title: Pha-4 emb input

status: Public on Jan 24 2009

department: Child Study Center

description: No ChIP just input DNA from the same preparation

data_processing: Enriched peak regions corresponding to transcription factor binding sites were identified by first extending all the uniquely mapped tags reads to the averaged sequenced DNA fragment size ~200bps and then accumulated into fragment density signal maps. Peaks in these maps are identified by comparison to a computer simulated null model for each Mb of each chromosome (accounting for the variability in mappability of sequence tags across the C. elegans genome. For potential target regions the number of sequenced tags is compared against the normalized number of sequence tags overlapping the region from the matching Input DNA reference sample. Fold enrichment ratios are computed from the ratio of these two sets of counts for each regions as well as p-value using the cumulative distribution function for the binomial distribution. P-value are corrected for multiple hypothesis testing using a Benjamini-Hochberg correction factor and a false discovery rate threshold of 0.05 is imposed. (See Rozowsky et al. Submitted)

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 Colifor 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 the indicated antisera. DNA and transcription factor complex was pull down, reversed cross-linking, ligated the adaptors to ChIP DNA, sequenced (gel purified 150-350bp) using Illumina Genome Analyzer.

treatment_protocol: Resuspend embryo or Lava stage samples  in 1% 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. Store at -80C

tag: growth stage

value: emrbyo

tag: antibody


title: Pha-4 emb GFP

type: SRA

city: New Haven

first: Flora

last: Vaccarino

state: CT

address: 230 South Frontage Road

country: USA

institute: Yale University

description: Chromatin IP against anti-GFP

library_source: genomic

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: pha-4 transgenic worm OP37

tag: strain

value: embryo

value: anti-GFP


title: Pha-4 L1 GFP

description: Chromatin IP against anti-GFP


title: Input

status: Public on Jan 22 2009

city: Salt Lake City

first: Dean

last: Tantin

state: UT

address: 15 North Medical Drive East

department: Department of Pathology

institute: University of Utah

description:
input DNA, both 26 and 36bp reads, 5 lanes.
variable: no treatment

data_processing:
The standard Illumina GAPipeline-0.3.0 was run to convert images to quality scored sequences and aligned reads. The USeq package http://useq.sourceforge.net was then used to identify enriched Oct1 binding peaks.
Each processed file contains a list of genomic regions (NCBI 36.1, H_sapiens_Mar_2006, hg18) enriched for Oct1 binding.
These files were generated by running the EnrichedRegionMaker on ScanSeqs window scored data, see http://useq.sourceforge.net/ .
Adjacent and overlapping windows with a q-value FDR of 0.0001 were joined into larger enriched regions.
The best scoring window's scores are used to represent the enriched region.

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: Normal culture conditions. Subconfluent cells were grown in DMEM

extract_protocol: Chromatin was fixed in 1% formaldehyde, sheared to 200-800bp, immunoprecipitated using Oct1 antibodies, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

treatment_protocol: no treatment

tag: no treatment


title: hepg2_tap_pasr

status: Public on Jan 26 2009

city: Cold Spring Harbor

first: Katalin

last: Fejes Toth

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Labs

description:
hepg2_tap_pasr
variable: standard protocol

library_source: transcriptomic

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).

molecule: total RNA

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_depl_cip_tap

description:
hepg2_depl_cip_tap
variable: rRNA depleted, CIP treated before TAP, 5pM cluster density


title: H2O2

description:
chromatin IP using Oct1 antibodies, both 26 and 36bp reads, 3 lanes.
variable: 1 hr H2O2 treatment

treatment_protocol: 1mM H2O2

tag: 1 hr H2O2 treatment


title: hela_nucl_t

description:
hela_nucl_t
variable: nuclear polyU enriched, alternative primers

source_name: HeLa

tag: cervix cc cell line


title: Footprints-starved-1

status: Public on Feb 12 2009

city: Berkeley

first: Nicholas

middle: T

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

state: CA

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

description:
Small RNA sequencing by polyadenylation and circularization: RNA fragments were dephosphorylated, purified by filtration followed by gel purification for ~30 bp fragments, tailed with poly-A polymerase, reverse transcribed with anchored oligo-dT primer, cDNA was circularized

Footprints: sucrose density gradient; mRNA: polyA

data_processing: Reads aligned to reference genome by first 21 nt, then extended to account for the poly-A tail

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: yeast BY4741, 20 min amino acid starved

growth_protocol: Yeast strain BY4741 (leu2D0 ura3D0 met15D0 his3D1) was grown at 30 C in YEPD to OD600 = 0.6-0.7, then 20 min into minimal media w/o amino acids at 30 C if indicated

extract_protocol: Footprints: cells were rapidly harvested, flash-frozen in polysome lysis buffer, and pulverized in a mixer mill, extracts were digested with 150 U Rnase I for 1 hour, monosomes were purified by sucrose density gradient, RNA was extracted from the monosome fraction by hot acid phenol; total RNA was prepared from flash-frozen cells by the hot acid phenol protocol, polyA RNA was purified by oligo-dT DynaBeads, and fragmented at 95 C under mild alkali conditions

treatment_protocol: All samples were treated for 2 min with cycloheximide 100 ug / ml

tag: BY4741 (leu2D0 ura3D0 met15D0 his3D1)


title: Pha-4 starved L1 input


title: nTreg-H3K4me3

status: Public on Jan 21 2009

city: DC

first: Weiqun

last: Peng

address: 725 21st street, NW

institute: The Georege Washington University

description:
Chromatin IP
T cells were treated with MNase to generate approximately 80% mononucleosomes and 20% dinucleosomes. Chromatin from 2 × 107 cells was used for each ChIP experiment, which yielded approximately 100 ng of DNA. Antibodies against histone H3K4me3 (ab8580, Abcam) and H3K27me3 (07-449, Upstate) were used. The ChIP DNA fragments were blunt-ended, ligated to the Solexa adaptors, and sequenced with the Illumina 1G Genome Analyzer.

data_processing: Sequence reads were obtained and mapped to the mouse (February, 2006) genomes using the Illumina Genome Analyzer Pipeline. More details as described in Wei et al., 2009 (PMID:19144320)

organism: Mus musculus

source_name: nTreg cells

growth_protocol: Growth protocol as described in Wei et al., 2009 (PMID:19144320)

extract_protocol: Extract protocol as described in Wei et al., 2009 (PMID:19144320)

treatment_protocol: Treatment protocol as described in Wei et al., 2009 (PMID:19144320)


title: iTreg-H3K27me3

source_name: iTreg cells


title: Th17-H3K27me3

source_name: Th17 cells


title: hela_10_1

description:
hela_10_1
variable: nuclear, PCR amplification with 10:1 ratio of GC:AT dNTPs, alternative primers


title: hela_phil_rd2

description:
hela_phil_rd2
variable: standard protocol with alternative primers


title: hela_tap_pasr

description:
hela_tap_pasr
variable: standard protocol


title: Th2-H3K27me3

source_name: Th2 cells


title: nTreg-H3K27me3


title: Th1-H3K27me3

source_name: Th1 cells


title: naïve-H3K27me3

source_name: Naive cells


title: Th1-H3K4me3


title: hela_5_1

description:
hela_5_1
variable: nuclear, PCR amplification with 5:1 ratio of GC:AT dNTPs, alternative primers


title: Th17-H3K4me3


title: hela_phil_smrna_nuc

description:
hela_phil_smrna_nuc
variable: nuclear fraction, alternative primers


title: naïve-H3K4me3


title: hela_chip_smrna_pure

description:
hela_chip_smrna_pure
variable: nuclear, enriched for PASRs with Affymetrix promotor array, alternative primers


title: E14Tg2a murine ES cells IgG

status: Public on Jan 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

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 enriched with mapped reads with p-value threshold E-10.

