title: Illumina: Human-superior frontal gyrus-8 years 2 days old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 2922 day old human individual

value: 2922 days


title: Illumina: Human-superior frontal gyrus-53 years 112 days old

status: Public on Jun 10 2010

type: SRA

city: shanghai

first: Song

last: Guo

address: 320 Yue Yang Road

country: China

institute: PICB

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 19457 day old human individual

library_source: transcriptomic

data_processing: supplementary files contain small RNA sequences from purified low molecular weight RNA

molecule: total RNA

organism: Homo sapiens

source_name: Dissected human post-mortem superior frontal gyrus

extract_protocol: Total RNA was isolated from the frozen prefrontal cortex tissue using the Trizol (Invitrogen, USA) protocol with no modifications. Low molecular weight RNA was isolated, ligated to the adapters, amplified, and sequenced following the Small RNA preparation protocol (Illumina, USA) with no modifications.

treatment_protocol: All human postmortem brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (NICHDBB)(Baltimore, MD, USA). All subjects were defined as normal controls by forensic pathologists at the NICHDBB. No subjects with prolonged agonal state were used.

tag: sex

value: male

tag: age

tag: tissue

value: superior frontal gyrus of the brain

tag: batch

value: human batch 1


title: Illumina: Human-superior frontal gyrus-34 days old rep1

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 34 day old human individual

value: 34 days


title: Illumina: Human-superior frontal gyrus-98 years old rep1

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 35770 day old human individual


title: dcr-2 homozygous, untreated

status: Public on Aug 03 2010

city: Worcester

first: Hervé

last: Seitz

state: MA

address: 364 Plantation Street

department: Biochemistry and Molecular Pharmacology

country: USA

institute: University of Massachusetts Medical School

description: This RNA sample was not treated before adapter ligation.

data_processing:
Small RNA sequences were extracted from the deep-sequencing reads by the following procedure: every 18-29-nt long sequence immediately followed by the 5´ heptanucleotide of the 3´ adapter (CTGTAGG) was extracted, then mapped on the Drosophila genome (assembly R5.5 from FlyBase). Only the perfectly-matching sequences were retained for subsequent analyses.
We then discarded every sequence that maps perfectly on a known Drosophila melanogaster abundant non-coding RNA (rRNAs and their frequent variants, tRNAs, snRNAs and snoRNAs).

organism: Drosophila melanogaster

source_name: dcr-2 homozygous heads

growth_protocol: Flies were grown at 25 ºC, on a light/darkness cycle of 12h/12h

extract_protocol: Total RNA was extracted using the mirVana kit (Ambion), then short (18-30 nt) RNAs were gel-purified. 2S rRNA was depleted as described in Seitz et al. (Curr. Biol. 18:147-151 (2008).

treatment_protocol: Heads were dissected as described in Seitz et al. (Curr. Biol. 18:147-151 (2008).

tag: heads were dissected from dcr-2 mutant adult flies (dcr-2^{l811fsx} allele described in lee et al. (2004) cell 117(1)

value: 69-81) as described in Seitz et al. (Curr. Biol. 18:147-151 (2008).


title: Illumina: Human-superior frontal gyrus-2 day old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 2 day old human individual

value: 2 day


title: ago2 homozygous, oxidized (technical replicate #2)

description: This RNA sample was oxidized (as described in Horwich et al. (2007) Curr. Biol. 17(14):1265-1272, except the final alcaline beta-elimination step was omitted) before adapter ligation.

source_name: ago2 homozygous heads

tag: heads were dissected from ago2 mutant adult flies (ago2^{414} allele described in okamura et al. (2004) genes dev. 18


title: ago2 homozygous, oxidized (technical replicate #1)


title: dcr-2 heterozygous, untreated

source_name: dcr-2 heterozygous heads

tag: heads were dissected from dcr-2 heterozygous adult flies (dcr-2^{l811fsx} allele described in lee et al. (2004) cell 117(1)

value: 69-81, over CyO balancer chromosome) as described in Seitz et al. (Curr. Biol. 18:147-151 (2008).


title: Illumina: Rhesus macaque-superior frontal gyrus-26 years 28 days old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 9518 day old human individual

organism: Macaca mulatta

source_name: Dissected rhesus macaque post-mortem superior frontal gyrus

treatment_protocol: Rhesus macaque brains were obtained from the SuZhou Experimental Animal Center (SuZhou, China). The dissections were made from the cortical region approximately corresponding to Brodmann area 9 of the prefrontal cortex (the superior frontal gyrus). We aimed to make dissections that contain 2:1 grey:white matter (60-70% grey matter).

value: female

value: macaque batch 1


title: dcr-2 heterozygous, oxidized


title: Illumina: Rhesus macaque-superior frontal gyrus-20 year 91 days old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 7391 day old human individual

value: 7391 days


title: Illumina: Rhesus macaque-superior frontal gyrus-4 year 27 days old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 1487 day old human individual

value: 1487 days


title: Illumina: Rhesus macaque-superior frontal gyrus-28 years old rep2

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 10220 day old human individual


title: Illumina: Rhesus macaque-superior frontal gyrus-310 days old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 310 day old human individual

value: 310 days


title: Illumina: Rhesus macaque-superior frontal gyrus-2 year 9 days old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 739 day old human individual

value: 739 days

value: macaque batch 2


title: Illumina: Rhesus macaque-superior frontal gyrus-20 days old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 20 day old human individual

value: 20 days


title: Illumina: Rhesus macaque-superior frontal gyrus-16 days old rep2

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 16 day old human individual

value: 16 days


title: Illumina: Rhesus macaque-superior frontal gyrus-9 year 104 days old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 3389 day old human individual

value: 3389 days


title: RNA_whole_worm_mixed_stages, RACE, H

status: Public on May 26 2010

city: New York

first: Kristin

middle: C

last: Gunsalus

state: NY

department: Biology

institute: NYU Center for Genomics and Systems Biology

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 3âUTR 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 3âUTR and GATC represents the DpnII restriction site. Ys represent part of the 3â linker sequence.

organism: Caenorhabditis elegans

source_name: N2 wildtype

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

extract_protocol: Total RNA was incubated at 55Â°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 94Â°C 30 sec, annealing 60Â°C 30 sec, extension 72Â°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 37Â°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: developmental stage

value: mixed stage

tag: clones

value: RACE


title: Illumina: Rhesus macaque-superior frontal gyrus-153 days old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 153 day old human individual

value: male

value: 153 days

value: superior frontal gyrus of the brain


title: Illumina: Rhesus macaque-superior frontal gyrus-16 days old rep1


title: Illumina: Rhesus macaque-superior frontal gyrus-22 years 74 days old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 8104 day old human individual

value: 8104 days


title: Illumina: Rhesus macaque-superior frontal gyrus-28 years old rep1


title: RNA_whole_worm_mixed_stages, RACE, D


title: RNA_whole_worm_mixed_stages, RACE, E


title: RNA_whole_worm_mixed_stages, RACE, F


title: RNA_whole_worm_mixed_stages, RACE, G


title: RNA_whole_worm_mixed_stages, RACE, C


title: RNA_whole_worm_mixed_stages, H

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).

extract_protocol: Total RNA was incubated at 55Â°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 94Â°C 30 sec, annealing 60Â°C 30 sec, extension 72Â°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 37Â°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.


title: RNA_whole_worm_mixed_stages, RACE, B


title: RNA_whole_worm_mixed_stages, F


title: RNA_whole_worm_mixed_stages, G


title: Illumina: Rhesus macaque-superior frontal gyrus-207 days old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 207 day old human individual

value: 207 days


title: Myers_K562_cell_2x75_200_2

status: Public on Sep 11 2010

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

data_processing: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeCaltechRnaSeq

molecule: polyA RNA

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/human/K562_protocol.pdf

extract_protocol: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeCaltechRnaSeq

tag: cell line

tag: cell organism

value: Human

tag: cell description

value: leukemia

tag: cell karyotype

value: cancer

tag: cell lineage

value: "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

tag: cell sex

value: F

tag: localization

value: cell

tag: readtype

tag: insertlength

tag: replicate


title: RNA_whole_worm_mixed_stages, C


title: RNA_whole_worm_mixed_stages, D


title: Colon and lung cancer pool

status: Public on May 20 2010

city: Rehovot

first: Einat

last: Sitbon

address: 10 Plaut St

country: Israel

institute: Rosetta Genomics

description:
Pool2 consists of samples:
4143-Colon (adenocarcinoma)
4119-Colon (adenocarcinoma)
4120-Colon (adenocarcinoma)
4144-Colon (adenocarcinoma)
4145-Colon (adenocarcinoma)
4121-Colon (adenocarcinoma)
4122-Colon (adenocarcinoma)
4146-Colon (adenocarcinoma)
4147-Colon (adenocarcinoma)
4123-Colon (adenocarcinoma)
4124-Colon (adenocarcinoma)
4148-Colon (adenocarcinoma)
4149-Colon (adenocarcinoma)
4125-Colon (adenocarcinoma)
4130-Lung (non-small; adenocarcinoma)
4154-Lung (non-small; adenocarcinoma)
4155-Lung (neuroendocrine; small)
4131-Lung (neuroendocrine; small)
4132-Lung (non-small; large)
4156-Lung (non-small; large)
4157-Lung (non-small; squamous)
4133-Lung (non-small; squamous)
4134-Lung (non-small; squamous)
4158-Lung (non-small; squamous)
4160-Lung (non-small; squamous)
4136-Lung (non-small; squamous)

data_processing: Adaptors were removed using a Perl script allowing internal polyN sequences within the adaptors and 1 mismatch. About 1000 sequences were removed since they were too short after adaptor removal (<10 bp). The sequences were mapped to the human genome (UCSC hg18 build) using BLAST, allowing maximum three bps mismatched to the genome and maximum insertion/deletion (indels) of three bps. For each aligned sequence the highest scoring hit was retrieved. All sequences with position overlap were clustered together using a Perl script. We assigned each genomic cluster of sequences the most abundant sequence in this cluster and demanded that for candidate miRNAs, the most abundant sequence will be mapped precisely to the genome (not allowing any mismatches/indels). The next step was to annotate known sequences. The following datasets were used for this task: RNA genes, sno/miRNA, RefSeq genes, and RepeatMasker tables were downloaded from the UCSC table browser {Karolchik, 2004 }, and known miRNA precursors were downloaded from miRBase  in order to mark whether the sequence is part of a noncoding gene, a snoRNA, a protein-coding gene exon, a genomic repeat, or a known miRNA precursor, respectively. The sequences of the novel miRNA candidates were extended by several hundred bp within their chromosomes in order to predict possible miRNA precursors. An extended sequence was intended to predict the folding of a pri-miRNA that contains a hairpin-folded pre-miRNA. The candidate pri-miRNAs were folded using the Vienna package  or mfold  programs. All hairpin structures that had at least six base pairs, were at least 55 nucleotides long and had a loop not longer than 20 nucleotides were extracted from the minimum free energy fold of the predicted pri-miRNA (excluding overlapping hairpins). Each hairpin was assigned a Palgrade and conservation score as described before {Bentwich, 2005}. Predicted miRNA precursors have either Palgrade>0 meaning it has structural characteristics of known miRNA) or have absolute value of conservation score>0.9 (conserved in mammals). In addition, only sequences with ten or less genomic copies, with a length of 17-25 bp and a GC content in known miRNA range (15-90%) were chosen as miRNA candidates.

