title: oocytes stage III, IV

description: Small RNAs were sequenced from Xenopus tropicalis oocytes stage III, IV

value: wild type

value: oocytes stage III, IV


title: oocytes stage V, VI

status: Public on Jul 10 2009

type: SRA

city: Cambridge

first: Mike

last: Gilchrist

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: Cambridge University

description: Small RNAs were sequenced from Xenopus tropicalis oocytes stage V, VI

library_source: transcriptomic

data_processing:
Reads stripped of adaptor sequence to make tags. Tags with exact mapping to genome submitted.

library strategy: RNA-Seq. 10µg RNA of miRvana size-selected RNA was again size-selected to 18-30 nucleotides on a denaturing polyacrylamide gel and small RNA libraries were cloned through ligation of a 5' and 3' adapter according to the manufacturerâ€™s protocol (Illumina, San Diego, CA, USA).
library source: RNA
library selection: 18-42 nucleotides

molecule: total RNA

organism: Xenopus tropicalis

source_name: Xenopus tropicalis oocytes stage V, VI

extract_protocol: Ovarian lobes were removed from Xenopus tropicalis females and collagenase treated for 3 h. Oocytes were staged and washed in modified Barth’s solution (8.8mM NaCl, 1mM KCl, 330µM Ca(NO3)2, 410µM CaCl2, 820µM MgSO4, 2.4mM NaHCO3, 10 mM HEPES-NaOH pH7.4). Total RNA was isolated from staged oocytes of Xenopus tropicalis or from different adult tissues of Xenopus tropicalis using Trizol reagent (Invitrogen, Carlsbad CA, USA) and according to the manufacturer’s protocol. Total RNA extracted was enriched for small RNAs using the miRVana kit (Ambion, Austin TX, USA), resolved in a 15% denaturing polyacrylamide gel and stained using SYBR green (Invitrogen). 10µg RNA of miRvana size-selected RNA was again size-selected to 18-30 nucleotides on a denaturing polyacrylamide gel and small RNA libraries were cloned through ligation of a 5' and 3' adapter according to the manufacturer’s protocol (Illumina, San Diego, CA, USA).

tag: genotype

tag: developmental stage

value: oocytes stage V, VI


title: Histone-Mnase Lane 10

status: Public on Jun 15 2009

city: Salt Lake City

first: Bradley

middle: R.

last: Cairns

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

country: USA

institute: HHMI and Huntsman Cancer Institute

description: Histone bound DNA enrichment via Mnase digestions and nucleosome purification

library_source: genomic

data_processing: Reads were aligned to Hg18/ NCBI 36.1/ H_sapiens_Mar_2006 using the Illumina Pipeline's ELAND extended aligner and enriched regions relative to input identified using the USeq analysis package (http://useq.sourceforge.net, Nix et al BMC Bioinfo Dec 5:9(1):523 (2008)).

molecule: genomic DNA

organism: Homo sapiens

source_name: Sperm Donor D3

growth_protocol: Sperm samples were obtained from four known fertile donors attending the University of Utah Andrology laboratory, consented for research.

extract_protocol: Sperm samples were collected after 2-5 days abstinence and subjected to an ISolate density gradient (to purify viable, motile, mature sperm) and treated with somatic cell lysis buffer (0.1% SDS, 0.5% Triton X in DEPC H2O) for 20 min on ice to eliminate white blood cell contamination. Samples were centrifuged at 10,000 G for 3 min and the sperm pellet was resuspended in 1X PBS and used immediately for chromatin preparation. Chromatin was prepared as previously described by Zalenskaya et al Biochem Biophys Res Commun 279, 213-8 (2000) in the absence of crosslinking reagent. Sperm was treated with sequential and increasing MNase (10U-160U), and centrifuged to sediment protamine-associated DNA, releasing mononucleosomes. The pooled mononucleosomes were used for chromatin immunopreciptation (below), or the DNA extracted and gel purified (~140-155bp) for  array analysis. All Chromatin IPs (ChIPs) were performed as previously described by Gordon et al Mol Cell Biol 27, 4058-69 (2007).

tag: cell type

value: sperm


title: Histone-Mnase Lane 9

source_name: Sperm Donor D2


title: Jurkat T cell RNA-Seq

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

description: RNA-seq

data_processing: Illumina Genome Analyzer Pipeline version 1.0 produced an output containing sequences in seq and prb formats. First 30 bases of sequences were matched to both the hg18 human genome and a library of (26+26)-bp exon junction sequences using ELAND. Exons sequences were retrieved from Ensembl database (version 50).

molecule: polyA RNA

source_name: Jurkat T cell mRNA

extract_protocol: polyA RNA purified from total RNA

value: T cell

tag: cell line

value: Jurkat


title: Histone-Mnase Lane 7

source_name: Sperm Donor D1


title: oocytes stage I, II

description: Small RNAs were sequenced from Xenopus tropicalis oocytes stage I, II

source_name: Xenopus tropicalis oocytes stage I, II

value: oocytes stage I, II


title: Histone-Mnase Lane 8


title: Histone-Mnase Lane 6


title: Histone-Mnase Lane 5


title: Histone-Mnase Lane 3


title: Histone-Mnase Lane 4


title: Illumina sequencing of small RNAs from irradiated planarians

status: Public on Jul 01 2009

city: Berlin

first: Marc

middle: Riemer

last: Friedlaender

state: Berlin

address: Robert-Rössle-Str. 10

country: Germany

institute: MDC, Berlin-Buch

description: small RNAs

data_processing: Output from Bustard application (part of Solexa/Illumina package), adapters clipped and reads with more than one uncalled nucleotide or homo-nucleotides stretches of 7 nt or longer were discarded, as were reads that did not map to the genome (for details on mapping protocol, see Friedlander et al. PNAS, 2009).

organism: Schmidtea mediterranea

source_name: planarian

extract_protocol: total RNA, ~15-40nt RNAs isolated using Novex 15% TBE-Urea gel (invitrogen)

value: irradiated whole-body planarians


title: 18dpp_hetero_tdrd6-KO

status: Public on Jul 25 2009

city: Cold Spring Harbor

first: Vasily

last: Vagin

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor

description:
19-33 nt RNA isolated from testes of 18 days old mice
library_strategy: sequential ligation of 3' and 5' linkers using T4 RNA ligase follwed by PCR amplification
library_source: small RNA
library_selection: other

data_processing: Reads were aligned to the reference genome allowing zero mismatches. Number of mapping in the genome and genomic annotation were extracted.

organism: Mus musculus

source_name: testes

extract_protocol: total RNA was size selected (19-33nt)

tag: tissue

value: 18dpp mouse testes


title: H3K27Me3 Lane 2

description: ChIP-Seq for H3K27Me3

source_name: Sperm Pooled Donors

tag: chip antibody


title: H3K27Me3 Lane 1

description: ChIP-Seq for H3K27Me3


title: H3K4Me3 Lane 3

description: ChIP-Seq for H3K4Me3


title: Histone-Mnase Lane 1


title: H3K4Me3 Lane 2

description: ChIP-Seq for H3K4Me3


title: H2Az

description: ChIP-Seq for H2Az


title: Col0_wholeplant_meDIP-seq

status: Public on Jun 12 2009

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
IP against 5-methylcytosine
Library Strategy: meDIP-seq. Libraries from immunoprecipitated DNA that was 100-200 bp or 200-300 bp in size were created following Illumina protocols.
Library Source: Genomic
Library Selection: meDIP
100-200 bp IPed DNA: Col0_s_8_sequence.fastq

data_processing: Reads were aligned to the TAIR8.0 version of the Arabidopsis thaliana genome using MAQ v.6.3 (*aln.txt files). Methylation profiles were created from uniquely mapping reads with a quality score greater than or equal to 20. Each read represents the end of an immunoprecipitated DNA fragment, and not the precise location of methylation. To compensate for this, the midpoint of each immunoprecipitated fragment was determined by adding half of the average size of the sequenced DNA fragments to the location of the read (i.e. 75 bp for 100-200 bp DNA, 125 bp for 200-300 bp DNA). Each read was distributed over length of the fragment using a Gaussian distribution centered at the fragment midpoint. Profiles were created using the kernel density estimation function in R, with a bandwidth of 50 bp, and divided into 100 bp bins. The total number of reads for each profile was set to 1, so that profiles made from different numbers of reads could be directly compared (*kdef.gff files). Methylation profiles were compared in overlapping 300 bp segments, sliding 100 bp each time. The methylation in each 300 bp segment represented the average methylation of the 3 100 bp bins comprising it. Values for all 300 bp segments were multiplied by one million. A difference score was calculated for each segment by subtracting the read value for profile B from profile A and dividing by the square root of the value of profile A plus the value of profile B (*diff.gff files)

organism: Arabidopsis thaliana

source_name: whole plant

growth_protocol: Plants were grown on soil in 16h days at 22 C.

extract_protocol: Seeds (1500-1800) from multiple individuals were hand-dissected and genomic DNA isolated using CTAB. DNA was sheared by sonication to less than 650 bp with an average size of 300-400 bp. 4 micrograms of DNA was incubated with 10 micrograms anti-5-methylcytosine antibody (Eurogentec) for 2.5 hours. IPed DNA was recovered using sheep anti-mouse IgG dynabeads.

treatment_protocol: no treatment

tag: Accession

value: Col-0, Tissue:aerial portion of plant, Age:21 days (bolted)


title: Input Lane 6

description: Input control


title: Ler_dme_endosperm_meDIP-seq

description:
IP against 5-methylcytosine
Library Strategy: meDIP-seq. Libraries from immunoprecipitated DNA that was 100-200 bp or 200-300 bp in size were created following Illumina protocols.
Library Source: Genomic
Library Selection: meDIP
100-200 bp IPed DNA: Ler_s_6_sequence.fastq
200-300 bp IPed DNA: Ler_s_7_sequence.fastq

source_name: dme endosperm

value: Ler, Tissue:dme-2 mutant endosperm, Age:Seeds arrested at heart stage


title: Leaf-Autotriploid

status: Public on Jul 15 2009

city: Wuhan

first: hai

last: peng

address: College of Life Sciences, Jianghan University

country: China

institute: Jianghan University

data_processing: The signatures were matched against the reference genome of Oryza sativa L. ssp. indica (http://rice.genomics.org.cn/rice/index2.jsp) and assigned to each location at which a perfect match was found. For the sequencing number normalization, 5s rRNA was chosen as internal control. The sRNA locus expression comparison between the autotriploids and diploids were conducted with the toolkit as described by Moxon et al. [38]. Except the parameter of minimum number of (weighted) hits in SiLoCo analysis was adjusted to 30, the other parameters were set as default. In addition, the log2 ratio of the SiLoCo result was adjusted according to the internal control of 5S rRNA gene.

organism: Oryza sativa

source_name: The middle part of the flag leaves

growth_protocol: The experiment was conducted during April - September in the filed and a greenhouse located in a geographical region with latitude of 30039N, longitude of 104005E and altitude of 500 m asl. The seeds of SARII-658 germinated indoors for screening twin-seedlings, which subsequently were pairwise planted in field in April. During the flowering stage, twin-seedlings with low seed-setting rates were selected out and the upper parts (about 2/3) of the tillers were cut off. The remaining parts were separated into two equal halves, one of which was pairwise rooted in fresh water supplemented with a little urea for ploidy confirmation. The other half was transplanted into an experimental greenhouse for ratoon growth. Plants were cultured in a tank (100×60×20 cm) filled with sand. Hoagland nutrient solution was used to irrigate the plant. The water level maintained at 3 to 5 cm above the sand surface. Air temperature was maintained at 30 oC at day time and 20 oC during night. Relative humidity (RH) ranged from 50% to 80%. Light/dark photoperiod and light intensity were about 13/11 h and 1,100 μmol•m-2•s-1 at noon, respectively. The nutrient solution was replaced every 3 to 7 days.