source_name: E14Tg2a murine ES cells

growth_protocol: E14 ES cells were cultured in Knockout Dulbecco’s modified eagle medium (Gibco, Cat# 10829) supplemented with 15% ES-qualified FBS (Invitrogen, Cat#16141-079), 2mM L-glutamine (Gibco #25030-081), 10mM HEPES (Gibco #15630-080), 100U/ml penicillin/streptomycin (Gibco #15070-063), 0.1mM non-essential amino acids (Gibco #11140-050), 0.1mM beta-mercaptoethanol (Gibco #21985-023) and 1000U/ml LIF (Esgro, Chemicon #ESG1107). ES cells were maintained at 37°C, 7% carbon dioxide, fed with fresh media daily, and passaged onto new plates following trypsin dissociation.

extract_protocol: For chromatin immunoprecipitation (ChIP) using a anti-Brg/Brm antibody (Clone J1, Khavari et al., 1993, Nature, PMID: 8232556), the formaldehyde cross-linked cells were sonicated to obtain DNA fragments ranging in size from ~200-500 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: ES cells


title: Footprints-starved-2


title: mRNA-starved-2


title: hela_5_pct

description:
hela_5_pct
variable: nuclear, PCR amplification with 5% ratio of ddATP, alternative primers


title: iTreg-H3K4me3


title: Footprints-rich-1

source_name: yeast BY4741, mid-exponential phase


title: mRNA-rich-2


title: mRNA-rich-1


title: Footprints-rich-2


title: CD36-H3K9me3

status: Public on Jan 09 2009

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

description:
Chromatin IP against H3K9me3
run53_lane3
run56_lane3
run133_lane4

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 Cui et al., 2008

source_name: CD36+ cells

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

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

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

tag: CD36 H3K9me3


title: CD36-H4K20me1

description:
Chromatin IP against H4K20me1
run53_lane6
run56_lane5
run134_lane4

tag: CD36 H4K20me1


title: CD36-PolII

description:
Chromatin IP against RNA Polymerase II
run53_lane7

tag: CD36 RNA Polymerase II


title: CD36-H3K4me1

description:
Chromatin IP against H3K4me1
run132_lane2
run145_lane4

tag: CD36 H3K4me1


title: CD36-H3K4me3

description:
Chromatin IP against H3K4me3
run50_lane6

tag: CD36 H3K4me3


title: CD36-H3K36me3

description:
Chromatin IP against H3K36me3
run52_lane4
run55_lane7
run134_lane2

tag: CD36 H3K36me3


title: hela_nucl_a

description:
hela_nucl_a
variable: nuclear, polyA enriched, alternative primers


title: CD36-H3K27me3

description:
Chromatin IP against H3K27me3
run51_lane5
run54_lane4
run132_lane6

tag: CD36 H3K27me3


title: E14Tg2a murine ES cells Brg J1


title: mRNA-starved-1

description:
Small RNA sequencing by polyadenylation and circularization: RNA fragments were dephosphorylated, purified by filtration followed by gel purification for ~30 bp fragments, tailed with poly-A polymerase, reverse transcribed with anchored oligo-dT primer, cDNA was circularized

Footprints: sucrose density gradient; mRNA: polyA


title: CD36-H3K9me1

description:
Chromatin IP against H3K9me1
run51_lane6
run55_lane6
run133_lane2

tag: CD36 H3K9me1


title: hela_phil_smrna_cyto

description:
hela_phil_smrna_cyto
variable: cytoplasmic fraciton, alternative primers


title: CD36-H3K27me1

description:
Chromatin IP against H3K27me1
run132_lane4
run145_lane6
run185_lane1

tag: CD36 H3K27me1


title: CD133-H4K20me1

description:
Chromatin IP against H4K20me1
run53_lane4
run56_lane4
run134_lane3

source_name: CD133+ cells


title: CD133-H3K4me3

description:
Chromatin IP against H3K4me3
run49_lane5

tag: CD133 H3K4me3


title: CD133-H3K9me1

description:
Chromatin IP against H3K9me1
run50_lane1
run55_lane5
run133_lane1

tag: CD133 H3K9me1


title: CD133-PolII

description:
Chromatin IP against RNA Polymerase II
run53_lane5

tag: CD133 RNA Polymerase II


title: CD133-H3K9me3

description:
Chromatin IP against H3K9me3
run50_lane2
run56_lane2
run133_lane3

tag: CD133 H3K9me3


title: CD133-H3K4me1

description:
Chromatin IP against H3K4me1
run132_lane1
run145_lane3

tag: CD133 H3K4me1


title: CD133-H3K27me3

description:
Chromatin IP against H3K27me3
run49_lane7
run54_lane3
run132_lane5


title: CD133-H2AZ

description:
Chromatin IP against H2A.Z
run50_lane4
run132_lane7

tag: CD133 H2A.Z


title: CD133-H3K36me3

description:
Chromatin IP against H3K36me3
run50_lane3
run57_lane8
run134_lane1


title: CD36-H2AZ

description:
Chromatin IP against H2A.Z
run54_lane5
run132_lane8

tag: CD36 H2A.Z


title: MEFF H3K27me3 ChIP-seq

status: Public on Dec 22 2008

city: Vienna

first: Florian

middle: M

last: Pauler

state: Vienna

address: Dr Bohrgasse 9/4

country: Austria

institute: CeMM

description: Chromatin IP against H3K27me3

data_processing: Density: A theoretical fragment density for each 25bp window was calculated. Uniquely aligned tags within a 200bp and oriented towards it were counted as 1 to the for each 25bp window and as 0.25 if they were within 200bp and 300bp. Window Counts: For each 200bp window the uniquely aligned tags were counted.

source_name: Mouse embryonic fibroblasts

growth_protocol: MEF cell lines were cultured according to standard protocols

extract_protocol: Native ChIP was performed as published (Regha et al., 2007 PMID: 17679087).

treatment_protocol: MEFF is a spontaneously immortalized 12.5dpc mouse embryo fibroblast cell. The 93Mb long Chr.17 sequence in the cell line is identical with the exception of the Thp deletion on the maternal chromosome. The Thp deletion spans at least 4,6Mbp spanning the region between the genes T and Sod2 (8,6Mbp-13,2Mbp Mouse July 2007 mm9) and contains the 400kb Igf2r imprinted gene cluster (Regha et al., 2007 PMID: 17679087).