source_name: Colon neoplasia and lung neoplasia

extract_protocol: Total RNA was extracted twice from each sample of 23 human formalin-fixed paraffin-embedded (FFPE) samples derived from cancerous tissue. RNA was isolated using ten 10-µm-thick tissue sections using the miRdicatorTM extraction protocol developed at Rosetta Genomics. Briefly, the sample was incubated repeatedly in xylene at 57oC to remove excess paraffin, followed by washing in ethanol. Proteins were degraded by incubation in proteinase K solution at 45oC for a few hours. The RNA was extracted with acid phenol:chloroform followed by ethanol precipitation and DNAse digestion. Total RNA quantity and quality were checked by spectrophotometry (Nanodrop ND-1000). Pools of samples of the small RNA fraction within the total RNA were labeled and hybridized on arrays. After ensuring the presence and expression of more than 100 miRNAs per cancerous tissue pool, tissues were pooled together, resulting in a bladder+breast tumor pool and a colon+lung tumor pool. Array expression revealed the presence of 157 miRNAs from bladder cancer FFPEs, 260 miRNAs from breast cancer FFPEs, 135 miRNAs from lung cancer FFPEs, and 239 miRNAs from colon cancer FFPEs. Total RNA (75 µg) of seven different colon cancer FFPEs were pooled together with 75 µg of six different lung cancer FFPEs, while 75 µg total RNA of five different bladder cancer FFPEs were pooled together with 75 µg of five different breast cancer FFPEs.

tag: tissue

value: colon tumors, lung tumors


title: ERG_AR_re_ChIP

status: Public on May 18 2010

city: Chicago

first: Jindan

last: Yu

state: IL

address: 303 E. Superior St.

department: Medicine - Hem/Onc

institute: Northwestern University

library_source: genomic

data_processing: Reads were aligned to the reference genome using Eland software   (Illumina). Enriched intervals were identified by a Hidden Markov   Model-based program named HPeak (Qin et al. unpublished).

molecule: genomic DNA

source_name: VCaP - Regular medium - Chromatin IP against ERG first followed by re-ChIP against AR

growth_protocol: Prostate cell lines were maintained in appropriate medium.  For androgen treatment experiment, LNCaP and VCaP cells were hormone starved for 48 hours prior to treatment with ethanol control or synthetic androgen R1881.  For RNA interference of ERG, VCaP cells were grown in regular medium and subjected to non-silencing control siRNA or siRNA specific for targeting ERG on two continuous days.  At 48 hour after the last siRNA transfection, cells were harvested for ChIP analysis.

extract_protocol: Chromatin was fixed in 1% formaldehyde, sheared to 200-700bp using an ultrasonic sonicator (Misonix), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

tag: Regular medium


title: VCaP_R1881_H3K9me3

description: Chromatin IP against H3K9me3

source_name: VCaP - R1881 - Chromatin IP against H3K9me3


title: Breast and bladder cancer pool

description:
Pool1 consists of samples:
4117-Bladder
4141-Bladder
4142-Bladder (transitional cell carcinoma)
4118-Bladder (transitional cell carcinoma)
4138-Bladder
4162-Bladder
4163-Bladder
4139-Bladder
4140-Bladder
4164-Bladder
4126-Breast
4150-Breast
4151-Breast
4127-Breast
4128-Breast
4152-Breast
4135-Breast
4159-Breast
4137-Breast
4161-Breast

source_name: Bladder neoplasia and breast neoplasia

value: bladder tumors, breast tumors


title: mouse epiblast#3

status: Public on May 10 2010

city: Foster City

first: Catalin

last: Barbacioru

address: 850 Lincoln Centre Dr

institute: Applied Biosystems

description:
Data was processed with base quality values set to 32
AB SOLiD system V3.0

data_processing:
srf conversion generated by SOLiD srt tool: http://solidsoftwaretools.com/gf/project/srf/
raw data alignet to Mouse genome (Jul. 2007 assembly of the mouse genome: mm9, NCBI Build 37) using SOLiD whole transcriptome pipeline: http://solidsoftwaretools.com/gf/project/transcriptome/
algorithm description: Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, Lao K, Surani MA., mRNA-Seq whole-transcriptome analysis of a single cell, Nat Methods. 2009 May;6(5):377-82.

organism: Mus musculus

source_name: E4.5 Epiblast

extract_protocol: whole cell lysis, Whole transcriptome Amplification by RT-PCR from a single cell, mRNA with poly(A) tail

tag: gender

value: female

tag: sample type

value: E4.5 Epiblast


title: Day5-Oct4- outgrowth#1

source_name: ICM outgrowth at Day 5 Oct4-positive

value: ICM outgrowth at Day 5 Oct4-positive


title: Day5-Oct4- outgrowth#2


title: Day3-Oct4+ outgrowth#1

source_name: ICM outgrowth at Day 3 Oct4-positive

value: ICM outgrowth at Day 3 Oct4-positive


title: Day5-Oct4+ outgrowth#2

source_name: ICM outgrowth at Day 5 Oct4-negative

value: ICM outgrowth at Day 5 Oct4-negative


title: Day5-Oct4- outgrowth#3


title: Day5-Oct4+ outgrowth#1


title: mouse epiblast#2


title: mouse epiblast#1


title: Day3-Oct4+ outgrowth#3


title: Day5-Oct4+ outgrowth#3


title: WT, oxidized

description: This RNA sample was oxidized (as described in Horwich et al. (2007) Curr. Biol. 17(14):1265-1272, except the final alcaline beta-elimination step was omitted) before adapter ligation.

source_name: WT heads

tag: heads were dissected from oregon r adult flies as described in seitz et al. (curr. biol. 18


title: dcr-2 homozygous, oxidized

tag: heads were dissected from dcr-2 mutant adult flies (dcr-2^{l811fsx} allele described in lee et al. (2004) cell 117(1)

value: 69-81) as described in Seitz et al. (Curr. Biol. 18:147-151 (2008).


title: mouse inner cell mass#9

source_name: E3.5 ICM

value: E3.5 ICM


title: mouse inner cell mass#8


title: C.rubella_5d-seedling_6hr-mock

status: Public on May 14 2010

city: Saint Louis

first: James

last: Carrington

state: MO

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description:
Wild type C. rubella 5d seedling small RNA after 6hr mock treatment.
CR03

data_processing: Small RNA sequences were parsed from 454 sequencing data files through identification of the 5' and 3' adaptor boundaries. For A. lyrata samples, only sequences that mapped perfectly to the reference genome (JGI v1.0;  http://genome.jgi-psf.org/Araly1/Araly1.info.html ; http://www.phytozome.net/alyrata) were included in the analysis.  All C. rubella small RNA are provided as there was no available draft genome at the time the experiment was done.

organism: Capsella rubella

source_name: 5d seedlings, mock

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 a Roche Genome Sequencer FLX instrument.

treatment_protocol: C. rubella 5d seedlings were either treated with 150mM NaCl for 6 hrs or mock treated for 6 hrs.

tag: strain

value: MTE

value: seedlings

tag: age

value: 5 days

tag: treatment

value: 6hr mock


title: Day3-Oct4+ outgrowth#2


title: mouse inner cell mass#7


title: A.lyrata_14d-seedling_rep1

description:
Wild type A. lyrata 14d seedling small RNA.
AL06

organism: Arabidopsis lyrata

source_name: 14d seedlings

value: 14 days


title: mouse inner cell mass#6


title: mouse inner cell mass#4


title: mouse inner cell mass#3


title: A.lyrata_14d-seedling_rep2

description:
Wild type A. lyrata 14d seedling small RNA.
AL07


title: A.lyrata_flowers-stage1-12_rep1

description:
Wild type A. lyrata flower small RNA.
AL04

source_name: flowers stage 1-12

value: flowers

value: stage 1-12


title: mouse inner cell mass#5


title: mouse inner cell mass#2

description:
Data was processed with base quality values
AB SOLiD system V3.0


title: C.rubella_5d-seedling_6hr-150mM-NaCl

description:
Wild type C. rubella 5d seedling small RNA after 6hr treatment with 150 mM NaCl.
CR04

source_name: 5d seedlings, NaCl

value: 6hr 150 mM NaCl


title: mouse embyronic stem cell#5

source_name: ES cell

value: ES cell


title: mouse embyronic stem cell#6


title: mouse embyronic stem cell#10


title: mouse embyronic stem cell#8


title: mouse embyronic stem cell#13


title: mouse embyronic stem cell#11


title: C.rubella_flowers-stage1-12

description:
Wild type C. rubella flower small RNA.
CR01


title: C.rubella_14d-seedling

description:
Wild type C. rubella 14d seedling small RNA.
CR02


title: mouse embyronic stem cell#9


title: mouse embyronic stem cell#12


title: A.lyrata_flowers-stage1-12_rep2

description:
Wild type A. lyrata flower small RNA.
AL05


title: mouse embyronic stem cell#7


title: mouse embyronic stem cell#3


title: mouse embyronic stem cell#2


title: mouse embyronic stem cell#1


title: mouse inner cell mass#1


title: mouse embyronic stem cell#4


title: undifferentiated human embryonic stem cells

status: Public on May 07 2010

city: Seattle

first: Muneesh

last: Tewari

state: WA

address: 1100 Fairview Ave, N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: Undiff hESC

data_processing:
Raw sequencing files (*reads.fna) are in fasta format as received from Roche.
Custom bioinformatic data analysis pipeline: The sequencing data was preprocessed by first trimming the 454 adaptor and 5'/3' linker sequences from each read, followed by removal of any sequences corresponding to spiked-in RNA size markers. The resulting set of reads contained both "forward" sequences (which contain the 5' and 3' linkers in that order) and "reverse complement" sequences (which contain the 3' linker and then the 5' linker in that order) that were combined into a single set of reads. The complete set of reads was then compiled into a set of unique (i.e., nonredundant) sequences, with the number of reads for each sequence reflecting relative abundance. The Undiff-hESC dataset contained 18,227 nonredundant sequences with 280,185 reads and the Diff-hESC dataset contained 16,096 nonredundant sequences with 143,124 reads. Both datasets contained sequences ranging in length from 10 to 32 nucleotides, with 82% of the sequences and 91% of the reads in the range of 18-26 nts. The unique sequences and their counts are provided in the supplementary *unique.fa file.
The data analysis pipeline next identifies sequences that match previously annotated features in the genome and sets those sequences aside for further analysis. We first compared our sequences using BLAST against a database constructed of known miRNA mature sequences and a database constructed of the precursor sequences (miRBase release 9.0). Many high-abundance sequences were not exact matches to known miRNAs, but were either super-sequences, sub-sequences, or had significant overlap with known miRNAs. As the great majority of these sequences exactly matched the precursor sequence of a single known miRNA, we decided to incorporate those reads into the set of sequences matching known miRNAs. Specifically, if the super-sequence exactly matched the precursor of the known miRNA, the numbers of reads for both sequences were summed. For the sub-sequences, if our sequence was a sub-sequence of exactly one known miRNA, the reads were added together. If a sequence was a sub-sequence of more than one known miRNA, then it was not included in the analysis. Of the 224 sub-sequences for the Undiff-hESC dataset and the 409 sub-sequences of the Diff-hESC dataset, there were just 16 and 13 sequences, respectively, which were sub-sequences of more than one known miRNA. If a sequence was not strictly a super- or sub-sequence of a known miRNA, but there was an overlap of more than 15 nt between our sequence and the known miRNA, and the sequence exactly matched the precursor of the known miRNA, its reads were incorporated. The remaining sequences were then BLASTed against a database constructed from the precursor sequences of known miRNAs from miRBase release 9.0 to identify potential star forms of known miRNAs. If one of our sequences did not match the mature sequence of a known miRNA but exactly matched the precursor sequence, we then checked where it appeared on the hairpin of the known miRNA. If it was found in the stem of the hairpin opposite the known mature sequence and had >50% complementarity with the known mature miRNA sequence, we annotated the sequence as a novel star form of a known miRNA. If not (i.e., it was found to be a loop sequence or sequence adjacent to the mature sequence), it was discarded as probable processing by-product of the precursor.

