FPKM values were obtained with cufflinks-2.2.1 using Ensembl gtf annotation.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files report only those reads aligned uniquely to one genomic location, and with alignment quality above 10
Supplementary_files_format_and_content: GSE57249_fpkm.txt includes normalized expression values (FPKM).

source_name: trophectoderm

growth_protocol: Adult female mice (C57BL/6) were super-ovulated by intraperitoneal hormone injections with the interval of 48 hours between injections. The hormones administered were either PMSG followed by hCG (5IU/0.1ml, Sigma-Aldrich), or 0.1ml of PG600 (Intervet) administered twice, equivalent to 2.5 IU of hCG and 5IU of PMSG. Following the second hormonal treatment, the females were mated with males (1:1, C57BL/6). Zygotes, 2-cell, 4-cell and blastocysts were collected 26, 48, 52 and 94 hours post hCG or the second injection of PG600.

extract_protocol:
The total RNA was extracted from ICM or TE cells with Trizol (Life Technologies) and the supplement of 1μg of Glycoblue (Invitrogen).
The zygotes, blastomeres and the RNA extracted from ICM and TE were used for cDNA amplification using the SMARTer Universal Low Input RNA kit (Clontech). For all samples, the total amplified cDNA was used for library preparation using Nextera XT DNA Sample Prep Kit (Illumina).

treatment_protocol: Prior to blastomere collection, the zona pelucida was removed by Tyrode’s acid solution. The 2- and 4-cell embryos were then immersed in Trypsin solution (Invitrogen) with RNAse inhibitor (1 IU/μl, Clontech) and BSA (50μg/μl) for the separation of the blastomeres. The separated blastomeres were snap frozen, and maintained at -80°C until processed. ICM was isolated by immunosurgery, using anti-mouse IgG and complement (Sigma-Aldrich), following previously described procedures (Handyside & Barton, 1977; Harlow & Quinn, 1979), and snap frozen in Trizol reagent (Invitrogen). TE was isolated by exposure of the blastocyst to concanavalin A conjugated to magnetic beads, followed by trypsin treatment for cell dismemberment. The cells were immersed in PBS (RNAse inhibitor 1IU/μl, BSA 50μg/μl). Following magnetic separation of the trophoblast cells, they were snap frozen in Trizol reagent.

tag: developmental stage

value: trophectoderm, from blastocyst


title: Trophectoderm sample 1


title: Trophectoderm sample 3


title: Four-cell Embryo 4 Blastomere 4

source_name: blastomere

value: Four-cell Embryo Blastomere


title: Four-cell Embryo 5 Blastomere 2


title: Four-cell Embryo 5 Blastomere 3


title: Four-cell Embryo 5 Blastomere 1


title: SABG1165-CC5

source_name: SABG 1165

value: SABG 1165


title: SABG1835-CC1

source_name: SABG 1835

value: SABG 1835


title: Four-cell Embryo 4 Blastomere 2


title: Four-cell Embryo 3 Blastomere 3


title: Four-cell Embryo 3 Blastomere 4


title: Four-cell Embryo 3 Blastomere 2


title: Four-cell Embryo 2 Blastomere 3


title: Four-cell Embryo 3 Blastomere 1


title: Four-cell Embryo 1 Blastomere 4


title: Four-cell Embryo 2 Blastomere 2


title: Four-cell Embryo 1 Blastomere 3


title: Four-cell Embryo 2 Blastomere 1


title: Four-cell Embryo 1 Blastomere 1


title: Two-cell Embryo 10 Blastomere 2

value: Two-cell Embryo Blastomere


title: Four-cell Embryo 1 Blastomere 2


title: Two-cell Embryo 10 Blastomere 1


title: Two-cell Embryo 9 Blastomere 2


title: Four-cell Embryo 5 Blastomere 4


title: Het_Tg_treated

city: Ann Arbor

first: Maureen

last: Sartor

state: MI

address: 100 Washtenaw Avenue

institute: University of Michigan

description:
Sample 2
mRNA-Seq (RSW)
processed data file: Tg_RSW_processed.txt

data_processing:
Illumina GAII (for Tg samples) and GAIIx (for Dtt samples) pipeline used for basecalling
Align reads using bowtie after trmming the last 2bp
Split unmapped reads using custom scripts
Realign split unmapped reads using Bowtie
Select candidate read split pairs meeting criteria using custom scripts
Remove false positive pairs
Consolidate reads using custom scripts
Report non-canonical spliced regions supported by two or more reads
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files reporting abundance measurements

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Cells were grown to 80% confluency then treated or not for 4hrs before harvesting.

extract_protocol:
RNA isolated using Trizol followed by Dnase treatment and cleanup
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Samples 1, 3 were untreated
Sample 2 was treated with thapsigargin 4hrs. 500nM
Sample 4 was treated with 1mM Dithiothreitol 4hrs.

value: MEF

tag: treatment

value: 500nM Thapsigargin Treated 4hrs.

tag: genotype/variation

value: Ire1a Heterozygous cells


title: Two-cell Embryo 8 Blastomere 2


title: Two-cell Embryo 8 Blastomere 1


title: Two-cell Embryo 7 Blastomere 1


title: Two-cell Embryo 7 Blastomere 2


title: Four-cell Embryo 4 Blastomere 3


title: SSP25-LKB1-2

city: Duarte

first: keqiang

last: zhang

address: 1500 East Duarte Road

department: Molecular Pharmacology

institute: City of Hope National Medical Center

data_processing:
Illumina Casava1.8 software used for basecalling. Raw short sequence fragments were accepted if they passed the quality filtering parameters used in the Illumina GA Pipeline GERALD stage.
Sequenced reads were mapped to hg19 whole genome using tophat-1.2.0 with parameters -p 16 -g 10 -a 8
Aligned reads was normalized by edgeR bioconductor package and outputed as normalized RPKB file
Genome_build: Genome Reference Consortium GRCh37
Supplementary_files_format_and_content: normalized RPKB in txt format for all 12 samples

source_name: Intrahepatic cholangiocarcinoma

growth_protocol: HuH-28 cells were kept in MEM medium with 10% fetal bovine serum (FBS) +1% penicillin-streptomycin (P/S), all others were kept in RPMI1640 with the same supplements.