tag: genotype

value: Thp/+, Age:cell line, Tissue:embryo, Strain:FVBN, Antibody:H3K27me3 (Thomas Jenuwein), Type:Native ChIP

tag: antibody

value: H3K27me3, Cell Type:MEF


title: Th2-H3K4me3

description:
Chromatin IP
T cells were treated with MNase to generate approximately 80% mononucleosomes and 20% dinucleosomes. Chromatin from 2 × 107 cells was used for each ChIP experiment, which yielded approximately 100 ng of DNA. Antibodies against histone H3K4me3 (ab8580, Abcam) and H3K27me3 (07-449, Upstate) were used. The ChIP DNA fragments were blunt-ended, ligated to the Solexa adaptors, and sequenced with the Illumina 1G Genome Analyzer.


title: xrn1 rrp6 lsm1 pat1 Rep 4

status: Public on Dec 18 2008

city: Stanford

first: Gavin

last: Sherlock

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

description: S. cerevisiae experimental RNA

data_processing: The Solexa Pipeline version 0.3.0 produced an output containing our sequences in fastq format.  Sequences were matched to both the genome and the ORF sequences using ELAND, tolerating up to 2 mismatches in the first 25 bases.

source_name: xrn1 rrp6 lsm1 pat1

growth_protocol: Our unpublished studies suggested that among two dozen or so different conditions that we assayed, exposure to high salt (0.8M NaCl) results in the expression of the greatest fraction of known and novel transcripts, and thus was chosen as the experimental condition to use to find previously unannotated and low abundance transcripts. Cells were grown at 30 degrees C in YPD to approximately 1x10^7 cells/ml as determined by a Beckman Coulter Z2 Particle Count and Size Analyzer. 1.6M NaCl (in YPD) was added in an equal volume of YPD prewarmed to 30 degrees C (final concentration 0.8M). Cells were harvested after 30 minutes by filtration, frozen in liquid nitrogen, and kept at minus 80 degrees C until RNA extraction and purification.

extract_protocol: RNA was extracted from the cells using a slightly modified version of the traditional hot phenol protocol (Schmitt et al. 1990) followed by ethanol precipitation and washing. Briefly, 5ml of lysis buffer (10mM EDTA ph 8.0, 0.5% SDS, 10mM Tris-HCl pH 7.5) and 5ml of acid phenol were added to frozen cells and incubated at 60 degrees C for 1 hour with occasional vortexing, then placed on ice. The aqueous phase was extracted after centrifugation and additional phenol extraction steps were performed as needed, followed by a chloroform extraction. Total RNA was precipitated from the final aqueous solution with 10% volume 3M sodium acetate pH 5.2 and ethanol, and resuspended in nuclease-free water. RNA was prepared for sequencing utilizing a protocol obtained from Shujun Luo at Affymetrix and Brian Williams from Barbara Wold's lab at CalTech. Briefly, the total RNA was polyA purified twice using oligo dT conjugated to magnetic beads, which were then fragmented and subjected to cDNA synthesis. Solexa linkers were ligated to the ends of the cDNA, and the cDNA was run on an agarose gel for size selection. An agarose gel slice corresponding to the appropriate size was excised the purified, and the cDNA was amplified via PCR using Solexa specific primers. The PCR product was purified, quantified, and submitted for sequencing.

treatment_protocol: The sequencing libraries were prepared following protocols issued by Illumina (developed by Shujun Luo at Illumina and Brian Williams from Barbara Wold's Lab at CalTech).

tag: strain

value: FY23 x FY86 (Winston et al. 1995), carrying the auxotrophic markers:his3-delta200, leu2-delta1, trp1-delta63, ura3-52.  The strain contains deletions in the genes XRN1, RRP6, LSM1, and PAT1.


title: Ethanol 4 replicates (2 non-crosslinked, 2 crosslinked)

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

description: library source : genomic

data_processing:
Mapped Reads: Unique reads mapped to the yeast genome, and extended to the average fragment length in the experiment (140-170 bp).
Normalized Tracks: For each Sample, we used the map reads to calculate at every basepair the log-ratio between the number of reads that cover that basepair and the average number of reads per basepair across the genome. We then set the genomic mean in each sample to zero by subtracting the genome-wide mean from every basepair. Finally, we averaged the replicates within each experimental condition, resulting in four tracks of log-normalized nucleosome coccupancy. One file for each biological condition, four files in total.

source_name: S. cerevisiae BY4741

growth_protocol: Cells were grown in YP media supplemented by 2% galactose or 2.8% ethanol.

extract_protocol: Samples were extracted as indicated in sample protocols.  All samples were then blunted using END-IT DNA Repair Kit #ER0720 from Epicentre (< 5µg DNA, 5uL 10x buffer, 5uL dNTP mix, 5uL ATP solution, 1uL enzyme mix, water to 50uL.  Incubated at room temp for 60 minutes, then cleaned up using Qiagen buffer QG on QiaQuick columns with 2 PE buffer washes, eluted with 30uL EB), then A-tailed using #KL06041K from Epicentre (Klenow Exo-minus) (30uL DNA solution, 5uL Klenow, 1uL 10mM dATP, 1uL Klenow, water to 50uL, 60 min at room temp, then cleaned up with Qiagen MinElute columns and eluted in 10uL EB).  Solexa adapters were ligated using a Fast Link Kit (#LK11025 from Epicentre) (10uL DNA, 1.5uL 10x buffer, 0.75 uL 10mM ATP, 1uL of Solexa adapters, 1uL ligase, and water to 50uL incubated for 60 min at room temp, then 7.5uL water, 1uL 10x buffer, 0.5uL 10mM ATP, and 1uL ligase were added and the entire reaction incubated at 16C overnight before purification on QiaQuick columns as in blunting reaction).  Samples were run out on a 2% agarose gel and the mononucleosome sized band (~147bp) was extracted using Qiagen Gel Extraction columns.  Samples were amplified by PCR (Stratagen PfuUltra II Fusion #600670) (30uL ligated DNA, 2uL Solexa PCR primers, 10uL 10x buffer, 10uL 2.5mM dNTP, 1uL enzyme, water to 100uL for PCR [95C 1 min, (95C 50'', 65C 1', 72C 30'') x 15 cycles, 72C 5min, 4C hold] and then cleaned on QiaQuick columns) before being sequenced on Illumina Genome Analyzer II machines.

treatment_protocol: As indicated in sample protocols

tag: yeast strain

tag: genomic dna

value: chromatin

tag: growth condition

value: Ethanol


title: Galactose 3 replicates (2 non-crosslinked, 1 crosslinked)

description: library source : genomic

value: Galactose


title: YPD 6 biological replicates (4 non-crosslinked, 2 crosslinked)

description: library source : genomic

growth_protocol: Mononucleosomes were isolated from S. cerevisiae were grown to an OD600 of 0.8 in YPD medium as described in Segal et. al, Nature 442, 772-8 (2006). For crosslinked sample, yeast were grown to an OD600 of 0.8 in YPD and fixed with 1% formaldehyde for 15 min at 30C before spheroplasting as in Segal et. al, Nature 2006.  Spheroplasts were treated with Mnase as in Shivaswamy et al, PLoS Biol 6, e65 (2008), and nucleosomal DNA isolated as in Sekinger, Moqtaderi, and Struhl, Mol Cell 18, 735-48 (2005).