source_name: undifferentiated hESC

growth_protocol: Human ESC were cultured in DMEM/F12 containing GlutaMax™ supplemented with 20% serum replacer (SR), 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 50 U/ml penicillin, 50 μg/ml streptomycin, (all from Invitrogen, Carlsbad, CA, USA), 0.1 mM β-mercaptoethanol (Sigma, St. Louis, MO, USA) and 2 ng/ml basic fibroblast growth factor (FGF, Peprotech, Rocky Hill, NJ, USA).  Primary mouse embryonic fibroblasts (MEF) from E12.5 CD-1 mice were used to make conditioned medium.  To condition medium, 50 ml of the hESC culture medium were placed on a confluent 10 cm plate of MEF cells and held at 37˚C in 5% CO2 in air for 3 days, after which the medium was collected and filtered through a 0.22 μm filter.  Human ESC were cultured on plates seeded with Matrigel (BD Biosciences, San Jose, CA, USA) following the manufacturer’s directions. Culture took place in conditioned medium.  Cells were passaged using 1.2 U/ml dispase (Invitrogen) dissolved in PBS supplemented with 10% fetal bovine serum (ES-qualified FBS, Invitrogen).  Once colonies began to lift from the plate, the cell layer was washed off using a pipette, collected in a centrifuge tube containing culture medium and washed twice by centrifugation before plating.   Cells were incubated at 37ºC in either 5% or 7.5% CO2 in air (Ware et al., 2005, 2006).

extract_protocol: Undifferentiated and differentiated hESC cells were rinsed with cold PBS, lysed in 600µl mirVana Lysis/Binding buffer (Ambion, Inc., Austin, TX) and total RNA was extracted using the mirVanaTM miRNA isolation kit (Ambion) per the manufacturer’s protocol.  MicroRNA cloning was performed as previously described ((Lau et al., 2001; PMID 11679671), http://web.wi.mit.edu/bartel/pub/protocols/miRNACloningUpdate0705.pdf), with modifications at the amplification steps to prepare the samples for massively parallel sequencing by 454 Life Sciences.  Briefly, 100 µg of total RNA was combined with 25 fmol of 5´-32P-labeled 18 and 24 nt RNA molecular weight markers.  These markers had the following sequences: 18nt: AGCGUGUAGGGAUCCAAA; 24nt: GGCCAACGUUCUCAACAAUAGUGA.  Samples were then electrophoresed through 15% denaturing polyacrylamide gels (SequaGel Sequencing System, National Diagnostics, Atlanta, Georgia, USA). Markers were visualized by phosphorimaging, and gel fragments containing the 18-24 nt fractions were excised with a scalpel.  RNAs were eluted in 300 µL 0.3M NaCl with shaking at room temperature overnight, polyacrylamide was removed from the eluate using 0.2 µm Nanosep columns and the eluate was ethanol-precipitated with 20 µg of glycogen as a carrier.  Precipitated RNAs were resuspended in DEPC-treated water and ligated at their 3’ ends with the DNA-based 3’ adaptor oligonucleotide, AppCTGTAGGCACCATCAATddC (Integrated DNA Technologies (IDT), Coralville, IA, USA) using T4 RNA ligase (Amersham Pharmacia Biotech (GE Healthcare Bio-Sciences), Piscataway, NJ, USA) in a 20 µl reaction at room temperature for 2 hours.  3’ ligated reaction products were resolved on a 12% denaturing polyacrylamide gel, imaged, excised, eluted and precipitated as above.  A second ligation was then performed with the 5´-adaptor oligonucleotide, ATCGTaggcaccugaaa (Dharmacon, Inc., Chicago, IL, USA; uppercase, DNA; lowercase RNA), using T4 RNA ligase and ATP (0.4 mM).  Doubly-ligated products were purified through 10% denaturing polyacrylamide gels, imaged, excised, eluted and precipitated as described above.  One quarter of the gel-purified doubly-ligated RNA was reverse-transcribed in a 50 µl reaction (SuperScript III, Invitrogen) using the RT primer ATTGATGGTGCCTAC. The cDNA was amplified by PCR (undifferentiated hESC: x25 cycles; differentiated hESC: x15 cycles), using AmpliTaq® DNA polymerase (Applied Biosystems, Inc., Foster City, CA, USA), the RT primer and a DNA version of the 5´-adaptor oligonucleotide.  The PCR products were gel purified through 3% metaphor agarose, purified using a Qiagen gel extraction kit (Qiagen, Valencia, CA, USA) and 1µl of the purified product was used as template for a second round of PCR using the same primers. Thirty parallel PCR reactions generated from each cDNA library were pooled, phenol/chloroform-extracted and purified through a native 12% polyacrylamide gel (AccuGel, National diagnostics). A five µg aliquot of each miRNA library PCR product pool was submitted for massively parallel pyrosequencing (454 Life Sciences, Inc., Branford, CT) (Margulies et al., 2005). Processing at 454 Life Sciences, Inc. included ligation with adaptors containing 454 sequencing primers followed by sequencing runs and filtering of data to select high-quality reads.

treatment_protocol: To differentiate hESC cultures, cells were lifted from the monolayer using dispase, as in the growth protocol.  One well-growing 35 mm plate was reseeded onto one 10 cm plate seeded with a Matrigel matrix, as described in the growth protocol.  Medium was switched to DMEM containing 15% fetal bovine serum (ES-qualified) and 50 U/ml penicillin, 50 μg/ml streptomycin (all from Invitrogen, Carlsbad, CA, USA), and allowed to differentiate for a specified number of days, day 0 being the day of initial seeding.  Plates were fluid changed every other day (Ware et al., 2005, 2006).  Differentiation was recognized by morphological changes including loss of colony structure that is typical of undifferentiated hESC colonies and acquisition of spindle shape by individual cells. Additional confirmation was obtained by observing loss of Oct-4 expression by qRT-PCR (data not shown).

tag: cell line

tag: cell type

value: human embryonic stem cell (hESC)

tag: differentiation state

value: undifferentiated


title: differentiated human embryonic stem cells

description: Diff hESC

source_name: differentiated hESC

value: differentiated


title: Tumor3_K36

status: Public on May 05 2010

city: Cambridge

first: Noam

last: Shoresh

address: 7 Cambridge Center

department: Epigenomics

institute: Broad Institute

description: Chromatin IP against H3K36me3

data_processing: wig files (signal tracks): Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and mapped to the human (March, 2006) genomes using MAQ. All reads mapping with two or fewer mismatches were retained. Reads with multiple best matches on the genome were discarded. Each read was extended in the direction of its strand out to 200bp, and with a fractional value of 0.25 between 200 and 300bps. Every 25pbs along the genome the number of overlapping tags was calculated. A value of -1 indicates locations for which signal cannot be obtained due to low complexity and the consequential multiple alignment hits for reads from that region.

source_name: WTX-mutated Wilms tumor

growth_protocol: Surgical samples of primary Wilms tumors, normal kidney, and fetal kidney were obtained from Boston Children’s Hospital. All samples were collected with institutional review board approval.

extract_protocol: ChIP DNA samples were quantified using PicoGreen (Invitrogen), and three to ten nanograms were used to prepare sequencing libraries, as described (Mikkelsen et al., 2007). Libraries were loaded onto flow cells and sequenced on the Illumina Genome Analyzer using standard operating procedures.

treatment_protocol: Frozen tissues corresponding to either sections of mature or fetal kidney, or to blastemal compartments of Wilms tumor were thawed and chopped into small fragments. Tissue fragments were crosslinked in 1% formaldehyde, quenched with glycine, washed and disaggregated into single cells using the 50mm medicones on the Medimachine (Beckon Dickinson) according to manufacturer’s protocol. Cells were then lysed and sonicated with a Branson 250 Sonifier to achieve a chromatin fragment size range from 200 to 700bp. Cell lysate was diluted 1:10 in ChIP dilution buffer and subjected to immunoprecipitation with respective antibodies against K4me3 (Abcam 8580), K27me3 (Upstate 07-449) or K36me3 (Abcam 9050). Whole cell lysate was retained for input control. All buffers were supplemented with protease inhibitor cocktail (Roche 14696200).

tag: disease state

value: primary Wilms tumor

tag: tumor region

value: blastemal compartments of Wilms tumor

tag: mutation

value: WTX

tag: chip antibody


title: Fetal Kidney_FK_K27

description: Chromatin IP against H3K27me3

source_name: 18-wk fetal kidney

value: normal

value: kidney

tag: developmental stage

value: fetal


title: mature Kidney_K27

description: Chromatin IP against H3K27me3

source_name: Mature kidney

tag: tissue

value: mature


title: G702N

status: Public on Apr 28 2010

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: NJ

address: Nelson Labs A125, 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

description: 5' monophosphate dependent small RNA cloning

data_processing: frequencies of  known and novel miRNAs expressed in human cervical cancer tissues and matched normal tissues calculated (see Series record)

source_name: normal cervix

growth_protocol: not applicable

extract_protocol: Small RNA isolation was performed using mirVana miRNA isolation kit (Applied Biosystems/Ambion, Austin, TX). Purified small RNAs were ligated to the 3’-adaptor [“Linker-1”, IDT Inc., Coralville, IA] and 5’ adaptor [5’-ACGCTCTTCCGATCTv-3’ (uppercase, DNA; v=barcodes with triple RNA molecules: aaa, ggg, ccc or uuu; IDT Inc., Coralville, IA)] oligonucleotides. Products from the second ligation were gel-purified and reverse transcribed using the RT primer [5'-ATTGATGGTGCCTACAG-3’]. cDNA was amplified with 16-20 PCR cycles, using a forward primer 5'- GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T-3' and a reverse primer 5’-CAA GCA GAA GAC GGC ATA CGA GCT CTT CCG ATC TAT TGA TGG TGC CTA CAG-3', to produce sequencing libraries that were subjected to Solexa/Illumina sequencing platform.

treatment_protocol: not applicable

tag: diagnosis

value: normal cervix


title: G702T

source_name: cervical cancer

value: squamous cell carcinoma

value: tumor


title: G761T

description:
5' monophosphate dependent small RNA cloning
uuu

value: adenocarcinoma


title: G761N

description:
5' monophosphate dependent small RNA cloning
ccc


title: G850T

description:
5' monophosphate dependent small RNA cloning
ggg


title: G576N

description:
5' monophosphate dependent small RNA cloning
aaa


title: G576T


title: Fetal Kidney_FK_K4

description: Chromatin IP against H3K4me3


title: Tumor WT1_K4

description: Chromatin IP against H3K4me3

source_name: WT1-mutated Wilms tumor


title: Tumor2_K4

description: Chromatin IP against H3K4me3


title: Tumor1_K4

description: Chromatin IP against H3K4me3


title: mature Kidney_K4

description: Chromatin IP against H3K4me3


title: Tumor2_K27

description: Chromatin IP against H3K27me3


title: G850N


title: G871N


title: G871T

value: adenosquamous cell carcinoma


title: G696T


title: G696N


title: Tumor1_K27

description: Chromatin IP against H3K27me3


title: Tumor3_K27

description: Chromatin IP against H3K27me3


title: G659N


title: G659T


title: Tumor3_K4

description: Chromatin IP against H3K4me3


title: G691N


title: G691T


title: G547N


title: G699T


title: G699N


title: G652N


title: G652T


title: G547T


title: FC115_L6_M7_TTC

status: Public on Apr 09 2010

description: Single plant

data_processing: Small RNA sequences were parsed from Illumina sequencing data files through identification of the 3' adaptor boundary and the 5' barcode. Only sequences that mapped perfectly to Arabidopsis thaliana or to TuMV genomes were included in the analysis.