extract_protocol:
Trizol RNA extraction protocol
Transcriptome libraries were constructed with TruSeq RNA Sample Preparation Kit V2  (Illumia, San Diego, USA) with minor modifications.

treatment_protocol: 45 pmal/6-well (5x10^5 cell) with 4.5 ul Lipofectamin RNAiMax following Lipofectamine® RNAiMAX Transfection Protocol

tag: cell type

value: Intrahepatic cholangiocarcinoma

tag: sirna knockdown

value: LKB1 siRNA

tag: cell line

tag: time


title: SSP25-LKB1-1


title: SSP25-Control-1

value: Control siRNA


title: SSP25-Control-2


title: KO_Tg_untreated

description:
Sample 1
mRNA-Seq (RSW)
processed data file: Tg_RSW_processed.txt

value: Untreated

value: Ire1a Knockout cells


title: RBE-LKB1-2

value: RBE


title: Two-cell Embryo 6 Blastomere 2


title: RBE-LKB1-1


title: Two-cell Embryo 6 Blastomere 1


title: RBE-Control-2


title: Two-cell Embryo 5 Blastomere 2


title: Two-cell Embryo 4 Blastomere 2


title: HuH28-Control-2


title: HUH28-LKB1-2


title: Two-cell Embryo 4 Blastomere 1


title: Inner cell mass sample 4

source_name: inner cell mass

value: inner cell mass, from blastocyst


title: HuH28-Control-1


title: Two-cell Embryo 9 Blastomere 1


title: Two-cell Embryo 3 Blastomere 2


title: Inner cell mass sample 3


title: Inner cell mass sample 1


title: R89_Germinating_Cotyledons_Stage6_BR2

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

data_processing:
Standard Illumina pipeline including CASSAVA
Sequenced reads were aligned to 78,773 Glyma1 cDNA soybean gene models determined by the Soybean Genome Project (Schmutz et al. 2010) using Bowtie (Langmead et al. 2009). Bowtie parameters allowed up to three mismatches and up to 25 alignments per read.
Reads per kilobase of gene model per million mapped reads (RPKM) were calculated according to Mortazavi et al. (2008).
Genome_build: Glyma1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Glycine max

source_name: Germinating cotyledons

growth_protocol: Plants were grown in optimal greenhouse conditions. Germinating cotyledons were collected at stated days after planting

extract_protocol:
Total RNA was extracted from tissues using phenol:chloroform and a lithium chloride precipitation (Gonzalez and Vodkin 2007). Sequencing was performed by the Keck Center (University of Illinois) using an Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Williams

tag: Stage

value: 5-6 days after planting

tag: preservation

value: lyophilized

tag: purification


title: Two-cell Embryo 2 Blastomere 1

tag: strain


title: Two-cell Embryo 1 Blastomere 2


title: R82_Germinating_Cotyledons_Stage7_BR1

value: 6-7 days after planting


title: Two-cell Embryo 1 Blastomere 1


title: RBE-Control-1


title: Inner cell mass sample 2


title: Two-cell Embryo 5 Blastomere 1


title: HuH28-LKB1-1


title: Zygote 8

source_name: zygote

value: zygote


title: R88_Germinating_Cotyledons_Stage5_BR2

value: 4-5 days after planting


title: R81_Germinating_Cotyledons_Stage6_BR1


title: Two-cell Embryo 2 Blastomere 2

value: Two-cell Embryo Blastomere


title: Zygote 9


title: R80_Germinating_Cotyledons_Stage5_BR1


title: Zygote 7


title: Two-cell Embryo 3 Blastomere 1


title: R87_Germinating_Cotyledons_Stage4_BR2

value: 3-4 days after planting


title: Zygote 5


title: Zygote 6


title: Zygote 4


title: STC1-/- KO (7FKO)

city: Davis

first: Sanchita

last: Bhatnagar

address: 1275 Health Sciences, Tupper Hall 3134

department: Medical Microbiology and Immunology

institute: University of California Davis

data_processing:
Images were analyzed using OLB 1.9 and CASAVA_v1.8.2
TopHat v2.0.6 was used to map the sequences to mm10
cuffdiff v2.0.1 was used to generate the differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: cuffdiff results

source_name: MEFs

growth_protocol: MEFs were grown in DMEM with 10% FCS and Pen/Strep

extract_protocol:
RNA was extracted using Qiagen columns
library constructed following Illumina TruSeq  Stranded mRNA Sample Prep guide.

tag: background strain

tag: genotype

value: STC1-/- KO

value: embryonic fibroblasts


title: STC1-/- KO (4.1 KO)


title: R79_Germinating_Cotyledons_Stage4_BR1


title: STC1-/- KO (5.1KO)


title: R90_Germinating_Cotyledons_Stage7_BR2


title: STC1+/+ WT (3.2WT)

value: STC1+/+ WT


title: Four-cell Embryo 4 Blastomere 1

value: Four-cell Embryo Blastomere


title: R86_Germinating_Cotyledons_Stage3_BR2

value: 2-3 days after planting


title: R85_Germinating_Cotyledons_Stage2_BR2

value: 2 days after planting


title: STC1+/+ WT (4FWT)


title: Zygote 1


title: R78_Germinating_Cotyledons_Stage3_BR1


title: Zygote 2


title: Zygote 3


title: STC1+/+ WT (4.6WT)


title: q96 gonads Replicate 8

city: Madison

first: Marco

middle: Antonio

last: Ortiz

state: Wisconsin

address: 433 Babcock Drive

department: Biochemistry

institute: University of Wisconsin-Madison

data_processing:
Basecalls performed using CASAVA version 1.8.2 with standard parameters.
We used TopHat2 v2.0.11 (with –g 1 option) to align reads to the C. elegans reference genome (WBcel235.75.fa) and gene annotations (WBcel235.75.gtf), both in Wormbase WS240 (Ensembl).
For compatibility to feature-counting software, we created sorted and indexed SAM versions of the BAM files (SAMtools).
To create a read-count dataset, we processed SAM files with python scripts described elsewhere (Anders and Huber 2010) using gene annotations gene annotations WBcel235.75.
Genome_build: WBcel235
Supplementary_files_format_and_content: Number of reads aligned per gene (wormbase)

organism: Caenorhabditis elegans

source_name: ~30 Extruded gonads from fem-3(q96) worms

growth_protocol: The fem-3(q96gf) stocks were maintained at 15°C; fog-2(q71) mutants were maintained at 22°C. Experimental animals were syncronized and grown at 22°C until 2 hours after L4/Adult molt.