extract_protocol: The middle parts of the flag leaves were collected for RNA extraction at 08:00 on the day when the flag leaf was fully extended (record the length of the flag leafs each morning until the length did not increase any longer). The total RNAs were isolated the operation instruction of the Trizol Reagent (Invitrogen, USA, Cat. No.18068). The equivalent amounts of total RNAs from three biological replica were sampled and mixed together for the construction of autotriploid and diploid sRNA libraries as described by Lu et al.  sRNA libraries were sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

tag: strain

value: SARII-658; Tissue:flag leafs; Age:about 120 days; Developmental stage:flowering stage


title: Input Lane 7

description: Input control


title: Colgl_dme_endosperm_meDIP-seq

description:
IP against 5-methylcytosine
Library Strategy: meDIP-seq. Libraries from immunoprecipitated DNA that was 100-200 bp or 200-300 bp in size were created following Illumina protocols.
Library Source: Genomic
Library Selection: meDIP
100-200 bp IPed DNA: Colgl_s_6_sequence.fastq
200-300 bp IPed DNA: Colgl_s_7_sequence.fastq

value: Col-gl, Tissue:dme-2 mutant endosperm, Age:Seeds arrested at heart stage


title: Ler_endosperm_meDIP-seq

description:
IP against 5-methylcytosine
Library Strategy: meDIP-seq. Libraries from immunoprecipitated DNA that was 100-200 bp or 200-300 bp in size were created following Illumina protocols.
Library Source: Genomic
Library Selection: meDIP
100-200 bp IPed DNA:Ler_s_3_sequence.fastq
200-300 bp IPed DNA: Ler_s_4_sequence.fastq

source_name: endosperm

value: Ler, Tissue:endosperm, Age:Torpedo stage seeds (6-7 DAP)


title: Ler_embryo_meDIP-seq

description:
IP against 5-methylcytosine
Library Strategy: meDIP-seq. Libraries from immunoprecipitated DNA that was 100-200 bp or 200-300 bp in size were created following Illumina protocols.
Library Source: Genomic
Library Selection: meDIP
100-200 bp IPed DNA: Ler_s_1_sequence.fastq
200-300 bp IPed DNA: Ler_s_2_sequence.fastq

source_name: embryo

value: Ler, Tissue:embryo, Age:Torpedo stage seeds (6-7 DAP)


title: D.rerio_adult_pooled infected fish_1,2,3 and 4 (s3)

status: Public on Jun 30 2009

city: Leiden

first: Anna

middle: Magdalena

last: Zakrzewska

address: Wassenaarseweg 64

department: IBL

country: Netherlands

institute: University of Leiden

data_processing: Image analysis, base calling, extraction of 17bp tags and tag counting were performed using the Illumina pipeline.

organism: Danio rerio

source_name: pooled whole adult fish (M.marinum-infected)

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org).

extract_protocol: Fish were snap frozen in liquid nitrogen, stored at -80°C, and homogenized in liquid nitrogen using a mortar and pestle. Portions of 50 -100 μg of powdered tissue were used for extraction of total RNA with 1 ml of TRIZOL® Reagent (Invitrogen) according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to clean up using RNeasy columns (Qiagen). The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies). The samples used had an average RIN value of 9.5 and a minimum RIN value of 8.9.

treatment_protocol: Adult male zebrafish were infected by intraperitoneal inoculation with approximately 1x 10-3 M. marinum bacteria

value: whole organism

tag: age

value: adult


title: Colgl_endopserm_meDIP-seq

description:
IP against 5-methylcytosine
Library Strategy: meDIP-seq. Libraries from immunoprecipitated DNA that was 100-200 bp or 200-300 bp in size were created following Illumina protocols.
Library Source: Genomic
Library Selection: meDIP
100-200 bp IPed DNA: Cogl_s_3_sequence.fastq
200-300 bp IPed DNA: Colgl_s_4_sequence.fastq
200-300 bp IPed DNA: Colgl_s_8_sequence.fastq

value: Col-gl, Tissue:endosperm, Age:Torpedo stage seeds (6-7 DAP)


title: Histone-Mnase Lane 13

source_name: Sperm Donor D4


title: Colgl_embryo_meDIP-seq

description:
IP against 5-methylcytosine
Library Strategy: meDIP-seq. Libraries from immunoprecipitated DNA that was 100-200 bp or 200-300 bp in size were created following Illumina protocols.
Library Source: Genomic
Library Selection: meDIP
100-200 bp IPed DNA: Colgl_s_1_sequence.fastq
200-300 bp IPed DNA: Colgl_s_2_sequence.fastq

value: Col-gl, Tissue:embryo, Age:Torpedo stage seeds (6-7 DAP)


title: D.rerio_adult_pooled control fish 1,2,3 and 4 (s6)

source_name: pooled whole adult fish (healthy control)


title: memory-CD8-TEM-H3K27me3

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

description:
Chromatin IP against H3K27me3
run57_lane7
run60_lane3

data_processing: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. More details as described in Araki et al., 2008

source_name: TEM H3K27me3

growth_protocol: Growth protocol as described in Araki et al., 2008

extract_protocol: Extract protocol as described in Araki et al., 2008

treatment_protocol: Treatment protocol as described in Araki et al., 2008

tag: memory CD8 T cells


title: memory-CD8-naive-H3K4me3

description:
Chromatin IP against H3K4me3
run42_lane1

source_name: naïve H3K4me3


title: memory-CD8-naive-H3K27me3

description:
Chromatin IP against H3K27me3
run57_lane5
run60_lane1

source_name: naïve H3K27me3


title: memory-CD8-TCM-H3K27me3

description:
Chromatin IP against H3K27me3
run57_lane6
run60_lane2

source_name: TCM H3K27me3


title: D.rerio_adult_pooled control fish 1,2,3 and 4 (s2)


title: D.rerio_adult_pooled infected fish_1,2,3 and 4 (s7)


title: memory-CD8-TEM-H3K4me3

description:
Chromatin IP against H3K4me3
run42_lane3

source_name: TEM H3K4me3


title: Leaf-Diploid


title: memory-CD8-TCM-H3K4me3

description:
Chromatin IP against H3K4me3
run42_lane2

source_name: TCM H3K4me3


title: N2_starved L1_rep 3

status: Public on Jun 11 2009

city: New Haven

first: Flora

last: Vaccarino

state: CT

address: 230 South Frontage Road

department: Child Study Center

institute: Yale University

data_processing: RNA-Seq libraries were prepared for sequencing using the Illumina protocol as described (Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344-9 (2008)).  RNA-seq scoring was performed as previously described (Hillier, L.W. et al. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res 19, 657-66 (2009)).

organism: Caenorhabditis elegans

source_name: N2 starved L1 RNA

growth_protocol: Worms were routinely grown on plates to obtain many adults with embryos. Bleach to obtain embryos. Hatch overnight in M9 Buffer to obtain L1s. Wash L1s and put into 500 ml liquid media (S medium+1X PSN antibiotics and nystatin) and grow at 20 oC in an incubator shaking at 230 rpm. Add concentrated E Coli for food as necessary during growth. It takes around 2.5-3 days to obtain adults with embryos. Collect adults and bleach to obtain embryos. Spin down embryos at 3000 g for 3 minutes. Resuspend pellet (embryos) and wash 2 more times with M9 Buffer. For L1 stage samples, After collect adults from liquid culture and bleach to obtain embryos, The embryos were hatched overnight in M9 Buffer without any food to obtain L1s. The pellet can be stored at -80 oC.

extract_protocol: Total RNA was extracted by TRIzol (Invitrogen) according to the manufacturer’s protocol (TRIzol: pellet= 2:1).  PolyA RNA was purified using the Applied Biosystem (Ambion) MicroPoly(A) Purist kit. PolyA RNA was fragmented using Fragmentation Reagent (Ambion).  First strand cDNA was synthesized from polyA RNA using a mixture of oligo dT and random primer (Invitrogen). Double stranded cDNA synthesis was performed using the SuperScript double stranded cDNA synthesis kit (Invitrogen).

tag: stage

value: Starved L3


title: N2_emb_rep 3

source_name: N2 embryo RNA

value: embryo


title: N2_starved L1_rep 2

value: Starved L2


title: N2_emb_rep 2


title: N2_emb_rep 1


title: N2_starved L1_rep 1

value: Starved L1


title: H3K27me3_ChIP-Seq_E14_10d-EB

status: Public on Jun 06 2009

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

description: Chromatin IP against H3K27me3

data_processing:
Reads (32 bp) were aligned to the Mouse (Mus muscules) reference genome. Tracks for the different cell lines or antibodies were equalized for the total number of mapped tags by random removal of sequenced tags. Wiggle files were generated from these bed files.
All ChIP-Seq sequence analyses were conducted based on Mus musculus NCBI m37 genome assembly (MM9) accessed from the Ensembl (release 49) or the UCSC (assembly July 2007) genome browsers.

source_name: Embryonic Stem cells

growth_protocol: ES cells were cultured in normal cell culture containing ES-grade serum supplemented with LIF. These cells were grown on gelatin-coated plates

extract_protocol: Chromatin was fixed in 1% formaldehyde for 10 minutes, sheared to 200-700bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

treatment_protocol: ES cells were either treated with atRA for 4 days or grown to EBs (removal of LIF) for 10 days

value: ES-cells

tag: antibody

value: H3K27me3 from T. Jenuwein


title: H3K27me3_ChIP-Seq_XT67E1_undiff

description: Chromatin IP against H3K27me3


title: H3K27me3_ChIP-Seq_E14_undiff

description: Chromatin IP against H3K27me3


title: H3K4me3_ChIP-Seq_XT67E1_10d-EB

description: Chromatin IP against H3K4me3

value: H3K4me3 Diagenode


title: H3K27me3_ChIP-Seq_LF2_10d-EB

description: Chromatin IP against H3K27me3


title: H3K27me3_ChIP-Seq_LF2_undiff

description: Chromatin IP against H3K27me3


title: H3K27me3_ChIP-Seq_XT67E1_10d-EB

description: Chromatin IP against H3K27me3


title: aerial_tissues_BS_seq

status: Public on Jun 16 2009

city: Berkeley

first: Toshiro

last: Nishimura

state: CA

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

description:
DNA methylation analysis of Arabidopsis tissue by bisulfite sequencing
library_strategy: Other (BS-seq)
library_source: genomic
library_selection: random

data_processing:
Processed data files (.gff): alignment, single_C_fractional_methylation, and 50bp_window_fractional_methylation files, are linked below as supplementary files.
Alignment: We used Perl scripts to convert all the Cs in the ‘forward’ reads (and in the scaffold) to Ts, and all the Gs in the ‘reverse’ reads and scaffold to As, and initially aligned the converted reads to the converted TAIR8 scaffold using SeqMap as individual reads, allowing up to two mismatches per read. We subsequently used a Perl script to insure that paired reads mapped to opposite strands within 300 bp of each other.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
Each processed data file has 9 tab-delimited columns (described in the README.txt file attached to the Series record).

