title: Mitochondrial ESTs from females of D. melanogaster

description:
Mitochondrial ESTs from females from reciprocal crosses of D. melanogaster strains 14021-0231.36 and 14021-0231.16.
Expression profiles of D. melanogaster mitochondrial protein coding genes and rRNA genes from the library prepared with female flies.
library strategy: EST
library source: non-genomic
library selection: cDNA

source_name: D. melanogaster females


title: 5' NCR from HCV isolated at week -4 from 4x0513 rep2

status: Public on Dec 03 2009

type: SRA

city: Hoersholm

first: Andreas

last: Petri

address: Kogle Alle 6

department: microRNA

country: Denmark

institute: Santaris Pharma

library_source: viral RNA

data_processing:
A single amplicon was analyzed for variations using the Roche/454 GS Amplicon Variant Analyzer.  Barcoded samples were demultiplexed by the software using gsMID tag definitions.
Processed data files include .fasta and .qual files (corresponding to phred quality scores for the fasta files).
Additional processed data available on the Series record include:
AMPLICON.txt, which contains the reference sequence of the amplicon that we have sequenced and the primer sequences
Condensed_all_variants_36x8.txt, which describes frequencies of variations relative to the reference sequence observed in the different samples

molecule: other

organism: Hepacivirus hominis

extract_protocol: The 5’ end of the viral RNA from serum was reverse transcribed into complementary DNA and the cDNA was amplified by hemi-nested polymerase chain reaction (PCR) to obtain a specific PCR product. RNA from 10 μl of serum was used for RT-PCR using RNA UltraSense OneStep Quantitative RT-PCR Kit (Invitrogen) for first round of PCR. The forward primer was 1-20MF (5’-gccagccgcctgatgggggc-3’ with a G/C change at nucleotide 8 to destabilize the step loop structure in the primer. The RT and reverse primer was 274R 5’-tcgcgacccaacactactcggc-3’. The cycles were 60ºC for 30 min, 95ºC for 10 min, and 45 cycles of 95ºC for 15 sec, 60ºC for 1 min, 72ºC for 30 sec with a final cycle of 72ºC for 5 min. One tenth of the PCR product was subjected to a hemi-nested PCR reaction using 1-20MF and 223R (5’-tccaggcattgagcgggtttat-3’) in a Vent Polymerase reaction for 25 cycles at 94ºC for 1 min, 60ºC for 1 min 30 sec, 72ºC for 3 min with a final cycle of 65ºC for 5 min. The PCR product was purified by running on a 1% TAE agarose gel, and by isolating the 223 bp product followed by purification using QIAquick Gel Extraction Kit (Qiagen). The purified PCR products were subjected to deep sequencing by 454 Titanium Sequencing (SeqWright, Houston TX). The samples were first modified to have unique sequence ends with Multiplex Identifiers (MIDs or bar coded).

tag: animal id

tag: treatment protocol

value: locked nucleic acid (LNA)-modified oligonucleotide (SPC3649) complementary to miR-122

tag: time (weeks of treatment)

tag: barcode

tag: region


title: Mitochondrial ESTs from males of D. pseudoobscura

status: Public on Dec 09 2009

city: Campinas

first: Tatiana

middle: Teixeira

last: Torres

state: SP

address: Rua Candido Rondon, 400

department: CBMEG

country: Brazil

institute: Unicamp

description:
Mitochondrial ESTs from males from reciprocal crosses of D. pseudoobscura strains 14011‑0121.94 and 14011‑0121.88.
Expression profiles of D. pseudoobscura mitochondrial protein coding genes and rRNA genes from the library prepared with male flies.
library strategy: EST
library source: non-genomic
library selection: cDNA

library_source: transcriptomic

data_processing:
Alignment of the 454-ESTs to annotated mitochondrial transcripts was performed on PanGEA (available at www.koﬂer.or.at/bioinformatics). We used the 5.5 release of transcript annotations of D. melanogaster as a reference data set, correcting the transcripts for the genes atp6, atp8, nad4 and nad4L that were not annotated as bi-cistronic transcripts. For D. pseudobscura we used the assembled and annotated mitochondrial genome (FJ899745). Only reads with at least 95% identity with a sequence in the database over at least 60% of their length were considered. The numberof ESTs that mapped to a given transcript was taken as the absolute expression level for that gene. Expression levels were normalized by dividing the number of ESTs mapped to each mitochondrial transcript by the total number of ESTs in the library (see Series GSE16651 supplementary file).
The Sample data tables represent the four libraries generated in our study. Each row contains one sequence, the the number of times it was sequenced and the mitochondrial gene it was mapped to. The 3' linker and the poly-A tail were removed from these sequences.

molecule: total RNA

organism: Drosophila pseudoobscura

source_name: D. pseudoobscura males

growth_protocol: Flies were grown at 20°C in standard cornmeal medium. Newly emerged males and females were collected separately and allowed to age from 3 to 7 days.

extract_protocol: Total RNA was extracted with Trizol (Invitrogen) from 30 flies (three replicates of 10 flies each). RNA samples were treated with DNase I (10 units/50 mg of total RNA) and the absence of contaminating genomic DNA was confirmed by PCR. First-strand cDNA was generated from approximately 5 mg of total RNA using the RevertAid H  Minus First Strand cDNA Synthesis Kit (Fermentas) according to manufacturer's instructions. The synthesis was carried out using a biotinylated oligo(dT) fused to the 454 sequencing primer B (5'-Biotin-GCCTTGCCAGCCCGCTCAG(T)17V-3', where V stands for any base but T).  Double-stranded cDNA was synthesized by addition of 30 U of E. coli DNA polymerase I, and 1 U of E. coli Ribonuclease H to the first- strand synthesis reaction, following Fermentas' suggested protocol  for second strand cDNA synthesis.

tag: gender

value: male

tag: strains

tag: developmental stage

value: Adults

tag: tissue

value: Whole body


title: Maa7-IR44_Chlamydomonas_rep2

status: Public on Feb 09 2010

city: Newark

first: Linda

last: Rymarquis

state: DE

address: 15 Innovation way rm 241

country: USA

institute: University of Delaware

description: Low molecular weight RNA gel-sized in the ~18-33 nt range

data_processing: Small RNA reads were analyzed after removal of 3' adapter (5' -TCGTATGCCGTCTTCTGCTTG) and filtering of 5' adapter (5'-GTTCAGAGTTCTACAGTCCGACGATC) or 3' adapter artifacts. Sequences were segregated into individual libraries according to their barcodes and the barcodes removed. Raw abundances were normalized according to the formula: normalized abundance (TPM)= raw/(total genome match - (t/r/sn/snoRNA/chloroplast/mitochondria)*1,000,000.

organism: Chlamydomonas reinhardtii

source_name: vegetative cells

growth_protocol: Cell were grown photoheterotrophically in Tris-Acetate-Phosphate (TAP) medium

extract_protocol: A conventional TRI Reagent extraction was performed to extract total RNA, followed by precipitation of the low molecular weight fraction

value: CU

tag: small rna library

value: Control line


title: 5' NCR from HCV isolated at week 23 from 4x0514 rep1


title: 5' NCR from HCV isolated at week 27 from 4x0513 rep2


title: Mut-68_Chlamydomonas_rep1

value: GA

value: Mutation in Mut-68 gene


title: 5' NCR from HCV isolated at week 17 from 4x0513 rep1


title: 5' NCR from HCV isolated at week -4 from 4x0514 rep1


title: 5' NCR from HCV isolated at week -4 from 4x0513 rep1


title: AU1054 SE2, Replicate 2

status: Public on Nov 21 2009

city: Boston

first: Deborah

middle: R.

last: Yoder-Himes

state: MA

address: 77 Louis Pasteur Ave, 1038 NRB

department: Microbiology and Molecular Genetics

institute: Harvard Medical School

data_processing: Sequencing reads were mapped to the genome using BlastN with a threshold e-value of 0.0001 and using the "-F F" parameter. Reads mapped to rRNA and reads not mapped under the mentioned parameters were removed from further analysis. The number of reads overlapping each gene based on GenBank annotation was recorded. Reads from replicate samples were pooled, and the number of reads per gene was normalized according to the total number of reads in each library and the gene size. The resulting number is the gene expression index (GEI, expressed as normalized reads per kilobase). Reproducibility was assessed by plotting replicate GEI values against each other.

organism: Burkholderia cenocepacia

source_name: AU1054 SE-grown cells

growth_protocol: All cells were grown on a rotary shaker in 125 mL flasks containing 30 mL of medium. The cultures grown on synthetic CF sputum medium (6) at 37°C were inoculated from cells grown on LB agar plates. The inoculum for the soil extract medium (SE) was grown overnight in 1/10th tryptic soy broth at 22°C, centrifuged at 6000 rpm at room temperature, and the pellets were resuspended in 2 mL spent supernatant. One ml was diluted into 30 mL of moderate soil medium (15), which contains 10% soil extract (prepared by autoclaving 400 g sieved maize rhizosphere soil per liter of water for 15 min, centrifuging, and filtering to remove particulates) and supplemented with 3 mM glucose (equal to the CF medium). The soil cultures were incubated at 22°C.

extract_protocol: Libraries were prepared for sequencing according to the manufacturer's instructions.

treatment_protocol: Cell growth was monitored in triplicate 30 mL cultures of each strain under each condition. When the O.D.600 reached approximately 1.0 or 0.8 for CF and SE conditions, respectively, cells were centrifuged at 6000 rpm at 4°C and cell pellets were resuspended in 3 mL phosphate-buffered saline. One mL of culture was subjected to RNA purification by RNeasy Midi Kit (Qiagen, Valencia, CA) and eluted in 500 uL of RNase-free water. Samples were treated with DNaseI to remove any residual DNA and purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. Ten micrograms from each total RNA sample was subjected to further purification by enriching for mRNA via the MICROBExpress kit (Ambion) according to the manufacturer’s instructions. Samples were resuspended in 15 uL RNase-free water. cDNA was generated according to instructions given in Invitrogen’s Superscript Double-Stranded cDNA Synthesis Kit. Briefly, each mRNA sample was mixed with 100 pmol random hexamers (Integrated DNA Technologies, Coralville, IA), incubated at 70°C for 10 min, chilled on ice, mixed with 5 uL First-Strand Reaction Buffer (Invitrogen), 2.5 uL 0.1 M DTT, 1.25 uL 10 mM RNase-free dNTP mix, 3 uL Superscript III reverse transcriptase, and incubated at 50°C for 2 h. To generate the second strand, the following Invitrogen reagents were added: 86 uL RNase-free water, 30 uL Second-Strand Reaction Buffer, 3 uL 10 mM RNase-free dNTP mix, 10 U E. coli DNA Ligase, 40 U E. coli DNA Polymerase, 2 U E. coli RNase H, and incubated at 16°C for 2 h. Ten units of T4 DNA Polymerase (Invitrogen) were added the reactions were incubated for an additional 5 min at 16°C. Reactions were stopped by adding 10 uL 0.5 M RNase-free EDTA and purified by phenol-chloroform extraction and ethanol precipitation. Residual RNA was removed by treating with RNaseH and RNaseA followed by phenol-chloroform extraction and ethanol precipitation.

tag: condition

value: soil environment

tag: strain

tag: growth phase

value: mid-log phase, OD600~0.75


title: HI2424 SE1, Replicate 1

source_name: HI2424 SE-grown cells


title: AU1054 CF2, Replicate 2

source_name: AU1054 CF-grown cells

value: cystic fibrosis lung environment

value: mid-log phase, OD600~1.0


title: AU1054 SE1, Replicate 1


title: HI2424 SE2, Replicate 2


title: HI2424 CF1, Replicate 1

source_name: HI2424 CF-grown cells


title: 5' NCR from HCV isolated at week 11 from 4x0513 rep1


title: RNA_whole_worm_mixed_stages, A

status: Public on Nov 13 2009

city: New York

first: Kristin

middle: C

last: Gunsalus

state: NY

department: Biology

institute: NYU Center for Genomics and Systems Biology

data_processing:
Aligned using bowtie aligner tool, v0.10.1, against the wormbase WS190 release of the genome.  Parameters:
-n 2 :allow max 2 mismatches in first 28 base pairs: 2 (-n 2)
-e 70: maximum permitted total quality values at mismatched position
-k 1: report 1 valid alignments per read, (chosen at random if more than one valid alignment is found).