extract_protocol:
Total RNA was extracted from the gonads using TRIzol (Invitrogen) and RNeasy Mini Kit (Qiagen), following the manufacturer's instructions.
The University of Wisconsin Biotechnology Center prepared libraries for each sample using the TruSeq Illumina sequencing protocol, which includes mRNA purification (poly-A selection) and fragmentation, cDNA synthesis, end repair, adapters ligation, and DNA fragment enrichment.  Each library was bar-coded and sequenced in four different lanes to obtain single-end 101-bp reads using Illumina HiSeq2000.

treatment_protocol: The synchronized young adults (0-2 hours past the L4 to adult molt) were first cut behind the pharynx in PBS-Tween (0.1% Tween20) with 0.25 mM Levamisole.Gonadal arms were then cut at or near the spermatheca to isolate them from the carcass.

value: fem-3(q96 gfts)

value: 95% germline tissue, 5% somatic tissue

tag: gametes

value: sperm

value: L4/Adult molt +2 hrs

tag: growth temperature


title: R77_Germinating_Cotyledons_Stage2_BR1

value: Williams


title: q96 gonads Replicate 7

tag: tissue


title: kc_suhw-gp60_2_hiseq

description: nuclear RNA

source_name: Kc167 cells

value: Kc167 cells

tag: machine

value: HiSeq 2000

tag: antibody

value: Su(Hw) Gp60

tag: quality score

tag: biological replicate


title: q96 gonads Replicate 2


title: q96 gonads Replicate 13


title: q96 gonads Replicate 5


title: q96 gonads Replicate 11


title: q96 gonads Replicate 10


title: q71 gonads Replicate 9

source_name: ~30 Extruded gonads from fog-2(q71) worms

value: oocytes


title: kc_shep-rb6_1_hiseq

description: nuclear RNA

value: Shep Rb6


title: kc_shep-rb6_2_hiseq

description: nuclear RNA


title: q96 gonads Replicate 4


title: kc_shep-rb5_3_hiseq

description: nuclear RNA

value: Shep Rb5


title: q71 gonads Replicate 8


title: kc_shep-gp01_1_hiseq

description: nuclear RNA

value: Shep Gp01


title: q71 gonads Replicate 7


title: kc_shep-gp01_2_hiseq

description: nuclear RNA


title: R84_Germinating_Cotyledons_Stage1_BR2

value: 1 day after imbibition

value: lyophilized


title: kc_suhw-gp60_3_hiseq

description: nuclear RNA


title: kc_input_3_hiseq

description: nuclear RNA

value: input


title: q71 gonads Replicate 5


title: q71 gonads Replicate 6


title: kc_input_4_hiseq

description: nuclear RNA


title: q71 gonads Replicate 2


title: bg3_suhw-gp60_2_hiseq

description: nuclear RNA

source_name: BG3 cells

value: BG3 cells


title: R76_Germinating_Cotyledons_Stage1_BR1


title: kc_input_5_hiseq

description: nuclear RNA


title: q71 gonads Replicate 3


title: q71 gonads Replicate 1


title: bg3_shep-rb5_1_hiseq

description: nuclear RNA


title: bg3_suhw-gp60_1_hiseq

description: nuclear RNA


title: bg3_shep-rb5_2_hiseq

description: nuclear RNA


title: JM13_1

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
GSE52462_Nfurzeri_MZM_brain_Normal_Ageing_counts_RPKM.xls - Illumina Casava software used for extraction of FASTQ files
GSE52462_Nfurzeri_MZM_brain_Normal_Ageing_counts_RPKM.xls - FASTQ files were mapped using Bowtie versus a transcriptome catalogue of N. furzeri containing 19,812 transcripts
GSE52462_Nfurzeri_MZM_brain_Normal_Ageing_counts_RPKM.xls - Uniquely mapped reads for each transcript were counted using R Statistical Language and Bioconductor.
GSE52462_Nfurzeri_MZM_brain_Normal_Ageing_counts_RPKM.xls - The read counts were normalized with respect to the size of the individual genes and to the total amount of mappable reads obtained in the sequencing process, resulting in RPKM-values (Mortazavi et al. 2008) for each gene.
GSE52462_Nfurzeri_MZM_brain_Normal_Ageing_counts_RPKM.xls - The transcripts were annotated additionally using Ensembl gene identifiers from D. rerio, while 13,561 shared a best bi-directional BLAST hit between both species.
GSE52462_Nfurzeri_MZM_brain_Normal_Ageing_counts_RPKM.xls - Genome_build: Transcriptome sequence published by Petzold et al. 2013 [PMID: 23496936]
GSE52462_Nfurzeri_MZM_brain_Normal_Ageing_counts_RPKM.xls - Supplementary_files_format_and_content: Excel file including raw counts and RPKM values for each sample
------------
GSE52462_counts_RPKMs_2015.xls - Illumina Casava software used for extraction of FASTQ files
GSE52462_counts_RPKMs_2015.xls - FASTQ files were mapped using Tophat (v2.0.6) to the N.furzeri genome.
GSE52462_counts_RPKMs_2015.xls - Uniquely mapped reads were counted for each gene_id using featureCounts v1.4.3-p1 (featureCounts -T 8 -a $GTF -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE)
GSE52462_counts_RPKMs_2015.xls - RPKM values were computed using exon lengths provided by featureCounts as described in Mortazavi et al. 2008.
GSE52462_counts_RPKMs_2015.xls - Genome_build: genome v20150522 and annotation v20140422 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (http://nfingb.fli-leibniz.de/)
GSE52462_counts_RPKMs_2015.xls - Supplementary_files_format_and_content: Excel file includes raw counts and RPKM values