source_name: Aerial tissues

growth_protocol: Standard long day growth conditions

extract_protocol: Seeds at the mid-torpedo stage to early-maturation stage (7-9 days after pollination, ecotype Col-0) were dissected in 0.3 M sorbitol, 5 mM MES (pH 5.7) on a slide under a dissecting microscope. We synthesized custom Illumina adapters in which cytosines were replaced by 5-methylcytosines, so that the adapters would survive bisulfite conversion. We chose to synthesize paired ends (PE) adapters, which allow each molecule to be sequenced from both ends, thus facilitating subsequent alignment to the genomic scaffold. We isolated 0.5-1 micrograms of genomic DNA from endosperm dissected from wild type and dme seeds, as well as control wild type embryos and aerial tissues. Specifically,plant tissues were ground in CTAB (cetyltrimethylammonium bromide) and genomic DNA was isolated as described by Murray and Thompson (Nucleic Acids Research. 8: 4321-4325, 1980, PMID: 7433111). DNA was sheared by sonication to fragments of 100-500 bp, and the adapters were ligated following the Illumina protocol. The library was then treated twice with sodium bisulfite (which converts unmethylated Cs to Us) using the Qiagen EpiTect kit, and amplified by 18 cycles of PCR using PfuTurboCx DNA polymerase (Stratagene), a proofreading enzyme that tolerates uracil in the template strand. Bands around 300 bp were gel-purified and cloned for validation.

tag: ecotype

value: wild-type

value: aerial tissues


title: H3K4me3_ChIP-Seq_XT67E1_undiff

description: Chromatin IP against H3K4me3


title: Illumina sequencing of small RNAs from untreated planarians

description: small RNAs

source_name: planarian

value: untreated whole-body planarians


title: H3K4me3_ChIP-Seq_XT67E1_4d-atRA

description: Chromatin IP against H3K4me3


title: H3K27me3_ChIP-Seq_XT67E1_4d-atRA

description: Chromatin IP against H3K27me3


title: Input Lane 1

description: Input control

source_name: Sperm Donor D1

value: sperm


title: H3K4Me3 Lane 1

description: ChIP-Seq for H3K4Me3

source_name: Sperm Pooled Donors


title: Pupae_INPUT_CBP

status: Public on May 29 2009

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

data_processing: Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300Â bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

organism: Drosophila melanogaster

source_name: Pupae

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of pupae at 1-2 days APF (after puparium formation), new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Embryos covered plates are then cut and placed back into regular fly medium bottles. 3. Pupae are collected 2 days after the first pupa formed on the wall of the bottle. They are collected with a brush humidified with EWB and placed into an eppendorf tube. They are rinsed extensively with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.

extract_protocol: Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. The DNA is directly used for Solexa library preparation.

treatment_protocol: No Treatment

tag: tissue/development stage

value: Pupae

tag: reference

value: INPUT


title: E12-16_INPUT_CBP


title: L3_INPUT_CBP

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of third instar larvae (L3), new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Plates are then kept at 25C for another 48 hours. 3. L3 larvae are collected at 8.45 am using a filter mesh and a brush. L3 larvae are the larvae not going through the first mesh. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.


title: AdultMale_CBP_ChIPSeq_1

source_name: AdultMale

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of Drosophila Adult Male 2-3 days old, new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Embryos covered plates are then cut and placed back into regular fly medium bottles. 3. Adult flies are collected 2 to 3 days after the first adult hatched. They are sorted for sex under a dissecting microscope after being put to sleep with CO2. Females and males are placed into different eppendorff tubes on ice and then rinsed with EWB before cross-linking in 1.8% formaldehyde at room temperature for 15 min.

value: AdultMale

value: CBP

tag: antibody provider

value: Dr. Mattias Mannervik in Stockholm University


title: E4-8_INPUT_CBP

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.2. For a 4-8 hours egg laying, new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 4 hours.3. Embryos are collected at 4.45 pm using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 5 pm in 1.8% formaldehyde at room temperature for 15 min.


title: L1_INPUT_CBP

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of first instar larvae, new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. 3. L1 larvae are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.


title: AdultMale_INPUT_CBP


title: L3_CBP_ChIPSeq_1

description:
CBP_ChIPSeq_1
corresponding input record: GSM408993


title: Pupae_CBP_ChIPSeq_1

description:
CBP_ChIPSeq_1
corresponding input record: GSM408995


title: E12-16_CBP_ChIPSeq_1

description:
CBP_ChIPSeq_1
corresponding input record: GSM408987


title: L1_CBP_ChIPSeq_1

description:
CBP_ChIPSeq_1
corresponding input record: GSM408991


title: AdultFemale_CBP_ChIPSeq_1

description:
CBP_ChIPSeq_1
corresponding input record: GSM408983

source_name: AdultFemale

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of Drosophila Adult Female 2-3 days old, new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Embryos covered plates are then cut and placed back into regular fly medium bottles. 3. Adult flies are collected 2 to 3 days after the first adult hatched. They are sorted for sex under a dissecting microscope after being put to sleep with CO2. Females and males are placed into different eppendorff tubes on ice and then rinsed with EWB before cross-linking in 1.8% formaldehyde at room temperature for 15 min.

value: AdultFemale


title: Whole-aerial_dcl1-7

status: Public on Jun 03 2009

city: Saint Louis

first: James

middle: C

last: Carrington

state: MO

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: dcl1-7 mutant plant

data_processing: Small RNA sequences were parsed from Illumina sequencing data files through identification of adaptor boundaries. Only sequences that mapped to the Arabidopsis thaliana Col-0 genome (TAIR8) were included in the analysis.

source_name: Whole aerial tissue, bolting

growth_protocol: Plants were maintained on soil in a standard greenhouse with 16 hr light/8 hr dark supplemental light cycle.

extract_protocol: Total RNA was isolated from whole aerial tissue, bolting, using Trizol and chloroform. Following isolation the RNA was purified by phenol-chloroform extraction. Small RNA were fractionated on denaturing 17% polyacrylamide gels. Amplicons for sequencing were prepared by 5' and 3' adaptor ligations followed by RT-PCR. Sequencing-by-synthesis was done using an Illumina 1G Genome Analyzer.

value: homozygous dcl1-7


title: AdultFemale_INPUT_CBP


title: Whole-aerial_dcl2-1dcl3-1dcl4-2

description: dcl2-1 dcl3-1 dcl4-2 mutant plant

value: homozygous dcl2-1 dcl3-1 dcl4-2


title: E4-8_CBP_ChIPSeq_1

description:
CBP_ChIPSeq_1
corresponding input record: GSM408989


title: Whole-aerial_Col-0

description: Wild type reference for dcl1-7 and dcl2-1 dcl3-1 dcl4-2 plants


title: Whole-aerial_Col-0_rep3

description: Technical replicate of rep1


title: Whole-aerial_Col-0_rep1

description: Biological replicate of rep2, technical replicate of rep3


title: BdR small RNA

status: Public on Jun 08 2009

city: beijing

first: bo

last: wei

institute: caas

description: Gel pufified small RNAs (16 -25 nt) were ligated to a 5’ adaptor and a 3’ adaptor sequentially, RT-PCR-amplified, and used for sequencing directly.

data_processing: Primers sequences were removed from raw sequences using either cross-match (Gordon et al. 2001) or Perl scripts. Small RNAs sequences of 16 to 25 nt were collected for analysis. Identical sequences were removed using an in-house Perl script. For stem-loop structure prediction, Repbase repeats (Jurka 2000), TIGR wheat repeats, RFam RNA sequences, and known miRNAs from miRBase were first screened from genomic or EST sequences using RepeatMasker. Small RNAs were then mapped to genomic sequences (BAC ends, ESTs) using BlastN. With one end anchored 10 bp away from the mapped small RNA location, sequences of 120 bp to 360 bp, with each extension of 20 bp, that cover the small RNA region were collected. Secondary structures of each sequence were predicted using MFold (Zuker 2003). Under conditions similar to those suggested by Allen et al. (2005), a stem-loop structure with ≤3 gaps involving ≤8 bases at the small RNA location was considered as a candidate miRNA precursor. Sequences of newly identified miRNA precursors from our full length cDNA have been submitted to GenBank under accession numbers FL488860 - FL488875. Sequences complementary to the novel miRNA were then checked for existence of miRNA*. Target genes of miRNAs were predicted using the first criterion used by Allen et al. (2005), in which mismatched bases were penalized according to their location in the alignment (Allen et al. 2005). All other data processing and graphical display were performed using in-house Perl scripts.

organism: Brachypodium distachyon

source_name: young spike (reproductive)

growth_protocol: Wheat cv. Chinese Spring was grown in normal field conditions. Brachypodium distachyon BD21-3 was provided by Dr. John Vogel, USDA. Seeds were sown in pots with soil and vernalized at 4℃ for 1-2 weeks. Pots were then transferred to light chambers with 16 h light at 22℃ and 8 h dark at 18℃ until mature.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen, USA). Small RNAs were enriched by PEG precipitation, separated on 15% denaturing PAGE, and visualized by SYBR-gold staining. Small RNAs of 16 - 28 nt were gel-purified.

tag: inbred line

value: young spike


title: Bmi1 KO MEF uH2A

status: Public on May 20 2009

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

description: Chromatin IP with anti-uH2A E6C5

data_processing: Sequenced 25-bp reads were mapped to the mouse genome (mm8) using the Solexa Analysis Pipeline. Reads that mapped to unique genomic locations with at most 2 mismatches were processed further to using the TIROE algorithm to identify genomic regions specifically enriched for mapped reads in the WT MEF sample 1 as compared to Bmi1 KO MEF Sample 2 with p-value threshold E-5.

source_name: Bmi1 KO C57BL/6 MEF cells

growth_protocol: TBX2 immortalized MEF cells were cultured in Dulbecco’s modified eagle medium (Gibco, Cat# 10829) supplemented with 10% FBS and were maintained at 37°C, 7% carbon dioxide, and passaged onto new plates following trypsin dissociation ever 3 days.

extract_protocol: For chromatin immunoprecipitation (ChIP) using a anti-uH2A(E6C5) (Cao et al., 2005, Mol Cell, PMID: 16359901), the formaldehyde cross-linked cells were sonicated and subjected to MNase digestion to obtain DNA fragments ranging in size from ~200-300 bp. Cluster generation and sequencing were performed as described earlier (Barski et al Cell, 2007) .

treatment_protocol: Cells were grown under standard conditions and were not subjected to further treatment before harvesting for ChIP-Seq experiments

tag: genotype

value: Bmi1 KO


title: Histone-Mnase Lane 2

description: Histone bound DNA enrichment via Mnase digestions and nucleosome purification

growth_protocol: Sperm samples were obtained from four known fertile donors attending the University of Utah Andrology laboratory, consented for research.


title: WT MEF uH2A

description: Chromatin IP with anti-uH2A E6C5

source_name: Bmi1 WT C57BL/6 MEF cells

value: Bmi1 WT


title: L2_H3K4Me1_ChIPSeq_1

status: Public on May 12 2009

description:
H3K4Me1_ChIPSeq_1
corresponding input record: GSM400669

data_processing: Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of second instar larvae (L2), new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Plates are then kept at 25C for another 24 hours.3. L2 larvae are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number

tag: antibody lot number


title: E20-24_H3K27Ac_ChIPSeq_1

description:
H3K27Ac_ChIPSeq_1
corresponding input record: GSM400673

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 20-24 hours egg laying, new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 4 hours.3. Embryos are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.