organism: Caenorhabditis elegans

source_name: N2 wildtype

growth_protocol: Mixed stage worms were grown on 10 cm2 NGM plates seeded with OP50.

extract_protocol:
RNA extraction was performed following the vendor’s protocol with the following modification: 3 times freeze/thaw/vortex and disruption with pellet pestle was included to increase worm lysis efficiency.
Total RNA was incubated at 55°C for one hour in presence of Superscript III Reverse Transcriptase (Invitrogen) and a universal VN poly-dT reverse primer, according the manufacture specifications. 3'UTR amplification were performed in 96-well plates format using transcript-specific forward primers and the universal reverse primer in presence of RNA prepared in the first strand reaction, using the following PCR parameters: denaturing 94°C 30 sec, annealing 60°C 30 sec, extension 72°C for 3 minutes. 3'UTRs were recombined into pDONR P2R-P3 entry vector using the BP Clonase II Enzyme Mix kit (Invitrogen) following the manufacturer's specifications and transformed into MultiShot Stripwell TOP 10 plates (Invitrogen). The transformed bacteria were grown overnight at 37°C under kanamycin selection.  6,912 minipools were manually streaked into large agar plates and 8 single colonies each minipool (total 55,296 colonies) were manually recovered, propagated and pooled in 8 different sets using the Aquarius automated multi-channel pipetting system (Tecan Trading AG, Switzerland). Each set contains none or one unique 3'UTR isoform.  Plasmid DNA was recovered using standard alkaline lysis procedure from overnight cultures of each of the 8 deconvoluted libraries . Each library was used as template for PCR reactions to produce eight amplicon libraries using the following primers: forward: GTT TCT CGT TCA ACT TTC TTG TAC AAA GTG GGA reverse: ATA ATG CCA ACT TTG TAT AAT AAA GTT GTT TTT TTT TTT. The eight libraries were then purified through Qiagen columns, adjusted to be blunt-end and incubated in presence of ligase overnight. Each library were then sonicated using bioruptor with the following parameters: 30 minutes, 30 sec ON, 30 sec OFF. Six of the resultant 8 fragmented libraries were prepared for Solexa sequencing using the manufacturer recommendations in Dr. Sachidanandam Laboratory in Mount Sinai, New York.

value: mixed stage


title: Ovules (on the day of anthesis 0 DPA)

status: Public on Nov 12 2009

city: South San Francisco

first: Vikram

last: Agarwal

state: CA

address: 1130 Veterans Blvd

institute: Calico Life Sciences

data_processing: The following adaptor sequence was cleaved from the 3' end of the small RNA if it was detected: TCGTATGCCGTCTTCTGCTTG.  The 5' nucleotide of the small RNA was used as an indexing base that denoted the tissue that the read was derived from: A --> Leaf tissue, G --> -3 DPA ovule tissue, C -->  0 DPA ovule tissue, T --> +3 DPA ovule tissue.  This nucleotide was cleaved to generate library-specific counts for each unique small RNA sequence, discarding small RNAs below 17 base pairs in length.  Contaminant RNAs were annotated and removed based on homology to: 1) the A. thaliana and B. napus mitochondrial genomes, 2) the G. hirsutum chloroplast genome, 3) plant snRNAs and snoRNAs deposited in NCBI, 4) A. thaliana tRNA sequences, and 5) annotated A. thaliana and G. hirsutum rRNA sequences.

organism: Gossypium hirsutum

source_name: 0 DPA ovules

growth_protocol: G. hirsutum L. cv. Texas Marker-1 (TM-1) cotton plants were grown in a greenhouse at The University of Texas at Austin or in field in College Station Texas.

extract_protocol: Total RNA was purified and verified using the CTAB extraction method.  Small RNAs (17-30-nt) were purified cloned barcoded using oligo adaptors and sequenced from 75 micrograms of cotton total RNA for each sample type using a protocol provided by Illumina

treatment_protocol: Ovules at 3 days prior to anthesis (- 3DPA) on the day of anthesis (0 DPA) and 3 days post-anthesis (+3 DPA) and seedling leaves were harvested for total RNA extraction.

value: 0 DPA ovules


title: Ovules (3 days prior to anthesis - 3 DPA)

source_name: -3 DPA ovules

value: -3 DPA ovules


title: RNA_whole_worm_mixed_stages, RACE, A

description:
linker removed processed files: blat coordinates and sequences
Use RACE clones to identify 3'UTR isoforms via deep sequencing.

data_processing: All sequences that didn't reach the polyA were removed. The remaining sequences were processed to remove the 5' and 3' adaptors, and only those with a length of at least 15bp were used for further analysis. Sequences were aligned to the genome using BLAT (downloaded from http://www.genome.ucsc.edu/, and run locally), with a maximum intron size of 1000, minimum window size of 5 and maximum Gap of 6. Best matches are selected; multiple alignments are reported if the best match is present in more than one genomic location.  Forward reads are identified by the following pattern - XXXX-GATCNNNNNNNNNNNNNN-XAAAAXAAAAXAAAAXAAAA where XXXX represents the corresponding 4bp barcode for the stage and Ns represent the sequence from DpnII site to the end of the 3’UTR and GATC represents the DpnII restriction site. Reverse reads are identified by the pattern XTTTTXTTTTXTTTTXTTTT-NNNNNNNNNNNNGATC-XXXX-YYYY where XXXX represents the corresponding barcode for the stage and Ns represent the reverse complemented sequence from the DpnII site to the end of the 3’UTR and GATC represents the DpnII restriction site. Ys represent part of the 3’ linker sequence.

extract_protocol: Total RNA was incubated at 55°C for one hour in presence of Superscript III Reverse Transcriptase (Invitrogen) and a universal VN poly-dT reverse primer, according the manufacture specifications. 3'UTR amplification were performed in 96-well plates format using transcript-specific forward primers and the universal reverse primer in presence of RNA prepared in the first strand reaction, using the following PCR parameters: denaturing 94°C 30 sec, annealing 60°C 30 sec, extension 72°C for 3 minutes. 3'UTRs were recombined into pDONR P2R-P3 entry vector using the BP Clonase II Enzyme Mix kit (Invitrogen) following the manufacturer's specifications and transformed into MultiShot Stripwell TOP 10 plates (Invitrogen). The transformed bacteria were grown overnight at 37°C under kanamycin selection.  6,912 minipools were manually streaked into large agar plates and 8 single colonies each minipool (total 55,296 colonies) were manually recovered, propagated and pooled in 8 different sets using the Aquarius automated multi-channel pipetting system (Tecan Trading AG, Switzerland). Each set contains none or one unique 3'UTR isoform.  Plasmid DNA was recovered for each set using the Wizard Plus miniprep Kit (Promega) and used as template for PCR amplification reaction with the following primers:   Generic Forward (adaptorA::Barcode:forward): GCC TCC CTC GCG CCA TCA GxxxxG TTT CTC GTT CAA CTT TCT TGT ACA AAG TGG GA.    Generic reverse (adaptorB::Barcode:reverse): GCC TTG CCA GCC CGC TCA GxxxxA TAA TGC CAA CTT TGT ATA ATA AAG TTG TTT TTT TTT TT   Primers for each set were tagged with the following barcodes (xxxx): A: CATG, B: TAGT, C: GATC, D: CACT, E: TACG, F: GAGC, G: CTGC, H: ATCG. Barcode-containing PCR amplicons were pooled purified using MinElute PCR purification kit (Qiagen) and quantified with the 2100 Agilent bioanalyzer platform (Agilent Technologies).  Because the FLEX platform (454-Roche) output obtained with samples of variable length is biased toward shorter reads, we split the sample into two identical batches. The first batch was treated with AMPure SPRI PCR purification kit (Agencourt Bioscience) to remove fragments below 100bp and enrich it with larger fragments (marco2). The second batch was kept untreated (marco1).

treatment_protocol: RNA extraction was performed following the vendor’s protocol with the following modification: 3 times freeze/thaw/vortex and disruption with pellet pestle was included to increase worm lysis efficiency.

tag: clones

value: RACE


title: Maa7-IR44_Chlamydomonas_rep1

value: AG


title: 5' NCR from HCV isolated at week 27 from 4x0513 rep1

value: locked nucleic acid (LNA)-modified oligonucleotide (SPC3649) complementary to miR-122


title: AU1054 CF1, Replicate 1


title: Young leaves from seedlings

source_name: Leaves

value: Leaves


title: Mitochondrial ESTs from males of D. melanogaster

description:
Mitochondrial ESTs from males from reciprocal crosses of D. melanogaster strains 14021-0231.36 and 14021-0231.15 .
Expression profiles of D. melanogaster mitochondrial protein coding genes and rRNA genes from the library prepared with male flies.
library strategy: EST
library source: non-genomic
library selection: cDNA

organism: Drosophila melanogaster

source_name: D. melanogaster males

value: male

value: Adults


title: RNAPII-Ser5P ChIP from WT Mus musculus

status: Public on Nov 04 2009

city: Singapore

first: Chia-Lin

last: Wei

address: 60 Biopolis Street #02-01

department: Genome Technology & Biology

country: Singapore

institute: Genome Institute of Singapore

description: RNAPII-Ser5P ChIP DNA from Mus musculus C57/BL6 wt anemic spleen

library_source: genomic

data_processing:
The PET sequences were extracted from raw sequence reads and mapped to the genome, defining the boundaries of each ChIP DNA fragment. The following specific mapping criteria were used: both 5' and 3' signatures must be present on the same chromosome; their 5' to 3' orientation must be correct; a minimal 17 bp match must exist for each 18 bp 5' and 3' signature; the tags must have genomic alignments within 7 Kb of each other. Due to the known possibility of MmeI slippage (+/- 1 bp) that leads to ambiguities at the PET signature boundaries, a minimal 17 bp match was set for each 18 bp signature. The total count of PET sequences mapped to the same locus but with slight nucleotide differences may reflect the expression level of the transcripts. Only PETs with specific mapping (one location) to the genome were considered. PETs that mapped to multiple locations may represent low complexity or repetitive sequences, and therefore were not included for further analysis.
Peak detection was performed as described in (Wei et al., Cell 124:207-219)

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse anemic spleen, WT

growth_protocol: Wt mice treated with phenylhydrazine to induce anemia

extract_protocol: RNAPII-S5P ChIP was performed on mouse anemic spleen. Nuclei were resuspended in sonication buffer (50 mM Tris-HCl, pH 8, 10 mM EDTA, 1% SDS, protease inhibitors (Roche)) and chromatin was sonicated to an average length of <1 kb. Nuclear debris was removed by centrifugation of 100 µg aliquots of chromatin in 1 ml ChIP buffer (16.7 mM Tris-HCl, pH 8, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton-X100, 0.01% SDS, protease inhibitors (Roche Complete, EDTA-free)), prior to immunoprecipitation with anti-RNAPII-S5P (Ab5131, Abcam), adsorbed to protein A-bound magnetic beads (Dynabeads, Invitrogen). Bound chromatin was washed 3x with 20 mM Tris-HCl, pH 8, 150 mM NaCl, 2 mM EDTA, 1% Triton-X100, 0.1% SDS, protease inhibitors, then 3x with the same buffer with 500 mM NaCl, and finally 3x with 10 mM Tris-HCl, pH 8, 1 mM EDTA. Chromatin was eluted from protein A beads by incubation at 50°C for 30 min with 1% SDS, 100 mM NaHCO3. Libraries were prepared according to Wei et al., Cell 124:207-219. In brief, ChIP DNA was end-polished and cloned into the plasmid vector, pGIS3. pGIS3 contains two MmeI recognition sites that flank the cloning site, which were used to produce a 36 bp PET from the original ChIP DNA fragments (18 bp from each of the 5' and 3' ends). Two 36 bp PETs were ligated as a unit (di-PET) and subjected to GS20 pyrosequencing.

value: C57/BL6 wild-type

value: anemic spleen


title: Mut-68_Chlamydomonas_rep2

value: UC


title: Ovules (3 days post anthesis +3 DPA)

source_name: +3 DPA ovules

value: +3 DPA ovules


title: small RNAs from wild type control for csr-1(tm892) and ego-1(om97)

status: Public on Oct 02 2009

city: Worcester

first: Julie

middle: M.