organism: Nothobranchius furzeri

source_name: total RNA extracted from brain

extract_protocol:
The whole fish brains were dissected and transferred into 2 ml tubes with 1 ml cooled QIAzol (Qiagen, Hilden, Germany) and one 5 mm stainless steel bead (Qiagen) was added. Homogenization was performed using a TissueLyzer II (Qiagen) at 20 Hz for 2-3x 1 min. After incubation for 5 min at room temperature 200 µl chloroform was added. The tube was shaken for (at least) 15 s and incubated for 3 min at room temperature. Phase separation was achieved by centrifugation at 12,000x g for 20 min at 4°C. The aqueous phase was transferred into a fresh cup and 10 µg of Glycogen (Invitrogen, Darmstadt, Germany), 0.16x volume NaAc (2 M; pH 4.0) and 1.1x volume isopropanol were added, mixed thoroughly and incubated for 10 min at room temperature. The RNA was precipitated by a centrifugation step with 12,000 x g at 4°C for 20 min. The supernatant was removed and the pellet was washed with 80% Ethanol twice and air dried for 10 min. The RNA was resuspended in 20 µl DEPC-treated water by pipetting up and down, followed by incubation at 65°C for 5 min. The RNA was quantified with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80°C until use.
Sequencing procedure was done using Illumina methodology [Bentley et al, 2008]. Around 2.5 µg of total RNA was used for library preparation (Illumina, TruSeq™ RNA Sample Prep Kit v2) using the manufacturer’s description.

tag: age

value: 39 weeks

value: brain


title: JM18_1


title: JM15_1


title: bg3_input_2_hiseq

description: nuclear RNA

tag: cell line


title: JM1_1


title: JM72_1

value: 27 weeks


title: JM69_1_w0w1


title: JM12_1_w0w1


title: JM66_1


title: bg3_input_1_hiseq

description: nuclear RNA


title: JM86_1_w0w1

value: 20 weeks


title: JM75_1


title: JM82_1


title: kc_input_6_hiseq

description: nuclear RNA


title: JM113_1

value: 12 weeks


title: JM84_1


title: JM79_1


title: JM109_1


title: JM107_1_w0w1


title: JM105_1_w0w1


title: JM104_1


title: Het_Dtt_treated

description:
Sample 4
mRNA-Seq (RSW)
processed data file: Dtt_RSW_processed.txt

tag: cell type

value: MEF

tag: treatment

value: 1mM Dithiothreiltol treated 4hrs.

tag: genotype/variation

value: Ire1a Heterozygous cells


title: JM103_1

value: 5 weeks


title: JM100_1


title: JM101_1


title: JM96_1_w0w1


title: worker bee small RNA

status: Public on Jul 28 2014

city: Stanford

first: Xiangqian

last: Guo

address: 300 Pasteur Dr.

department: Department of Pathology

institute: Stanford University

description: Experiment type: small RNA sequencing

data_processing:
Low-quality reads and 5’/3’ adaptor sequences were filtered out and discarded before mapping the small RNA reads to the honeybee genome with SOAP. Only perfect matches were accepted and retained for the following analysis.
To identify known miRNAs, we aligned all the small RNA reads to mature miRNAs and miRNA hairpins in miRBase13.0 with blast using an E-value threshold of 0.01. As a miRNA gene could have different isoforms, the sum of all sequence reads corresponding to a miRNA gene was used as a digital measure of the gene expression level.
For other known non-coding RNAs and coding genes, we collected all the non-coding RNAs such as rRNAs, tRNAs, snoRNAs, and snRNAs from NCBI, and Rfam, and all coding genes from UCSC, and aligned the small RNA reads to these sequences with blast using an E-value threshold of 0.01.
All the remaining unannotated distinct small RNAs were tested for their miRNA-encoding potential with “MIREAP” (https://sourceforge.net/projects/mireap/). Given that a miRNA could have different isoforms, we took the predominant small RNA from “MIREAP” as the novel representative miRNA.
The Audic and Claverie test was used to compare small RNA expression differences between worker and royal jelly .
Genome_build: apiMel2
Supplementary_files_format_and_content: expressional matrix with sample by column and gene by row

organism: Apis mellifera

source_name: Worker bee

growth_protocol: Three healthy 10-frame colonies of ‘Zhenongda No.1’- a high-yielding royal jelly breed of Apis mellifera ligustica , were maintained at the Huajiachi campus of Zhejiang University. In each colony, the queen laid eggs over a period of 24 hours in one empty frame which was subsequently moved to an egg-free super-chamber. After 66 hours (less than 18 hours after hatching), we transferred 150 larvae into queen cups to rear queens in each colony and put the queen cup frames into their corresponding colonies. 40-60 worker larvae and queen larvae were collected from each colony after 4 days (73~90 h after hatching), 5 days (97~114 h after hatching) and 6 days (121~138 h after hatching).

extract_protocol:
Total RNAs were extracted from the Queen and Worker samples with Trizol (Invitrogen) as per the manual. For small RNA library construction, total RNA was size fractionated on a 15% Tris-Borate-EDTA (TBE) urea polyacrylamide gel and the 18-30nt fraction was excised. Small RNAs were eluted in 0.3 M NaCl by rotating the slice at room temperature for 4 hours. The eluted RNAs were precipitated and washed in ethanol, and resuspended in ultrapure water.
The gel-purified small RNAs were ligated to the 5’ RNA adapter with T4 RNA ligase, and the ligation products were gel fractionated and purified, before ligating to the 3’ RNA adapter. The final ligation products were purified and amplified by RT-PCR. The amplification products were gel fractionated and purified by electrophoresis on a 6% polyacrylamide gel in TBE buffer, and a gel slice corresponding to the amplified library was eluted in 0.3 M NaCl by rotating the mixture at room temperature for 4 hours. The purified PCR products were then precipitated using ethanol, and resuspended in nuclease-free water. The purified PCR products were sequenced on the Solexa sequencing platform.

treatment_protocol: The larval samples were collected into 50 ml tubes, immediately frozen in liquid nitrogen and stored at -80C until being used for RNA extraction.