organism:
Arabidopsis thaliana
Turnip mosaic virus

source_name: TuMV

growth_protocol: Plants were grown in a greenhouse with a 16-hr light/8-hr dark cycle.

extract_protocol:
Small RNAs were separated 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.
5' adaptor GUUCAGAGUUCUACAGUCCGACGAUC and 3' adaptor CTGTAGGCACCATCAAT

treatment_protocol: Plants were inoculated with enriched TuMV virion preparations or with buffer (mock).

tag: time point

value: 10 dpi

tag: genotype


title: FC115_L6_M7_CCC

description: Single plant


title: FC115_L4_M6_TTC

description: Single plant

value: 7 dpi


title: FC115_L4_M6_AAC

description: Single plant


title: FC115_L8_M9_GGC

description: Single plant

source_name: Mock


title: FC115_L6_M7_AAC

description: Single plant


title: FC115_L8_M9_TTC

description: Single plant


title: FC115_L6_M7_GGC

description: Single plant


title: newly transcribed_270' post LPS_experiment 2

status: Public on Apr 25 2010

type: RNA

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

country: Germany

institute: University Hospital Erlangen

description: Gene expression data from bone marrow derived macrophages

hyb_protocol: 5 µg of biotinylated DNA were hybridized to Mouse Gene ST 1.0 GeneChips overnight, followed by washing and staining procedures, and scanning, following Affymetrix protocols.

scan_protocol: scanning following Affymetrix protocols

data_processing: For generation of probe set expression values, CEL files containing probe level data were normalized using RMA (Affymetrix Expression Console).

label: biotin

source_name: bone marrow derived macrophages from C3H/HeN mice

label_protocol: To investigate the changes in nascent and total mRNA after LPS stimulation of macrophages, RNA samples from two independent experiments were processed and hybridised to Affymetrix Mouse Gene ST 1.0 GeneChips according to the manufacturer’s protocols. In brief, 200 ng total RNA and 100 ng nascent RNA were reverse transcribed introducing by random priming a T7-binding site into the cDNA that allows in vitro transcription. The resulting cRNA was subjected to a second round of random primed cDNA synthesis in the presence of dUTP, that allow fragmentation of the cDNA with uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1. Biotinylation of the fragmented cDNA was accomplished by incubation with Terminal Deoxynucleotidyltransferase (TdT).

growth_protocol: Bone marrow cells from C3H/HeN mice were isolated and cultured in medium for 17 days: After overnight depletion of adherent cells non-adherent cells were expanded by addition of recombinant murine IL-3 (10 mg/L), IL-6 (10 mg/L) and SCF (50 mg/L) (Tebu-Bio) in the presence of 10 % L-cell conditioned medium (LCCM) as a source of macrophage colony stimulating factor (M-CSF) on 10 cm bacteriological plates, starting with 1 x 107 cells per plate. M-CSF was included in the cultures from the beginning to favor the differentiation of macrophages. Cultures were split every 2 to 3 days. After 13 days cells were plated in medium with 10 % LCCM without cytokines to complete differentiation into macrophages for 3 days. On day 16 non-adherent cells were discarded and 25 x 106 adherent cells were plated on 15 cm cell culture plates (Falcon) without LCCM for stimulation the next day.

extract_protocol: Cells were lysed by addition of 10 ml Trifast (PeqLab, Germany) and total RNA was extracted. Biotinylation of 4sU labeled RNA was performed in a total volume of 1 ml containing 120 µg RNA, 10 mM Tris (pH 7.4), 1 mM EDTA and 0.2 mg/ml Biotin-HPDP (Pierce) by rotation at RT for 90 min, followed by two rounds of phenol-chloroform extraction and precipitation. For separation of biotinylated nascent and pre-existing unlabelled RNA paramagnetic streptavidin-coated beads and MACS columns were used (Miltenyi, Germany). RNA and beads were mixed and incubated at RT for 15 min, transferred to the columns and washed extensively with washing buffer. The flow through and the first wash volume were collected for recovery of unlabelled, pre-existing RNA. Labelled RNA was eluted with two rounds of 100 µl DTT (100 mM) into buffer RLT (Qiagen, Germany) and cleaned up using RNeasy MinElute Spin Columns. Concentration and integrity of total and labelled RNA were determined by spectrophotometry (Nanodrop) and Experion automated electrophoresis system (Biorad, Munich, Germany).

treatment_protocol: Metabolic labelling and purification of nascent RNA were performed essentially as described (Dolken et al., 2008), with minor modifications for use with primary macrophages. In brief, 4 x 107 bone marrow derived macrophages differentiated under the same conditions as for the phosphoproteome analysis (except SILAC) were stimulated on 15 cm dishes with 100 ng/ml LPS Escherichia coli (Sigma Aldrich) for 45 min or 4.5 h or were left untreated. For metabolic labelling, the medium was supplemented with 200 µM 4-thiouridine (4sU, Sigma Aldrich, Cat. No. T4509) during the last 35 min of stimulation.

value: C3H/HeN mice

value: bone marrow cells


title: newly transcribed_not stimulated_experiment 1


title: newly transcribed_not stimulated_experiment 2


title: FC115_L4_M6_CCC

description: Single plant


title: total RNA_45' post LPS_experiment 2


title: total RNA_not stimulated_experiment 2


title: newly transcribed_45' post LPS_experiment 1


title: total RNA_270' post LPS_experiment 2


title: FC115_L8_M9_CCC

description: Single plant


title: total RNA_45' post LPS_experiment 1


title: total RNA_not stimulated_experiment 1


title: total RNA_270' post LPS_experiment 1


title: newly transcribed_270' post LPS_experiment 1


title: newly transcribed_45' post LPS_experiment 2


title: FC115_L8_M9_AAC

description: Single plant


title: FC115_L4_M6_GGC

description: Single plant


title: 454-sequenced Cymbidium Ringspot Virus (CymRSV)-derived siRNAs

status: Public on Apr 12 2010

city: Norwich

first: Simon

last: Moxon

state: Norfolk

address: University of East Anglia

country: United Kingdom

institute: University of East Anglia

description: CymRSV-derived small RNAs from early systemic leaves of Nicotiana benthamiana.

data_processing: Removed adaptors. Sequences without adapters were discarded. Small RNA sequences were mapped to the CymRSV genome (GenBank: X15511.1).

organism:
Nicotiana benthamiana
Cymbidium ringspot virus

source_name: Early systemic leaves of CymRSV-infected Nicotiana benthamiana

growth_protocol: 3 weeks old Nicotiana benthamiana plants grown in soil under normal growth conditions were used for virus infection. After infection with CymRSV, plants were grown in fitotrons under a 14 h light (50 E µm-2s-1) and 10 h dark regime at 21°C

extract_protocol: Total RNA was extracted from early systemic leaves of Nicotiana benthamiana infected with CymRSV. The homogenized plant materials were resuspended in 600 \u03bcL of extraction buffer (0.1 M glycine-NaOH, pH 9.0, 100 mM NaCl, 10 mM EDTA, 2% SDS, and 1% sodium lauroylsarcosine) and mixed with an equal volume of phenol. The aqueous phase was treated with equal volumes of phenol and chloroform, precipitated with ethanol, and resuspended in sterile water and used in subsequent reactions.

value: early systemic leaves

value: CymRSV infection


title: FC112_L8_M5_CCC

description: Single plant


title: FC112_L8_M5_GGC

description: Single plant


title: 454-sequenced P19 silencing suppressor mutant Cymbidium Ringspot Virus (Cym19stop)-derived siRNAs

description: Cym19stop-derived small RNAs from early systemic leaves of Nicotiana benthamiana.

source_name: Early systemic leaves of Cym19stop-infected Nicotiana benthamiana

growth_protocol: 3 weeks old Nicotiana benthamiana plants grown in soil under normal growth conditions were used for virus infection. After infection with Cym19stop, plants were grown in fitotrons under a 14 h light (50 E µm-2s-1) and 10 h dark regime at 21°C

extract_protocol: Total RNA was extracted from early systemic leaves of Nicotiana benthamiana infected with Cym19stop. The homogenized plant materials were resuspended in 600 \u03bcL of extraction buffer (0.1 M glycine-NaOH, pH 9.0, 100 mM NaCl, 10 mM EDTA, 2% SDS, and 1% sodium lauroylsarcosine) and mixed with an equal volume of phenol. The aqueous phase was treated with equal volumes of phenol and chloroform, precipitated with ethanol, and resuspended in sterile water and used in subsequent reactions.

value: Cym19stop infection


title: FC115_L7_M9_CCC

description: Single plant


title: FC115_L7_M8_GGC

description: Single plant


title: FC112_L8_M5_AAC

description: Single plant


title: FC112_L7_M4_CCC

description: Single plant


title: FC112_L7_M4_TTC

description: Single plant


title: FC112_L7_M4_AAC

description: Single plant


title: FC112_L7_M4_GGC

description: Single plant


title: FC115_L7_M8_TTC

description: Single plant


title: FC115_L7_M8_AAC

description: Single plant


title: FC112_L6_M3_CCC

description: Single plant


title: FC112_L6_M3_GGC

description: Single plant


title: FC112_L6_M3_AAC

description: Single plant


title: FC112_L4_M2_GGC

description: Single plant


title: FC112_L8_M5_TTC

description: Single plant


title: FC112_L4_M2_TTC

description: Single plant


title: FC112_L4_M2_CCC

description: Single plant


title: FC112_L4_M2_AAC

description: Single plant


title: FC112_L6_M3_TTC

description: Single plant


title: FC102_L006_M1_CCC

description: Single plant


title: FC102_L006_M1_TTC

description: Single plant


title: FC102_L006_M1_GGC

description: Single plant


title: FC102_L006_M1_AAC

description: Single plant


title: A.lyrata_flowers-stage1-12_rep1

description:
Wild type A. lyrata flower small RNA.
AL02

data_processing:
Small RNA sequences were parsed from Illumina sequencing data files through identification of the 3' adaptor boundary (the first six nucleotides of the 3' adaptor: CTGTAG). Only sequences that mapped perfectly to the A. thaliana (TAIR8; http://www.arabidopsis.org) or A. lyrata (v1.0; http://genome.jgi-psf.org/Araly1/Araly1.info.html ; http://www.phytozome.net/alyrata) genomes were included in the analysis.
********Raw data (fastq file) unavailable for this Sample********

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: flowers

value: stage 1-12


title: A.lyrata_flowers-stage1-12_rep2

description:
Wild type A. lyrata flower small RNA.
AL03


title: AP1-GRap1cal_8hr Mock vs. Dex_set4_4000B

status: Public on Apr 02 2010

city: Bellaterra

first: Jose Luis

last: Riechmann

state: Barcelona

address: Campus UAB - Edifici CRAG

country: Spain

institute: Center for Research in Agricultural Genomics

description: s39_AP1GRap1cal_8hMockDex_G460R600_set4_JLR4000B.gpr

hyb_protocol: Dye-labeled antisense RNA was hybridized to microarrays using a MAUI hybridization system (BioMicro Systems, Salt Lake City, UT, USA) as previously described (Wellmer et al. (2006) PLoS Genetics 2, e117). Specifically, hybridizations were done as follows: dye-labeled antisense RNA preparations were dried down and the resulting pellets were re-suspended in 5 ul 10 mM EDTA and 45 ul SlideHyb Buffer #1 (Ambion, Austin, Texas, United States) and hybridized for 14 h to microarrays at 48C using a MAUI hybridization system (BioMicro Systems, Salt Lake City, Utah, United States) according to the manufacturer's instructions.