last: Claycomb

address: 373 Plantation Street Biotech2 Suite 219

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description:
small RNAs, 18 to 26 nt
18 to 26 nt small RNAs from DA1316 animals
Tar file of Illumina *_seq.txt files provided as supplementary file

data_processing: Small RNA sequences bigger than 17 nt were mapped to the Caenorhabditis elegans genome (WS192, www.wormbase.org). Sequences that matched tRNA or rRNA sequences were then removed. Only full-length complete matches were allowed. siRNA-targeted loci were defined as a region containing at least 25 reads per million matching reads. Relative abundance at each locus was determined by calculating (22G-RNAs in mutant(or)IP)/(22G-RNAs in wt+22G-RNAs in mutant(or)IP ).

source_name: DA1316 adult animals

growth_protocol: animals were grown at 20 C for approximately 60h. Csr-1(tm892), ego-1(om97) and DA1316 animals were counter selected on ivermectin

extract_protocol:
[CSR-1 IP samples] RNA was eluted from CSR-1 immunopercipitated complex by extraction with TRI Reagent (MRC Reagents, Inc). RNA was extracted as described in the manufacturer’s protocol. Small RNAs from the immunopercipitated complex, and wild type input, were resolved in a 15% polyacrylamide 7M Urea Gel, along with 20 picomoles of RNA standard (18- and 26-nt) in separate lanes. Ethidium Bromide staining was used to visualize the RNA standards. A gel fragment was excised from the sample lanes in the migration range between the two standards. RNA was eluted from the gel fragment in (0.3M NaCl-TE pH7.5) solution overnight and ethanol-precipitated using 20mg of glycogen as the carrier. Gel purified RNA was incubated with 0.05 Unit/µl Tobacco Acid Pyrophosphatase (Epicenter Biotechnologies) in 10µl reaction buffer containing 1 Unit/µl SUPERase Inhibitor (Ambion) for 1h at 37°C. After phenol extraction, the RNA was ethanol precipitated. The gel purified RNA and 1µM of each standard were incubated with 20µM of 3’-end linker, 1 Unit of SuperRNaseIN, 10% DMSO and 3 Units T4 RNA ligase (Takara) in 10µl ligation buffer (50mM Tris-Cl pH7.5, 10mM MgCl2, 6mg/mL BSA, 10mM DTT). The 3’ ligated products were gel purified and the RNAs were incubated in the presence of 30µM of 5’ adapter oligonucleotide, 1 Unit SuperRNaseIN (Ambion) and 1.5 Units of T4 RNA ligase in ligation buffer (50mM Tris-HCI (pH7.5), 10mM MgCI2, 10mM DTT, 1mM ATP and 10% Dimethyl sulfoxide). The ligated products were gel purified as described above and reverse transcribed in a standard 50µl reaction (SuperScript III, Invitrogen). The cDNA was amplified by PCR and purified in a 10% acrylamide gel. PCR products generated for all the samples were sequenced on a Solexa sequencing platform (Illumina, Inc.)
[csr-1(tm892), ego-1(om97) and DA1316 samples] RNA was resolved in a 15% polyacrylamide 7M Urea Gel, along with 20 picomoles of RNA standard (18- and 26-nt) in separate lanes. Ethidium Bromide staining was used to visualize the RNA standards. A gel fragment was excised from the sample lanes in the migration range between the two standards. RNA was eluted from the gel fragment in (0.3M NaCl-TE pH7.5) solution overnight and ethanol-precipitated using 20mg of glycogen as the carrier.  Gel purified RNA was treated with 1 Unit/µl of Alkaline Phosphatase, Calf Intestine (NEB) in 100mM NaCl, 50mM Tris-HCl, 10mM MgCl2, 1mM Dithiothreitol, pH 7.9 at 25°C and 1 Unit/µl SuperRNaseIn (Ambion) for 1 hour at 37 °C. After phenol extraction, the gel purified RNA and 1µM of each standard were incubated with 20µM of 3’-end linker, 1 Unit of SuperRNaseIN, 10% DMSO and 3 Units T4 RNA ligase (Takara) in 10µl ligation buffer (50mM Tris-Cl pH7.5, 10mM MgCl2, 6mg/mL BSA, 10mM DTT).  The 3’ ligated products were gel purified and treated with 1 Unit/µl Polynucleotide Kinase in 1x Polynucleotide Kinase buffer (70mM Tris-HCl, 10mM MgCl2, 5mM Dithiothreitol, pH 7.6 at 25°C), 2mM ATP, 1 Unit/µl SuperRNAseIN. After phenol extraction, RNAs were incubated in the presence of 30µM of 5’ adapter oligonucleotide, 1 Unit SuperRNaseIN (Ambion) and 1.5 Units of T4 RNA ligase in ligation buffer (50mM Tris-HCI pH7.5), 10mM MgCI2, 10mM DTT, 1mM ATP) and 10% Dimethyl sulfoxide). The ligated products were gel purified as described above and reverse transcribed in a standard 50µl reaction (SuperScript III, Invitrogen). The cDNA was amplified by PCR and purified in a 10% acrylamide gel. PCR products generated for all the samples were sequenced on a Solexa sequencing platform (Illumina, Inc.)


title: S96ChIP_rep3

status: Public on Feb 18 2010

city: New Haven

first: Wei

last: Zheng

state: CT

address: Suite 503, 300 George Street

institute: Yale University

data_processing:
Sequence reads were parsed by barcodes, and mapped to the S. cerevisiae S288C (Oct 2003) genome using the Illumina Genome Analyzer Pipeline. Uniquely mapped reads with at most 2 mismatches are retained for downstream analysis.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: Yeast cells were grown in 500ml YPAD medium to mid-log phase (O.D. = 0.6).

extract_protocol: Chromatin immunoprecipitation was performed as in Aparicio et al., Curr Protoc Cell Biol (2004). Sequencing library was constructed as in Lefrancois et al., BMC Genomics (2009).

treatment_protocol: Incubation at 30C for 30 minutes in presence of 5uM alpha factor.

tag: treatment

value: alpha factor

tag: chip antibody


title: HI2424 CF2, Replicate 2


title: Bacteroides thetaiotaomicron-Minimal media plus amino acids-2

status: Public on Sep 16 2009

city: St. Louis

first: Andrew

middle: L

last: Goodman

state: MO

address: Campus Box 8510, 4444 Forest Park Ave

department: Center for Genome Sciences

institute: Washington University School of Medicine

description: Transposon-adjacent DNA isolated by insertion sequencing (INSeq)

data_processing: Raw reads were parsed by barcode if necessary. Reads were then mapped and quantified using the MapSAM custom software package (processed_data.txt files). The format for these processed_data.txt files is as follows: Column 1 = Full 32bp sequence used for mapping insertion location; Column 2 = trimmed read sequence from tag 5' of insertion location; Column 3 = trimmed read sequence from tag 3' of insertion location; Column 4 = non-normalized read count for 5' tag; Column 5 = non-normalized read count for 3' tag; Column 6 = insertion coordinate (for "T" of "TA" dinucleotide insertion site); Column 7 = GenBank ID for reference sequence.

organism: Bacteroides thetaiotaomicron

source_name: INSeq DNA

extract_protocol: Genomic DNA was purified, digested with MmeI, and separated by PAGE. Transposon-sized fragments were extracted from the gel and ligated to a double-stranded DNA adapter bearing a 3’-NN overhang. PAGE-purified adapter-ligated library molecules were PCR amplified for 18 cycles using a transposon-specific and an adapter-specific primer. The 125bp product was purified by PAGE and sequenced using an Illumina Genome Analyzer as described in the user’s manual. Sequence images were converted into raw reads using Illumina software with default settings.

tag: environment

value: Minimal media, batch culture

tag: defined microbiota

value: In vitro

tag: mouse genotype

value: GCTA


title: Bacteroides thetaiotaomicron-Minimal media plus amino acids-3

value: CGAT


title: Bacteroides thetaiotaomicron-Firmicutes+Actinobacteria community-Wt mouse-Experiment AGE3_D, mouse 5

value: C57Bl/6J male mouse

value: Firmicutes+Actinobacteria

value: wildtype


title: Bacteroides thetaiotaomicron-Minimal media plus amino acids-4

value: TCAG


title: Bacteroides thetaiotaomicron-Firmicutes+Actinobacteria community-Wt mouse-Experiment AGE3_D, mouse 4


title: Bacteroides thetaiotaomicron-Firmicutes+Actinobacteria community-Wt mouse-Experiment AGE3_D, mouse 1


title: Bacteroides thetaiotaomicron-Bacteroides community-Wt mouse-Experiment AGE3_C, mouse 9

value: Bacteroides


title: Bacteroides thetaiotaomicron-Bacteroides community-Wt mouse-Experiment AGE3_C, mouse 10


title: Small Pdf cells from adult biological replicate 2

status: Public on Oct 31 2009

type: RNA

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

description: Sorted small GFP positive cells from Pdf-Gal4;UAS-GFP line.

hyb_protocol: Following fragmentation, 15 or 20 ug of cRNA were hybridized for 18 hr at 45C on GeneChip Drosophila v2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneArray Scanner G3000.

data_processing: The data were processed with GCRMA algorithm in the Bioconductor with default settings.

label: biotin

source_name: brain, Small Pdf-GFP positive cells

label_protocol: Biotinylated cRNA were prepared using two rounds of T7 in vitro transcription based aRNA amplification (Affymetrix Small Sample Target Labeling Assay Version II) from about 0.1 to 0.4 ng of total RNA.

growth_protocol: Flies were growth under standard conditions in 12hs light and 12hs dark cycles

extract_protocol: PicoPure RNA Isolation Kit (Arcturus) was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: About 50 larval or adult heads were dissected at around ZT12, digested with protease, dissociated and GFP positive cells were collected.

tag: source

value: brain

value: adult

tag: cell type

value: small Pdf-GAL4


title: Bacteroides thetaiotaomicron-Bacteroides community-Wt mouse-Experiment AGE3_C, mouse 7

tag: barcode


title: Bacteroides thetaiotaomicron-Minimal media plus amino acids-1

value: AAAA


title: Large Pdf cells from adult biological replicate 1

description: Sorted large GFP positive cells from Pdf-Gal4;UAS-GFP line.

source_name: brain, Large Pdf-GFP positive cells

value: large Pdf-GAL4


title: Small Pdf cells from adult biological replicate 1


title: small RNAs from csr-1 mutant animals

description:
small RNAs, 18 to 26 nt
18 to 26 nt small RNAs from csr-1(tm892) mutant animals
Tar file of Illumina *_seq.txt files provided as supplementary file

source_name: csr-1(tm892) adult animals


title: Large Pdf cells from adult biological replicate 2


title: Elav cells from adult biological replicate 2

description: Sorted GFP positive cells from Elav-Gal4;UAS-GFP line.

source_name: brain, Elav-GFP positive cells


title: Bacteroides thetaiotaomicron-Bacteroides+Firmicutes+Actinobacteria community-Wt mouse-Experiment AGE3_B, mouse 14

value: Bacteroides+Firmicutes+Actinobacteria


title: Bacteroides thetaiotaomicron-Minimal media no amino acids-4

value: TTAA


title: Bacteroides thetaiotaomicron-Bacteroides+Firmicutes+Actinobacteria community-Wt mouse-Experiment AGE3_B, mouse 13


title: Bacteroides thetaiotaomicron-Minimal media no amino acids-3

value: CATG


title: Elav cells from adult biological replicate 1


title: Large Pdf cells from adult biological replicate 3


title: Bacteroides thetaiotaomicron-Minimal media no amino acids-1

value: Minimal media, batch culture

value: AGTC


title: Bacteroides thetaiotaomicron-Minimal media no amino acids-2

value: In vitro

value: GGGG


title: Bacteroides thetaiotaomicron-Bacteroides+Firmicutes+Actinobacteria community-Wt mouse-Experiment AGE3_B, mouse 11

value: C57Bl/6J male mouse


title: Bacteroides thetaiotaomicron-Firmicutes+Actinobacteria community-Wt mouse-Experiment AGE3_D, mouse 2

value: Firmicutes+Actinobacteria


title: panicles_UD

status: Public on Feb 15 2010

city: Saint Louis

first: James

last: Carrington

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: wild type B. distachyon panicle small RNA

data_processing: Small RNA sequences were parsed from Illumina sequencing data files through identification of the 3' adaptor boundary. Only sequences that mapped perfectly to the B. distachyon genome were included in the analysis.

organism: Brachypodium distachyon

source_name: panicles

extract_protocol: Small RNA were extracted from total RNA by size fractionation and converted to DNA amplicons by serial adaptor ligation to both ends followed by RT-PCR.  DNA amplicons were sequenced using an Ilumina Genome Analyzer.