tag: sample collection

value: pool of day4, day5,day6

tag: tissue archive method

value: fresh frozen

tag: Stage

value: larva


title: queen bee small RNA

description: Experiment type: small RNA sequencing

source_name: Queen bee


title: JM52_1

tag: strain


title: WT2

city: Callaghan

first: Peter

last: Lewis

address: University Dr

country: Australia

institute: University of Newcastle

description: wild-type replicate 2

data_processing:
Analysis of the RNAseq was performed by Micromon at Monash University
The raw reads of 50 bp were clipped for Phred quality greater than or equal to 10.
Illumina adaptor sequences were removed from the ends of the reads and any reads shorter than 24 bp were removed
The reads were aligned to the reference genome A. baylyi ADP1 using SHRiMP 2.0, and alignments to annotated genes (called tags) were counted.
Alignment counts were analysed with EdgeR from the Bioconductor package
Genome_build: ASM4684v1
Supplementary_files_format_and_content: Excel file including log2 fold changes, RPKM values, p-values, gene information and COG analysis

organism: Acinetobacter baylyi

source_name: wild-type cells

growth_protocol: Overnight culture were diluted 1:100 in LB and cultured to an OD(600nm) of 1.0

extract_protocol:
Total RNA was isolated using a RiboPure-Bacteria kit (Ambion) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: wildtype


title: 2924_1

description: atfA knockout replicate 1

source_name: atfA knockout

value: atfA knockout


title: WT1

description: wild-type replicate 1


title: JM62_1


title: Mir212/132ILN/ILN

city: Freiburg

first: Yoko

middle: Fukuda

last: Yuzawa

address: Stübeweg 51

institute: Max-Planck Institute of Immunobiology

data_processing:
Illumina Casava1.8 software was used for basecalling. Reads that failed to pass filtering were removed.
Genome mapping was carried out using Bowtie (version 0.12.3) and Tophat (version 1.4.1) with default parameters. Resulting data was processed with BEDtools and visualized in the UCSC Genome Browser.
Sequences in fastq files are converted to reverse-complementary strand. NEUMA (version 1.1.2) program was performed to estimate whole mRNA expression using Refseq dataset with strand-specific analysis option.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include LVKM values (gene-level) for each Sample.
LVKM = log FVKM, where FVKM = fragments per virtual kilobase per million sequenced reads.
gFVKM = mRNA abundance estimated at the gene level.
gLVKM = gLVKM values are the final adjustment of gene-level estimates.

source_name: Mammary gland

extract_protocol: mammary gland was isolated, total RNA was extracted using Qiashredder and Rneasy kit. polyA(+) RNA was isolated by Dynabeads mRNA Purification Kit (Invitrogen) and fragmented by incubation at 94°C for 3min in fragmentation buffer (40mM TrisOAc pH8.2, 100mMKOAc, 30mM MgOAc).  cDNA was synthesized using SuperScriptTM III First-Strand Synthesis System for RT-PCR (Invitrogen) with random hexamers for first-strand, Second Strand Buffer (Invitrogen) and dNTPs with dTTP replaced by dUTP (Roche) for second-strand. End repair, dA-Tailing, and adapter-ligation were performed by NEBNext ChIP-Seq Sample Prep Master Mix Set1 (NEB). After size selection of fragments around 200-bp in length and Uracil–DNA glycosylase (NEB) treatment, cDNA was enriched by Phusion polymerase. We used the standard Illumina adaptors, PCR and sequencing primers. 2 lanes were used for each sample to obtain enough reads.

value: mammary gland

value: post natal week 6

value: Mir212/132ILN/ILN (insertion of an IRES-LacZ-Neo (ILN) cassette into the locus)


title: H3K27me3 in Ngn3+ cells

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

description:
raw files: 10.csfasta, 10.qual
Endocrine progenitors

data_processing: Gene Ontology was determined using DAVID and setting an FDR control of 10%. Resulting categories were merged if they contained the same genes, using the title of the more significantly called GO term.

growth_protocol: Pdx1-gfp (Gu et al., 2004) and Ngn3-gfp (Lee et al., 2002; White et al., 2008) mice were used for sequencing material.

extract_protocol:
H3K27me3 ChIP using low cell numbers was as described (Xu et al., 2011).  We used chromatin from 0.5-1 X 10^5 sorted cells, pooled from many embryos harvested on multiple dates.  Five µl of H3K27me3 antibody were used with the MAGnify™ Chromatin Immunoprecipitation System (Invitrogen 49-2024).
The preparations of multiplex libraries for sequencing were as per “NEBNext ChIP-Seq Library Prep Set for SOLiD” (NEB E6260S). Sequencing was performed on the SOLiD4.0 platform with input and H3K27me3-immunoprecipitated libraries.

treatment_protocol: Endoderm cells were purified by FACS with the ENDM1 antibody as described (Xu et al., 2011).  Embryos or pancreas tissue at later developmental stages were dissected from Pdx1-GFP or Ngn3-GFP stains, dissociated with trypsin for 5 minutes at 37ºC, then stopped with 0.4 volumes of FBS.  The cells were filtered through a Nylon mesh.  GFP+ cells were then analyzed or purified on a BD FACSDiva cell sorter.