value: Dextrose


title: CD133-H3K27me1

description:
Chromatin IP against H3K27me1
run132_lane3
run145_lane5


title: In_vitro (2 biological replicates)

description: library source : genomic

source_name: S. cerevisiae genomic DNA and histone octamer from chicken erythrocytes

growth_protocol: S. cerevisiae genomic DNA was purified from strain YLC8 using standard methods with additional methods to remove contaminating RNA.  After recovery by ethanol precipitation, the sample was resuspended in TE buffer and the DNA concentration determined by agarose gel electrophoresis using ethidium stain followed by comparison to mass standards using quantitative fluorometry.  The sample was then digested with 100µg of RNase A for every 10µg of DNA overnight at 50C and then the DNA was ethanol precipitated.  After resuspension in TE the genomic DNA was sheared twice each through a 25 gauge and then 27.5 gauge needle.  The mixture was then run out on a 1% agarose gel at 100V for 6-8 hours.  The genomic DNA band was cut out and the agarose slab was re-electrophoresed inside a dialysis bag to elute DNA.  The resulting DNA was then reconstituted into nucleosomes by salt gradient dialysis using 40µg histone octomer + 100 µg DNA in 200uL volume.  The resulting nucleosomes were then isolated by micrococcal nuclease digestion using 6x10^-3 units MNase per 10µg reconstituted DNA in 10mM Tris pH 8.0, 1mM CaCl2 for 5 min at 37C.

value: YLC8 [MAT(a) ura3(∆) leu2(∆) his3(∆) met15(∆)]

value: purified DNA


title: xrn1 rrp6 lsm1 pat1 Rep 2

description: S. cerevisiae experimental RNA


title: xrn1 rrp6 lsm1 pat1 Rep 3

description: S. cerevisiae experimental RNA


title: ski2 ski8 rrp6 Rep 4

description: S. cerevisiae experimental RNA

source_name: ski2 ski8 rrp6

value: FY23 x FY86 (Winston et al. 1995), carrying the auxotrophic markers:his3-delta200, leu2-delta1, trp1-delta63, ura3-52.  The strain contains deletions in the genes SKI2, SKI8, and RRP6.


title: xrn1 rrp6 lsm1 pat1 Rep 1

description: S. cerevisiae experimental RNA


title: ski2 ski8 rrp6 Rep 3

description: S. cerevisiae experimental RNA


title: rrp6 lsm1 pat1 Rep 4

description: S. cerevisiae experimental RNA

source_name: rrp6 lsm1 pat1

value: FY23 x FY86 (Winston et al. 1995), carrying the auxotrophic markers:his3-delta200, leu2-delta1, trp1-delta63, ura3-52.  The strain contains deletions in the genes RRP6, LSM1, and PAT1.


title: ski2 ski8 rrp6 Rep 2

description: S. cerevisiae experimental RNA


title: rrp6 lsm1 pat1 Rep 3

description: S. cerevisiae experimental RNA


title: rrp6 lsm1 pat1 Rep 2

description: S. cerevisiae experimental RNA


title: rrp6 lsm1 pat1 Rep 1

description: S. cerevisiae experimental RNA


title: Isogenic wild-type Rep 4

description: S. cereviae control RNA

source_name: Isogenic wild-type

value: FY23 x FY86 (Winston et al. 1995), carrying the auxotrophic markers:his3-delta200, leu2-delta1, trp1-delta63, ura3-52.


title: Ciona larva miR309

status: Public on Jan 18 2009

city: Corvallis

first: David

middle: Anthony

last: Hendrix

state: OR

address: 2011 Ag & Life Sciences Bldg

department: Biochemistry and Biophysics/EECS

institute: Oregon State University

description: small RNA sequenced from larva expressing exogenous D. melanogaster miR309 locus

data_processing: Each read was trimmed to optimize total read quality and to remove any 3' adapter sequence.  Trimmed reads were then aligned to the Ciona intestinalis genome (JGI V1.0) via gapless BLAST with E=0.001.

organism: Ciona intestinalis

source_name: larva

growth_protocol: Adult Ciona intestinalis animals were collected from Half Moon Bay, California and maintained in an artificial seawater tank.

extract_protocol: Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion). From ~30 µg of total RNA, only 17-25-nt RNAs were size selected via 15% denaturing PAGE. The 3’ “modban-1” adaptor (IDT) was ligated to this fraction with RNA ligase (Ambion) in the presence of ATP-free reaction buffer, and appropriately ligated RNAs were size selected via 15% denaturing PAGE. The modified RNAs were subsequently ligated to a 5’ linker (Solexa linker) in the presence of RNA ligase and reaction buffer with ATP. The resulting RNA library was reverse transcribed to a cDNA library with SuperScript II (Invitrogen).

tag: developmental stage

value: larva expressing Drosphila melanogaster miR309


title: Isogenic wild-type Rep 3

description: S. cereviae control RNA


title: ski2 ski8 rrp6 Rep 1

description: S. cerevisiae experimental RNA


title: MNase-digested DNA from HeLa S3 cells

first: Raymond

middle: K

last: Auerbach

address: 266 Whitney Ave

description:
size selected, MNase-digested genomic DNA from HeLa S3 cells
size selected for 100-200 bp

data_processing: Raw data from the Illumina Genome Analyzer and Illumina Genome Analyzer II were analyzed with Illumina’s Firecrest, Bustard and GERALD modules for image analysis, basecalling and run metrics respectively. Replicates were combined for each sample.  All reads were aligned against human genome build hg18. The PolII, Sono-Seq (large fragment, small fragment, and interferon-gamma treated), and normal IgG were scored relative to naked DNA using PeakSeq (see "Peak-Seq - Systematic Scoring of ChIP-Seq Experiments Relative to Controls by Rozowsky et al. Nature Biotechnology. In press). Signal files were created using a 200 bp sliding window for all samples other than Sono-Seq/Input DNA-Large Fragment (575 bp).  Two peak lists were created for each sample: an unfiltered list of all hits with p-value < 0.05 and a subset of this list that was filtered based upon sample tag count and enrichment versus naked DNA.  Cutoff values were scaled for each sample relative to the number of reads.  For PolII, normal mouse IgG, and Sono-Seq/Input DNA (small fragments), we required all peaks to have at least 20 sample tags and an enrichment of at least 5.0 versus the naked DNA reference.  For Sono-Seq (interferon-gamma stimulated), cutoffs of 16 sample tags and 4.0x enrichment were used.  For Sono-Seq (large fragments), cutoffs of 13 sample tags and 3.0x enrichment were used.  MNase-digested DNA was not scored.

source_name: MNase-digested DNA

growth_protocol: HeLaS3 cells were grown in Minimum Essential Medium modified for Suspension (SMEM, Invitrogen), supplemented with glutamine, 10% FBS, and antibiotics (penicillin-streptomycin) at 37C in 5% CO2, to a density of 5 x10^5 cells/ml.