scan_protocol: Microarrays were scanned and the data acquired with an Axon GenePix 4000B scanner using GenePix Pro 5.1.0.19 analysis software.

data_processing: Data were processed with the Resolver version 7.1 data analysis system (Rosetta Biosoftware, Seattle, WA), using the Axon/GenePix Ratio data processing pipeline with default settings. Resolver uses an error model-based approach to stabilize the variance estimation to improve the specificity and sensitivity in differential gene expression detection (Weng, L., Dai, H., Zhan, Y., He, Y., Stepaniants, S.B., and Bassett, D.E. (2006). Rosetta error model for gene expression analysis. Bioinformatics 22, 1111-1121).

organism: Arabidopsis thaliana

source_name: AP1-GRap1cal_8hr Mock_set4

label_protocol: Dye-labeled antisense RNA was generated from the total RNA preparation. The Amino Allyl MessageAmpII aRNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) was used for labeling of RNA samples with Cy3 and Cy5 fluorescent dyes, following manufacturer's instructions.

growth_protocol: Plants were grown on a soil:vermiculite:perlite (2:1:1) mixture at 20ºC under constant illumination with cool white fluorescent light.

extract_protocol: Total RNA was isolated from tissue samples using the Plant Total RNA kit (Sigma-Aldrich) according to the manufacturer’s instructions. Quality of RNA samples was evaluated using a Bioanalyzer and a RNA Nano 6000 kit (Agilent). RNA concentrations were determined using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: For all experiments, we used approximately 4 week-old 35S:AP1-GR ap1-1 cal-1 plants. For each sample, inflorescence tissue from ~25 plants was collected using jeweler’s forceps. Four biologically independent sets of samples were generated. Inflorescences were treated with a solution containing 10 μM dexamethasone (Sigma-Aldrich), 0.01% (v/v) ethanol, and 0.015% (v/v) Silwett L-77 (De Sangosse), or with an identical mock solution that lacked dexamethasone. We then collected inflorescence tissue after 2, 4, 8, and 12 hours, as well as from untreated plants (0 hour time point).

tag: genome/variation

value: AP1-GR ap1 cal inflorescences

tag: treatment group

value: Mock

tag: treatment time

source_name: AP1-GRap1cal_8hr Dex_set4

value: Dex


title: AP1-GRap1cal_4hr Dex vs Mock_set5_4000B

description: s68_AP1GRap1cal_4hDexMock_G420R580_set5_4000B_JLR.gpr

source_name: AP1-GRap1cal_4hr Dex_set5

source_name: AP1-GRap1cal_4hr Mock_set5


title: AP1-GRap1cal_4hr_Dex vs Mock_set3_4000B

description: s43_AP1GRap1cal_4hDexMock_G460R600_set3_JLR4000B.gpr

source_name: AP1-GRap1cal_4hr Dex_set3

source_name: AP1-GRap1cal_4hr Mock_set3


title: AP1-GRap1cal_2hr Dex vs Mock_set5_4000B

description: s67_AP1GRap1cal_2hDexMock_G420R550_set5_4000B_JLR.gpr

source_name: AP1-GRap1cal_2hr Dex_set5

source_name: AP1-GRap1cal_2hr Mock_set5


title: AP1-GRap1cal_4hr Mock vs. Dex_set2_4000B

description: s46_AP1GRap1cal_4hMockDex_G420R600_set2_JLR4000B.gpr

source_name: AP1-GRap1cal_4hr Mock_set2

source_name: AP1-GRap1cal_4hr Dex_set2


title: AP1-GRap1cal_12hr_Mock vs.Dex_set4_4000B

description: s40_AP1GRap1cal_12hMockDex_G430R600_set4_JLR4000B.gpr

source_name: AP1-GRap1cal_12hr Mock_set4

source_name: AP1-GRap1cal_12hr Dex_set4


title: AP1-GRap1cal_0hr Mock vs. Dex_set4_4000B

description: s36_AP1GRap1cal_0hMockDex_G470R600_set4_JLR4000B.gpr

source_name: AP1-GRap1cal_0hr Mock_set4

source_name: AP1-GRap1cal_0hr Dex_set4


title: AP1-GRap1cal_2hr Mock vs Dex_set4_4000B

description: s37_AP1GRap1cal_2hMockDex_G440R600_set4_JLR4000B.gpr

source_name: AP1-GRap1cal_2hr Mock_set4

source_name: AP1-GRap1cal_2hr Dex_set4


title: AP1-GRap1cal_12hr Mock vs. Dex_set2_4000B

description: s57_AP1GRap1cal_12hMockDex_G420R590_set2_4000B_JLR.gpr

source_name: AP1-GRap1cal_12hr Mock_set2

source_name: AP1-GRap1cal_12hr Dex_set2


title: AP1-GRap1cal_2hr_Dex vs. Mock_set3_4000B

description: s42_AP1GRap1cal_2hDexMock_G400R600_set3_JLR4000B.gpr

source_name: AP1-GRap1cal_2hr Dex_set3

source_name: AP1-GRap1cal_2hr Mock_set3


title: AP1-GRap1cal_0hr Mock vs. Dex_set2_4000B

description: s53_AP1GRap1cal_0hMockDex_G440R600_set2_4000B_JLR.gpr

source_name: AP1-GRap1cal_0hr Mock_set2

source_name: AP1-GRap1cal_0hr Dex_set2


title: AP1-GRap1cal_12hr_Dex vs Mock_set5_4000B

description: s70_AP1GRap1cal_12hDexMock_G420R570_set5_4000B_JLR.gpr

source_name: AP1-GRap1cal_12hr Dex_set5

source_name: AP1-GRap1cal_12hr Mock_set5


title: AP1-GRap1cal_8hr Dex vs. Mock_set3_4000B

description: s44_AP1GRap1cal_8hDexMock_G430R600_set3_JLR4000B.gpr

source_name: AP1-GRap1cal_8hr Dex_set3

source_name: AP1-GRap1cal_8hr Mock_set3


title: AP1-GRap1cal_0hr_Dex vs. Mock_set3_4000B

description: s41_AP1GRap1cal_0hDexMock_G430R600_set3_JLR4000B.gpr

source_name: AP1-GRap1cal_0hr Dex_set3

source_name: AP1-GRap1cal_0hr Mock_set3


title: AP1-GRap1cal_12hr Dex vs. Mock_set3_4000B

description: s45_AP1GRap1cal_12hDexMock_G430R590_set3_JLR4000B.gpr

source_name: AP1-GRap1cal_12hr Dex_set3

source_name: AP1-GRap1cal_12hr Mock_set3


title: AP1-GRap1cal_8hr Mock vs. Dex_set2_4000B

description: s47_AP1GRap1cal_8hMockDex_G420R600_set2_JLR4000B.gpr

source_name: AP1-GRap1cal_8hr Mock_set2

source_name: AP1-GRap1cal_8hr Dex_set2


title: AP1-GRap1cal_8hr_Dex vs Mock_set5_4000B

description: s69_AP1GRap1cal_8hDexMock_G420R570_set5_4000B_JLR.gpr

source_name: AP1-GRap1cal_8hr Dex_set5

source_name: AP1-GRap1cal_8hr Mock_set5


title: AP1-GRap1cal_0hr Dex vs Mock_set5_4000B

description: s71_AP1GRap1cal_0hDexMock_G420R540_set5_4000B_JLR.gpr

source_name: AP1-GRap1cal_0hr Dex_set5

source_name: AP1-GRap1cal_0hr Mock_set5


title: AP1-GRap1cal_0hr Dex vs Mock_set5_4200A

description: S71_AP1GRap1cal_0hDexMock_G460R470_set5.gpr

scan_protocol: Microarrays were scanned and the data acquired with an Axon GenePix 4200A scanner using GenePix Pro 5.1.0.19 analysis software.