tag: strain background

tag: developmental stage

tag: tissue source

value: Embryonic mouse endoderm

tag: tissue/cell type

value: Endocrine progenitors

tag: sorted cell type

tag: chip antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: WT

tag: tissue

tag: age

value: wild type


title: Input in Ngn3+ cells

description:
raw files: 9.csfasta, 9.qual
Endocrine progenitors


title: JM97_1

value: brain


title: Input in Pdx1+Liv2- cells

description:
raw files: 7.csfasta, 7.qual
Pancreatic progenitors

value: unknown (M) X B6C3F1 (F)

value: Pancreatic progenitors


title: Input in ENDM1+ cells

description:
raw files: 1.csfasta, 1.qual
Endoderm progenitors

value: Endoderm progenitors


title: EY-RNA_-Glu15_polyA_Replicate2

city: La Jolla

first: Brian

middle: Matthew

last: Zid

state: California

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

institute: University of California San Diego

description:
PolyA selected RNA
-Glucose15m

data_processing:
Reads were trimmed of their polyA tail and then aligned to the S. cerevisiae genome using Bowtie-0.12.8.
Reads were aligned to a library of RNA genes
Remaining reads were aligned to the S. cerevisiae genome R64-1-1
Genome_build: http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-1-1_20110203.tgz
Supplementary_files_format_and_content: Each line in the tab deliminated txt file has the following columns: Systematic Name: Name: Descript: Start:  End: Length: RNA-Glu/RNA+Glu(log2)-BY4741-mRNA Fold Change Replicate 1: Ribo-Glu/RNA-Glu/Ribo+Glu/RNA+Glu(log2)-BY4741-Ribosome Occupancy Fold Change Replicate 1: RNA-Glu/RNA+Glu(log2)-EY0690-mRNA Fold Change Replicate 1: Ribo-Glu/RNA-Glu/Ribo+Glu/RNA+Glu(log2)-EY0690-Ribosome Occupancy Fold Change Replicate 1: RNA(pA)-Glu/RNA(pA)+Glu(log2)-BY4741-mRNA Fold Change Replicate 1: Ribo-Glu/RNA(pA)-Glu/Ribo+Glu/RNA(pA)+Glu(log2)-BY4741-Ribosome Occupancy Fold Change Replicate 1: RNA(pA)-Glu/RNA(pA)+Glu(log2)-BY4741-mRNA Fold Change Replicate 2: Ribo-Glu/RNA(pA)-Glu/Ribo+Glu/RNA(pA)+Glu(log2)-BY4741-Ribosome Occupancy Fold Change Replicate 2: RNA(pA)-Glu/RNA(pA)+Glu(log2)-EY0690-mRNA Fold Change Replicate 1: Ribo-Glu/RNA(pA)-Glu/Ribo+Glu/RNA(pA)+Glu(log2)-EY0690-Ribosome Occupancy Fold Change Replicate 1: RNA(pA)-Glu/RNA(pA)+Glu(log2)-EY0690-mRNA Fold Change Replicate 2: Ribo-Glu/RNA(pA)-Glu/Ribo+Glu/RNA(pA)+Glu(log2)-EY0690-Ribosome Occupancy Fold Change Replicate 2:  Ribo+Glu_RPKM-BY4741 - Replicate 1: Ribo-Glu_RPKM-BY4741 - Replicate 1: RNA+Glu_RPKM-BY4741 TotalRNA - Replicate 1: RNA-Glu_RPKM-BY4741 TotalRNA - Replicate 1: Ribo+Glu_RPKM-EY0690 - Replicate 1: Ribo-Glu_RPKM-EY0690 - Replicate 1: RNA+Glu_RPKM-EY0690 TotalRNA - Replicate 1: RNA-Glu_RPKM-EY0690 TotalRNA - Replicate 1: RNA+Glu_RPKM-BY4741 polyA_RNA - Replicate 1: RNA-Glu_RPKM-BY4741 polyA_RNA - Replicate 1: Ribo+Glu_RPKM-BY4741 - Replicate 2: Ribo-Glu_RPKM-BY4741 - Replicate 2: RNA+Glu_RPKM-BY4741 polyA_RNA - Replicate 2: RNA-Glu_RPKM-BY4741 polyA_RNA - Replicate 2: RNA+Glu_RPKM-EY0690 polyA_RNA - Replicate 1: RNA-Glu_RPKM-EY0690 polyA_RNA - Replicate 1: Ribo+Glu_RPKM-EY0690 - Replicate 2: Ribo-Glu_RPKM-EY0690 - Replicate 2: RNA+Glu_RPKM-EY0690 polyA_RNA - Replicate 2: RNA-Glu_RPKM-EY0690 polyA_RNA - Replicate 2:  Ribo+Glu_InitiationRegion-BY4741 Replicate 1: Ribo+Glu_DownstreamRegion-BY4741 Replicate 1: Ribo-Glu_InitiationRegion-BY4741 Replicate 1: Ribo-Glu_DownstreamRegion-BY4741 Replicate 1: RNA+Glu_InitiationRegion-BY4741_TotalRNA Replicate 1: RNA+Glu_DownstreamRegion-BY4741_TotalRNA Replicate 1: RNA-Glu_InitiationRegion-BY4741_TotalRNA Replicate 1: RNA-Glu_DownstreamRegion-BY4741_TotalRNA Replicate 1: Ribo+Glu_InitiationRegion-EY0690 Replicate 1: Ribo+Glu_DownstreamRegion-EY0690 Replicate 1: Ribo-Glu_InitiationRegion-EY0690 Replicate 1: Ribo-Glu_DownstreamRegion-EY0690 Replicate 1: RNA+Glu_InitiationRegion-EY0690_TotalRNA+RiboZeroRNA Replicate 1: RNA+Glu_DownstreamRegion-EY0690_TotalRNA+RiboZeroRNA Replicate 1: RNA-Glu_InitiationRegion-EY0690_TotalRNA+RiboZeroRNA Replicate 1: RNA-Glu_DownstreamRegion-EY0690_TotalRNA+RiboZeroRNA Replicate 1: RNA+Glu_InitiationRegion-BY4741_polyA_RNA Replicate 1: RNA+Glu_DownstreamRegion-BY4741_polyA_RNA Replicate 1: RNA-Glu_InitiationRegion-BY4741_polyA_RNA Replicate 1: RNA-Glu_DownstreamRegion-BY4741_polyA_RNA Replicate 1: Ribo+Glu_InitiationRegion-BY4741 Replicate 2: Ribo+Glu_DownstreamRegion-BY4741 Replicate 2: Ribo-Glu_InitiationRegion-BY4741 Replicate 2: Ribo-Glu_DownstreamRegion-BY4741 Replicate 2: RNA+Glu_InitiationRegion-BY4741_polyA_RNA Replicate 2: RNA+Glu_DownstreamRegion-BY4741_polyA_RNA Replicate 2: RNA-Glu_InitiationRegion-BY4741_polyA_RNA Replicate 2: RNA-Glu_DownstreamRegion-BY4741_polyA_RNA Replicate 2: RNA+Glu_InitiationRegion-EY0690_polyA_RNA Replicate 1: RNA+Glu_DownstreamRegion-EY0690_polyA_RNA Replicate 1: RNA-Glu_InitiationRegion-EY0690_polyA_RNA Replicate 1: RNA-Glu_DownstreamRegion-EY0690_polyA_RNA Replicate 1: Ribo+Glu_InitiationRegion-EY0690 Replicate 2: Ribo+Glu_DownstreamRegion-EY0690 Replicate 2: Ribo-Glu_InitiationRegion-EY0690 Replicate 2: Ribo-Glu_DownstreamRegion-EY0690 Replicate 2: RNA+Glu_InitiationRegion-EY0690_polyA_RNA Replicate 2: RNA+Glu_DownstreamRegion-EY0690_polyA_RNA Replicate 2: RNA-Glu_InitiationRegion-EY0690_polyA_RNA Replicate 2: RNA-Glu_DownstreamRegion-EY0690_polyA_RNA Replicate