extract_protocol: HeLa S3 cells were resuspended in MNase buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 1 mM CaCl2, 4% NP-40, and 1 mM DTT) and treated with 50 units of micrococcal nuclease (USB) at 37°C for 1 h.  The samples were treated with proteinase K for 2 h at 37°C, extracted twice with phenol-chloroform, and subjected to ethanol precipitation. After centrifugation, the samples were treated with RNase A (Qiagen) and centrifuged through G50 sephadex spin columns.  Each sample was treated with 30 units of calf intestinal alkaline phosphatase (NEB) for 2 h at 37°C to remove 3' phosphate groups left by the MNase.  After a second ethanol precipitation, the samples were treated with 30 units T4 polynucleotide kinase (NEB). DNA samples were run though Qiagen MinElute PCR columns, eluted with 15 μl of Qiagen buffer EB and size-selected (100-200 bp) on 2% agarose E-gels (Invitrogen).  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: HeLa S3 cells (ATCC/Snyder Lab)


title: Isogenic wild-type Rep 2

description: S. cereviae control RNA


title: Isogenic wild-type Rep 1

description: S. cereviae control RNA


title: Reconstituted and Input pool

status: Public on Dec 24 2008

description: library source: Synthetic

data_processing: The log-ratio of counts: For each oligonucleotide, we counted the number of times it was sequenced in each of the Input and Reconstituted samples. We used only oligonucleotides which appeared between 1 and 500 times in each of the samples. For each of the two replicates, we then calculated for each oligonucleotide the ratio between its counts in the Reconstituted and Input samples. Finally, we averaged the count ratios from the two replicates and took its log.

molecule: other

organism: synthetic construct

source_name: Reconstituted pool (DT and ES sequences)

extract_protocol: 170-mer oligonucleotides containing a 150 base variable sequence and a 20 bp common sequence (5’- TCTCCCTATAGTGAGTCGTA-3’) were synthesized by Agilent Technologies.  10ng (0.2pmol) of the single stranded oligo pools was double stranded via primer extension.  Briefly, 2pmol of the reverse complement of the common sequence (5’-CTAATACGACTCACTATAGGG-3’) was first annealed to the oligos.  Sequences were double stranded using 1mM dNTP, 3U T4 DNA polymerase (NEB), 5U Klenow fragment (NEB), 1X NEB2 buffer, 1X BSA, and incubated at 30°C for 30 minutes.  The reaction product was phenol:chloroform extracted, precipitated with ammonium acetate and ethanol, washed with 70% ethanol, dried, and resuspended in dH2O.  10pmol of an M13 primer duplex (5’-CAGGAAACAGCTATGAGC-3’/5’-P-GCTCATAGCTGTTTCCTG-3’) was then ligated to the double stranded oligos using 400U T4 DNA ligase (NEB) overnight at 16°C. Ligation products were end-labeled with T4 polynucleotide kinase and [γ-32P] ATP and the expected 188bp product was isolated from a 4% polyacrylamide gel.  To remove potential concatamers, ligation products were PCR amplified using extended primers containing the SwaI restriction site:  Forward primer, 5’ GCATGATCGACTGCGAATTTGATTTAAATCTAATACGACTCACTATAGGG -3’; Reverse primer,  5’-ATGACACATTATGACCAAAGATCGATTTAAATCAGGAAACAGCTATGAGC-3’.   PCR products were digested with SwaI (NEB).   The resultant 197bp product was gel purified from a 2.8% agarose gel and assembled into nucleosomes  via salt gradient dialysis,  using 6 µg histone octamer + 12 µg DNA in a 200 µl volume.  The resulting nucleosomes were separated away from the remaining naked DNA by native polyacrylamide gel electrophoresis (5% (w/v) polyacrylamide) in 1/3x TBE buffer (TBE is 90 mM Tris, 90 mM boric acid, 2 mM EDTA, pH 8.3).  The nucleosome-containing band was excised from the gel, and its DNA extracted by crushing and soaking into 0.3 M NaOAc, 0.5 M NH4OAc, 0 .1 mM EDTA, 0.1% (w/v) SDS, followed by ethanol precipitation.  For the oligos to be sequenced, common priming sites on both ends had to be removed. Restriction sites for the NruI restriction enzyme were introduced into the common sites via PCR using the following primers: 5’-GTAGAGACTATCCAGGAAATCGCGATGAGC-3’(forward),  5’-CTAGAACAGACTAATACGACTCGCGATAGGG-3’ (reverse).  PCR products were digested with NruI to obtain a 169 bp digestion product, which was gel purified and sent for sequencing.

tag: Nucleosome-reconstituted pool

tag: synthetic oligonucleotide

value: mononucleosome

label: not applicable

source_name: Input pool (DT and ES sequences)

label_protocol: not applicable

tag: Starting oligonucleotide pool (before nucleosome reconstitution)

tag: Synthetic oligonucleotide:Input


title: Locusta migratoria gregarious sRNA

status: Public on Jan 16 2009

city: Beijing

first: Yuanyuan

last: Wei

address: Datun Road, Chaoyang District

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing: extraction of sequences flanked by perfect matches to the expected adjacent adapter sequences

organism: Locusta migratoria

source_name: Locusta migratoria gregarious sRNA

extract_protocol: total RNA extracted using standard Trizol extraction, ~18-30nt RNAs isolated using PAGE, 3' and 5' adaptors sequentially ligated

tag: Locusta migratoria_gregarious whole body except midgut (mixure of all developmental stages) 18-30 nt


title: Large fragment Sono-Seq DNA (350-800 bp)

description:
size selected, sonicated, crosslinked chromatin from HeLa S3 cells
size selected for 350-800 bp

source_name: Sono-Seq DNA (350-800 bp)

extract_protocol: HeLa S3 cells were fixed with 1% formaldehyde at room temperature for 10 min and the fixation was terminated by the addition of glycine to a final concentration of 125 mM. The fixed cells were washed in cold 1x Dulbecco’s PBS (Invitrogen) and swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8.0, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x108 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle for 7x 30 s intervals) to an average size of less than 500 bp as verified on a 2% agarose gel. Lysates were then clarified by centrifugation for 15 min at 20,000 xg at 4°C. For Sono-Seq DNA, aliquots of clarified lysate were reserved for reversal of crosslinking, followed by RNase and proteinase K treatments. Sono-Seq DNA was further purified by phenol-chloroform extraction and ethanol precipitation. DNA samples were run though Qiagen MinElute PCR columns, eluted with 15 μl of Qiagen buffer EB and size-selected (350-800 bp) on 2% agarose E-gels (Invitrogen).  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: HeLa S3 cells (ATCC/National Cell Culture Center)


title: Naked DNA from HeLa S3 cells

description:
size selected, sonicated genomic DNA from deproteinized HeLa S3 cells
size selected for 100-350 bp

source_name: Naked DNA

extract_protocol: HeLa S3 cells were collected by centrifugation, resuspended in digestion buffer (100 mM NaCl, 10 mM Tris-HCl, pH 8.0, 25 mM EDTA pH 8.0 and 0.5% SDS) and digested overnight at 50°C with 0.1 mg/ml proteinase K (Ambion, Austin, TX). The digest was extracted twice with phenol-chloroform, once with chloroform and ethanol precipitated. The DNA was recovered, treated with RNase (Qiagen) for 3 h at 37°C, extracted once with phenol-chloroform, once with chloroform, ethanol precipitated and resuspended at 2.5 x 108 cell equivalents in 5 ml of 1x TE pH 7.5 (10 mM Tris, 1 mm EDTA). A 2.5 ml aliquot was sonicated once for 30 s with a Branson 250 Sonifier (power setting 2, 100% duty cycle) to an average size of less than 500 bp as verified on a 2% agarose gel. DNA samples were run though Qiagen MinElute PCR columns, eluted with 15 μl of Qiagen buffer EB and size-selected (100-350 bp) on 2% agarose E-gels (Invitrogen).  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: Normal Mouse IgG ChIP