tag: tissue

value: Embryos

tag: time point


title: L2_H3K9Ac_ChIPSeq_1

description:
H3K9Ac_ChIPSeq_1
corresponding input record: GSM400669


title: Whole-aerial_Col-0_rep2

description: Biological replicate of rep1


title: L1_H3K9Ac_ChIPSeq_1

description:
H3K9Ac_ChIPSeq_1
corresponding input record: GSM400663


title: L2_H3K27Ac_ChIPSeq_1

description:
H3K27Ac_ChIPSeq_1
corresponding input record: GSM400669


title: L3_H3K9Ac_ChIPSeq_1

description:
H3K9Ac_ChIPSeq_1
corresponding input record: GSM400661


title: L3_H3K27Ac_ChIPSeq_1

description:
H3K27Ac_ChIPSeq_1
corresponding input record: GSM400661


title: Pupae_H3K9Ac_ChIPSeq_1

description:
H3K9Ac_ChIPSeq_1
corresponding input record: GSM400665


title: Pupae_H3K27Ac_ChIPSeq_1

description:
H3K27Ac_ChIPSeq_1
corresponding input record: GSM400665


title: Pupae_H3K4Me1_ChIPSeq_1

description:
H3K4Me1_ChIPSeq_1
corresponding input record: GSM400665


title: AdultFemale_H3K27Ac_ChIPSeq_1

description:
H3K27Ac_ChIPSeq_1
corresponding input record: GSM400671


title: AdultMale_H3K4Me1_ChIPSeq_1

description:
H3K4Me1_ChIPSeq_1
corresponding input record: GSM400667


title: BdV small RNA

source_name: root, shoot, leaf (vegetative)

value: root, shoot, leaf


title: AdultMale_H3K27Ac_ChIPSeq_1

description:
H3K27Ac_ChIPSeq_1
corresponding input record: GSM400667


title: E0-4_H3K4Me1_ChIPSeq_1

description:
H3K4Me1_ChIPSeq_1
corresponding input record: GSM400657

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 0-4 hours egg laying, new plates are added after a 2hours pre-egglaying at 10 am and flies are allowed to lay eggs for 4 hours. 3. Embryos are collected at 1.45 pm using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 2 pm in 1.8% formaldehyde at room temperature for 15 min.


title: E0-4_H3K9Ac_ChIPSeq_1

description:
H3K9Ac_ChIPSeq_1
corresponding input record: GSM400657


title: E0-4_H3K27Ac_ChIPSeq_1

description:
H3K27Ac_ChIPSeq_1
corresponding input record: GSM400657


title: E16-20_H3K4Me1_ChIPSeq_1

description:
H3K4Me1_ChIPSeq_1
corresponding input record: GSM400659

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.2. For a 16-20 hours egg laying, new plates are added after a 2hours pre-egglaying at 1 pm and flies are allowed to lay eggs for 4 hours.3. Embryos are collected at 8.45 pm using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.


title: E16-20_H3K9Ac_ChIPSeq_1

description:
H3K9Ac_ChIPSeq_1
corresponding input record: GSM400659


title: E4-8_H3K9Ac_ChIPSeq_1

description:
H3K9Ac_ChIPSeq_1
corresponding input record: GSM400675


title: E4-8_H3K4Me1_ChIPSeq_1

description:
H3K4Me1_ChIPSeq_1
corresponding input record: GSM400675


title: E4-8_H3K27Ac_ChIPSeq_1

description:
H3K27Ac_ChIPSeq_1
corresponding input record: GSM400675


title: Tae small RNA

description: Gel pufified small RNAs (16 -25 nt) were ligated to a 5’ adaptor and a 3’ adaptor sequentially, RT-PCR-amplified, and used for sequencing directly.

organism: Triticum aestivum

source_name: root, shoot, leaf, young spike

tag: cultivar

value: Chinese Spring

value: root, shoot, leaf, young spike


title: E20-24_INPUT

value: input


title: AdultFemale_INPUT


title: E4-8_INPUT


title: E4-8_H3K4Me3_ChIPSeq_1

description:
H3K4Me3_ChIPSeq_1
corresponding input record: GSM400675


title: E20-24_H3K4Me3_ChIPSeq_1

description:
H3K4Me3_ChIPSeq_1
corresponding input record: GSM400673


title: L2_INPUT


title: L2_H3K4Me3_ChIPSeq_1

description:
H3K4Me3_ChIPSeq_1
corresponding input record: GSM400669


title: AdultMale_INPUT


title: Pupae_INPUT

value: Pupae


title: E20-24_H3K9Ac_ChIPSeq_1

description:
H3K9Ac_ChIPSeq_1
corresponding input record: GSM400673


title: Pupae_H3K4Me3_ChIPSeq_1

description:
H3K4Me3_ChIPSeq_1
corresponding input record: GSM400665


title: L1_INPUT


title: E16-20_INPUT


title: L3_INPUT


title: L1_H3K4Me3_ChIPSeq_1

description:
H3K4Me3_ChIPSeq_1
corresponding input record: GSM400663


title: L3_H3K4Me3_ChIPSeq_1

description:
H3K4Me3_ChIPSeq_1
corresponding input record: GSM400661


title: E16-20_H3K4Me3_ChIPSeq_1

description:
H3K4Me3_ChIPSeq_1
corresponding input record: GSM400659


title: E0-4_INPUT


title: E0-4_H3K4Me3_ChIPSeq_1

description:
H3K4Me3_ChIPSeq_1
corresponding input record: GSM400657


title: Mid-log_air_rep1_Illumina

status: Public on May 01 2009

city: Atlanta

first: Nicholas

last: Bergman

state: GA

address: 310 Ferst Dr., Rm 231

department: Biology

institute: Georgia Institute of Technology

description: variable = atmosphere: air

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

organism: Bacillus anthracis

source_name: vegetative cells

growth_protocol: Standard growth in Modified G medium

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

tag: strain

tag: growth phase

value: mid-log

tag: optical density


title: Mili-wt-associated

status: Public on May 24 2009

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description:
library_strategy: Illumina small RNA library preparation kit
library_source: Protein-associated small RNAs
library_selection: Immunoprecipitation and gel elution of ~28-30 nt RNAs by radioactive spike labelling

data_processing: Alignment with mouse genome July 2007, mm9 assembly

source_name: Testes

growth_protocol: Mouse testes extract

extract_protocol: Immunoprecipitation

treatment_protocol: Lysate preparation

tag: age

value: Adult

value: testes


title: AdultMale_H3K4Me3_ChIPSeq_1

description:
H3K4Me3_ChIPSeq_1
corresponding input record: GSM400667

value: AdultMale

tag: antibody


title: AdultFemale_H3K4Me3_ChIPSeq_1

description:
H3K4Me3_ChIPSeq_1
corresponding input record: GSM400671

value: AdultFemale


title: L3_H3K4Me1_ChIPSeq_1

description:
H3K4Me1_ChIPSeq_1
corresponding input record: GSM400661


title: Tdrd1-associated

description:
library_strategy = Illumina small RNA library preparation kit
library_source: Protein-associated small RNAs
library_selection: Immunoprecipitation and gel elution of ~28-30 nt RNAs by radioactive spike labelling

treatment_protocol: Immunoprecipitated Tdrd1 complexes were treated with Proteinase K and associated RNAs were extracted by phenol. Small RNA libraries were prepared with Illumina small RNA preparation kit.


title: E16-20_H3K27Ac_ChIPSeq_1

description:
H3K27Ac_ChIPSeq_1
corresponding input record: GSM400659


title: Mid-log_CO2_rep1_Illumina

description: variable = atmosphere: 15% CO2


title: Drosophila OSS cell small RNA libraries, rep3

status: Public on Jun 09 2009

city: New York

first: Nicolas

last: Robine

address: 1275 York Avenue, Box 252

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description: Small RNA data (technical replicate).

data_processing: raw sequences were clipped by 3' linker sequences recognition, and clipped sequences longer than 18 nt were selected for analysis.

source_name: Drosophila OSS cells

extract_protocol: total RNA extracted with Trizol (Invitrogen) from OSS cells, ~18-30nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: cell line

value: Ovary Somatic Sheet (OSS) cell line


title: Drosophila OSS cell small RNA libraries, rep4

description: Small RNA data (technical replicate).

value: Ovary Somatic Sheet (OSS) cell line.


title: Drosophila OSS cell small RNA libraries, rep2

description: Small RNA data (technical replicate).


title: atxr5/atxr6 double mutant

status: Public on Jun 01 2009

city: Los Angeles

first: matteo

last: Pellegrini

address: 621 Charles Young Drive South

department: MCD Biology

institute: UCLA

description:
reads of bisulfite converted DNA
library strategy: BS-seq
library source: genomic
library selection: bisulfite

data_processing: Sequencing data was first processed using initial steps of version 0.2.2.4 of the Solexa Analysis Pipeline, and then by previously published customized software that performs basecalling, bisulfite alignment, and non-conversion filtration.  We removed a five base tag at the start of the read.

source_name: leaves

growth_protocol: Plants were grown under cool-white fluorescent light (~100 µmol/m-2 sec-1) under long-day (16 hours light followed by 8 hours darkness) or short-day conditions (8 hours light followed by 16 hours darkness).

extract_protocol: Plant DNeasy Maxi Kit (Qiagen) was used to isolate genomid DNA

value: leaf

value: atxr5/atxr6 double mutant


title: Wild type

value: wild-type


title: SpnE Mutant

status: Public on Apr 30 2009

first: Colin

middle: Dean

last: Malone

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

department: Skirball Institute - Developmental Genetics

institute: NYU Medical Center

description: small RNA sequencing

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

source_name: ovaries

growth_protocol: 24 degrees C

extract_protocol: Trizol

treatment_protocol: Trizol/Phenol Cholorofom extractions

value: ovaries


title: Zuc Mutant

description: small RNA sequencing


title: H3K36me3_ChIPSeq_root

status: Public on Apr 28 2009

first: Xiangfeng

last: Wang

address: 352 OML, 165 Prospect st

department: MCDB

data_processing: Sequencing reads were mapped to genome using MAQ software. ChIP-enriched regions were detected by MACS software. Further details found at http://www.plantcell.org/cgi/content/abstract/tpc.109.065714v1?papetoc

organism: Zea mays

source_name: seedling roots

growth_protocol: Maize inbred line B73 was obtained from the USDA-ARS North Central Regional Plant Introduction Station in Ames, IA. Seeds were planted in individual pots containing a mixture of three parts soil (Premier Pro-Mix Bx Professional, Premier Horticulture, Quakertown, PA) and two parts vermiculite (D3 Fine Graded Horticultural Vermiculite, Whittemore Co., Lawrence, MA). Plants were grown under controlled environmental conditions (15 hours light/25 ºC, 9 hours dark/20 ºC) in a growth chamber, and the soil mixture was kept moist by watering the pots with 0.7mM Ca(NO3)2. Seedlings were harvested after 14 days, separated into shoots and roots, frozen in liquid nitrogen and stored at –80 ºC or processed directly after harvesting for ChIP.

extract_protocol: Maize tissue from 10 different seedlings was ground in liquid nitrogen, and genomic DNA was extracted from 1 g pooled tissue using a Qiagen DNeasy plant maxi kit. To enrich for methylated genomic DNA, 20 mg genomic DNA were digested with 200 units McrBC (New England Biolabs) overnight, and fragments 500 nucleotides and smaller were gel purified and used for library construction following the manufacturer's instructions, but adding a final gel purification step. To enrich for histonemodified regions, ChIP was conducted using 5 g fresh maize tissue from 10 seedlings following a previously described procedure (Lee et al., 2007). The following antibodies were used: H3K9ac (Upstate; 07-352), H3K27me3 (Upstate; 07-449), H3K4me3 (Abcam; ab8580), and H3K36me3 (Abcam; ab9050). For each 1-mL ChIP reaction, 5 mL antibody were added. The ChIPed DNA from three reactions was pooled to construct Solexa libraries essentially following the manufacturer's standard protocol but running 18 PCR cycles before gel purification of the samples. Total RNA was isolated using TRIzol reagent (Invitrogen) following the manufacturer's instructions. mRNA was extracted from total RNA using Dynabeads Oligo(dT) (Invitrogen Dynal) following the manufacturer's directions. After elution from the beads, first- and secondstrand cDNA was generated using SuperscriptII reverse transcriptase (Invitrogen), and the standard Solexa protocol was followed thereafter to create mRNA libraries. smRNA was extracted by running total RNA on a 15% PAGE gel and cutting out bands in the ;19- to 24-nucleotide size range. Libraries for smRNAs were constructed following previously published procedures (Mi et al., 2008; see Supplemental Methods online for details). All samples were prepared for sequencing following the manufacturer's standard protocol.