source_name: yeast EY0690

growth_protocol: Yeast strains BY4741 and EY0690 (w303) was grown at 30C in synthetic complete + glucose media to OD600 =0.3-0.4. Then 15min into SC -glucose media as indicated.

extract_protocol:
Footprints: cells were rapidly harvested, flash-frozen in polysome lysis buffer, and pulverized in a mixer mill, extracts were digested with 100 U Rnase I for 30 min, monosomes were purified by sucrose density gradient or by sucrose cushion, RNA was extracted from the monosome fraction by hot acid phenol; total RNA was prepared from flash-frozen cells by the hot acid phenol protocol, polyA RNA was purified by oligo-dT DynaBeads, or RiboZero selected RNA or Total RNA, and fragmented at 95 C under mild alkali conditions
Libraries were prepared by polyA tailing 28mers followed by reverese transcription with either OTi225 or OTi9pA, see Methods in Zid et al, in submission

treatment_protocol: All samples were treated for 1 min with cycloheximide 100ug/ml

tag: strategy

value: RNA-seq

tag: treatment


title: KO_Dtt_untreated

description:
Sample 3
mRNA-Seq (RSW)
processed data file: Dtt_RSW_processed.txt

source_name: Mouse Embryonic Fibroblasts

tag: cell type

value: MEF

value: Untreated

tag: genotype/variation

value: Ire1a Knockout cells


title: H3K27me3 in Liv2+Pdx1- cells

description:
raw files: 6.csfasta, 6.qual
Immature hepatocytes

value: Immature hepatocytes


title: H3K27me3 in ENDM1+ cells

description:
raw files: 2.csfasta, 2.qual
Endoderm progenitors


title: Input in Liv2+Pdx1- cells

description:
raw files: 5.csfasta, 5.qual
Immature hepatocytes


title: 2924_2

description: atfA knockout replicate 2

value: atfA knockout


title: Input in ENDM1- cells

description:
raw files: 3.csfasta, 3.qual
Non-Endoderm

value: Embryonic mouse tissue

value: Non-Endoderm


title: EY-Ribo_logphase_Replicate2

description:
Ribosome protected mRNA
+Glucose

value: Ribosome Profiling

value: +Glucose


title: EY-Ribo_-Glu15_Replicate2

description:
Ribosome protected mRNA
-Glucose15m


title: ribosome footprinting nmf205-/-; n-Tr20J/J rep1

city: Farmington

first: Jeffrey

last: Chuang

state: CT

address: 263 Farmington Avenue

department: Computational Biology

institute: The Jackson Laboratory for Genomic Medicine

data_processing:
library strategy: ribosome footprinting
fastx_clipper -Q33 -a CTGTAGGCACCATCAAT -l 25 -c -n -v -i $fastqfile -o temp_clipped.fastq
fastx_trimmer -Q33 -f 2 -l 100 -i temp_clipped.fastq -o temp_trimmed.fastq
Mouse ribosomal RNA sets were obtained by searching Genbank for known rRNAs and then filtering these out using the command: bowtie -p 16 rRNA temp_trimmed.fastq -l 23 --un temp_noRRNA.fastq > /dev/null.
Reads with unique mapping to the mm10 genome were computed using tophat and Illumina igenome annotations: tophat -p 16 -a 8 -m 0 -i 70 -I 500000 -g 1 --no-novel-juncs --library-type fr-firststrand –GTF /IlluminaGTF/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf /IlluminaGTF/Mus_musculus/UCSC/mm10/Sequence/BowtieIndex/genome/ temp_noRRNA.fastq. Manual inspection of coding loci with high read counts also revealed an additional rRNA overlapping a coding region, which was removed from consideration in further data analysis (LSU-rRNA_Hsa, on mm10 chr6).
Genome_build: mm10
Supplementary_files_format_and_content: bam files

extract_protocol:
Tissue homogenization was performed with a mixer mill (Retsch MM400) in 1.0 ml of 20 mM Tris-Cl (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% (v/v) Triton X-100, 25 U/ml Turbo DNase I, 100 mg/ml cycloheximide, and 2 mg/ml harringtonine. RNase I-treated lysates were ultracentrifuged through a sucrose cushion to obtain the ribosome pellet from which RNA was extracted. 26 nt to 34-nt RNA fragments were purified by electrophoresis on 15% polyacrylamide TBE-urea gel.
Linker addition and cDNA generation and circularization were then performed. Subtraction of rRNA with a pool of oligos was performed as indicated in the protocol. The resulting DNAs were amplified with different indexing primers to distinguish each sample as indicated in the protocol. The libraries were analyzed by sequencing on an Illumina HiSeq 2000 platform.

treatment_protocol: Cerebella were immediately frozen in liquid nitrogen upon dissection and three cerebella were pooled from mice of each genotype for library generation.