description:
size selected, normal mouse IgG ChIP DNA from HeLa S3 cells
size selected for 100-350 bp

source_name: Normal Mouse IgG ChIP

extract_protocol: HeLa S3 cells were fixed with 1% formaldehyde at room temperature for 10 min and the fixation was terminated by the addition of glycine to a final concentration of 125 mM. The fixed cells were washed in cold 1x Dulbecco’s PBS (Invitrogen) and swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8.0, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x108 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle for 7x 30 s intervals) to an average size of less than 500 bp as verified on a 2% agarose gel. Lysates were then clarified by centrifugation for 15 min at 20,000 xg at 4°C. For normal mouse IgG ChIP samples, 12 mg of normal mouse IgG (Santa-Cruz sc-2025) were added to 1 x108 cells. Chromatin immunoprecipitations were conducted as previously described (Hartman et al. 2005; Euskirchen et al. 2007). The IgG ChIP DNA samples were run though Qiagen MinElute PCR columns, eluted with 15 μl of Qiagen buffer EB and size-selected (100-350 bp) on 2% agarose E-gels (Invitrogen).  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: DH 18_RNAPII_Day6_3T3L1_ChIP-seq

status: Public on Dec 10 2008

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

description:
Chromatin IP against RNAPII
Antibody RNAPII
Day of adipocyte differentiation

data_processing: Reads (32 bp) were aligned to the Mouse (Mus muscules) reference genome. The July 2007 mouse (Mus musculus) genome data were obtained from the Build 37 assembly by NCBI and the Mouse Genome Sequencing Consortium. . RNAPII tracks for the different days were equalized for the total number of mapped tags by random removal of sequenced tags. The same was done for the transcription factor binding sites. For PPARg and RXR, enriched intervals were identified using Findpeaks. For RNAPII number of tags within ENSEMBLE genes (from +250 from TSS to end of gene) were counted and gene regulation was expressed as ratio of tags on a given day divided by tags in same gene region on day 0.

source_name: 3T3L1 cells

growth_protocol: 3T3-L1 fibroblasts were differentiated to adipocytes by standard DMI procedure (stimulation with 3-isobutyl-1-methylxanthine, dexamethasone, and insulin; Helledie et al., 2002, J. Biol. Chem. 277: 26821-26830).

extract_protocol: Chromatin was harvested at Day0, 1, 2, 3, 4 and 6 during adipocyte differentiation. Chromatin was fixed in 1% formaldehyde for 10 minutes, sonicated for 8x30sec at high power using a Bioruptor (Diagenode), immunoprecipitated PPARg (Sc-7196, Santa Cruz), RXR (Sc-774, Santa Cruz) and RNAPII ((AC-0555-100, Diagenode) antibodies, purified and sequenced using Illumina Genome Analyzer as recommended by the manufacturer.

tag: DMI induced day6


title: DH 16_RNAPII_Day3_3T3L1_ChIP-seq

tag: DMI induced day3


title: DH 13_RNAPII_Day0_3T3L1_ChIP-seq

tag: DMI induced day0


title: DH 12_RXR_Day6_3T3L1_ChIP-seq

description:
Chromatin IP against RXR
Antibody RXR
Day of adipocyte differentiation


title: DH 14_RNAPII_Day1_3T3L1_ChIP-seq

tag: DMI induced day1


title: DH 11_RXR_Day4_3T3L1_ChIP-seq

tag: DMI induced day4


title: DH 10_RXR_Day3_3T3L1_ChIP-seq


title: Ciona Adult

description: small RNA sequenced from Adult

source_name: Adult

value: adult


title: DH 9_RXR_Day2_3T3L1_ChIP-seq

tag: DMI induced day2


title: DH 8_RXR_Day1_3T3L1_ChIP-seq


title: Locusta migratoria solitary sRNA

source_name: Locusta migratoria solitary sRNA

tag: Locusta migratoria_solitary whole body except midgut (mixure of all developmental stages) 18-30 nt

tag: phase

value: solitary

tag: tissue

value: whole body except midgut

tag: stage

value: mixture of all developmental stages (including embryoes, larva, and adults)


title: DH 6_PPARg_Day6_3T3L1_ChIP-seq

description:
Chromatin IP against PPARg
Antibody PPARg
Day of adipocyte differentiation


title: DH 7_RXR_Day0_3T3L1_ChIP-seq


title: DH 17_RNAPII_Day4_3T3L1_ChIP-seq


title: DH 5_PPARg_Day4_3T3L1_ChIP-seq


title: DH 1_PPARg_Day0_3T3L1_ChIP-seq


title: Ciona Egg

description: small RNA sequenced from unfertilized egg

data_processing: Each read was trimmed to optimize total read quality and to remove any 3' adapter sequence.  Trimmed reads were then aligned to the Ciona intestinalis genome (JGI V1.0) via gapless BLAST with E=0.01.

source_name: Unfertilized egg

tag: developmental stage

value: egg


title: DH 3_PPARg_Day2_3T3L1_ChIP-seq


title: DH 2_PPARg_Day1_3T3L1_ChIP-seq


title: GRO-seq rep2

status: Public on Dec 04 2008

city: Ithaca

first: Leighton

middle: James

last: Core

address: 417 Biotechnology Building

department: Moleular Biology and Genetics

institute: Cornell University

description:
Nuclear run on with 5-BromoUTP for immunopurification
Supplementary Raw data files :lib2_s6_tag.txt
lib2_s6_sequence.txt.gz
lib2_s7_tag.txt.gz
lib2_s7_sequence.txt.gz
lib2_s8_tag.txt.gz
lib2_s8_sequence.txt.gz

data_processing: Reads were aligned with ELAND to the hg18 non-repeat masked reference human genome and alignments to rDNA repeats were then removed.

molecule: nuclear RNA

source_name: primary lung fibroblasts

growth_protocol: Cells are maintained in Minimal essential medium (Eagle) with Earle's balance salt solution, 2mM L-glutamine, 1mM sodium pyruvate, 1.5 g/L sodium bicarbonate, 0.1mM non-essential amino acids, and 10% fetal bovine serum.  Cells are grown at 37 degrees Celsius at 5% CO2.  Cells were harvested at 80% confluency for all assays.

extract_protocol: Nuclei isolation and run-on reactions are performed using standard protocols with the exception that 5-Bromo-UTP is used in place UTP, and the concentration of CTP is adjusted to 1µM.  Samples are treated with Rnase-free RQ1 DNase (promega) and Proteinase K (invitrogen). RNA is then extracted twice with Leder phenol and once with chloroform, then precipitated.  Isolated RNA is then base hydrolyzed to the desired size and RNA fragments are then isolated by binding to anti-deoxy-BrU beads, washed several times, and eluted from the beads.  The RNAs are treated at low pH with tobacco acid pyrophosphatase and then are treated at low pH with T4 polynucleotide kinase (PNK).  The pH is then raised and the RNA is treated again with PNK, except now in the presence of ATP.  A standard Illumina adapter is then added to the 5’-end with T4-RNA ligase and the RNA is bound to anti-deoxy-BrU beads.  This process is then repeated for the addition of the Illumina 3’-adapter.  The affinity-enriched RNAs are then reverse transcribed, amplified, and PAGE purified.  This cDNA was then sequenced on the Illumina Genome Analyzer.