title: AP1-GRap1cal_4hr Mock vs. Dex_set4_4000B

description: s38_AP1GRap1cal_4hMockDex_G440R600_set4_JLR4000B.gpr

source_name: AP1-GRap1cal_4hr Mock_set4

source_name: AP1-GRap1cal_4hr Dex_set4


title: AP1-GRap1cal_2hr Dex vs Mock_set5_4200A

description: S67_AP1GRap1cal_2hMockDex_G440R460_set5.gpr

source_name: AP1-GRap1cal_2hr Dex_set5

source_name: AP1-GRap1cal_2hr Mock_set5


title: AP1-GRap1cal_12hr_Dex vs Mock_set5_4200A

description: S70_AP1GRap1cal_12hMockDex_G430R460_set5.gpr

source_name: AP1-GRap1cal_12hr Dex_set5

source_name: AP1-GRap1cal_12hr Mock_set5


title: AP1-GRap1cal_4hr Dex vs Mock_set5_4200A

description: S68_AP1GRap1cal_4hDexMock_G430R460_set5.gpr

source_name: AP1-GRap1cal_4hr Dex_set5

source_name: AP1-GRap1cal_4hr Mock_set5


title: AP1-GRap1cal_12hr_Mock vs.Dex_set4_4200A

description: S40_AP1GRap1cal_12hMockDex_G430R480_set4.gpr

source_name: AP1-GRap1cal_12hr Mock_set4

source_name: AP1-GRap1cal_12hr Dex_set4


title: AP1-GRap1cal_8hr Mock vs. Dex_set4_4200A

description: S39_AP1GRap1cal_8hMockDex_G430R440_set4.gpr

source_name: AP1-GRap1cal_8hr Mock_set4

source_name: AP1-GRap1cal_8hr Dex_set4


title: AP1-GRap1cal_4hr Mock vs. Dex_set4_4200A

description: S38_AP1GRap1cal_4hMockDex_G420R440_set4.gpr


title: AP1-GRap1cal_8hr Dex vs. Mock_set3_4200A

description: S44_AP1GRap1cal_8hDexMock_G430R450_set3.gpr

source_name: AP1-GRap1cal_8hr Dex_set3

source_name: AP1-GRap1cal_8hr Mock_set3


title: AP1-GRap1cal_8hr Mock vs. Dex_set2_4200A

description: S47_AP1GRap1cal_8hMockDex_G420R470_set2.gpr

source_name: AP1-GRap1cal_8hr Mock_set2

source_name: AP1-GRap1cal_8hr Dex_set2


title: AP1-GRap1cal_2hr_Dex vs. Mock_set3_4200A

description: S42_AP1GRap1cal_2hDexMock_G410R470_set3.gpr

source_name: AP1-GRap1cal_2hr Dex_set3

source_name: AP1-GRap1cal_2hr Mock_set3


title: AP1-GRap1cal_0hr Mock vs. Dex_set4_4200A

description: S36_AP1GRap1cal_0hMockDex_G440R440_set4.gpr

source_name: AP1-GRap1cal_0hr Mock_set4

source_name: AP1-GRap1cal_0hr Dex_set4


title: AP1-GRap1cal_4hr_Dex vs Mock_set3_4200A

description: S43_AP1GRap1cal_4hDexMock_G450R470_set3.gpr

source_name: AP1-GRap1cal_4hr Dex_set3

source_name: AP1-GRap1cal_4hr Mock_set3


title: AP1-GRap1cal_2hr Mock vs Dex_set4_4200A

description: S37_AP1GRap1cal_2hMockDex_G410R440_set4.gpr

source_name: AP1-GRap1cal_2hr Mock_set4

source_name: AP1-GRap1cal_2hr Dex_set4


title: AP1-GRap1cal_4hr Mock vs. Dex_set2_4200A

description: S46_AP1GRap1cal_4hMockDex_G420R460_set2.gpr

source_name: AP1-GRap1cal_4hr Mock_set2

source_name: AP1-GRap1cal_4hr Dex_set2


title: C15_omegaUV2zf_rep1

status: Public on Nov 13 2010

first: Scot

last: Wolfe

address: 364 Plantation Street, LRB 619

department: MCCB

institute: UMass Medical School

library_source: synthetic

data_processing:
Two barcoded, multiplexed samples were sequenced using Illumina Genome Analyzer machines.  Each experiment was associated with one or more expected sequence.  Expected sequences were determined based on the restriction enzyme and barcode used to uniquely identify each experimental sample.  Each read was assigned to an experiment if it matched the constant region of an expected sequence exactly.  Reads that did not match one of the expected sequences exactly were placed in the 'unassigned' category.
The Sample tables contain two columns. The first column contains all of the observed unique randomized regions for an experiment.  The second column contains an integer values which indicates the number of times each unique randomized region was observed.
Note: Randomized regions which contained 'N' characters were discarded.  Only reads which matched an expected sequence exactly were considered.  The sequences from multiple experiments were pooled and multiplexed.  The sequences from each experiment were uniquely labeled using a combination of different restriction enzymes and different barcodes.  The expected sequence for each experimental data set is determined by the restriction enzyme and barcode used. In order to be assigned to a specific experiment, a read had to match an expected sequence exactly at all constant (i.e. non randomized) bases.  For example, the expected sequence for the Zen2_omegaUV2zf_rep1 data set is GGTCATGGATCCNNNNNNNNNNTGGGCGGCTGATAG.  The read GGTCATGGATCCGTCCAGATTGTGGGCGGCTGATAG matches the expected sequence for Zen2_omegaUV2zf_rep1, but the sequence GGTCATGGATCCGTCCAGATTGTGGGCAAAAAAAAA does not.

molecule: other

source_name: B1H selection; homeodomain protein: C15

extract_protocol: After each selection, all of the cells were scraped of the plate.  The randomized portion of the prey vector containing the selected transcription factor binding sites were extracted and amplified using PCR.  The PCR products from different experiments were digested with different restriction enzymes  in the first step of uniquely encoding sequences from different experiments.  The restriction enzyme fragments were then barcoded, pooled and sequenced using the Illumina Genome Analyzer II or IIx.  the supplemental material of Noyes et al. (2008). Cell. 133(7):1277-1289 for a more detailed description of the experimental protocol employed.

tag: homeodomain protein

tag: iptg concentration

value: 10 uM

tag: 3-at concentration

tag: duration of experiment

value: 36-48 hours

tag: bait_plasmid variant


title: AP1-GRap1cal_0hr_Dex vs. Mock_set3_4200A

description: S41_AP1GRap1cal_0hDexMock_G410R460_set3.gpr

source_name: AP1-GRap1cal_0hr Dex_set3

source_name: AP1-GRap1cal_0hr Mock_set3


title: AP1-GRap1cal_0hr Mock vs. Dex_set2_4200A

description: S53_AP1GRap1cal_0hMockDex_G570R470_set2.gpr

source_name: AP1-GRap1cal_0hr Mock_set2

source_name: AP1-GRap1cal_0hr Dex_set2


title: AP1-GRap1cal_12hr Dex vs. Mock_set3_4200A

description: S45_AP1GRap1cal_12hDexMock_G430R450_set3.gpr

source_name: AP1-GRap1cal_12hr Dex_set3

source_name: AP1-GRap1cal_12hr Mock_set3


title: AP1-GRap1cal_2h Mock vs. Dex_set2_4200A

description: S52_AP1GRap1cal_2hMockDex_G430R460_set2.gpr

source_name: AP1-GRap1cal_2hr Mock_set2

source_name: AP1-GRap1cal_2hr Dex_set2


title: AP1-GRap1cal_12hr Mock vs. Dex_set2_4200A

description: S57_AP1GRap1cal_12hMockDex_G420R470_set2.gpr

source_name: AP1-GRap1cal_12hr Mock_set2

source_name: AP1-GRap1cal_12hr Dex_set2


title: AP1-GRap1cal_4hr Dex vs Mock_set5

description: GEC_251778410021_S01_GE2-v5_95_Feb07_1_3.txt

hyb_protocol: Agilent microarrays were used following manufacturer's instructions. Microarray hybridizations (65ºC, 16h) and washes were performed with Agilent reagents and following standard protocols.

scan_protocol: Microarrays were scanned using an Agilent DNA Microarray Scanner G2565CA, and data were acquired using Agilent's Feature Extraction Software version 9.5.3.1.

data_processing: Data were processed with the Resolver version 7.1 data analysis system (Rosetta Biosoftware, Seattle, WA), using the Agilent Ratio data processing pipeline with default settings. Resolver uses an error model-based approach to stabilize the variance estimation to improve the specificity and sensitivity in differential gene expression detection (Weng, L., Dai, H., Zhan, Y., He, Y., Stepaniants, S.B., and Bassett, D.E. (2006). Rosetta error model for gene expression analysis. Bioinformatics 22, 1111-1121).

source_name: AP1-GRap1cal_4hr Dex_set5

label_protocol: Agilent microarrays were used following manufacturer's instructions. RNA samples were labeled with fluorescent dyes using the Quick Amp Labeling Kit (Agilent).

source_name: AP1-GRap1cal_4hr Mock_set5


title: AP1-GRap1cal_12hr_Mock vs.Dex_set4

description: GEC_251778410015_S01_GE2-v5_95_Feb07_1_1.txt

source_name: AP1-GRap1cal_12hr Mock_set4

source_name: AP1-GRap1cal_12hr Dex_set4


title: AP1-GRap1cal_8hr_Mock vs Dex_set5

description: GEC_251778410021_S01_GE2-v5_95_Feb07_1_4.txt

source_name: AP1-GRap1cal_8hr Mock_set5

source_name: AP1-GRap1cal_8hr Dex_set5


title: AP1-GRap1cal_12hr_Mock vs Dex_set5

description: GEC_251778410001_S01_GE2-v5_95_Feb07_1_1.txt

source_name: AP1-GRap1cal_12hr Mock_set5

source_name: AP1-GRap1cal_12hr Dex_set5


title: AP1-GRap1cal_8hr_Dex vs Mock_set5_4200A

description: S69_AP1GRap1cal_8hMockDex_G430R460_set5.gpr


title: AP1-GRap1cal_4hr Mock vs. Dex_set4

description: GEC_251778410014_S01_GE2-v5_95_Feb07_1_3.txt

source_name: AP1-GRap1cal_4hr Mock_set4

source_name: AP1-GRap1cal_4hr Dex_set4


title: AP1-GRap1cal_12hr Dex vs. Mock_set3

description: GEC_251778410017_S01_GE2-v5_95_Feb07_1_4.txt


title: AP1-GRap1cal_8hr Mock vs. Dex_set4

description: GEC_251778410014_S01_GE2-v5_95_Feb07_1_4.txt

source_name: AP1-GRap1cal_8hr Mock_set4

source_name: AP1-GRap1cal_8hr Dex_set4


title: AP1-GRap1cal_2hr Dex vs Mock_set5

description: GEC_251778410021_S01_GE2-v5_95_Feb07_1_2.txt

source_name: AP1-GRap1cal_2hr Dex_set5

source_name: AP1-GRap1cal_2hr Mock_set5


title: AP1-GRap1cal_0hr Dex vs Mock_set5

description: GEC_251778410021_S01_GE2-v5_95_Feb07_1_1.txt

source_name: AP1-GRap1cal_0hr Dex_set5

source_name: AP1-GRap1cal_0hr Mock_set5


title: AP1-GRap1cal_2h Mock vs. Dex_set2_4000B

description: s52_AP1GRap1cal_2hMockDex_G430R590_set2_JLR4000B.gpr

source_name: AP1-GRap1cal_2hr Mock_set2

source_name: AP1-GRap1cal_2hr Dex_set2


title: AP1-GRap1cal_2hr_Dex vs. Mock_set3

description: GEC_251778410015_S01_GE2-v5_95_Feb07_1_3.txt

source_name: AP1-GRap1cal_2hr Dex_set3

source_name: AP1-GRap1cal_2hr Mock_set3


title: AP1-GRap1cal_8hr Dex vs. Mock_set3

description: GEC_251778410017_S01_GE2-v5_95_Feb07_1_3.txt

source_name: AP1-GRap1cal_8hr Dex_set3

source_name: AP1-GRap1cal_8hr Mock_set3


title: AP1-GRap1cal_0hr Mock vs. Dex_set4

description: GEC_251778410014_S01_GE2-v5_95_Feb07_1_1.txt

source_name: AP1-GRap1cal_0hr Mock_set4

source_name: AP1-GRap1cal_0hr Dex_set4


title: AP1-GRap1cal_12hr Dex vs. Mock_set2

description: GEC_251778410019_S01_GE2-v5_95_Feb07_1_1.txt

source_name: AP1-GRap1cal_12hr Dex_set2

source_name: AP1-GRap1cal_12hr Mock_set2


title: AP1-GRap1cal_2hr Mock vs Dex_set4

description: GEC_251778410014_S01_GE2-v5_95_Feb07_1_2.txt

source_name: AP1-GRap1cal_2hr Mock_set4

source_name: AP1-GRap1cal_2hr Dex_set4


title: AP1-GRap1cal_4hr Mock vs. Dex_set2

description: GEC_251778410018_S01_GE2-v5_95_Feb07_1_3.txt

source_name: AP1-GRap1cal_4hr Mock_set2

source_name: AP1-GRap1cal_4hr Dex_set2


title: Bsh_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Bsh

value: Bsh


title: AP1-GRap1cal_4hr_Dex vs Mock_set3

description: GEC_251778410015_S01_GE2-v5_95_Feb07_1_4.txt

source_name: AP1-GRap1cal_4hr Dex_set3

source_name: AP1-GRap1cal_4hr Mock_set3


title: Treg, infected, replicate 3

status: Public on Mar 31 2010

description: Gene expression data from lymph nodes of mice infected with Schistosoma mansoni

hyb_protocol: Biotinylated cRNA was hybridized on MOE430A 2.0 GeneChips, that were stained, washed and scanned following Affymetrix standard procedures.