value: panicles

value: University of Delaware

tag: growth conditions

value: Plants were grown in long-day conditions (20 h days/4 h nights) at 20°C for 42 days


title: Bacteroides thetaiotaomicron-Bacteroides+Firmicutes+Actinobacteria community-Wt mouse-Experiment AGE3_B, mouse 15

value: wildtype


title: Bacteroides thetaiotaomicron-monoassociation-Rag1-/- mouse-Experiment AGE3_F, mouse 12

value: Monoassociation


title: Bacteroides thetaiotaomicron-monoassociation-Rag1-/- mouse-Experiment AGE3_F, mouse 4


title: Bacteroides thetaiotaomicron-monoassociation_Wt mouse-Experiment AGE3_A, mouse 5


title: Bacteroides thetaiotaomicron-Bacteroides community-Wt mouse-Experiment AGE3_C, mouse 8

value: Bacteroides


title: Bacteroides thetaiotaomicron-Bacteroides community-Wt mouse-Experiment AGE3_C, mouse 6


title: Bacteroides thetaiotaomicron-monoassociation_Wt mouse-Experiment AGE3_A, mouse 4


title: Elav cells from adult biological replicate 3

value: brain

value: adult


title: Bacteroides thetaiotaomicron-monoassociation-Myd88-/- mouse-Experiment AGE3_G, mouse 8


title: Bacteroides thetaiotaomicron-monoassociation-Myd88-/- mouse-Experiment AGE3_G, mouse 7


title: Bacteroides thetaiotaomicron-monoassociation_Wt mouse-Experiment AGE3_A, mouse 2


title: Bacteroides thetaiotaomicron-Bacteroides+Firmicutes+Actinobacteria community-Wt mouse-Experiment AGE3_B, mouse 12

value: Bacteroides+Firmicutes+Actinobacteria


title: Bacteroides thetaiotaomicron-monoassociation_Wt mouse-Experiment AGE3_A, mouse 3


title: Bacteroides thetaiotaomicron-Bacteroides+Firmicutes+Actinobacteria community-Wt mouse-Experiment AGE2, mouse 14


title: Bacteroides thetaiotaomicron-monoassociation-Myd88-/- mouse-Experiment AGE3_G, mouse 1


title: Bacteroides thetaiotaomicron-Bacteroides+Firmicutes+Actinobacteria community-Wt mouse-Experiment AGE2, mouse 11


title: Bacteroides thetaiotaomicron-monoassociation_Wt mouse-Experiment AGE2, mouse 3


title: Bacteroides thetaiotaomicron-monoassociation_Wt mouse-Experiment AGE2, mouse 2


title: Bacteroides thetaiotaomicron-Bacteroides+Firmicutes+Actinobacteria community-Wt mouse-Experiment AGE2, mouse 12


title: Bacteroides thetaiotaomicron-monoassociation-Rag1-/- mouse-Experiment AGE3_F, mouse 11


title: Bacteroides thetaiotaomicron-monoassociation-Rag1-/- mouse-Experiment AGE3_F, mouse 9


title: Bacteroides thetaiotaomicron-monoassociation-Rag1-/- mouse-Experiment AGE3_F, mouse 7


title: Bacteroides thetaiotaomicron-monoassociation_Wt mouse-Experiment AGE3_A, mouse 1


title: Bacteroides thetaiotaomicron-arrayed mutant library pools 2-24

value: TYG, pooled overnight cultures

value: Pool13:TTGG, Pool14:CCTT, Pool15:GCTA, Pool16:GGAA, Pool17:GGGG, Pool18:GTAC, Pool19:GTCA, Pool20:AAAA, Pool21:TCAG, Pool22:TATA, Pool23:TCGA, Pool24:AACC


title: Bacteroides thetaiotaomicron-monoassociation-Myd88-/- mouse-Experiment AGE3_G, mouse 6


title: Bacteroides thetaiotaomicron-arrayed mutant library pools 1-12

value: Pool1:TTTT, Pool2:ACCA, Pool3:AGGA, Pool4:ACGT, Pool5:AGTC, Pool6:ATCG, Pool7:GAAG, Pool8:CATG, Pool9:CCAA, Pool10:CCCC, Pool11:CGAT, Pool12:TTAA


title: Bacteroides thetaiotaomicron-monoassociation_Wt mouse-Experiment AGE1, mouse 11


title: Bacteroides thetaiotaomicron-TYG chemostat-45h-1

value: TYG chemostat, 45h


title: Bacteroides thetaiotaomicron-monoassociation_Wt mouse-Experiment AGE1, mouse 8


title: Bacteroides thetaiotaomicron-TYG chemostat-45h-2

value: In vitro


title: Bacteroides thetaiotaomicron-Bacteroides+Firmicutes+Actinobacteria community-Wt mouse-Experiment AGE2, mouse 15


title: Bacteroides thetaiotaomicron-Bacteroides+Firmicutes+Actinobacteria community-Wt mouse-Experiment AGE2, mouse 13


title: Bacteroides thetaiotaomicron-monoassociation_Wt mouse-Experiment AGE2, mouse 5


title: S2 pKF63 transiently transfected

status: Public on Sep 14 2009

city: Munich

first: Klaus

last: Förstemann

address: Feodor-Lynen 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilians University

description:
pKF63: GFP expression construct under control of ubiquitin promotor
library_strategy:  (small RNA sequencing, 3'- and 5'-Adaptor ligation followed by cDNA synthesis and PCR amplification)
library_source:  18-30 nt small RNAs (gel-purified)
linker sequences: 3'- (AMP-5’p=5’pCTGTAGGCACCATCAATdideoxyC-3’) and 5'- (5'-rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrC rUrCrUrUrCrCrGrArUrCrU-3' + 3 nt Barcode (-GAU)

data_processing: 3'-adapter sequences were removed, multiplexed samples were separated and the 5'-sequence tags removed, length selection for 20-24 nt, files were converted from fastq to fasta format

source_name: Schneider cells

extract_protocol: Extraction of total RNA with Trizol. Gel purification of small RNAs (15-30nt).

tag: cell line

value: S2B2 + pKF63


title: Bacteroides thetaiotaomicron-monoassociation_Wt mouse-Experiment AGE2, mouse 1

value: C57Bl/6J male mouse


title: Bacteroides thetaiotaomicron-monoassociation_Wt mouse-Experiment AGE1, mouse 10


title: Bacteroides thetaiotaomicron-monoassociation_Wt mouse-Experiment AGE1, mouse 9


title: Bacteroides thetaiotaomicron-monoassociation_Wt mouse-Experiment AGE1, mouse 7


title: Bacteroides thetaiotaomicron-TYG chemostat-15h-2

value: TYG chemostat, 15h


title: Bacteroides thetaiotaomicron-TYG chemostat-15h-1


title: Bacteroides thetaiotaomicron-Additional library

value: Initial plated population


title: Illumina sequenced synthetic miRNA sample A with barcode 4

status: Public on Sep 08 2009

city: Kgs. Lyngby

first: Hanni

last: Willenbrock

address: Kemikalievej, bygning 208

department: Center for Biological Sequence Analysis

institute: DTU

description:
Illumina barcode 4 (TACA)
Illumina multiplexed sequencing

data_processing:
The GAPipeline-1.0 was used starting from the IPAR-1.01 calculated intensities.
The adapter sequences were trimmed in 3 steps:
(NB: 3' special adapter: CTGTAGGCACCATCAATCGTA)
1) The 21nt adapter sequence is used, which permits to identify “inserts” of 11nt or less.
2) If no adapter sequence was found, in successive steps the last base of the adapter was removed and the sequence was searched at the end of the reads. The minimum adapter size of 6 bases permits identifying inserts of up to 26 bases.
3) Finally the remaining reads are search for notexact matches of the adapter. The first 5 bases of the adapter were searched within the full reads sequences and at least 80% of the following bases must be identical to the adapter sequence (max 26 bp).

organism: Homo sapiens

source_name: Sample A

tag: sample

value: synthetic miRNA


title: Illumina sequenced synthetic miRNA sample B with barcode 2

description:
Illumina barcode 2 (CGGA)
Illumina multiplexed sequencing

source_name: Sample B


title: Illumina sequenced synthetic miRNA sample A with barcode 2


title: Illumina sequenced synthetic miRNA sample A with barcode 3

description:
Illumina barcode 3 (GTAA)
Illumina multiplexed sequencing


title: Illumina sequenced synthetic miRNA sample B

data_processing:
The GAPipeline-1.0 was used starting from the IPAR-1.01 calculated intensities.
First the data sets are screened for the sequence of the 5' adapter (We sometime observed that parts of the 5' adapter can be cloned instead of a small RNA insert) with the same method than described below using the last 10 bases of this adapter. This was not observed for your samples so all reads were processed for the 3prime adapter location and removal.
The adapter sequences were trimmed in 3 steps:
1) The 21nt adapter sequence is used, which permits to identify “inserts” of 15nt or less.
2) If no adapter sequence was found, in successive steps the last base of the adapter was removed and the sequence was searched at the end of the reads. The minimum adapter size of 6 bases permits identifying inserts of up to 30 bases.
3) Finally the remaining reads are search for notexact matches of the adapter. The first 4 bases of the adapter were searched within the full reads sequences and at least 75% of the following bases must be identical to the adapter sequence (max 31 bp).


title: Illumina sequenced synthetic miRNA sample A

source_name: sample A


title: Bacteroides thetaiotaomicron-monoassociation_Wt mouse-Experiment AGE2, mouse 4


title: S2 pKF63 stably transfected

description:
pKF63: GFP expression construct under control of ubiquitin promotor
library_strategy:  (small RNA sequencing, 3'- and 5'-Adaptor ligation followed by cDNA synthesis and PCR amplification)
library_source:  18-30 nt small RNAs (gel-purified)
linker sequences: 3'- (AMP-5’p=5’pCTGTAGGCACCATCAATdideoxyC-3’) and 5'- (5'-rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrC rUrCrUrUrCrCrGrArUrCrU-3' + 3 nt Barcode (-CUG)


title: S2 parental

description:
S2 parental
library_strategy: (small RNA sequencing, 3'- and 5'-Adaptor ligation followed by cDNA synthesis and PCR amplification)
library_source:  18-30 nt small RNAs (gel-purified)
linker sequences: 3'- (AMP-5’p=5’pCTGTAGGCACCATCAATdideoxyC-3’) and 5'- (5'-rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrC rUrCrUrUrCrCrGrArUrCrU-3' + 3 nt Barcode (-CCU)


title: Donor 3, EBNA-3A mutant A infected LCL, line 3

status: Public on Sep 05 2009

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

institute: University Hospital Erlangen

description: donor 3, EBNA-3A mutant A infected LCL, line 3

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The probe level data (CEL files) were processed for global normalization and generation of expression values using the robust multi-array average algorithm (RMA) of the “affy package” in the R software environment (http://www.R-project.org).

source_name: human lymphoblastoid cell line (EBV transformed)

label_protocol: 1 µg total cellular RNA was reverse transcribed and biotinylated cRNA generated according to Affymetrix protocols.

growth_protocol: Human primary B cells were isolated from adenoids, depleted of T cells by rosetting with sheep erytrocytes, and purified by Ficoll-Hypaque density-gradient centrifugation.

extract_protocol: Total cellular RNA was extracted from established cell lines using the the peqGOLD Trifast kit according to the manufacturer's protocol.

treatment_protocol: 1-2 x 10e5 CD19 positive B cells were infected with 1000 GRUs of EBVwt or different viral mutants and plated on lethally irradiated MRC5 feeder layer in a total volume of 200µl/well in a 96-well cluster plate. Once per week 100µl of the culture medium was replaced with fresh medium. 28-35 days p.i. proliferating B-cell cell cultures  were removed from feeder layers and expanded indefinetly in suspension.