value: B73 Strain

value: 14 day-old

tag: tissue type

value: seedling roots


title: Piwi Mutant

description: small RNA sequencing


title: DNAmeth_McrBCSeq_root


title: H3K27me3_ChIPSeq_root


title: Aub Mutant

description: small RNA sequencing


title: Krimp Mutant

description: small RNA sequencing


title: mRNASeq_root

description: mRNA


title: Drosophila OSS cell small RNA libraries, rep1

description: Small RNA data (technical replicate).


title: H3K9ac_ChIPSeq_root


title: dmel_imaginal-disc-brain

description:
Small RNA data.
library strategy: RNA-Seq
library source: total RNA

data_processing: raw sequences were clipped by 3' linker sequences recognition, and select clipped sequences longer than 18 nt

source_name: imaginal disc/brain

extract_protocol: total RNA from adult bodies, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

value: imaginal disc/brain


title: H3K4me3_ChIPSeq_root


title: DNAmeth_McrBCSeq_shoot

source_name: seedling shoots

value: seedling shoots


title: Vasa Mutant

description: small RNA sequencing


title: H3K27me3_ChIPSeq_shoot


title: Mili-Tdrd1 KO associated

description:
15 dpp
library_strategy: Illumina small RNA library preparation kit
library_source: Protein-associated small RNAs
library_selection: Immunoprecipitation and gel elution of ~28-30 nt RNAs by radioactive spike labelling


title: H3K9ac_ChIPSeq_shoot


title: Squ Mutant

description: small RNA sequencing


title: H3K4me3_ChIPSeq_shoot


title: Vasa Heterozygote

description: small RNA sequencing

value: vasD5/cyo and vasPH165/cyo


title: Piwi Heterozygote

description: small RNA sequencing

value: piwi1/cyo and piwi2/cyo


title: pool4-run3

status: Public on Apr 26 2009

city: Seoul

first: Jinkuk

last: Kim

address: 50 Irwon-dong, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

description: PCR amplification reactions for each of selected SNPs were performed individually (Phusion Hot Start polymerase, NEB).  All PCR reactions done with cDNA were accompanied by a matching no-RT control.  Because gDNA-templated, liver-mRNA-templated, and muscle-mRNA-templated amplicons all shared the same primers, they needed to be sequenced in separate pools, so that they could be distinguished from one another.  Because one pyrosequencing plate can be divided into four segments without contamination between segments, the amplicons were mixed into 4 pools.  Each pool had ~60 amplicons, mixed in equimolar amounts following determination of each amplicon concentration (Bioanalyzer, Agilent Technologies).  Each pool was deproteinated (phenol, chloroform with iso-amyl-alcohol), purified by native PAGE gel, taking precautions to avoid denaturing the double-stranded PCR products, and submitted to the 454 Life Sciences for sequencing.

data_processing:
Sequencing reads of the amplicons were mapped to 3'-terminal 10-nt fragments of the primer pairs to identify the origin of the reads. Any amplicons of the four pools are for either miR-1, miR-122, miR-133 or control sites. For each amplicon, the number of reads for each allele was calculated.
The processed data file for each pool-run is linked below as a supplementary file.

source_name: muscle or liver from F1 progeny of either one of the five inter-strain crosses

growth_protocol: The Jackson laboratory performed five inter-strain crosses (CAST/EIJ × PWD/PHJ, FVB/NJ × PWD/PHJ, A/J × C57BL/6J, WSB/EiJ × MOLF/EiJ, A/J × DBA/2J) and dissected liver and skeletal muscle from two 4-week-old F1 littermates of each cross.

extract_protocol: For each cross and tissue, ~0.6 g tissue (~0.3 g from each littermate) was homogenized for RNA extraction (RNeasy Maxi kit, Qiagen), and cDNA was synthesized from total RNA in RT reactions (Superscript III, Invitrogen) primed with random hexamers.  For each cross, gDNA was isolated from ~50 mg of either liver or muscle from either littermate (DNeasy Blood and Tissue kit, Qiagen).

value: muscle or liver


title: dmel_male_body

source_name: male body

value: male body


title: Flam Mutant

description: small RNA sequencing


title: Armi Mutant

description: small RNA sequencing


title: Squ Heterozygote

description: small RNA sequencing

value: squHE47/cyo and squPP32/cyo


title: pool4-run2


title: High-throughput sequencing of small RNAs in chicken somite embryos

city: Oxford

first: Helio

last: Pais

address: Jonh Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

description: The somites where taken from chick embryos between stages HH14 and HH21.

data_processing: Chicken genome [chicken genome assembly WASHUC2] was downloaded from Ensembl database. Small RNA sequences were mapped to genomic sequence.

organism: Gallus gallus

source_name: White leghorn chicken embryos

extract_protocol:
Dissected tissue white leghorn chicken embryos was disaggregated and RNA extracted using the miRVana kit (Ambion). Small RNA fraction between 19 and 24 nt was isolated from 15% denaturing polyacrylamide gel and 15 micro gram was ligated to Solexa adaptors (Illumina) without de-phosphorylating and re-phosphorylating.
The short RNAs were converted to DNA by RT-PCR following the Illumina protocol.

tag: developmental stage

value: somite embryos (stages HH14 and HH21)


title: pool4-run1


title: pool3-run2

source_name: muscle from F1 progeny of either one of the five inter-strain crosses

value: muscle


title: Aub Heterozygote

description: small RNA sequencing

value: aubHN2/cyo and aubQC42/cyo


title: SpnE Heterozygote

description: small RNA sequencing

value: spnE1/TM3 and spnE100.37/TM3


title: pool3-run3


title: pool3-run1


title: pool2-run3

description:
NOTE: Both gDNA-templated and liver-mRNA-templated amplicons represented.
PCR amplification reactions for each of selected SNPs were performed individually (Phusion Hot Start polymerase, NEB).  All PCR reactions done with cDNA were accompanied by a matching no-RT control.  Because gDNA-templated, liver-mRNA-templated, and muscle-mRNA-templated amplicons all shared the same primers, they needed to be sequenced in separate pools, so that they could be distinguished from one another.  Because one pyrosequencing plate can be divided into four segments without contamination between segments, the amplicons were mixed into 4 pools.  Each pool had ~60 amplicons, mixed in equimolar amounts following determination of each amplicon concentration (Bioanalyzer, Agilent Technologies).  Each pool was deproteinated (phenol, chloroform with iso-amyl-alcohol), purified by native PAGE gel, taking precautions to avoid denaturing the double-stranded PCR products, and submitted to the 454 Life Sciences for sequencing.

library_source: other

molecule: other

value: amplicons derived from genomic DNA or total RNA


title: pool2-run1


title: pool1-run3


title: pool2-run2


title: pool1-run1


title: Krimp Heterozygote

description: small RNA sequencing


title: pool1-run2


title: Flam Heterozygote

description: small RNA sequencing


title: Lai Kc167 cells Sample Kc-48 (Replicate 1) extraction1_seq1 aliquote 1

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

source_name: Kc cell line

extract_protocol: total RNA from Kc cells, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

value: Kc


title: Pha-4 emb replicate 2 POL II

status: Public on Apr 11 2009

description: Chromatin IP against anti-Pol II

data_processing: Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200 bp.

source_name: pha-4 transgenic worm OP37

growth_protocol: Transgenic worms were routinelly grow on plates to obtain as many adults with embryos. Bleach to obtain embryos. Hatch overnight in M9 Buffer to obtain L1s. Wash L1s and put into 500 ml liquid media (S medium+1X PSN antibiotics and nystatin) and grow at 20 oC in an incubator shaking at 230 rpm. Add concentrated E Coli for food as necessary during growth. It takes around 2.5-3 days to obtain adults with embryos. Collect adults and bleach to obtain embryos. Spin down embryos at 3000 g for 3 minutes. Resuspend pellet (embryos) and wash 2 more times with M9 Buffer. For embryo stage samples continue with cross-linking steps. For L1 stage samples, After collect adults from liquid culture and bleach to obtain embryos, The embryos were hatched overnight in M9 Buffer without any food to obtain L1s. Continue with the same wash and cross-linking steps.

extract_protocol: Chromatin was sheared to 200-800 bp using a Branson sonifier microtip, immunoprecipitated using anti-POL II antibody, purified for the DNA fragments bound by transcription factor, and sequenced it using Illumina Genome Analyzers.

treatment_protocol: Resuspend embryo or Lava stage samples  in 2% formaldehyde solution. Place on a shaker (50-100 rpm) and incubate for 30 minutes at room temperature. Wash samples once with 100 mM Tris pH 7.5 (to quench excess formaldehyde), 2 times with M9 Buffer, and once with FA buffer supplemented with protease inhibitors.

tag: growth stage

value: embryo

value: anti-Pol II


title: Pha-4 starved L1 replicate 2 POL II

description: Chromatin IP against anti-Pol II

value: starved L1


title: Armi Heterozygote

description: small RNA sequencing

value: ovaries

value: armi1/TM3 and armi72.1/TM3


title: MAB-5 L3 replicate 2 Input

description: No ChIP just input DNA from the same preparation

source_name: mab-5 transgenic worm OP26

growth_protocol: Transgenic worms were routinelly grow on plates to obtain as many adults with embryos. Bleach to obtain embryos. Hatch overnight in M9 Buffer to obtain L1s. Wash L1s and put into 500 ml liquid media (S medium+1X PSN antibiotics and nystatin) and grow at 20 oC in an incubator shaking at 230 rpm. Add concentrated E. Coli for food as necessary during growth. When worms reaches to L3 stage, spin down worms at 3000 g for 3 minutes. Resuspend the worm pellet and wash 2 more times with M9 Buffer. Continue with the same wash and cross-linking steps.

extract_protocol: Chromatin was sheared to 200-800 bp using a Branson sonifier microtip, immunoprecipitated using anti-GFP antibody, purified for the DNA fragments bound by transcription factor, and sequenced it using Illumina Genome Analyzers.


title: H3K36me3_ChIPSeq_shoot

value: B73 Strain

value: 14 day-old

value: seedling shoots


title: MAB-5 L3 replicate 1 Input


title: MAB-5 L3 replicate 2 GFP

description: Chromatin IP against anti-GFP

value: anti-GFP


title: MAB-5 L3 replicate 1 GFP

description: Chromatin IP against anti-GFP


title: mRNASeq_shoot

description: mRNA


title: Pha-4 emb replicate 1 POL II

description: Chromatin IP against anti-Pol II


title: dmel_Kc167_rep2

source_name: Drosophila melanogaster Kc167 cells

extract_protocol: total RNA from Kc167 cells, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH


title: DAF-16 L4/Young adult replicate 1 POL II

description: Chromatin IP against anti-POL II

source_name: daf-16 transgenic worm TJ356

growth_protocol: Transgenic worms were routinelly grow on plates to obtain as many adults with embryos. Bleach to obtain embryos. Hatch overnight in M9 Buffer to obtain L1s. Wash L1s and put into 500 ml liquid media (S medium+1X PSN antibiotics and nystatin) and grow at 20 oC in an incubator shaking at 230 rpm. Add concentrated E. Coli for food as necessary during growth. When worms reaches to L4/young adult stage, spin down worms at 3000 g for 3 minutes. Resuspend the worm pellet and wash 2 more times with M9 Buffer. Continue with the same wash and cross-linking steps.