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: mesenteric lymph node CD4+ cells

label_protocol: Per sample, 200 ng total RNA was processed using Ambion’s MessageAmp II Biotin Enhanced labeling kit according to the manufacturer’s instructions.

growth_protocol: Female specific pathogen-free (spf) C57Bl/6 mice were purchased from Harlan Winkelmann GmbH (Germany).

extract_protocol: Bulk lymphocyte cells from the MLN of infected or naïve mice were isolated following standard erythrocyte-depletion protocols. T cell populations were then enriched by depleting MHC class II+ cells using specific microbeads (Miltenyi). Thereafter, cells were subjected to an Fc blocking step using anti-CD16/CD32 and after thorough washing stained with a combination of anti-CD4 APC and anti-CD25 PE antibody (Natutec, Germany). After a further washing step, populations of CD4+CD25- and CD4+CD25hi T cells were isolated using the MoFloTM cell sorter (Beckmann-Coulter, Germany).Total RNA was prepared from MoFlo-separated Treg and Teff using the RNA isolation kit from Qiagen (Hilden, Germany). Biological replicates of independent sorts from two naïve mice and three infected mice were used for microarray analysis using the Affymetrix GeneChip platform.

treatment_protocol: Mice were infected subcutaneously with 100 cercariae from a Brazilian strain of S. mansoni from Biomphalaria glabrata snails (Brazilian origin) kept in the institute’s laboratory and killed after nine weeks of infection.

tag: cell type

tag: t cell type

value: regulatory

tag: strain


title: AP1-GRap1cal_0hr_Dex vs. Mock_set3

description: GEC_251778410015_S01_GE2-v5_95_Feb07_1_2.txt

source_name: AP1-GRap1cal_0hr Dex_set3

source_name: AP1-GRap1cal_0hr Mock_set3


title: Treg, infected, replicate 1


title: AP1-GRap1cal_2h Mock vs. Dex_set2

description: GEC_251778410018_S01_GE2-v5_95_Feb07_1_2.txt

source_name: AP1-GRap1cal_2hr Mock_set2

source_name: AP1-GRap1cal_2hr Dex_set2


title: Treg, infected, replicate 2


title: AP1-GRap1cal_0hr Mock vs. Dex_set2

description: GEC_251778410018_S01_GE2-v5_95_Feb07_1_1.txt

source_name: AP1-GRap1cal_0hr Mock_set2

source_name: AP1-GRap1cal_0hr Dex_set2


title: Teff, infected, replicate 3

value: effector


title: ap1_vs_Ler_inflorescences_set2

description: US23502418_251778410004_S01_GE2-v5_95_Feb07_1_3.txt

source_name: ap1 inflorescences

growth_protocol: Plants were grown on a soil:vermiculite:perlite mixture under constant illumination at 21°C

extract_protocol: Sets of tissue samples from the homeotic mutant and from wild-type plants were prepared. Tissue collection for the different sets was done on different days but at the same time of day. For each sample, floral buds (corresponding to floral stages 1-13) from approximately 50 plants were collected. RNA was isolated from 100 mg of tissue with the RNeasy RNA Isolation Kit (Qiagen). RNA quality was assessed by gel electrophoresis.

value: ap1 inflorescences

source_name: Ler inflorescences

value: Ler inflorescences


title: AP1-GRap1cal_8hr Dex vs. Mock_set2

description: GEC_251778410018_S01_GE2-v5_95_Feb07_1_4.txt

source_name: AP1-GRap1cal_8hr Dex_set2

source_name: AP1-GRap1cal_8hr Mock_set2


title: Treg, resting, replicate 2

description: Gene expression data from lymph nodes of naive mice


title: Ler_vs_ap1_inflorescences_set1

description: US23502418_251778410004_S01_GE2-v5_95_Feb07_1_4.txt


title: Teff, infected, replicate 1


title: ap1_vs_Ler_inflorescences_set3

description: US23502418_251778410005_S01_GE2-v5_95_Feb07_1_4.txt


title: Teff, infected, replicate 2


title: Treg, resting, replicate 1


title: Teff, resting, replicate 1


title: Replicate 2 of FLAG AGO4 associated small RNAs immunopurified from a transgene expressed in Columbia ecotype Arabidopsis

status: Public on Feb 21 2010

first: Krys

last: Kelly

address: Downing Street

department: Plant Sciences

institute: University of Cambridge

description:
small RNA sequencing
AGO4IP isolated with FLAG Antibody
AGO4_April_06_B.fa (fasta file)

data_processing: After adapter removal, reads were aligned to the Arabidopsis thaliana genome (TAIR v8) using SSAHA v3.1.

source_name: IP mixed stage inflorescence

growth_protocol: standard growth conditions (16hr light, 21 C)

extract_protocol: The FLAG epitope was used to immunopurify AGO4 and small RNAs were isolated using Trizol Reagent.

treatment_protocol: These samples are from 3 wild-type Col-0 Arabidopsis transgenic lines that express AGO4 with a FLAG epitope.  The epitope was used to immunopurify AGO4 and small RNAs were isolated using Trizol Reagent.  A 5' 454 adapter was ligated on, followed by gel purification.  The 3' adapter was ligated on, followed by gel purification.  cDNA was made using RT-PCR and the library was amplified using approximately 22 cycles of PCR.

value: mixed stage inflorescence

value: Col-0, wildtype

tag: fraction

value: IP

tag: antibody

value: FLAG Antibody


title: Teff, resting, replicate 2


title: antiAGO4 associated sRNAs (SL26)

description:
small RNA sequencing
IP with endogenous AGO4 Antibody
raw data file: SL26.fq (fastq file)

data_processing: Small RNA adapters were removed using an exact match to the first 8bp of the 3' adapter (or the barcode + 3' adapter for multiplexed samples SL234B/C/F and SL235B/H). After adapter removal, reads were aligned to the Arabidopsis thaliana genome (TAIR v8) using SSAHA v3.1.

source_name: IP aerial

extract_protocol: The extract protocol varies for total sRNA and for immunopurifications (IP).  If IP, proteins were purified with appropriate antibody and associated RNA was purified with Trizol reagent.  If total sRNA, total RNA was extracted using Trizol reagent and small RNAs purified using mirVana (Ambion).  For both of these types of samples, a 5' adapter was ligated, gel purified, followed by 3' adapter ligation, gel purification, 1st strand synthesis of RNA to create a cDNA library which was amplified with approximately 15 cycles of PCR.  The PCR amplified library was then gel purified.

treatment_protocol: These samples are from immunopurifications of either AGO4, AGO6 and AGO9 in Arabidopsis thaliana or small RNAs isolated, cloned and sequenced from Arabidopsis.

tag: tissue

value: aerial (stem, cauline leaves, silique, inflorescence)

value: endogenous AGO4 Antibody


title: antiAGO4 associated sRNAs (SL32)

description:
small RNA sequencing
IP with endogenous AGO4 Antibody
raw data file: SL32.fq (fastq file)

source_name: IP floral


title: Col-0 sRNAs (SL23_1)

description:
small RNA sequencing
Total sRNA sample; technical rep with SL23_2; biological replicate with SL5 and SL24_1
raw data file: SL23_1.fq (fastq file)

source_name: total floral

value: total


title: Col-0 sRNAs (SL5)

description:
small RNA sequencing
Total sRNA sample; biological replicate with SL24_1 and technical replicates SL23_1 and SL23_2
raw data file: SL5.fq (fastq file)


title: drd3-1 sRNAs (SL235B)

description:
small RNA sequencing
Total sRNA sample
raw data file: SL235_BH.fq (fastq file)


title: Replicate 3 of FLAG AGO4 associated small RNAs immunopurified from a transgene expressed in Columbia ecotype Arabidopsis

description:
small RNA sequencing
AGO4IP isolated with FLAG Antibody
AGO4_C_combined_July06.fa (fasta file)


title: Dyak-KNI_ChIP-Seq

status: Public on Feb 18 2010

city: Berkeley

first: Michael

last: Eisen

address: Stanley Hall 304B

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: chromatin IP against KNI

data_processing: We used the Apr. 2006 assembly (dm3, BDGP Release 5) of the D. melanogaster genome, downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/dm3/bigZips/chromFa.tar.gz and the Nov. 2005 assembly (droYak2) of the D. yakuba genome, downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/droYak2/bigZips/chromFa.tar.gz. We trimmed all sequenced tags to 20 bp and mapped the tags to the genomes using Bowtie v0.9.9.1 [22] with command-line options ‘-v 1 -m 1’, thereby keeping only tags which mapped uniquely to the genome with at most one mismatch. We called peaks for each experiment using MACS v1.3.5 [25] with the option ‘--pvalue 0.00001’. We used total chromatin as background controls, and set the ‘--mfold’ option to the maximum value for which MACS could find a sufficient number of paired peaks. In order to only consider peaks for which we could reliably assign orthology and to control for potential assembly errors in the draft D. yakuba genome, we used exonerate [35] to search for peaks whose associated sequence was duplicated in either genome. For each peak, we 1) searched for duplicated sequence in the genome where the peak was called, and 2) used the whole-genome alignment to pull out the orthologous sequence in the other genome and searched for duplicates of that sequence in the other genome, which frequently indicated a potential assembly error due to the unfinished nature of the D. yakuba assembly. We discarded any peaks whose associated sequence was duplicated in either genome.

organism: Drosophila yakuba

source_name: blastoderm embryos

growth_protocol: Embryos collected from large population cages for 1 hour, aged to appropriate stage, fixed in formaldehyde, chromatin isolated by CsCl gradient ultracentrifugation, fragmented and immunoprecipitated with affnity-purified antibody

extract_protocol: DNA fragments were converted to phosphorylated blunt ends using T4 DNA polymerase, Klenow DNA polymerase, and T4 polymerase kinase, a 3' A base overhang was added using Klenow DNA polymerase exo- (3' to 5' exo minus), and Illumina adapters were ligated to the fragments. We carried out the PCR step for enrichment of adapter-modified DNA prior to the library size selection, and limited the amplification to 10-13 cycles to minimize the potential bias associated with PCR amplification. After the amplification step, we size-selected DNA fragments of 150-500 bp (including the adapter sequence) for BCD, HB, GT, and KNI samples, and 200 - 500 bp for KR and CAD.

tag: developmental stage

value: blastoderm embryo

tag: developmental time

tag: fragment (size-selected)

value: KNI


title: Dyak-KR2_ChIP-Seq

description: chromatin IP against KR - antibody 2

value: KR - antibody 2


title: Dyak-CAD_ChIP-Seq

description: chromatin IP against CAD

value: CAD


title: Dyak-Input250

description: input

value: none (input fraction)


title: Dyak-KR1_ChIP-Seq

description: chromatin IP against KR - antibody 1

value: KR - antibody 1


title: Dyak-Input225

description: input


title: Dyak-GT_ChIP-Seq

description: chromatin IP against GT

value: GT


title: Replicate 1 of FLAG AGO4 associated small RNAs immunopurified from a transgene expressed in Columbia ecotype Arabidopsis

description:
small RNA sequencing
AGO4IP isolated with FLAG Antibody
AGO4_A_combined.fa (fasta file)


title: AGO4 Promoter:FLAG AGO6 associated sRNAs (SL234C)

description:
small RNA sequencing
IP with FLAG Antibody
raw data file: SL234_BCF.fq (fastq file)


title: AGO4 Promoter:FLAG AGO9 associated sRNAs (SL234F)


title: Dyak-BCD_ChIP-Seq

description: chromatin IP against BCD

value: BCD


title: Dyak-HB1_ChIP-Seq

description: chromatin IP against HB - antibody 1

value: HB - antibody 1


title: SEG48input

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: Dyak-HB2_ChIP-Seq

description: chromatin IP against HB - antibody 2

value: HB - antibody 2


title: SEG42input


title: SEG44input


title: SEG40input


title: SEG50input


title: SEG37input


title: SEG38input


title: SEG46input


title: SEG47input


title: SEG36input


title: AGO4 Promoter:FLAG AGO4 associated sRNAs (SL234B)

value: mixed stage inflorescence


title: ago4-3 AGO4P:AGO4 D660A sRNAs (SL235H)


title: SEG34input


title: SEG45input


title: SEG41input


title: SEG32input


title: SEG35input


title: SEG33input


title: antiAGO9 associated sRNAs (SL12)

description:
small RNA sequencing
IP with endogenous AGO9 Antibody
raw data file: SL12.fa (fasta file)

value: IP

value: endogenous AGO9 Antibody


title: FLAG AGO6 associated sRNAs (SL10)

description:
small RNA sequencing
IP with FLAG Antibody
raw data file: SL10.fq (fastq file)

value: FLAG Antibody


title: ago4-3 sRNAs (SL25_1)