tag: time in culture

value: 3 months

value: lymphoblastoid

tag: infection

value: EBNA-3A mutant A


title: Illumina sequenced synthetic miRNA sample B with barcode 4


title: Illumina sequenced synthetic miRNA sample B with barcode 3


title: Donor 2, EBNA-3A mutant B infected LCL, line 1

description: donor 2, EBNA-3A mutant B infected LCL, line 1

value: 4 months

value: EBNA-3A mutant B


title: Donor 3, EBNA-3A mutant B infected LCL, line 1

description: donor 3, EBNA-3A mutant B infected LCL, line 1


title: Donor 3, EBNA-3A mutant A infected LCL, line 4

description: donor 3, EBNA-3A mutant A infected LCL, line 4


title: Donor 1, EBNA-3A mutant A infected LCL

description: donor 1, EBNA-3A mutant A infected LCL

value: 6 months


title: Illumina sequenced synthetic miRNA sample B with barcode 1

description:
Illumina barcode 1 (ACTA)
Illumina multiplexed sequencing


title: Donor 3, EBNA-3A mutant A infected LCL, line 1

description: donor 3, EBNA-3A mutant A infected LCL, line 1


title: Donor 1, EBVwt infected LCL

description: donor 1, EBVwt infected LCL

value: EBV wild type


title: Donor 2, EBNA-3A mutant B infected LCL, line 3

description: donor 2, EBNA-3A mutant B infected LCL, line 3


title: Donor 3, EBNA-3A mutant A infected LCL, line 2

description: donor 3, EBNA-3A mutant A infected LCL, line 2


title: Donor 2, EBNA-3A mutant B infected LCL, line 2

description: donor 2, EBNA-3A mutant B infected LCL, line 2


title: Donor 2, EBVwt infected LCL, line 1

description: donor 2, EBVwt infected LCL, line 1


title: Illumina sequenced synthetic miRNA sample A with barcode 1


title: Donor 3, EBVwt infected LCL, line 2

description: donor 3, EBVwt infected LCL, line 2


title: Donor 3, EBVwt infected LCL, line 1

description: donor 3, EBVwt infected LCL, line 1


title: Donor 2, EBVwt infected LCL, line 2

description: donor 2, EBVwt infected LCL, line 2


title: X.tropicalis Single Egg Small RNAs, sample A4

status: Public on Sep 01 2009

city: Waltham

first: Nelson

last: Lau

address: 415 South St MS029

institute: Brandeis University

description:
Sample A4 in one multiplexed flowcell lane.
cDNA library was sequenced on a Illumina GA-II platform, according to Bentley et. al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008 Nov 6;456(7218):53-9. Analysis of this file is described in the manuscript "Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi".

data_processing: Base quality filtering, linker sequence removal, and structural RNA culling was performed with in-house scripts developed by Toshihiro Ohsumi and Mark Borowsky.

organism: Xenopus tropicalis

source_name: Small RNAs from a X.tropicalis Single Egg

extract_protocol: Small RNA library from a single X.tropicalis egg. A single de-jellied egg was mixed with Trizol to obtain total RNA. Small RNAs were ligated with linkers and converted to cDNA by reverse transcription. cDNA library was amplified by PCR.

tag: tissue

value: single egg

tag: sequencing technology

value: Illumina


title: X. tropicalis Microtubules Small RNAs

description: cDNA library was sequenced on a 454 Genome Sequencer FLX platform, according to Margulies et. al. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005 Sep 15;437(7057):376-80. Epub 2005 Jul 31. Analysis of this file is described in the manuscript "Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi".

source_name: Small RNAs from Microtubules from X.tropicalis Egg Extract

extract_protocol: Small RNA library from purified microtubules from X.tropicalis egg extract. Microtubules were polymerized by taxol from Xenopus egg extract and purified by pellting thorugh a glycerol cushion.  Pellet was extracted with Trizol to obtain total RNA.  Small RNAs were ligated with linkers and converted to cDNA by reverse transcription. cDNA library was amplified by PCR.

value: egg extract

tag: subcellular structure

value: microtubules


title: X. tropicalis Egg Extract Small RNAs

source_name: Small RNAs from X.tropicalis Egg Extract

extract_protocol: Small RNA library from X.tropicalis egg extract. Xenopus egg extract was prepared by crushing mature eggs laid in frog water in a centrifuge and pulling cytoplasmic layer with a needle and syringe.  The egg extract was mixed with Trizol to obtain total RNA. Small RNAs were ligated with linkers and converted to cDNA by reverse transcription. cDNA library was amplified by PCR.


title: X.laevis Egg Extract Small RNAs

organism: Xenopus laevis

source_name: Small RNAs from X.laevis Egg Extract

extract_protocol: Small RNA library from X.laevis egg extract. Xenopus egg extract was prepared by crushing mature eggs laid in frog water in a centrifuge and pulling cytoplasmic layer with a needle and syringe. The egg extract was mixed with Trizol to obtain total RNA. Small RNAs were ligated with linkers and converted to cDNA by reverse transcription. cDNA library was amplified by PCR.


title: X.tropicalis Single Egg Small RNAs, sample B1

description:
Sample B1 in one multiplexed flowcell lane.
cDNA library was sequenced on a Illumina GA-II platform, according to Bentley et. al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008 Nov 6;456(7218):53-9. Analysis of this file is described in the manuscript "Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi".


title: X.tropicalis Single Egg Small RNAs, sample B2

description:
Sample B2 in one multiplexed flowcell lane.
cDNA library was sequenced on a Illumina GA-II platform, according to Bentley et. al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008 Nov 6;456(7218):53-9. Analysis of this file is described in the manuscript "Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi".


title: small_RNA_rat_liver

status: Public on Jul 29 2009

city: Utrecht

first: Elzo

last: de Wit

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing: Sequencing reads were mapped to the known miRNA and miRNA* species in miRBase v11.0 using SHRiMP. Reads with 3 or less colorspace errors were included in the further analysis.

organism: Rattus norvegicus

source_name: rat liver

extract_protocol: SREK: SREK was performed according to the manufacturer’s protocol (Ambion, Inc, Austin, TX). Two replicates were produced with the 15-40 nt fraction derived from 0.5 μg small RNA (<200 nt) as input material.

value: liver

tag: strain

value: BN-Lx


title: small_RNA_rat_spleen

source_name: rat spleen

value: spleen


title: X.laevis Microtubules Small RNAs

source_name: Small RNAs from Microtubules from X.laevis Egg Extract

extract_protocol: Small RNA library from purified microtubules from X.laevis egg extract. Microtubules were polymerized by taxol from Xenopus egg extract and purified by pellting thorugh a glycerol cushion. Pellet was extracted with Trizol to obtain total RNA. Small RNAs were ligated with linkers and converted to cDNA by reverse transcription. cDNA library was amplified by PCR.


title: X.laevis Xiwi IP Small RNAs

description: cDNA library was sequenced on a Illumina GA-II platform, according to Bentley et. al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008 Nov 6;456(7218):53-9. Analysis of this file is described in the manuscript "Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi".

source_name: Immunoprecipitation of Xiwi from X.laevis Egg Extract

extract_protocol: Small RNA library from Xiwi IP from X.laevis egg extract. A polyclonal antibody against Xiwi was coupled to magnetic beads, mixed with Xenopus egg extract, and beads were extensively washed. The antibody immunoprecipitate was eluted and mixed with Trizol to obtain total RNA. Small RNAs were ligated with linkers and converted to cDNA by reverse transcription. cDNA library was amplified by PCR.

tag: antibody

value: polyclonal antibody against Xiwi


title: 3UTR_EMB_L1toL4_Adult_polyAcapture, L1

status: Public on Sep 02 2009

description: This run comprised of mixed barcoded sequences from embryo, L1 to L4, and adult hermaphrodite.

data_processing:
Forward reads are identified by the following pattern - XXXX-GATCNNNNNNNNNNNNNN-XAAAAXAAAAXAAAAXAAAA where XXXX represents the corresponding 4bp barcode for the stage and Ns represent the sequence from DpnII site to the end of the 3'UTR and GATC represents the DpnII restriction site. Reverse reads are identified by the pattern XTTTTXTTTTXTTTTXTTTT-NNNNNNNNNNNNGATC-XXXX-YYYY where XXXX represents the corresponding barcode for the stage and Ns represent the reverse complemented sequence from the DpnII site to the end of the 3'UTR and GATC represents the DpnII restriction site. Ys represent part of the 3' linker sequence. This run comprised of mixed barcoded sequences from the following stages (56,717 sequences in embryo; 47,504 sequences in L1; 74,047 sequences in L2; 48,713 sequences in L3; 69,296 sequences in L4; 75,546 sequences in adult hermaphrodite).
The sequences that didn't reach the polyA were removed(1,457 sequences in embryo; 1,634 sequences in L1; 1,737 sequences in L2; 1,320 sequences in L3; 2,462 sequences in L4; 2,143 sequences in adult hermaphrodite)
The remaining sequences were processed with custom written perl script to remove the 5' and 3' adaptor sequences and adaptor removed sequences of length less than 15 were discarded (2,461 sequences in embryo; 728 sequences in L1; 133 sequences in L2; 670 sequences in L3; 175 sequences in L4; 179 sequences in adult hermaphrodite).
The remaining sequences reached the polyA and were of length greater than or equal to 15 (52,797 sequences in embryo;45,142 sequences in L1; 72,177 sequences in L2; 46,723 sequences in L3; 66,659 sequences in L4; 73,224 sequences in adult hermaphrodite) and were used for further analysis.

molecule: polyA RNA

source_name: N2 wildtype

growth_protocol: N2 wildtype worms were grown on 10 cm2 NGM plates seeded with OP50 and synchronized by alkaline/hypochride.  A fraction of eggs (mixed embryos) were frozen down in TriReagent (Ambion, Cat# AM9738) and the remaining ones were hatched overnight in M9 buffer. Starved L1 larvae were then plated on 10 cm2 plates (OP50 as food) raised at 20C.  Samples were taken at ~8 hr (L1), ~20hr (L2), ~30hr (L3), ~45hr (L4), ~70hr (adult). Worms were collected in M9, washed 3 times with M9 to remove residue bacteria and frozen down in TriReagent.

extract_protocol:
RNA extraction was performed following the vendor's protocol with the following modification: 3 times freeze/thaw/vortex was included to increase worm lysis efficiency; isopropanol precipitation of RNA was carried out at -80°C for one hour.
A biotinylated oligo-dT primer was annealed to the 3' ends of the polyA mRNAs, followed by first strand synthesis with SuperScript III (Invitrogen).  Second strand synthesis was carried out, followed by phenol-chloroform extraction.  cDNAs were DpnII digested for 1 hr.  Biotinylated cDNAs were bound to  Streptavidin-Dynabeads and washed.  Linkers were added to the cDNA-bead solution, followed by phenol-chloroform extraction.  Ligation product was used in two rounds of PCR amplification with same primer as in labeling, plus a barcoded label.  DNA was phenol-chloroform precipitated and quantified using a Nanodrop spectrophotometer.  Linkers are comprised of two complementary oligos with barcodes to distinguish the samples: 5'-GCCTCCCTCGCGCCATCAGXXXX-3' and 5'PHOS-GATCXXXXCTGATGGCGCGAGGGAGGC-3', and PCR primers are: 5'-GCCTCCCTCGCGCCATCAGXXXX-3' and 5'-GCCTTGCCAGCCCGCTCAGXttttXttttXttttXtttt-3'.  Barcodes for the pilot run are as follows:  CATG embryo, TAGT L1, GATC L2, CACT L3, TACG L4, GAGC adult hermaphrodites.  Barcodes for the full runs are as follows: CATG embryo, TAGT L1, GATC L2, CACT L3, TACG L4, GAGC adult hermaphrodite, TACG adult male, CATG daf-2, TACT daf-7, GATC daf-9, CACT daf-11.  Sequencing was run per-stage so only the adult and dauer runs contained more than one sample.

tag: developmental stage


title: X.tropicalis Single Egg Small RNAs, sample B1_l7

description:
Sample B1 in one flowcell lane.
cDNA library was sequenced on a Illumina GA-II platform, according to Bentley et. al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008 Nov 6;456(7218):53-9. Analysis of this file is described in the manuscript "Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi".


title: X.tropicalis Single Egg Small RNAs, sample A3

description:
Sample A3 in one multiplexed flowcell lane.
cDNA library was sequenced on a Illumina GA-II platform, according to Bentley et. al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008 Nov 6;456(7218):53-9. Analysis of this file is described in the manuscript "Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi".


title: 3UTR_EMB_L1toL4_Adult_polyAcapture, embryo

value: embryo


title: smallRNA_rat_brain_SREK_rep1

source_name: rat brain

value: brain

tag: library preparation

value: SREK


title: synthetic_miRNAs_modban_amplified_rep3

data_processing: Sequencing reads were mapped to the reference set of miRNAs using SHRiMP. Reads with 3 or less mismatches were included in the further analysis.