extract_protocol: Chromatin was sheared to 200-800 bp using a Branson sonifier microtip, immunoprecipitated using anti-GFP antibody and anti-POL II antibody, purified for the DNA fragments bound by transcription factor, and sequenced it using Illumina Genome Analyzers.

treatment_protocol: Resuspend L4/young adult stage samples  in 2% formaldehyde solution. Place on a shaker (50-100 rpm) and incubate for 30 minutes at room temperature. Wash samples once with 100 mM Tris pH 7.5 (to quench excess formaldehyde), 2 times with M9 Buffer, and once with FA buffer supplemented with protease inhibitors.

value: L4/young adult

value: anti-POL II


title: DAF-16 L4/Young adult replicate 2 Input


title: DAF-16 L4/Young adult replicate 1 GFP

description: Chromatin IP against anti-GFP


title: DAF-16 L4/Young adult replicate 1 Input


title: DAF-16 L4/Young adult replicate 2 POL II

description: Chromatin IP against anti-POL II


title: ama-1 L4/young adult replicate 2 GFP

description: Chromatin IP against anti-GFP

source_name: ama-1 transgenic worm OP34


title: DAF-16 L4/Young adult replicate 2 GFP

description: Chromatin IP against anti-GFP


title: ama-1 L4/young adult replicate 1 GFP

description: Chromatin IP against anti-GFP


title: ama-1 L4/young adult replicate 2 Input


title: ML-DmBG3-c2-122

status: Public on Apr 08 2009

city: Farmington

first: Brenton

middle: R

last: Graveley

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

description: Oligo-dT selected, double stranded cDNA, Paired-end sequencing

data_processing: Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .bedgraph files which indicate the number of reads that map to each base in the genome.

source_name: ML-DmBG3-c2 cell line, biological replicate 1

growth_protocol: Schneider's medium + 10% heat-inactivated FCS + 10 ug/ml insulin

extract_protocol:
Paired-End RNA-Seq Library Preparation:
mRNA Purification from Total RNA
Fragmentation of mRNA: Assemble the following reaction: 2 µl 10 x fragmentation buffer (Ambion #AM8740), 11 µl mRNA (100ng/µL), 7 µl Spike-ins. Incubate the tube in a PCR thermocycler at 70°C for 5 minutes, add 1 µL of stop buffer, and put the tubes on ice. Transfer the solution to a 1.5 ml microcentrifuge tube. Add 1 µL of 3M NaOAC, 2 µL of glycogen, and 30 µL of 100% EtOH. Incubate the tube at -80°C for 30 minutes.Spin at 14000rmp for 25 minutes at 4°C in a microcentrifuge. Wash the pellet with 70% EtOH, and air dry the pellet. Resuspend the RNA in 10.5µL of water.
First strand cDNA synthesis:
Assemble the following reaction: 1.0 µl  N6 primer (3µg/µl), 10.5 µl  mRNA (100ng/µl). Incubate the tube in a PCR thermocycler at 65°C for 5 minutes, and put the tubes on ice. Mix the following in order, make 10% extra reagent for multiple samples: 4.0 µl 5 1st strand buffer, 2.0 µl 100 mM DTT, 1.0 µl dNTP Mix (10 mM), 0.5 µl (RNaseOUT (40U/µl) Add 7.5µL mixture to the tube, mix well, and heat the sample at 25°C in a thermocycler for 2 min. Add 1 µL SuperscriptII (200U/ µL) to the sample, and incubate the sample in a thermocycler with following program: 10 minutes 25C, 50 minutes 42C, 15 minutes 70C, Hold 4C.
Second strand cDNA synthesis:
Put the tubes on ice. Add 51µL of H2O to the first strand cDNA synthesis mix. Add the following reagents: 20µL 5 second strand buffer, 3µL dNTP mix (10mM). Mix well, incubate on ice 5 minutes or until well chilled, and add:1 µL RNaseH (2U/µL), 5 µL DNA pol I (10U/µL). Mix well, and incubate at 16°C in a thermocycler for 2.5 hours. Purify the DNA with a Qiaquick PCR spin column, and elute in 30µL of EB solution. Note: The remaining steps use reagents that are part of the Illumina Genomic DNA Sample Prep kit.
End Repair:
Prepare the following reaction mix: 50ul DNA sample, 25ul water, 10ul T4 DNA ligase buffer with 10mM ATP, 4ul dNTP mix (10 mM), 5ul T4 DNA polymerase, 1ul Klenow DNA polymerase, 5ul T4 PNK (10U/ul). Incubate in thermal cycler 30 min. at 20C. Purify on one QIAquick PCR Purification column (Qiagen part #28104) eluting in 32ul EB. Add 'A' Bases to 3' End of DNA Fragments: Prepare the following reaction mix: 32ul DNA sample, 5ul Klenow buffer, 10ul dATP(1mM), 3ul Klenow 3' to 5' exonuclease. Incubate for 30 min. at 37C. Purify on one Qiaquick MinElute column (Qiagen part #28004), eluting in 19ul EB. Ligate Adapters: Prepare the following reaction mix: 19 ul DNA sample, 25 ul DNA ligase buffer, 1 ul PE Adapter oligo mix, 5 ul DNA ligase (1U/ul). Incubate for 15 min. at room temp. Purify on one Qiaquick PCR purification column, eluting in 10ul EB.
Purify Ligation Products:
Prepare a 2% agarose gel in a final volumn of 50mL 1x TAE buffer. Load 10µL of the sample into one well, and 1µL 100bp DNA ladder into another. (To prevent cross contamination, leave at least 2 wells between samples). Run gel at 120V for 45~60 minutes. Cut the gel at 300bp (+/- 25bp), and purify the DNA with Qiaquick gel extraction kit (Qiagen part #28604). Elute the DNA into 30µL of EB solution.
Enrich Adapter Modified DNA fragments by PCR:
Prepare the following reaction mix: 23 ul DNA, 25 ul Phusion DNA polymerase, 1 ul PCR primer 1.1, 1 ul PCR primer 2.1. Amplify using the following protocol= 30 seconds at 98C, 10 seconds at 98C, 30 seconds at 65C, 30 seconds at 72C go to #2 15 more times, 5 minutes at 72C. Hold forever at 4C. Purify with one QIAquick pcr purification column and elute in 30ul EB.
Gel purification:
Prepare a 2% agarose gel in a final volumn of 50mL 1x TAE buffer. Load the 10µL of sample into one well, and 1µL 100bp DNA ladder into another. (To prevent cross contamination, leave at least 2 wells between samples). Run gel at 120V for 45~60min. Cut the gel at 300 bp (+/- 25bp), and purify the DNA with Qiaquick gel extraction kit. Elute the DNA into 30µL of EB solution. Load onto Solexa flowcell. Dilute sample to 10nM concentration in EB. Load onto flow cell at a 2-4pM concentration.


title: S2-DRSC-16

source_name: S2-DRSC cell line, biological replicate 2

growth_protocol: Schneider's medium + 10% heat-inactivated FCS


title: dmel_female_body

source_name: female body

value: female body


title: small RNA from S2 cells (S2-NP)

description: Small RNA data.

source_name: Drosophila melanogaster S2 cells

extract_protocol: total RNA from S2R+ cells, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: cell type

value: S2 cells


title: ama-1 L4/young adult replicate 1 POL II

last: Vaccarino

description: Chromatin IP against anti-POL II


title: CME_W1_Cl.8+-60

source_name: CME_W1_Cl.8+ cell line, biological replicate 1

growth_protocol: M3 medium + 2% heat-inactivated FCS + 5 ug/ml insulin + 2.5% fly extract


title: CME_W1_Cl.8+-62

source_name: CME_W1_Cl.8+ cell line, biological replicate 2


title: ama-1 L4/young adult replicate 1 Input


title: Kc167-2

source_name: Kc167 cell line, biological replicate 1


title: Kc167-4

source_name: Kc167 cell line, biological replicate 2


title: ama-1 L4/young adult replicate 2 POL II

description: Chromatin IP against anti-POL II


title: S2-DRSC-14

source_name: S2-DRSC cell line, biological replicate 1


title: DPY-27 emb replicate 2 input

status: Public on Apr 03 2009

source_name: dpy-27 transgenic worm OP32

growth_protocol: Transgenic worms were routinelly grow on plates to obtain as many adults with embryos. Bleach to obtain embryos. Hatch overnight in M9 Buffer to obtain L1s. Wash L1s and put into 500 ml liquid media (S medium+1X PSN antibiotics and nystatin) and grow at 20 oC in an incubator shaking at 230 rpm. Add concentrated E Coli for food as necessary during growth. It takes around 2.5-3 days to obtain adults with embryos. Collect adults and bleach to obtain embryos. Spin down embryos at 3000 g for 3 minutes. Resuspend pellet (embryos) and wash 2 more times with M9 Buffer. Continue with the same wash and cross-linking steps.


title: DPY-27 emb replicate 2 GFP

description: Chromatin IP against anti-GFP


title: ML-DmBG3-c2-124

source_name: ML-DmBG3-c2 cell line, biological replicate 2

growth_protocol: Schneider's medium + 10% heat-inactivated FCS + 10 g/ml insulin


title: DPY-27 emb replicate 1 input


title: ColxLer_5d_silique

status: Public on Mar 24 2009

city: Cambridge

first: Rebecca

middle: A

last: Mosher

address: Downing Street

department: Plant Sciences

institute: Cambridge University

description: small RNA library

data_processing: The data were processed by searching the raw reads for adapter sequence and trimming it off, leaving only small RNA sequences

source_name: 5d post-fertilization siliques ColxLer

growth_protocol: standard growth conditions

extract_protocol: standard RNA extraction

value: 5 day post-fertilization silique

tag: cross

value: ColxLer


title: LerxCol_5d_silique

description: small RNA library

source_name: 5d post-fertilization siliques LerxCol

value: LerxCol


title: DPY-27 emb replicate 1 GFP

first: Flora

address: 230 South Frontage Road

institute: Yale University

description: Chromatin IP against anti-GFP


title: LerxLer_5d_silique

description: small RNA library

source_name: 5d post-fertilization siliques LerxLer

value: LerxLer


title: ColxCol_5d_silique

description: small RNA library

source_name: 5d post-fertilization siliques ColxCol

value: ColxCol


title: HeLa S3 STAT1 ChIP unstimulated_7

status: Public on Mar 23 2009

city: Vancouver

first: Eric

last: Chuah

state: BC

address: 570 West 7th Ave

institute: BC Genome Sciences Centre

data_processing: We extracted sequences from the resulting image files using the open source Firecrest and Bustard applications on a 32-CPU cluster running Red Hat Enterprise Linux 4 and Sun Microsystems Grid Engine 6. Reads were aligned (mapped) to the unmasked human reference genome (NCBI v36, hg18) using the Eland application (Illumina). Eland achieves high throughput by permitting no more than two mismatches per read sequence. We maximized the number of mapped reads by iteratively discarding two bases from the end of a rejected read and resubmitting the truncated read to Eland, until either all reads had been aligned to the genome or the lengths of all unmapped reads were less than 20 bp. Only uniquely mapped reads were retained. DNA fragments were represented by a mapped sequence read of length 27 bp. Because a relatively small number of PCR cycles was used in library preparation and DNA-fragment end locations were weakly clustered rather than random (data not shown), we allowed reads with identical start coordinates to be present in a profile. We combined uniquely aligned reads from the three biological replicates into a single set of reads. We transformed mapped sequence reads into profiles of the number of overlapped DNA fragments at each nucleotide in the reference genome. Because a 27-bp read directionally represents one end of a DNA fragment (SET), we approximated the fragment that produced a read sequence by extending the read to generate an XSET. We chose the XSET length to be the mean fragment length of the size selected DNA. From distances between mapped reads, we estimated this length to be 174 bp. A peak's height was the maximum number of overlapped XSETs for that peak. A random expectation for the probability of observing peaks with a particular height was generated from a numerical background model that generated peaks by randomly placing onto a hypothetical genome several fragments equivalent to the actual uniquely mapped number. Each fragment's length was the estimated mean fragment length, that is, the XSET length. Because 27-bp reads can be mapped uniquely to approx90% of the human genome (data not shown), the background simulations used a mappable genome length that was 90% of 3.08 Gb. For a peak height, we estimated the FDR as the ratio of the number of peaks that the background model indicated should occur by chance, to the number observed.