description:
small RNA sequencing
Total sRNA sample
raw data file: SL25_1.fq (fastq file)


title: SEG26input


title: antiAGO9 associated sRNAs (SL11)

description:
small RNA sequencing
IP with endogenous AGO9 Antibody
raw data file: SL11.fa (fasta file)

value: aerial (stem, cauline leaves, silique, inflorescence)


title: FLAG AGO6 associated sRNAs (SL9)

description:
small RNA sequencing
IP with FLAG Antibody
raw data file: SL9.fa (fasta file)


title: SEG43input


title: SEG21input


title: SEG16input


title: SEG17input


title: SEG18input


title: SEG30input


title: SEG28input


title: SEG22input


title: SEG11input


title: SEG14input


title: SEG13input


title: SEG10input


title: SEG31input


title: SEG8input


title: SEG7input


title: SEG3input


title: SEG6input


title: SEG12input


title: SEG4input


title: SEG25input


title: SEG1input


title: SEG2input


title: S96_sli15D_ChIP

value: S96 sli15D


title: S96_noalpha_ChIP

value: rich medium


title: Col-0 sRNAs (SL4_2)

description:
small RNA sequencing
Total sRNA sample
raw data file: SL4_2.fq (fastq file)

source_name: total aerial

value: total


title: Col-2 sRNAs (SL24_1)

description:
small RNA sequencing
Total sRNA sample; biological replicate with SL25 and technical replicates SL23_1 and SL23_2
raw data file: SL24_1.fq (fastq file)


title: JM789input


title: S96input


title: HS959input


title: JM789_noalpha_ChIP


title: S96_sla1D_ChIP

value: S96 sla1D


title: S96_sct1D_ChIP

value: S96 sct1D


title: S96_hir1D_ChIP

value: S96 hir1D


title: S96_ics2D_ChIP

value: S96 ics2D


title: S96_gle2D_ChIP

value: S96 gle2D


title: S96_flo8D_ChIP

value: S96 flo8D


title: S96_ctf19D_ChIP

value: S96 ctf19D


title: S96_alk2D_ChIP

value: S96 alk2D

value: alpha factor


title: Col-0 sRNAs (SL23_2)

description:
small RNA sequencing
Total sRNA sample; technical rep with SL23_1; biological replicate with SL5 and SL24_1
raw data file: SL23_2.fq (fastq file)

value: mixed stage inflorescence


title: S96_pdr3D_ChIP

value: S96 pdr3D


title: HS959_pdr3D_ChIP

value: HS959 pdr3D


title: HS959_sla1D_ChIP

value: HS959 sla1D


title: SEG5input


title: S96_ldb7D_ChIP

value: S96 ldb7D


title: HS959_hir1D_ChIP

value: HS959 hir1D


title: HS959_ctf19D_ChIP

value: HS959 ctf19D


title: SEG50ChIP_rep2


title: S96_amn1D_ChIP

value: S96 amn1D


title: HS959_sct1D_ChIP

value: HS959 sct1D


title: HS959_sli15D_ChIP

value: HS959 sli15D


title: SEG50ChIP_rep1


title: SEG24input


title: HS959_amn1D_ChIP

value: HS959 amn1D


title: HS959_gle2D_ChIP

value: HS959 gle2D


title: HS959_ldb7D_ChIP

value: HS959 ldb7D


title: SEG47ChIP_rep2


title: SEG48ChIP_rep1


title: HS959_alk2D_ChIP

value: HS959 alk2D


title: HS959_flo8D_ChIP

value: HS959 flo8D


title: SEG45ChIP_rep2


title: SEG48ChIP_rep2


title: SEG44ChIP_rep1


title: SEG46ChIP_rep1


title: SEG45ChIP_rep1


title: SEG47ChIP_rep1


title: HS959_ics2D_ChIP

value: HS959 ics2D


title: SEG46ChIP_rep2

value: alpha factor


title: SEG43ChIP_rep2


title: SEG43ChIP_rep1


title: SEG44ChIP_rep2


title: SEG42ChIP_rep2


title: SEG42ChIP_rep1


title: SEG41ChIP_rep1


title: SEG41ChIP_rep2


title: SEG40ChIP_rep2


title: SEG40ChIP_rep1


title: SEG38ChIP_rep2


title: SEG36ChIP_rep1


title: SEG36ChIP_rep2


title: SEG37ChIP_rep2


title: SEG35ChIP_rep2


title: SEG38ChIP_rep1


title: SEG35ChIP_rep1


title: SEG36ChIP_rep3


title: SEG34ChIP_rep1


title: SEG34ChIP_rep2


title: SEG33ChIP_rep2


title: SEG33ChIP_rep1


title: SEG32ChIP_rep2


title: SEG32ChIP_rep1


title: SEG31ChIP_rep1


title: SEG31ChIP_rep2


title: SEG28ChIP_rep2


title: SEG30ChIP_rep2


title: SEG26ChIP_rep3


title: SEG25ChIP_rep2


title: SEG25ChIP_rep3


title: SEG28ChIP_rep1


title: SEG26ChIP_rep1


title: SEG26ChIP_rep2


title: SEG37ChIP_rep1


title: SEG24ChIP_rep3


title: SEG25ChIP_rep1


title: SEG24ChIP_rep2


title: SEG22ChIP_rep2


title: SEG24ChIP_rep1


title: SEG21ChIP_rep3


title: SEG22ChIP_rep1


title: SEG21ChIP_rep2


title: SEG18ChIP_rep2


title: SEG17ChIP_rep1


title: SEG17ChIP_rep2


title: SEG18ChIP_rep1


title: SEG30ChIP_rep1


title: SEG16ChIP_rep2


title: SEG15ChIP_rep2


title: SEG15ChIP_rep1


title: SEG13ChIP_rep2


title: SEG14ChIP_rep1


title: SEG14ChIP_rep2


title: SEG11ChIP_rep1


title: SEG10ChIP_rep3


title: SEG12ChIP_rep2


title: SEG13ChIP_rep1


title: SEG11ChIP_rep2


title: SEG12ChIP_rep1


title: SEG21ChIP_rep1


title: SEG10ChIP_rep1


title: SEG10ChIP_rep2


title: SEG16ChIP_rep1


title: SEG9ChIP_rep1


title: SEG9ChIP_rep3


title: SEG9ChIP_rep2


title: SEG7ChIP_rep2


title: SEG14ChIP_rep3


title: SEG6ChIP_rep2


title: SEG5ChIP_rep2


title: SEG5ChIP_rep1


title: SEG4ChIP_rep2


title: SEG4ChIP_rep3


title: SEG6ChIP_rep1


title: SEG3ChIP_rep2


title: SEG4ChIP_rep1


title: SEG2ChIP_rep2


title: SEG3ChIP_rep1


title: SEG2ChIP_rep1


title: SEG1ChIP_rep2


title: SEG8ChIP_rep2


title: SEG1ChIP_rep1


title: HS959ChIP_rep3


title: HS959ChIP_rep1


title: SEG8ChIP_rep1


title: S96ChIP_rep2


title: SEG7ChIP_rep1


title: SEG9input


title: S96ChIP_rep1


title: Dmel-Input250

description: input

value: Oregon R

value: blastoderm embryo

value: 2 - 3 hrs

value: none (input fraction)


title: Dmel-CAD_ChIP-Seq

description: chromatin IP against CAD

value: CAD


title: Dmel-KNI_ChIP-Seq

description: chromatin IP against KNI

value: KNI


title: SEG15input


title: Dmel-KR1_ChIP-Seq

description: chromatin IP against KR - antibody 1

value: KR - antibody 1


title: Dmel-HB2_ChIP-Seq

description: chromatin IP against HB - antibody 2

value: HB - antibody 2


title: Dmel-GT_ChIP-Seq

description: chromatin IP against GT

value: GT


title: Dmel-HB1_ChIP-Seq

description: chromatin IP against HB - antibody 1

value: HB - antibody 1


title: Dmel-BCD_ChIP-Seq

description: chromatin IP against BCD

value: BCD


title: control male 1 (barcode: GTTA)

status: Public on Jan 13 2010

data_processing:
The parsed reads correspond to the RNA captured between the 3' and 5' adapters. The 3'-adapter sequences were trimmed off by scanning from the 3' end of the 36-nt reads for the first instance of the first 4 nt of the adapter: CTGT. Reads that lacked CTGT in the 3'-most 13 nt were excluded from further analysis. After barcode sorting, the 4 nt of barcode were trimmed off the 5'  ends to yield 19- to 28-nt reads corresponding to the captured small RNAs.
The alignments contain genomic alignments produced from the parsed reads and can be uploaded for viewing on the UCSC genome browser. A local installation of BLAT was used with the C. elegans WS190 genome sequence as a reference. The BLAT parameters were set to default except -tileSize=10 and -stepSize=5.

source_name: whole males

growth_protocol: All animals were raised to young adult stage at 25°C on solid media with E. coli (OP50) as food.

extract_protocol: Libraries were prepared using a protocol similar to miRNA cloning methods in which small RNA species are flanked between adapter sequences to allow for PCR and sequencing. Unlike miRNA capture methods, this protocol does not select for small RNAs with 5' monophosphates and hence captures mainly the secondary-type, triphosphorylated endo siRNAs. The small RNA was extracted from frozen tissue using the mirVana miRNA Isolation kits.To remove the bias for 5' monophosphorylated species but preserve the bias towards 3' hydroxylated species, we treated the small RNAs with Antarctic phosphatase following addition of the 3' adapter with T4 RNA ligase 1. The resulting hydroxylated 5' ends were phosphorylated by treatment with T4 polynucleotide kinase and ATP in order to form a subtrate for T4 RNA ligase 1-mediated addition of the 5' adapter. After ligation of both the 3' and 5' adapters, the adapters were extended during the reverse transcription and PCR steps to include complete primer binding sites for subsequent amplification and sequencing reactions. To protect against cross-contamination and to allow for pooling of samples, we modified the 5' adapter sequence to include the Illumina genomic sequencing primer immediately followed by a 4-nt barcode.

value: whole organism

tag: genotype


title: control male 2 (barcode: TATG)


title: rrf-3 male 2 (barcode: GTTA)


title: rrf-3 male 1 (barcode: TATG)


title: sperm (barcode: AGCG)

source_name: isolated spermatogenic cells

value: spermatogenic cell


title: Dmel-Input225

description: input


title: Dmel-KR2_ChIP-Seq

description: chromatin IP against KR - antibody 2

value: KR - antibody 2


title: 5' NCR from HCV isolated at week 27 from 4x0514 rep2

status: Public on Dec 03 2009

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

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: 5' NCR from HCV isolated at week 23 from 4x0514 rep2


title: 5' NCR from HCV isolated at week -4 from 4x0514 rep2


title: 5' NCR from HCV isolated at week 11 from 4x0514 rep2


title: SEG1ChIP_rep3


title: HS959ChIP_rep2


title: 5' NCR from HCV isolated at week 17 from 4x0513 rep2


title: 5' NCR from HCV isolated at week 27 from 4x0514 rep1


title: Mitochondrial ESTs from females 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 females from reciprocal crosses of D. pseudoobscura strains 14011‑0121.94 and 14011‑0121.89.
Expression profiles of D. pseudoobscura mitochondrial protein coding genes and rRNA genes from the library prepared with female flies.
library strategy: EST
library source: non-genomic
library selection: cDNA

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.

organism: Drosophila pseudoobscura

source_name: D. pseudoobscura females

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: female

tag: strains

value: Adults

value: Whole body


title: 5' NCR from HCV isolated at week 11 from 4x0514 rep1


title: 5' NCR from HCV isolated at week 11 from 4x0513 rep2