source_name: synthetic miRNAs

extract_protocol: Modban: The original protocol, as described by Lau et al. 2001, was followed.

value: synthetic miRNAs


title: 3UTR_EMB_L1toL4_Adult_polyAcapture, L3


title: polyA_miRNA_profiling 2

data_processing: Sequencing reads were mapped to the known miRNA and miRNA* species in miRBase v11.0 using SHRiMP. Reads with 3 or less errors were included in the further analysis.

extract_protocol: polyA: The 15-40 nt fraction derived from 1 μg small RNA (<200 nt) was polyadenylated, purified and treated with periodic acid (as in 2) for 3` termination of the poly(A) tail. After ligation of the 5` linker, the >70 nt fraction was excised from 10% denaturing polyacrylamide gel (for replicate 1) or this step was omitted (replicate 2). Reverse-transcription was performed with the poly(A) RT primer, followed by 15 cycli of PCR (replicate 1) or 1/10 of the RT reaction was amplified by 17 cycles of PCR  (replicate 2). We produced 454 compatible libraries with ~0.3 ng of each library.  Primers used were barcoded primers (454solid_bc) in the forward orientation and the 454solid_reverse primer in the reverse orientation. 8 rounds of PCR were performed for each library as the PCR in the modban and poly(A) library preparation, with the exception that all reagents were 5x concentrated. The libraries, each carrying a unique barcode in the 5` adapter, were equimolarly mixed and submitted for 454 sequencing. 454solid_bc: 5` GCC TCC CTC GCG CCA TCA G  barcode C CAC TAC GCC TCC GCT TTC CTC TCT ATG 3` Barcodes:Bc1 GCTA;Bc2 CGTA;Bc3 CGAT;Bc4 GCAT;Bc5 TAGC;Bc6 ATGC

value: polyA


title: smallRNA_rat_brain_polyA_rep2

extract_protocol: polyA: The 15-40 nt fraction derived from 1 μg small RNA (<200 nt) was polyadenylated, purified and treated with periodic acid (as in 2) for 3` termination of the poly(A) tail. After ligation of the 5` linker, the >70 nt fraction was excised from 10% denaturing polyacrylamide gel (for replicate 1) or this step was omitted (replicate 2). Reverse-transcription was performed with the poly(A) RT primer, followed by 15 cycli of PCR (replicate 1) or 1/10 of the RT reaction was amplified by 17 cycles of PCR  (replicate 2).


title: modban_miRNA_profiling 1

extract_protocol: Modban: The original protocol, as described by Lau et al.1, was followed. We used as input the 15-40 nt fraction of 1 μg of small RNA isolated using the miRVana kit. A preadenylated modban adapter was ligated to the to the RNA in the absence of ATP. The 30-50 nt fraction was excised from a 15% denaturing polyacrylamide gel. After elution in 0.3M NaCL and EtOH precipitation, the 5` linker was ligated in the presence of ATP. The 70-90 nt fraction was gel-excised from a 10% denaturing polyacrylamide gel, eluted and precipitated. Reverse-transcription was performed with the modban RT primer and 15 cycles of PCR were performed to amplify the library. 8 rounds of PCR were performed for each library as the PCR in the modban and poly(A) library preparation, with the exception that all reagents were 5x concentrated. The libraries, each carrying a unique barcode in the 5` adapter, were equimolarly mixed and submitted for 454 sequencing. 454solid_bc: 5` GCC TCC CTC GCG CCA TCA G  barcode C CAC TAC GCC TCC GCT TTC CTC TCT ATG 3` Barcodes:Bc1 GCTA;Bc2 CGTA;Bc3 CGAT;Bc4 GCAT;Bc5 TAGC;Bc6 ATGC

value: Modban


title: modban_miRNA_profiling 2


title: SREK_miRNA_profiling 2

extract_protocol: SREK: SREK was performed according to the manufacturer’s protocol (Ambion, Inc, Austin, TX). Two replicates were produced with the 15-40 nt fraction derived from 0.5 μg small RNA (<200 nt) as input material. 8 rounds of PCR were performed for each library as the PCR in the modban and poly(A) library preparation, with the exception that all reagents were 5x concentrated. The libraries, each carrying a unique barcode in the 5` adapter, were equimolarly mixed and submitted for 454 sequencing. 454solid_bc: 5` GCC TCC CTC GCG CCA TCA G  barcode C CAC TAC GCC TCC GCT TTC CTC TCT ATG 3` Barcodes:Bc1 GCTA;Bc2 CGTA;Bc3 CGAT;Bc4 GCAT;Bc5 TAGC;Bc6 ATGC


title: Adult_herm_3UTR_polyAcapture

description: Mixed barcoded sequences from adult hermaphrodite and adult male, forward read

data_processing: Forward reads are identified by the following pattern - XXXX-GATCNNNNNNNNNNNNNN-XAAAAXAAAAXAAAAXAAAA where XXXX represents the corresponding 4bp barcode for the stage and Ns represent the sequence from DpnII site to the end of the 3’UTR and GATC represents the DpnII restriction site. Reverse reads are identified by the pattern XTTTTXTTTTXTTTTXTTTT-NNNNNNNNNNNNGATC-XXXX-YYYY where XXXX represents the corresponding barcode for the stage and Ns represent the reverse complemented sequence from the DpnII site to the end of the 3’UTR and GATC represents the DpnII restriction site. Ys represent part of the 3’ linker sequence. This run comprised of mixed barcoded sequences from the following stages (56,717 sequences in embryo; 47,504 sequences in L1; 74,047 sequences in L2; 48,713 sequences in L3; 69,296 sequences in L4; 75,546 sequences in adult hermaphrodite).  The sequences that didn't reach the polyA were removed(1,457 sequences in embryo; 1,634 sequences in L1; 1,737 sequences in L2; 1,320 sequences in L3; 2,462 sequences in L4; 2,143 sequences in adult hermaphrodite)  The remaining sequences were processed with custom written perl script to remove the 5' and 3' adaptor sequences and adaptor removed sequences of length less than 15 were discarded (2,461 sequences in embryo; 728 sequences in L1; 133 sequences in L2; 670 sequences in L3; 175 sequences in L4; 179 sequences in adult hermaphrodite).  The remaining sequences reached the polyA and were of length greater than or equal to 15 (52,797 sequences in embryo;45,142 sequences in L1; 72,177 sequences in L2; 46,723 sequences in L3; 66,659 sequences in L4; 73,224 sequences in adult hermaphrodite) and were used for further analysis.

growth_protocol: N2 protocol: N2 wildtype worms were grown on 10 cm2 NGM plates seeded with OP50 and synchronized by alkaline/hypochride.  A fraction of eggs (mixed embryos) were frozen down in TriReagent (Ambion, Cat# AM9738) and the remaining ones were hatched overnight in M9 buffer. Starved L1 larvae were then plated on 10 cm2 plates (OP50 as food) raised at 20C.  Samples were taken at ~8 hr (L1), ~20hr (L2), ~30hr (L3), ~45hr (L4), ~70hr (adult). Worms were collected in M9, washed 3 times with M9 to remove residue bacteria and frozen down in TriReagent.

value: young adult hemaprhodite


title: 3UTR_EMB_L1toL4_Adult_polyAcapture, L2


title: 3UTR_EMB_L1toL4_Adult_polyAcapture, young adult hemaprhodite


title: smallRNA_rat_brain_polyA_rep1


title: smallRNA_rat_brain_modban_rep2

extract_protocol: Modban: The original protocol, as described by Lau et al. 2001, was followed. We used as input the 15-40 nt fraction of 1 μg of small RNA isolated using the miRVana kit. A preadenylated modban adapter was ligated to the to the RNA in the absence of ATP. The 30-50 nt fraction was excised from a 15% denaturing polyacrylamide gel. After elution in 0.3M NaCL and EtOH precipitation, the 5` linker was ligated in the presence of ATP. The 70-90 nt fraction was gel-excised from a 10% denaturing polyacrylamide gel, eluted and precipitated. Reverse-transcription was performed with the modban RT primer and 15 cycles of PCR were performed to amplify the library.


title: synthetic_miRNAs_SREK_amplified_rep3

data_processing: Sequencing reads were mapped to the reference set of miRNAs using SHRiMP. Reads with 3 or less colorspace errors were included in the further analysis.

source_name: synthetic miRNA

extract_protocol: SREK: SREK was performed according to the manufacturer’s protocol (Ambion, Inc, Austin, TX).

value: synthetic miRNA


title: L4_3UTR_polyAcapture

description: Sequences from L4, forward and reverse read


title: SREK_miRNA_profiling 1


title: smallRNA_rat_brain_modban_rep1


title: synthetic_miRNAs_modban_amplified_rep2


title: synthetic_miRNAs_SREK_amplified_rep1


title: smallRNA_rat_brain_SREK_rep2


title: Dauer_daf11_3UTR_polyAcapture

description: Mixed barcoded sequences from dauer daf2, daf7, daf9, and daf11 mutants, forward read

source_name: N2 daf mutants

growth_protocol: dauer protocol: For dauer larvae preparation, daf mutants from starved plates were collected, resuspended in M9 buffer containing 1% SDS, and incubated in this solution for 15-30 min at room temperature. The suspension was then washed with M9 buffer and worms were placed on a fresh, unseeded plate at 20°C for 12 h. Because dauer larvae were resistant to SDS, the dauer larvae that had crawled away from the dead worms were collected in M9 buffer.

value: dauer


title: synthetic_miRNAs_modban_amplified_rep1


title: Dauer_daf9_3UTR_polyAcapture


title: Dauer_daf2_3UTR_polyAcapture


title: polyA_miRNA_profiling 1


title: Tobacco rattle virus (TRV) derived small RNAs

status: Public on Jul 10 2009

city: Garchinig

first: Yu

last: Wang

address: Boltzmannstrasse 1

department: High performance computing

institute: Leibniz Supercomputing Centre

description:
Virus: TRV Genus: Tobravirus Genome type: (+)-ssRNA bipartite
barcode: CGAC
5' ADAPTOR: GCCTCCCTCGCGCCATCAGATCGTAGCGACCTGATA
accesion number for virus isolate used:  (NC_003805, NC_003811)
processed file: smallRNA hit name - number after the virus name indicates how many times sRNA sequence was recovered.

data_processing: sRNA sequences were parsed from FASTA formatted files and assigned to specific libraries through identification of the sRNA/adapter boundaries and barcode analysis. The adapter sequences in the 454 sequencing reads were removed by using python scripts and the biopython library (http://biopython.org/). The viral genomic sequences were downloaded from NCBI (http://www.ncbi.hlm.nih.gov). vsRNA reads were mapped to the viral genomic sequences by using Blast and Vmatch (http://www.vmatch.de/)

organism: Tobacco rattle virus

source_name: Inflorescences from Arabidopsis thaliana infected with TRV

growth_protocol: Plants were grown under standard conditions

extract_protocol: Total RNA was extracted using Trizol reagent and ~300 microgrames were used for construction of sRNAs libraries. The 3’ adapter was a pre-activated 5’ adenylated oligo (5’ rAppCTGTAGGCACCATCAAT3ddC 3’) to avoid the circularization of sRNAs. The 5' adpaters were chimeric RNA/DNA oligonucleotide generated by modification of the four-nucleotide identifier. After each ligation step, sRNA was purified using 17 % denaturing PAGE. The purified-ligated sRNA was reverse transcribed and the cDNA was amplified using Taq DNA polymerase and 3’ PCR FusionB and 5’ PCR FusionA primers. PCR primers contained the “A” and “B” tag sequences used by 454 Life Science during sequencing. DNA amplicons were gel-purified using 12 % native polyacrylamide and eluted in 0.3M NaCl. Quantity and quality of DNA amplicons were measured using ND-1000 spectrophotometer (Nanodrop) and Experion Automated Electrophoresis System (BioRad), respectively. Same quantity of DNA amplicon from each library was pooled and sequenced by 454 Life Science technology (Lifesequencing, http://lifesequencing.com).

treatment_protocol: Plants were infected by mechanical inoculation

value: upper noninoculated systemically infected inflorescences from Arabidopsis thaliana

tag: virus

value: TRV


title: Cucumber mosai virus (CMV) derived small RNAs

description:
Virus: CMV Genus: Cucumovirus Genome type: (+)-ssRNA tripartite
barcode: CGTG
5' ADAPTOR: GCCTCCCTCGCGCCATCAGATCGTAGCGTGCTGATA
accesion number for virus isolate used: (NC_002035, NC_002034, D10538)
processed file: smallRNA hit name - number after the virus name indicates how many times sRNA sequence was recovered.