tag: background strain

value: Cerebellum


title: EY-RNA_logphase_polyA_Replicate2

description:
PolyA selected RNA
+Glucose

tag: strain


title: ribosome footprinting nmf205-/-; n-Tr20J/J rep2


title: ribosome footprinting nmf205-/-; n-Tr20N/N rep2


title: EY-RNA_-Glu15_Total_Replicate1

description:
Total RNA
-Glucose15m

data_processing:
Reads were trimmed of their polyA tail and then aligned to the S. cerevisiae genome using Bowtie-0.12.8.
Reads were aligned to a library of RNA genes
Remaining reads were aligned to the S. cerevisiae genome R64-1-1
Genome_build: http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-1-1_20110203.tgz
Supplementary_files_format_and_content: Each line in the tab deliminated txt file has the following columns:  Systematic Name:Name:Descript:Start: End :Length: RNA-Glu:RNA+Glu(log2)-BY4741-mRNA Fold Change:Ribo-Glu/RNA-Glu/Ribo+Glu/RNA+Glu(log2)-BY4741-Ribosome Occupancy Fold Change: RNA-Glu/RNA+Glu(log2)-EY0690-mRNA Fold Change: Ribo-Glu/RNA-Glu/Ribo+Glu/RNA+Glu(log2)-EY0690-Ribosome Occupancy Fold Change: Ribo+Glu_InitiationRegion-BY4741: Ribo+Glu_DownstreamRegion-BY4741: Ribo-Glu_InitiationRegion-BY4741: Ribo-Glu_DownstreamRegion-BY4741: RNA+Glu_InitiationRegion-BY4741_TotalRNA: RNA+Glu_DownstreamRegion-BY4741_TotalRNA: RNA-Glu_InitiationRegion-BY4741_TotalRNA: RNA-Glu_DownstreamRegion-BY4741_TotalRNA: Ribo+Glu_InitiationRegion-EY0690: Ribo+Glu_DownstreamRegion-EY0690: Ribo-Glu_InitiationRegion-EY0690: Ribo-Glu_DownstreamRegion-EY0690: RNA+Glu_InitiationRegion-EY0690_TotalRNA+RiboZeroRNA: RNA+Glu_DownstreamRegion-EY0690_TotalRNA+RiboZeroRNA: RNA-Glu_InitiationRegion-EY0690_TotalRNA+RiboZeroRNA: RNA-Glu_DownstreamRegion-EY0690_TotalRNA+RiboZeroRNA: Ribo+Glu_RPKM-BY4741: Ribo-Glu_RPKM-BY4741: RNA+Glu_RPKM-BY4741: RNA-Glu_RPKM-BY4741: Ribo+Glu_RPKM-EY0690: Ribo-Glu_RPKM-EY0690: RNA+Glu_RPKM-EY0690: RNA-Glu_RPKM-EY0690

growth_protocol: Yeast strain BY4741 was grown at 30C in synthetic complete + glucose media to OD600 =0.3-0.4. Then 15min into SC -glucose media as indicated.


title: ribosome footprinting B6J;n-Tr20J/J rep2

source_name: ribosome footprinting B6J;n-Tr20J/J


title: Four-cell Embryo 2 Blastomere 4

source_name: blastomere

value: Four-cell Embryo Blastomere


title: EY-RNA_-Glu15_polyA_Replicate1

description:
PolyA selected RNA
-Glucose15m


title: ribosome footprinting nmf205-/-; n-Tr20N/N rep1


title: EY-RNA_-Glu15_RiboZero_Replicate1

description:
RiboZero selected RNA
-Glucose15m


title: ribosome footprinting B6J;n-Tr20N/N rep2

source_name: ribosome footprinting B6J;n-Tr20N/N


title: EY-Ribo_-Glu15_Replicate1

description:
Ribosome protected mRNA
-Glucose15m


title: H3K27me3 in ENDM1- cells

description:
raw files: 4.csfasta, 4.qual
Non-Endoderm

value: wild type

value: Millipore


title: EY-RNA_logphase_polyA_Replicate1

description:
PolyA selected RNA
+Glucose


title: S2_PolII_TRIMKD_rep2

city: RTP

first: David

last: Fargo

department: HHS

institute: National Institute of Environmental Health Sciences

data_processing:
Basecalls performed using standard Illumina pipeline
Reads with mean Phred quality <20 were filtered
Reads were aligned to mm9 assembly using bowtie 0.12.8 employing parameters -v2 -m1
Duplicates reads were removed using Picard tools 1.74
Reads were extended to mean fragment length (150 nt), replicates were merged, and read coverage tracks were generated using bedtools 2.16.2
Genome_build: mm9
Supplementary_files_format_and_content: bigWig, read coverage

source_name: Embryonic Stem Cells

growth_protocol: ES cells were cultured in M10 medium as described in the manuscript

extract_protocol:
ES cells were crosslinked with formaldehyde and lysed. Chromatin was sonicated, and ChIP was performed as described in the manuscript.
Libraries were constructed using the SPRI-TE Nucleic Acid Extractor (Beckman Coulter, Indianapolis, IN) with a size selection of 200-400bp

treatment_protocol: ES cells were transfected with siRNAs at 50 nM concentration with lipofectamine 2000

value: S2 PolII, (ab5095, Abcam)

value: Trim28 siRNA


title: S2_PolII_WT_rep2

value: luciferase siRNA


title: EY-RNA_logphase_RiboZero_Replicate1

description:
RiboZero selected RNA
+Glucose

value: RNA-seq


title: BY-RNA_logphase_Total_Replicate1

description:
Total RNA
+Glucose

source_name: yeast BY4741


title: EY-RNA_logphase_Total_Replicate1

description:
Total RNA
+Glucose


title: S2_PolII_WT_rep1


title: S2_PolII_TRIMKD_rep1


title: Total_PolII_TRIMKD_rep1

value: Total PolII, (sc-899, Santa Cruz Biotechnology)


title: Total_PolII_WT_rep1


title: H3K27me3 in Pdx1+Liv2- cells

description:
raw files: 8.csfasta, 8.qual
Pancreatic progenitors

value: unknown (M) X B6C3F1 (F)

value: Embryonic mouse endoderm

value: Pancreatic progenitors


title: Total_PolII_WT_rep2


title: Input_WT_rep2


title: Input_WT_rep1


title: EY-Ribo_logphase_Replicate1

description:
Ribosome protected mRNA
+Glucose