source_name: HeLa S3

extract_protocol: To prepare immunoprecipated DNA for 1G sequencing, we size-fractionated 5?50 ng of immunoprecipate by 12% PAGE and excised a gel slice containing the 100?300 bp fragments. We eluted DNA from the gel slice overnight at 4 °C in 300 mul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl (pH 7.5), 0.2 mM EDTA)-7.5 M ammonium acetate) and recovered the DNA using a QIAquick PCR purification kit (Qiagen). Then we repaired the DNA ends using a 1:5 mixture of T4 and Klenow DNA polymerases (Illumina) following the manufacturer's instructions. After a 30-min incubation at 20 °C, we subjected the reaction to phenol?chloroform?isoamyl alcohol (pH 8.0; 100 mul; Fisher) extraction in 0.5-ml phase-lock gel tubes (heavy; Eppendorf) and precipitated the reactions by adding 250 ml of 100% EtOH, 3 ml of mussel glycogen (Invitrogen) and 10 ml of 7.5 M NH4OAc, and incubating at -20 °C for 20 min. We recovered the precipitate by centrifugation at 20,200g for 15 min at 4 °C in an benchtop refrigerated centrifuge (Eppendorf model 5417R). We added a single adenine base to the DNA using Klenow exo? (3' and 5' exo minus; Illumina) following the manufacturer's instructions.

tag: ChIP Antibody

tag: Cell Line

value: HeLa S3

tag: Treatment

value: unstimulated


title: HeLa S3 STAT1 ChIP unstimulated_5


title: HeLa S3 STAT1 ChIP unstimulated_6


title: HeLa S3 STAT1 ChIP unstimulated_3


title: HeLa S3 STAT1 ChIP unstimulated_4


title: dmel_Kc167_rep1

source_name: Drosophila melanogaster Kc167 cells


title: Pha-4 starved L1 replicate 1 POL II

city: New Haven

description: Chromatin IP against anti-Pol II

source_name: pha-4 transgenic worm OP37

value: starved L1

value: anti-Pol II


title: HeLa S3 STAT1 ChIP IFNgamma_3

value: IFNgamma stimulated


title: HeLa S3 STAT1 ChIP IFNgamma_6


title: HeLa S3 STAT1 ChIP IFNgamma_1


title: RNAPII Fulv

status: Public on Mar 09 2009

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

institute: Radboud University

description: Chromatin IP against RNA polymerase II

data_processing: Reads (32 bp) were aligned to the human (Homo sapiens, hg18) reference genome and extended to 133 bp. RNAPII tracks for the different ligands were equalized for the total number of mapped tags by random removal of sequenced tags. For ERalpha enriched regions were identified using Findpeaks. For RNAPII the number of tags within each ENSEMBL gene body was counted and gene regulation of each gene was expressed as the ratio of tags of ligand induced versus control.

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were hormone starved for 48h in DMEM w/o phenolred supplemented with 5% charcoal treated serum.

extract_protocol: Chromatin was harvested after 1h induction. Chromatin was fixed in 1% formaldehyde for 30 minutes, sonicated for 15x30sec at high power using a Bioruptor (Diagenode), immunoprecipitated ERalpha (AC-066-100, Diagenode) and RNAPII ((AC-0555-100, Diagenode) antibodies, purified and sequenced using Illumina Genome Analyzer as recommended by the manufacturer.

treatment_protocol: MCF-7 cells were treated for 1h with the different compounds

tag: Fulvestrant treated 100 nM

tag: Antibody RNAPII


title: Zuc Heterozygote

description: small RNA sequencing

source_name: ovaries

tag: tissue

value: ovaries

value: zucHM27/cyo and zucDf(2l)PRL/cyo


title: RNAPII control

description: Chromatin IP against RNA polymerase II

tag: mock treated


title: RNAPII E2

description: Chromatin IP against RNA polymerase II

tag: E2 treated 10 nM 1h


title: ERalpha Fulv

description: Chromatin IP against ERalpha

tag: Antibody ERalpha


title: ERalpha Tam

description: Chromatin IP against ERalpha

tag: Tamoxifen treated 1 uM 1h


title: HeLa S3 STAT1 ChIP unstimulated_2


title: ERalpha control

description: Chromatin IP against ERalpha


title: 1hr_Recovery_8WG16

status: Public on Feb 27 2009

city: Durham

first: L.

middle: Ryan

last: Baugh

address: 4314 French Family Science Center

institute: Duke University

data_processing: Data were analyzed using the Python package ERANGE. 6hr_Starved_S2 and 6hr_Starved_S2#2 were pooled prior to analysis and analyzed under the name 6hr_Starved_S2. The number of reads was counted over each gene model and over a 200 bp window spanning the most 5’ transcription start site for the input and each of the samples. Read density was computed from these counts by normalizing to reads per million per kilobase of sequence. The variance in input read density correlates with the variance in sample read density even after subtracting input read density from sample density, as if sequence-specific biases have a multiplicative effect during library preparation and sequencing. GC content is one possible explanation for this phenomenon. We therefore chose to divide sample read density for each region by input read density, rather than using subtraction, resulting in data with fold-enrichment (relative to input) as the unit. To avoid undefined and volatile ratios, we actually used the larger of the input read density or the median of all input read densities, making a conservative adjustment to fold-enrichment assessments. 5’ bias was defined as the ratio of fold-enrichment in the 200 bp window spanning the transcription start site to fold-enrichment over the gene model. To avoid undefined ratios in computing 5’ bias, fold-enrichments in the denominator (gene model) of zero were changed to 0.1.

source_name: 1hr recovery from 12hr L1 arrest

growth_protocol: Nematode cultures were maintained, passaged, and collected at 20°C.  A fresh thaw of C. elegans strain N2 from the Sternberg laboratory strain collection was used for microarray analysis; this N2 strain was obtained from the Caenorhabditis Genetics Center in 1987, expanded and frozen.  The worms were thawed and expanded on agar plates with E. coli OP50 as food {Lewis, 1995 #5}.  Populations of worms were synchronized in liquid culture for two generations prior to staging for ChIP analysis.  A starved 5 cm plate was used to inoculate a 10 ml liquid culture (S-complete plus 40 mg/ml E. coli HB101), and the liquid culture was incubated for 3 d and then bleached to produce a clean preparation of embryos {Lewis, 1995 #5}.  One million embryos were suspended in 100 ml of S-complete plus 40 mg/ml HB101 and they were cultured for 70 hr at 180 rpm.  Cultures were bleached resulting in approximately 10 embryos per worm bleached.  Bleached embryos were examined to ensure that they were clean and healthy and resuspended in S-complete at 10 embryos/microliter with no HB101.  They were cultured at 180 rpm for either 18 hr (for 6 hr L1 arrest) or 24 hr (for 12 hr L1 arrest) allowing them to hatch and enter L1 arrest, and then they were crosslinked.  Alternatively, after 24 hr of culture, 25 mg/ml HB101 was added to recovery the worms from arrest and they were cross-linked after 1 hr.

extract_protocol: In preparation for sonication, larvae were thawed on ice, washed once in Farnham Lysis Buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40, Roche Protease Inhibitor Cocktail, and Thermo Scientific HALT Phosphatase Inhibitor Cocktail), suspended in 2 ml of Farnham Lysis Buffer, and incubated on ice for 15 min with occasional mixing.  Larvae were pelleted, washed once with RIPA Buffer (1xPBS, 1% NP40, 0.5% Sodium Deoxycholate, 0.1% SDS, Roche Protease Inhibitor Cocktail, and Thermo Scientific HALT Phosphatase Inhibitor Cocktail), and re-suspended in 0.6 ml RIPA buffer.  Sonication was performed on a Misonic 3000 in a 15 ml centrifuge tube (Corning) submerged in 95% ethanol on dry ice with the following regimen:  6 x 30 sec at setting #7 with 1 min cooling intervals, 2 x 30 sec at setting #2.5 with 1 min cooling intervals, 4 x 30 sec at setting #5 with 1 min cooling intervals, and 30 sec at setting #7.  Sonicates were transferred to 1.5 ml microcentrifuge tubes (Eppendorf) and spun at 14,000 RPM for 30 min at 4°C to pellet debris.  Cleared supernatants were transferred to clean microcentrifuge tubes and their volumes were adjusted with RIPA buffer so that each 0.3 ml of sonicate contained chromatin from ~400,000 larvae.  1% of this chromatin was aliquoted, frozen and saved as an input control for sequencing.  For each immunoprecipitation, 2 micrograms of the appropriate antibody was added to 0.3 ml of sonicate and incubated overnight at 4°C on a nutator.  The following day, 150 microliters of magnetic beads with the appropriate immunoglobulin (Dynal/Invitrogen) were added and incubated for 3-4 hr on a nutator.  Beads were collected with the Dynal magnet and the supernatants were saved.  Beads were washed five times in LiCl Wash Buffer (100 mM Tris, 500 mM LiCl, 1% NP40, 1% Sodium Deoxycholate) for 3 min each, followed by a brief wash in TE.  The beads were then suspended in TE, transferred to a clean microcentrifuge tube, and TE was removed.  300 microliters of IP Elution Buffer (1% SDS and 0.1 M NaHCO3) and 2 microliters of Proteinase K (20 mg/ml; Ambion) were added to the beads and they were incubated at 42°C for 1-2 hr with periodic re-suspension of the beads and then overnight at 65°C.  Eluate was transferred to a clean tube, and a second elution was performed with 100 microliters IP Elution Buffer at 65°C for 1 hr, and the two were combined.  Eluate DNA was extracted with phenol/chloroform/isoamyl alcohol followed by chloroform/isoamyl alcohol.  25 micrograms of GenElute Linear Polyacrylamide (Sigma) was added as carrier, and DNA was precipitated with ethanol.  Precipitated DNA was dissolved in 100 microliters Tris (10 mM, pH 8.0) and interrogated by QPCR and Fluorometry (NanoDrop) using PicoGreen (Molecular Probes/Invitrogen).

treatment_protocol: Larvae were cross-linked for 30 min in 2% Formaldehyde (Polysciences, Inc.) in a shaking incubator at 20°C.  Formaldehyde was quenched by adding 0.1 volume of 1 M Tris pH 7.4.  Larvae were washed in ice-cold S-basal plus 125 mM Glycine, followed by ice-cold S-basal, and they were spun down to a small volume and frozen.