organism: Cucumber mosaic virus

source_name: Inflorescences from Arabidopsis thaliana infected with CMV

value: CMV


title: Potato virus X (PVX) derived small RNAs

description:
Virus: PVX Genus: Potexvirus Genome type: (+)-ssRNA monopartite
barcode: GCTG
5' ADAPTOR: GCCTCCCTCGCGCCATCAGATCGTAGGCTGCTGATA
accesion number for virus isolate used: (NC_001455)
processed file: smallRNA hit name - number after the virus name indicates how many times sRNA sequence was recovered.

organism: Potato virus X

source_name: Leaves from Nicothiana benthamiana infected with PVX

value: upper noninoculated systemically infected leaves from Nicothiana benthamiana

value: PVX


title: Cymbidium ringspot virus (CymRSV) derived small RNAs

description:
Virus: CymRSV Genus:Tombusvirus Genome type: (+)-ssRNA monopartite
barcode: GCAC
5' ADAPTOR: GCCTCCCTCGCGCCATCAGATCGTAGGCACCTGATA
accesion number for virus isolate used: (NC_003532)
processed file: smallRNA hit name - number after the virus name indicates how many times sRNA sequence was recovered.

organism: Cymbidium ringspot virus

source_name: Leaves from Nicothiana benthamiana infected with CymRSV

value: CymRSV


title: Melon necrotic spot virus (MNSV) derived small RNAs

description:
Virus: MNSV Genus: Carmovirus Genome type: (+)-ssRNA monopartite
barcode: ACGC
5' ADAPTOR: GCCTCCCTCGCGCCATCAGATCGTAGACGCCTGATA
accesion number for virus isolate used: (AY122286)
processed file: smallRNA hit name - number after the virus name indicates how many times sRNA sequence was recovered.

organism: Melon necrotic spot virus

source_name: Cotyledons from Cucumis melo infected with MNSV

value: inoculated cotyledons from Cucumis melo

value: MNSV


title: synthetic_miRNAs_SREK_amplified_rep2


title: L2_3UTR_polyAcapture

description: Sequences from L2, forward and reverse read


title: MEF

status: Public on Aug 25 2009

city: Cambridge

first: Christine

last: Mayr

address: 9 Cambridge Center

institute: Whitehead Institute

data_processing: Reads containing linker matches were mapped (after removing linkers) to predicted pre-miRNAs (MirBase version 12.0)

source_name: cell line

growth_protocol: RNA was harvested from exponentially growing cells

extract_protocol: Total RNA extracted using standard Trizol extraction. Total RNA fractionated on 15% polyacrylamide gel and 3' and 5' adaptors sequentially ligated requiring a 3' hydroxyl group and 5' phosphate

value: MEF


title: 3UTR_EMB_L1toL4_Adult_polyAcapture, L4


title: Tomato yellow leaf curl virus (TYLCV) derived small RNAs

description:
Virus: TYLCV Genus: Begomovirus Genome type: ssDNA circular
barcode: CGCA
5' ADAPTOR: GCCTCCCTCGCGCCATCAGATCGTAGCGCACTGATA
accesion number for virus isolate used: (NC_004005)
processed file: smallRNA hit name - number after the virus name indicates how many times sRNA sequence was recovered.

organism: Tomato yellow leaf curl virus

source_name: Leaves from Solanum lycopersicum infected with TYLCV

value: upper noninoculated systemically infected leaves from Solanum lycopersicum

value: TYLCV


title: Turnip mosaic virus (TuMV) derived small RNAs

description:
Virus: TuMV Genus: Potyvirus Genome type: (+)-ssRNA monopartite
barcode: ACGC
5' ADAPTOR: GCCTCCCTCGCGCCATCAGATCGTAGACGCCTGATA
accesion number for virus isolate used: (AB194802)
processed file: smallRNA hit name - number after the virus name indicates how many times sRNA sequence was recovered.

organism: Turnip mosaic virus

source_name: Inflorescences from Arabidopsis thaliana infected with TuMV

value: TuMV


title: X.tropicalis Xiwi IP Small RNAs

source_name: Immunoprecipitation of Xiwi from X.tropicalis Egg Extract

extract_protocol: Small RNA library from Xiwi IP from X.tropicalis egg extract. A polyclonal antibody against Xiwi was coupled to magnetic beads, mixed with Xenopus egg extract, and beads were extensively washed.  The antibody immunoprecipitate was eluted and mixed with Trizol to obtain total RNA. Small RNAs were ligated with linkers and converted to cDNA by reverse transcription. cDNA library was amplified by PCR.

value: polyclonal antibody against Xiwi

value: egg extract

value: Illumina


title: L1_3UTR_polyAcapture

description: Sequences from L1, forward and reverse read

organism: Caenorhabditis elegans


title: Watermelon mosaic virus (WMV) derived small RNAs

description:
Virus: WMV Genus: Potyvirus Genome type: (+)-ssRNA monopartite
barcode: GCCA / GCGT
5' ADAPTOR: GCCTCCCTCGCGCCATCAGATCGTAGGCCACTGATA / GCCTCCCTCGCGCCATCAGATCGTAGGCGTCTGATA
accesion number for virus isolate used: (AY437609)
processed file: smallRNA hit name - number after the virus name indicates how many times sRNA sequence was recovered.

organism: Watermelon mosaic virus

source_name: Cotyledons from Cucumis melo infected with WMV

value: WMV


title: Dauer_daf7_3UTR_polyAcapture

value: dauer


title: Melon necrotic spot virus (MNSV) chimeric virus derived small RNAs

description:
Virus: MNSV Genus: Carmovirus Genome type: (+)-ssRNA monopartite
barcode: ACCG / AGGC
5' ADAPTOR: GCCTCCCTCGCGCCATCAGATCGTAGACCGCTGATA / GCCTCCCTCGCGCCATCAGATCGTAGAGGCCTGATA
processed file: smallRNA hit name - number after the virus name indicates how many times sRNA sequence was recovered.

source_name: Cotyledons from Cucumis melo infected with MNSV chimeric virus

value: MNSV chimeric virus


title: Adult_male_3UTR_polyAcapture

value: adult male


title: L3_3UTR_polyAcapture

description: Sequences from L3, forward and reverse read


title: Endogenous small RNAs from mature leaf of rice - replicate 2

status: Public on Jun 08 2009

city: Davis

first: Venkatesan

last: Sundaresan

address: One Shields Ave

department: Plant Biology

institute: University of California Davis

description: 18-34nt small RNAs

data_processing: 5' and 3' adapter sequences were identified by alignment, and RNA sequences between these were extracted. Often more than one RNA sequence could be obtained from a single 100nt sequence read.

organism: Oryza sativa

extract_protocol: Small RNA libraries were constructed using a method that requires the 5’ end of the small RNAs to be phosphorylated  [Lau, N.C., Lim, L.P., Weinstein, E.G., Bartel, D.P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans Science, 294, 858–862].  Total cellular RNA was fractionated on a 15% acrylamide gel run in 8M urea and 1X TBE, and the region of the gel containing 16 to 28 nt RNAs was excised.  The small RNAs were eluted in 0.3 M NaCl and ethanol precipitated with 2.8 volumes of ethanol.  The small RNAs were ligated to one of three alternative RNA-DNA chimeric pre-adenylylated 3´-adaptor oligonucleotides (see elsewhere for specific adapter) in a reaction containing 20 uM 3´-adaptor, 50 mM Hepes pH 8.3, 5 mM MgCl2, 3 mM DTT, 5 ug/ ml BSA and 8% glycerol for 2 hr.  The ligated small RNAs were gel isolated as described above and ligated to an RNA 5’ adaptor (ATCGTAGGCACCTGAAA) and subsequently gel isolated.  The resulting RNAs were reversed transcribed and amplified by PCR.  The resulting DNAs were gel purified and sequenced by 454 Life Sciences.

value: 60 cm mature leaf

tag: stage

value: early immergence of inflorescence

tag: 3' adapter

value: CACTCGGGCACCAAGGA


title: Endogenous small RNAs from shoot apex of rice - replicate 1

description: 18-34nt small RNAs

value: mostly P4 shoot primordia some P3

value: 13-14 day old seedlings

value: CTGTAGGCACCATCAAT


title: Endogenous small RNAs from root apex of rice - replicate 3

description: 18-34nt small RNAs

value: ~250 micrometers root tip

value: TTTAACCGCGAATTCCAG


title: Late-sporulation_CO2_SOLiD

status: Public on May 01 2009

city: Atlanta

first: Nicholas

last: Bergman

state: GA

address: 310 Ferst Dr., Rm 231

institute: Georgia Institute of Technology

description: Variable= atmosphere: CO2

data_processing: Reads were aligned to B. anthracis Ames ancestor and sequence census of the reference genome was calculated using SOCS. SOCS output files are attached - in these files, each line corresponds to a single nucleotide in the reference genome (NC_007530.2 and pxO1 plasmid NC_007322.2).  The first column is the position (counting from 1... using the FASTA reference sequence), and the second column is the number of times that position is represented in the data set being mapped (i.e., the sequence coverage depth).

organism: Bacillus anthracis

source_name: sporulating cells

growth_protocol: Standard growth in Modified G medium

extract_protocol: Samples were enriched for mRNA by depleting the 16S and 23S ribosomal RNAs and converted to cDNA.

tag: growth phase

value: late sporulation

tag: optical density


title: Endogenous small RNAs from root apex of rice - replicate 1

description: 18-34nt small RNAs


title: Endogenous small RNAs from mature leaf of rice - replicate 1

description: 18-34nt small RNAs


title: Endogenous small RNAs from shoot apex of rice - replicate 3

description: 18-34nt small RNAs


title: Endogenous small RNAs from developing inflorescence of rice - replicate 3

description: 18-34nt small RNAs

value: 1-2.5 cm length inflorescence

value: mid stage 7


title: Endogenous small RNAs from developing inflorescence of rice - replicate 1

description: 18-34nt small RNAs


title: EMB_3UTR_polyAcapture

city: New York

first: Kristin

last: Gunsalus

institute: NYU Center for Genomics and Systems Biology

description: Sequences from embryo, forward and reverse read

source_name: N2 wildtype

value: embyro


title: Col-0 (Mock)

status: Public on Mar 24 2009

city: Lubbock

first: Zhixin

last: Xie

state: TX

institute: texas tech university

description:
Small RNAs captured from mock-infected host tissues.

The processed data below represent the sequence and normalized abundance of virus-derived small RNAs.

Since this sample was a "mock-infected" negative control, no virus-derived small RNAs would be expected. Therefore, there was no processed data file associated with this particular sample.