tag: cell line

value: lung

tag: antibody

value: Br-dUTP


title: DH 4_PPARg_Day3_3T3L1_ChIP-seq


title: DH 15_RNAPII_Day2_3T3L1_ChIP-seq


title: Ciona Early Embryo

description: small RNA sequenced from early embryo

source_name: Early embryo

value: early embryo


title: Ovary_rep1_NA(fem)_x_Har(male)_F1

status: Public on Nov 28 2008

city: New York

first: Colin

middle: Dean

last: Malone

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

department: Skirball Institute - Developmental Genetics

institute: NYU Medical Center

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

organism: Drosophila melanogaster

source_name: Ovary, female progeny of a cross between strain Na (female) and Harwich (male), 3-5 days old, 24 degrees C

growth_protocol: 21 or 24 degrees C

extract_protocol: Trizol

treatment_protocol: Trizol/Phenol Cholorofom extractions

tag: female progeny of a cross between strain Na (female) and Harwich (male), females, 3-5 days old


title: Ovary_rep1_LK(fem)_x_Har(male)_F1

source_name: Ovary, female progeny of a cross between strain LK (female) and Harwich (male), 3-5 days old, 24 degrees C

tag: female progeny of a cross between strain LK (female) and Harwich (male), females, 3-5 days old


title: Ovary_rep1_w1118(fem)_x_Har(male)_F1

source_name: Ovary, female progeny of a cross between strain w1118 (female) and Harwich (male), 3-5 days old, 24 degrees C

tag: female progeny of a cross between strain w1118 (female) and Harwich (male), females, 3-5 days old


title: Ovary_rep1_wK(fem)_x_w1118(male)_F1

source_name: Ovary, female progeny of a cross between strain wK (female) and w1118 (male), 3-5 days old, 21 degrees C

tag: female progeny of a cross between strain wK (female) and w1118 (male), females, 3-5 days old


title: Ovary_rep1_w1118(fem)_x_wK(male)_F1

source_name: Ovary, female progeny of a cross between strain w1118 (female) and wK (male), 3-5 days old, 21 degrees C

tag: female progeny of a cross between strain w1118 (female) and wK (male), females, 3-5 days old


title: Embryo_0-2hrs_rep1_wK_0_2hr_Emb

source_name: Embryos, strain wK, 0-2hrs post-laying embryos, 21 degrees C

tag: strain wK, females, 0-2hrs post-laying


title: GRO-seq rep 1

description:
Nuclear run on with 5-BromoUTP for immunopurification
Supplementary Raw data files :lib1_s6_tag.txt
lib1_s6_sequence.txt.gz
lib1_s7_tag.txt.gz
lib1_s7_sequence.txt.gz
lib1_s8_tag.txt.gz
lib1_s8_sequence.txt.gz


title: Ovary_rep1_NA_P

source_name: Ovary, strain NA, 3-5 day old ovaries, 24 degrees C

tag: strain NA, females, 3-5 days old


title: Embryo_0-2hrs_rep1_w1118_0_2hr_Emb

source_name: Embryos, strain w1118, 0-2hrs post-laying embryos, 21 degrees C

tag: strain w1118, females, 0-2hrs post-laying


title: Ciona Late Embryo

description: small RNA sequenced from Late Embryo

source_name: Late Embryo

value: late embryo


title: Ovary_rep1_LK_P

source_name: Ovary, strain LK, 3-5 day old ovaries, 24 degrees C

tag: strain LK, females, 3-5 days old


title: Ovary_rep1_Har_P

source_name: Ovary, strain Harwich, 3-5 day old ovaries, 24 degrees C

tag: strain Harwich, females, 3-5 days old


title: Ovary_rep1_wK_P

source_name: Ovary, strain wK, 3-5 day old ovaries, 21 degrees C

tag: strain wK, females, 3-5 days old


title: Drosophila melanogaster S2-GMR, second biological replicate

first: Nicolas

last: Robine

address: 1275 York Avenue, Box 252

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description: Small RNA data.

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

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: S2 cells from Gerard Rubin's lab


title: Ovary_rep1_w1118_P

source_name: Ovary, strain w1118, 3-5 day old ovaries, 21 degrees C

tag: strain w1118, females, 3-5 days old


title: skeletal muscle

status: Public on Nov 19 2008

city: Toronto

first: Weijun

last: Gao

address: 10 King's College Rd.

country: Canada

institute: University of Toronto

data_processing: not applicable

source_name: Human skeletal muscle tissue

extract_protocol: mRNA is purified from total RNA with oligo-dT magnetic beads. cDNA is synthesized with random primer priming. ds-cDNA is sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

tag: individual human skeletal muscle


title: lung

source_name: Human lung tissue

tag: individual human lung


title: liver

source_name: Human liver tissue

tag: individual human liver


title: brain

source_name: Human brain tissue

tag: individual human brain


title: Medicago_truncatula_sample1

status: Public on Dec 11 2008

city: Norwich

first: Simon

last: Moxon

state: Norfolk

address: University of East Anglia

country: United Kingdom

institute: University of East Anglia

description: Total endogenous small RNAs from Medicago truncatula Gaertn. cv. Jemalong seedlings

data_processing: Removed adaptors. Sequences without adapters were discarded.

organism: Medicago truncatula

source_name: Medicago truncatula Gaertn. cv. Jemalong leaves and stem

growth_protocol: Plants were grown in pots with soil in a growth chamber having a photoperiod of 16/8h day/night, a thermoperiod of 25/18ºC day/night and humidity of 40%.

extract_protocol: Total RNA was extracted from the aerial part (including stems and leaves) of nine week old Medicago truncatula Gaertn. cv. Jemalong seedlings

tag: RNA extracted from stems and leaves


title: endogenous small RNA associated to human Argonaute 1

status: Public on Nov 21 2008

city: Martinsried

first: Gunter

last: Meister

address: Am Klopferspitz 18

department: Center for Integrated Protein Science Munich (CIPSM)

country: Germany

institute: Max Planck Institute of Biochemistry

data_processing: Processed data file contains the reads with 5' and 3' adapters removed

source_name: HEK293 cells

extract_protocol: Argonaute complexes were immunoprecipitated with beads coated with anti-Ago1 or anti-Ago2 complexes. RNA was isolated by adding 40 μg  Proteinase K in 200 μl Proteinase K buffer (300 mM NaCl, 25 mM EDTA, 2% SDS, 200 mM  Tris HCl pH 7.5) directly onto beads followed by Phenol/Chloroform extraction and Ethanol precipitation. Small RNA cloning was performed by Vertis Biotechnologie AG (Weihenstephan, Germany)

tag: antibody

value: anti-Ago1 4B8


title: Embryo_0-2hrs_rep1_LK_0_2hr_Emb

source_name: Embryos, strain LK, females, 0-2hrs post-laying embryos, 24 degrees C

tag: strain LK, females, 0-2hrs post-laying


title: cerebral cortex

source_name: Human cerebral cortex tissue

tag: individual human cerebral cortex


title: heart

source_name: Human heart tissue

tag: individual human heart


title: endogenous small RNA associated to human Argonaute 2

value: anti-Ago2 11A9


title: whole_fly_rp_rep1

status: Public on Nov 04 2008

city: St Louis

first: Marijke

middle: Jeltje

last: van Baren

state: MO

address: One Brookings Drive

department: CSE

institute: Washington University

description: Double Stranded cDNA, Random Primed, run using a 2 p-mol concentration

data_processing: Reads were aligned to the genome and also to the predicted transcripts so that splice sites were included.