tag: wild-type strain N2

tag: variable

value: condition:1 hr recovery from 12 hr L1 arrest; antibody:8WG16 (ab817)


title: HeLa S3 STAT1 ChIP IFNgamma_5


title: 12hr_Starved_Input

source_name: 12hr L1 arrest

value: time:12 hr; condition:L1 arrest; antibody:Input


title: 6hr_Starved_Input

source_name: 6hr L1 arrest

value: time:6 hr; condition:L1 arrest; antibody:Input


title: 1hr_Recovery_Input

source_name: 1hr recovery after 12hr L1 arrest

value: condition:1 hr recovery after 12 hr L1 arrest; antibody:Input


title: HeLa S3 STAT1 ChIP unstimulated_1


title: 6hr_Starved_Input#2


title: HeLa S3 STAT1 ChIP IFNgamma_2


title: 1hr_Recovery_4H8

value: condition:1 hr recovery from 12 hr L1 arrest; antibody:4H8 (ab5046)


title: HeLa S3 STAT1 ChIP IFNgamma_4


title: 12hr_Starved_8WG16

value: time:12 hr; condition:L1 arrest; antibody:8WG16 (ab817)


title: 1hr_Recovery_S2

value: condition:1 hr recovery from 12 hr L1 arrest; antibody:S2 (ab5095)


title: RNAPII Tam

description: Chromatin IP against RNA polymerase II


title: 12hr_Starved_S2

value: time:12 hr; condition:L1 arrest; antibody:S2 (ab5095)


title: 12hr_Starved_4H8

value: time:12 hr; condition:L1 arrest; antibody:4H8 (ab5046)


title: 12hr_Starved_4H8#2


title: 6hr_Starved_S2#2

value: time:6 hr; condition:L1 arrest; antibody:S2 (ab5095)


title: ERalpha E2

description: Chromatin IP against ERalpha


title: 1hr_Recovery_4H8#2


title: Forebrain_p300_ChIP-seq

status: Public on Feb 11 2009

city: Berkeley

first: Matthew

middle: James

last: Blow

address: 1 Cyclotron Road

department: Genomics Division

institute: Lawrence Berkeley National Laboratory

description: Tissue pooled from ~150 embryos  Chromatin IP against p300

data_processing: Sequence reads were aligned to the mouse reference genome (mm9) using BLAT.  Uniquely aligned reads were extended to 300bp in the 3' direction and used to determine the read coverage at individual nucleotides at 25bp intervals throughout the mouse genome.  p300-enriched regions (peaks) with an estimated false discovery rate of 0.01, were identified by comparison with a random distribution of the same number of reads. Candidate peaks mapping to repetitive regions were removed as likely artifacts.

source_name: Mouse embryonic day 11.5 (e11.5) forebrain

extract_protocol: Embryonic forebrain, midbrain and limb tissue was isolated from CD-1 mouse embryos at e11.5.  Tissue samples were cross linked and cells were dissociated and subject to  chromatin isolation, sonication and immunoprecipitation using an anti-p300 antibody.  ChIP DNA was sheared by sonication, end-repaired, ligated to solexa sequencing adapters and amplified by emulsion PCR.  Gel purified amplified ChIP DNA between 300 and 500bp was sequenced on the Solexa / Illumina Genome Analyzer to generate 36 bp reads.

tag: strain

value: CD1  Gender:Mixed male / female  Age:embryonic day 11.5 (e11.5)  Tissue:forebrain


title: Midbrain_p300_ChIP-seq

source_name: Mouse embryonic day 11.5 (e11.5) midbrain

value: CD1  Gender:Mixed male / female  Age:embryonic day 11.5 (e11.5)  Tissue:midbrain


title: 6hr_Starved_S2


title: Limb_p300_ChIP-seq

source_name: Mouse embryonic day 11.5 (e11.5) limb

value: CD1  Gender:Mixed male / female  Age:embryonic day 11.5 (e11.5)  Tissue:limb


title: Endogenous small RNAs from Arabidopsis thaliana col-0, wild type, seedlings

status: Public on Feb 02 2009

city: PARIS

first: Alexis

last: Sarazin

address: 46 rue d'Ulm

department: Ecole Normale Supérieure, Département de Biologie

country: France

institute: CNRS UMR 8186 - Biologie Moléculaire des Organismes Photosynthétiques

description: Total endogenous small RNAs from Arabidopsis thaliana col-0 wild type

data_processing: Sequence reads were matched against the Arabidopsis thaliana nuclear genome (TAIR7, www.arabidopsis.org) using MUMmer v3.0, only full-length complete matches were allowed.

source_name: seedlings WT

growth_protocol: Plants were grown under long-day conditions

extract_protocol: Small RNA isolation, gel purification and cloning were performed as described in Curr Protoc Mol Biol by Pfeffer et al. in 2005.

value: Columbia-0 wild type  Tissue:seedlings  Development stage:10-days-old


title: NPC sample from patient2 (male)

status: Public on Feb 07 2009

city: Martinsried

first: Gunter

last: Meister

address: Am Klopferspitz 18

department: Center for Integrated Protein Science Munich (CIPSM)

institute: Max Planck Institute of Biochemistry

description: Total endogenous small RNAs between 15 and 30 bases from NPC sample of patient2

data_processing: Processed data file contains the reads with 5' and 3' adapters removed. Same reads are sorted together and the numbers of repetitivity are illustrated

source_name: Nasopharyngeal Carcinoma

extract_protocol: From all samples, RNA species smaller than 200 bases were enriched with the mirVana  miRNA isolation kit (Ambion, Austin, Texas, USA). The small RNAs from all 4 samples were  separated on a denaturing 12,5% polyacrylamide (PAA) gel and stained with SYBRgreenII.  As molecular mass standard a mixture of oligonucleotides was used that range in size  between 15 and 30 bases. The population of miRNAs with a length of 15 – 30  bases was obtained by passive elution of the RNAs from the gel. The miRNAs were then  precipitated with ethanol and dissolved in water. For cDNA synthesis the RNAs were first poly(A)-tailed using poly(A) polymerase followed by  ligation of a RNA adapter to the 5´-phosphate of the miRNAs. First-strand cDNA synthesis  was then performed using an oligo(dT)-linker primer and M-MLV-RNase H- reverse  transcriptase. The resulting cDNAs were then PCR-amplified to about 20 ng/μl using the high fidelity polymerase Phusion (Finnzymes). The fusion primers used for PCR amplification were designed for amplicon sequencing  according to the instructions of 454 Live Sciences. Barcode sequences for each cDNA  species are attached to the 5'-ends of the cDNAs. cDNAs of 4 samples were mixed in  equal amounts. The correct size range was obtained by separation of the mixed cDNAs on  and electroelution of the 120 – 135 bp fraction from 6% PAA-gels followed by purification of  the eluted cDNAs using Nucleospin Extract II (Macherey and Nagel). The cDNAs were pooled (Volume: 30 μl; Concentration: 13 ng/μl; dissolved in 5 mM Tris pH:8,5) and sent for 454 sequencing. Small RNA cloning was performed by Vertis Biotechnologie AG (Weihenstephan, Germany)

treatment_protocol: clinical dissection, frozen samples.

value: undifferentiated NPC


title: healthy control tissue from patient2 (male)

description: Total endogenous small RNAs between 15 and 30 bases from control tissue of patient2

source_name: healthy nasopharyngeal tissue

value: clinically negative of NPC


title: Endogenous small RNAs from Arabidopsis thaliana col-0, ddm1 mutant, seedlings

description: Total endogenous small RNAs from Arabidopsis thaliana col-0 ddm1 mutant

source_name: seedlings ddm1 mutant

value: Columbia-0 ddm1 mutant  Tissue:seedlings  Development stage:10-days-old


title: healthy control tissue from patient1 (female)

description: Total endogenous small RNAs from control tissue of patient1


title: NPC sample from patient1 (female)

description: Total endogenous small RNAs between 15 and 30 bases from NPC sample of patient1


title: small RNA from 12-24hr embryo

status: Public on Jan 30 2009

description: Small RNA data.

source_name: Drosophila melanogaster 12-24hr embryo

extract_protocol: total RNA from 12-24hr embryo, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: 12-24hr embryo

tag: Canton S


title: hepg2_bindASP_hl_2

status: Public on Jan 26 2009

city: Cold Spring Harbor

first: Katalin

last: Fejes Toth

address: 1 Bungtown Rd

institute: Cold Spring Harbor Labs

description:
hepg2_bindASP_hl_2
variable: cap-capture supernatant, standard protocol, alternative primers

data_processing: Reads were aligned to the reference genome (hg18 assembly version), and the fragment count at any given position (25-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

growth_protocol: HeLa cells were grown in suspension culture, HepG2 cells on plates in DMEM containing 10% FBS, 1% Penn/Strep and harvested at subconfluent concentration.

extract_protocol: RNA was extraceted with phenol, other column purified, TAP treated, adapters were addad by C-tailing, 5' ligation and RT using primer with a polyG stretch. PCR amplificaiton was used for enrichment and followed by gel purification of expected size range.

tag: liver carcinoma cell line


title: hepg2_biotin_el_hl_b

description:
hepg2_biotin_el_hl_b
variable: cap-capture eluate with TAP, standard protocol, alternative primers


title: HepG2_tot_up

description:
HepG2_tot_up
variable: whole cell RNA size range 50-200 nt


title: hepg2_untreated_b

description:
hepg2_untreated_b
variable: no TAP treatment


title: hepg2_biotin_el_hl_a

description:
hepg2_biotin_el_hl_a
variable: cap-capture eluate with TAP, standard protocol, alternative primers


title: HepG2_nucl_low

description:
HepG2_nucl_low
variable: nuclear other size range <50 nt


title: hepg2_cip_tap_pasr_b

description:
hepg2_cip_tap_pasr_b
variable: CIP treatment prior to TAP


title: hepg2_cip_tap_pasr_a

description:
hepg2_cip_tap_pasr_a
variable: CIP treatment prior to TAP


title: HepG2_tot_low

description:
HepG2_tot_low
variable: whole cell RNA size range <50 nt


title: hepg2_biotin_hl_2a

description:
hepg2_biotin_hl_2a
variable: cap-capture eluate with heat, standard protocol, alternative primers


title: hepg2_tap_pasr_b

description:
hepg2_tap_pasr_b
variable: standard protocol


title: HepG2_nucl_up

description:
HepG2_nucl_up
variable: nuclear other size range 50-200 nt


title: hepg2_biotin_hl_2b

description:
hepg2_biotin_hl_2b
variable: cap-capture eluate with heat, standard protocol, alternative primers


title: hepg2_tap_pasr_a

description:
hepg2_tap_pasr_a
variable: standard protocol


title: hepg2_untreated_a

description:
hepg2_untreated_a
variable: no TAP treatment


title: HepG2_TAP_depl

description:
HepG2_TAP_depl
variable: rRNA depleted RNA 3pM cluster density


title: HepG2_TAP_AFFY_depl

description:
HepG2_TAP_AFFY_depl
variable: rRNA depleted RNA with alternative primers, 3 pM cluster density


title: m3m7G_ip

description:
m3m7G_ip
variable: m3m7G immunoprecipitated RNA, 3 pM cluster density


title: HepG2_3pM_5

description:
HepG2_3pM_5
variable: nuclar other size range <50nt, 3pM cluster density


title: HepG2_3pM_7

description:
HepG2_3pM_7
variable: nuclar other size range <50nt, 3pM cluster density


title: HepG2_3pM_6

description:
HepG2_3pM_6
variable: nuclar other size range <50nt, 3pM cluster density


title: HepG2_2pM_2

description:
HepG2_2pM_2
variable: nuclar other size range <50nt, 2pM cluster density


title: HepG2_2pm_3

description:
HepG2_2pm_3
variable: nuclar other size range <50nt, 2pM cluster density


title: HepG2_3pM_4

description:
HepG2_3pM_4
variable: nuclar other size range <50nt, 3pM cluster density


title: hepg2_phil_rd2

description:
hepg2_phil_rd2
variable: standard protocol with alternative primers


title: HepG2_2pM_1

description:
HepG2_2pM_1
variable: nuclar other size range <50nt, 2pM cluster density


title: hepg2_untrtd

description:
hepg2_untrtd
variable: no TAP treatment


title: hepg2_cip_tap_pasr

description:
hepg2_cip_tap_pasr
variable: CIP treatment prior to TAP