Host genetic background: Wil type; Viral pathogen: None

data_processing: The small RNA sequences were computationally extracted from the raw sequence tags generated by Illumina and parsed into the four source libraries using Python scripts, based on the 5’-adapter index and the partial 3’-adapter sequence.  For each source library, small RNAs with sequence that perfectly matched the TMV-Cg genome, in either the sense or antisense orientation, were computationally extracted and designated as TMV-Cg-derived small RNAs.  The remaining small RNAs with sequence perfectly matching either the Arabidopsis nuclear genome or the organelle genomes were designated as Arabidopsis small RNAs.  Small RNAs with a sequence matching neither the virus nor the host genome were discarded without further analysis. TMV-Cg small RNA reads added with host small RNA reads as the total small RNA reads for each sample was normalized per million.

organism: Youcai mosaic virus

source_name: Mock-infected Arabidopsis thaliana Col-0 host.

growth_protocol: The Arabidopsis thaliana Plants were grown in a commercial soil mix (SunGrow complete mix No.1; BWI Inc.) in a growth chamber with a cycle of 16h light at 24 ºC and 8h dark at 22 ºC.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Inc), followed by column purification (RNA/DNA midi-kit, QIAGEN).  Total RNA samples(250ug) were separated on 17% denaturing PAGE gel and the zone corresponding to 16- to 28-nt small RNAs was excised and transferred to DE-81 paper (Whatman) and eluted.

treatment_protocol: Four-week-old plants, typically with 10-11 expanded rosette leaves prior to bolting were used for virus infection.  Briefly, five expanded leaves (the 4-8th true leaves) per plant were manually inoculated with purified TMV-Cg (10µg/mL in 10mM sodium phosphate buffer, pH 7.5).  A parallel set of control plants were mock-inoculated with the buffer following the same procedure.  Systemic tissues consisting of leaves and young inflorescences were collected at 3 dpi for RNA extraction. The local inoculated leaves were also collected in parallel for infection analysis. Each sample consists of pooled tissues from a group of 6 plants (from a total of 18 plants).

tag: Wild type Arabidopsis thaliana host, Non-infected control.

tag: Crucifer-infecting tobamovirus TMV-Cg is synonymous with Youcai Mosaic Virus, Accession number D38444


title: Late-sporulation_air_SOLiD

description: Variable= atmosphere: air


title: Late-log_CO2_SOLiD

description: Variable= atmosphere: CO2

source_name: vegetative cells

value: mid-log


title: Mid-log_air_SOLiD

description: Variable= atmosphere: air


title: Endogenous small RNAs from developing inflorescence of rice - replicate 2

description: 18-34nt small RNAs


title: Endogenous small RNAs from mature leaf of rice - replicate 3

description: 18-34nt small RNAs


title: Mid-log_CO2_SOLiD

description: Variable= atmosphere: CO2


title: Pepper mild mottle virus (PMMoV) derived small RNAs

description:
Virus: PMMoV Genus: Tobamovirus Genome type: (+)-ssRNA monopartite
barcode: GCCA
5' ADAPTOR: GCCTCCCTCGCGCCATCAGATCGTAGGCCACTGATA
accesion number for virus isolate used: (NC_003630)
processed file: smallRNA hit name - number after the virus name indicates how many times sRNA sequence was recovered.

organism: Pepper mild mottle virus

source_name: Leaves from Nicothiana benthamiana infected with PMMoV

value: upper noninoculated systemically infected leaves from Nicothiana benthamiana

value: PMMoV


title: Endogenous small RNAs from shoot apex of rice - replicate 2

description: 18-34nt small RNAs


title: Endogenous small RNAs from root apex of rice - replicate 2

description: 18-34nt small RNAs


title: Col-0 (TMV-Cg, 3dpi)

description:
The processed data below represent the sequence and normalized abundance of virus-derived small RNAs

For the ease of retrieving the small RNA data, we organized the processed small RNAs captured from TMV-Cg-infected Col-0 tissues into multiple files, each containing a distinct size class ranging from 18- to 25-nt.
_18nt.txt file is small RNAs of 18-nt in size
_19nt.txt file is small RNAs of 19-nt in size
_20nt.txt file is small RNAs of 20-nt in size
_21nt.txt file is small RNAs of 21-nt in size
_22nt.txt file is small RNAs of 22-nt in size
_23nt.txt file is small RNAs of 23-nt in size
_24nt.txt file is small RNAs of 24-nt in size
_25nt.txt file is small RNAs of 25-nt in size

Host genetic background: Wild type; Viral pathogen: TMV-Cg

source_name: TMV-Cg infected Arabidopsis thaliana Col-0 host.

tag: Wild type Arabidopsis thaliana host, TMV-Cg-infected.


title: Early-log_air_SOLiD

description: Variable= atmosphere: air

value: early-log


title: Adult liver Hpa II MethylSeq

status: Public on Mar 09 2009

city: Stanford

first: Rami

last: Rauch

address: 300 Pasteaur Dr

institute: Stanford U

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library17, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)

data_processing: Usable sequence reads were mapped to CCGG sites predicted in silico.  Sites with four or more MspI tags occurring in either the forward or reverse direction were retained in the analysis.  These assayable sites were then grouped with neighboring sites that were within 35-75 bp.  Regions therefore represent any number of digestion sites (between 2 and 18) that have neighboring sites within 35-75 bp of each other.  Methylation calls were made by using HpaII tag data from all assayable cut sites.  The larger of either the forward read count or reverse read count for each site was averaged across each region.  Regions that had an average of zero or one reads per digestion site were called methylated, and regions with more than one sequence read per site were considered unmethylated.

organism: Homo sapiens

source_name: adult liver

extract_protocol: In Methyl-seq, 5 µg genomic DNA was digested with HpaII or MspI.  Fragments were made into next-gen sequencing libraries by using adapters and reagents from Illumina's Library Construction Kit.  After an initial round of PCR, DNA bands (fragments with adapters) of 100-350 bp were isolated by gel extraction (Supplemental Fig. 2).  Size-selected libraries were then PCR-amplified prior to sequencing.  For meDIPSeq, 5 µg genomic DNA was digested with MspI and immunoprecipitated with anti-methylcytosine antibody (Calbiochem); fragments were made into Illumina libraries as described above.

value: liver

value: adult


title: H9 conditioned medium Hpa II MethylSeq

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library10, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)

source_name: H9 conditioned medium

tag: cell type

value: H9 conditioned medium


title: 454 sequencing of small RNAs from irradiated planarians

status: Public on Jul 01 2009

city: Berlin

first: Marc

middle: Riemer

last: Friedlaender

state: Berlin

address: Robert-Rössle-Str. 10

institute: MDC, Berlin-Buch

description: small RNAs

data_processing: These sequences are the output from the 454 Genome Sequencer FLX after base-calling was performed. No adapter sequences have been removed. 5' adapter sequence: CTGTAGG(C/T)(G/A)CCTGAAA. 3' adapter sequence: CTGTAGG(C/T)(G/A)CCTGAAA (identical). Adapters and intervening miRNA can also be in reverse complement orientation.

organism: Schmidtea mediterranea

source_name: planarian

extract_protocol: total RNA, ~15-25 nt RNAs isolated using Novex 15% TBE-Urea gel (invitrogen)

value: irradiated whole-body planarians


title: 454 sequencing of small RNAs from untreated planarians

description: small RNAs

value: untreated whole-body planarians


title: HEK293

tag: cell line


title: rdr1-1 (TMV-Cg, 3dpi)

description:
The processed data below represent the sequence and normalized abundance of virus-derived small RNAs

For the ease of retrieving the small RNA data, we organized the processed small RNAs captured from TMV-Cg-infected rdr1-1 tissues into multiple files, each containing a distinct size class ranging from 18- to 25-nt.
_18nt.txt file is small RNAs of 18-nt in size
_19nt.txt file is small RNAs of 19-nt in size
_20nt.txt file is small RNAs of 20-nt in size
_21nt.txt file is small RNAs of 21-nt in size
_22nt.txt file is small RNAs of 22-nt in size
_23nt.txt file is small RNAs of 23-nt in size
_24nt.txt file is small RNAs of 24-nt in size
_25nt.txt file is small RNAs of 25-nt in size

Host genetic background: rdr1-1; Viral pathogen: TMV-Cg

source_name: TMV-Cg infected Arabidopsis thaliana rdr1-1 host.

tag: rdr1 mutant Arabidopsis thaliana host, TMV-Cg-infected.


title: BG02 EB-derived cells rep2 Hpa II MethylSeq

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library14, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)

source_name: BG02 EB-derived cells

value: BG02 EB-derived cells


title: BG02 EB-derived cells rep1 Hpa II MethylSeq

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library13, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)


title: H9 EB-derived cells Hpa II MethylSeq

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library11, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)

source_name: H9 EB-derived cells

value: H9 EB-derived cells


title: BG02 hESC Hpa II MethylSeq

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library12, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)

source_name: BG02 hESC

value: BG02 hESC


title: Fetal liver 11 weeks Hpa II MethylSeq

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library15, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)

source_name: fetal liver 11 weeks

tag: tissue

value: fetal

tag: age

value: 11 wk


title: H9 embryoid bodies Hpa II MethylSeq

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library9, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)

source_name: H9 embryoid bodies

value: H9 embryoid bodies


title: rdr6-15 (TMV-Cg, 3dpi)

description:
The processed data below represent the sequence and normalized abundance of virus-derived small RNAs

For the ease of retrieving the small RNA data, we organized the processed small RNAs captured from TMV-Cg-infected rdr6-15 tissues into multiple files, each containing a distinct size class ranging from 18- to 25-nt.
_18nt.txt file is small RNAs of 18-nt in size
_19nt.txt file is small RNAs of 19-nt in size
_20nt.txt file is small RNAs of 20-nt in size
_21nt.txt file is small RNAs of 21-nt in size
_22nt.txt file is small RNAs of 22-nt in size
_23nt.txt file is small RNAs of 23-nt in size
_24nt.txt file is small RNAs of 24-nt in size
_25nt.txt file is small RNAs of 25-nt in size

Host genetic background: rdr6-15; Viral pathogen: TMV-Cg

source_name: TMV-Cg infected Arabidopsis thaliana rdr6-15 host.

tag: rdr6 mutant Arabidopsis thaliana host, TMV-Cg-infected.


title: mouse Dicer- knockout oocyte#1

status: Public on Feb 23 2009

city: Foster City

first: Catalin

last: Barbacioru

address: 850 Lincoln Centre Dr

institute: Applied Biosystems

description: library strategy: mRNA-Seq

data_processing: ABI gene expression pipeline

organism: Mus musculus

source_name: Dicer knockout oocyte

growth_protocol: extracted from mouse

extract_protocol: Whole transcriptome Amplification by RT-PCR from a single cell

treatment_protocol: whole cell lysis

tag: female mouse


title: mouse Ago2- knockout oocyte

description: library strategy: mRNA-Seq

source_name: Ago2 knockout oocyte


title: H9 endoderm Hpa II MethylSeq

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library6, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)

source_name: H9 endoderm

value: H9 endoderm


title: mouse Dicer- knockout oocyte#2

description: library strategy: mRNA-Seq

source_name: Dicer-knockout oocyte


title: Piwi IP from Armi Mutant

status: Public on Jun 05 2009

first: Colin

middle: Dean

last: Malone

address: NYUMC, Skirball Institute, 540 1st Ave, 4-10

department: Skirball Institute - Developmental Genetics

institute: NYU Medical Center

description:
small RNA sequencing
library strategy: ChIP-Seq

data_processing: The 36nt long Illumina reads were stripped of the 3’ linker and the resulting small RNA sequences were mapped to the Release 5 genome excluding the Uextra portion. Only reads matching the fly genome 100% were used for further analysis. For annotation, we used Flybase for protein coding genes, UCSC for non-coding RNAs and transposons/repeats (repeat masker tracks) and the most recent miRNA catalog. To control for sequencing depth, small RNA counts were normalized to the same total number after subtracting those matching abundant cellular RNAs such as rRNAs and tRNAs. For the piRNA analysis, we selected small RNAs, which exceeded 22 nt in length and were not annotated as miRNA, tRNA, rRNA, snoRNA, snRNA or smRNA.

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: 24 degrees C

extract_protocol: Trizol

treatment_protocol: Trizol/Phenol Cholorofom extractions

value: ovaries

tag: strain


title: mouse mature wild-type oocyte#2

description: library strategy: mRNA-Seq

source_name: wild-type mature oocyte


title: HCT116 rep3 Msp I MethylSeq

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library3, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)


title: Fetal liver 24 weeks Hpa II MethylSeq

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library16, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)

source_name: fetal liver 24 weeks

tag: developmental stage

value: 24 wk


title: H9 AFP+ hESC-derived cells Hpa II MethylSeq

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library7, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)

source_name: H9 AFP+ hESC-derived cells

value: H9 AFP+ hESC-derived cells


title: mouse mature wild-type oocyte#1

description:
library strategy: mRNA-Seq
The raw data file for this record was truncated and it could not be uploaded at SRA. It has been added as a supplementary file to this record.


title: mouse 4-cell blastomer

description: library strategy: mRNA-Seq

source_name: blastomere from 4-cell


title: HCT116 meDIPSeq data

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call meDIP (library4)  NOTE 0=methylated (tag average>1), 1=unmethylated (tag average<=1)


title: H9 AFP- hESC-derived cell negative Hpa II MethylSeq

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library8, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)

source_name: H9 AFP- hESC-derived cell negative

value: H9 AFP- hESC-derived cell negative


title: H9 hESC Hpa II MethylSeq

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library5, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)

source_name: H9 hESC

value: H9 hESC


title: HCT116 rep2 Msp I MethylSeq

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library2, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)


title: 454 sequencing of small RNAs from FACS-sorted planarian neoblasts

description: small RNAs

source_name: planarian

value: FACS-sorted neoblast stem cells


title: HCT116 rep1 Msp I MethylSeq

description:
please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library1, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)