source_name: whole fly - ds-cDNA - random-primed - 2pmol

growth_protocol: M3+BPYE + 5% FCS,CCM3

extract_protocol: TRIzol Dnase Rneasy

tag: Whole mixed sex adult flies, pooled


title: whole_fly_rp_rep2


title: whole_fly_odt_2pmol

description: Single Stranded cDNA, Oligo-DT Primed, run using a 2 p-mol concentration

source_name: whole fly - ss-cDNA - oligo-dt-primed - 2pmol


title: whole_fly_odt_4pmol

description: Single Stranded cDNA, Oligo-DT Primed, run using a 4 p-mol concentration

source_name: whole fly - ss-cDNA - oligo-dt-primed - 4pmol


title: whole_fly_odt_1pmol

description: Single Stranded cDNA, Oligo-DT Primed, run using a 1 p-mol concentration

source_name: whole fly - ss-cDNA - oligo-dt-primed - 1pmol


title: Drosophila Toll 10b mutant embryos

description: small RNA sequenced from Toll 10b mutant embryos

source_name: Toll 10b mutant embryos

tag: developmental stage

value: embryo

tag: genotype

value: Toll 10b mutant


title: mES_RING1B_ChIPSeq

status: Public on Nov 01 2008

city: Cambridge

first: Tarjei

middle: S

last: Mikkelsen

state: MA

address: 7 Cambridge Center

institute: Broad Institute

description: Chromatin IP against Ring1b

data_processing: Primary sequence data were filtered and aligned as described in (Mikkelsen et al. 2007, PMID 17603471).

source_name: Chromatin IP against Ring1b

growth_protocol: Embryonic stem cells were cultured as described in (Mikkelsen et al. 2007, PMID 17603471) and (Thomson et al. 1998, PMID 9804556 )

extract_protocol: All ChIP experiments were performed as described in (Mikkelsen et al. 2007, PMID 17603471), except for Suz12 and Ezh2, for which an additional nucleus isolation step was included, as described in (Weinmann et al. 2001, PMID 11564866).

tag: Embyonic stem cells (V6.5)

value: 129SvJae x C57BL/6


title: mES_EZH2_ChIPSeq

description: Chromatin IP against Ezh2

source_name: Chromatin IP against Ezh2


title: hES_RING1B_ChIPSeq

description: Chromatin IP against RING1B

source_name: Chromatin IP against RING1B

tag: Embyonic stem cells

tag: line

value: H9 (passage 45)


title: hES_EZH2_ChIPSeq

description: Chromatin IP against EZH2

source_name: Chromatin IP against EZH2


title: mES_SUZ12_ChIPSeq

description: Chromatin IP against Suz12

source_name: Chromatin IP against Suz12


title: hES_H3K36me3_ChIPSeq

description: Chromatin IP against H3K36me3

source_name: Chromatin IP against H3K36me3


title: hES_H3K27me3_ChIPSeq

description: Chromatin IP against H3K27me3

source_name: Chromatin IP against H3K27me3


title: hES_H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3

source_name: Chromatin IP against H3K4me3


title: Embryo_0-2hrs_rep1_HAR_0_2hr_Emb

source_name: Embryos, strain Harwich, 0-2hrs post-laying embryos, 24 degrees C

tag: strain Harwich, females, 0-2hrs post-laying


title: Scp160_(2)_oligo_EDTA_RBP40paper

status: Public on Oct 28 2008

type: RNA

first: Daniel

last: Hogan

address: 279 Campus Dr B439

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65974.gif
Genotype: Scp160

hyb_protocol: not provided

scan_protocol: Scanning software = AxImageIO; Scanner Make = Axon Instruments (V1.00)

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: total rna extract

label_protocol: Gerber et al. (2004) PLoS Biology; The protocol can be accessed from the web-site; Protocol Type = Extract preparation; Performer: Andre,,Gerber

extract_protocol: not provided

tag: total rna extract

source_name: affinity purified rna

tag: affinity purified rna


title: Cbf5_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67907.gif
Genotype: Cbf5

source_name: CBF5-TAP total RNA from extract

tag: CBF5-TAP total RNA from extract

source_name: CBF5-TAP affinity purified RNA

tag: CBF5-TAP affinity purified RNA


title: Medicago_truncatula_sample2

source_name: Medicago truncatula Gaertn. cv. Jemalong leaves and stem


title: Gbp2_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67857.gif
Genotype: Gbp2

source_name: GBP2-TAP total RNA from extract

tag: GBP2-TAP total RNA from extract

source_name: GBP2-TAP affinity purified RNA

tag: GBP2-TAP affinity purified RNA


title: Puf3_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67846.gif
Genotype: Puf3

source_name: PUF3-TAP total RNA from extract

tag: PUF3-TAP total RNA from extract

source_name: PUF3-TAP affinity purified RNA

tag: PUF3-TAP affinity purified RNA


title: Col-0 biological replicate 3

status: Public on Nov 17 2008

city: Saint Louis

first: James

middle: C

last: Carrington

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: Col-0 biological replicate 3

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 were included in the analysis.

organism: Arabidopsis thaliana

source_name: Inflorescence tissue: flower stages 1-12

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 Inflorescence tissue (flower stages 1-12) 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.

tag: Col-0 ecotype


title: Pub1_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67866.gif
Genotype: Pub1

source_name: PUB1-TAP total RNA from extract

tag: PUB1-TAP total RNA from extract

source_name: PUB1-TAP affinity purified RNA

tag: PUB1-TAP affinity purified RNA


title: Cbc2_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67856.gif
Genotype: Cbc2

source_name: CBC2-TAP total RNA from extract

tag: CBC2-TAP total RNA from extract

source_name: CBC2-TAP affinity purified RNA

tag: CBC2-TAP affinity purified RNA


title: Msl5_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65976.gif
Genotype: Msl5


title: Nrd1_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67875.gif
Genotype: Nrd1

source_name: NRD1-TAP total RNA from extract

tag: NRD1-TAP total RNA from extract

source_name: NRD1-TAP affinity purified RNA

tag: NRD1-TAP affinity purified RNA


title: Nsr1_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67901.gif
Genotype: Nsr1

source_name: NSR1-TAP total RNA from extract

tag: NSR1-TAP total RNA from extract

source_name: NSR1-TAP affinity purified RNA

tag: NSR1-TAP affinity purified RNA


title: Embryo_0-2hrs_rep1_NA_0_2hr_Emb

source_name: Embryos, strain NA, females, 0-2hrs post-laying embryos, 24 degrees C

tag: strain NA, females, 0-2hrs post-laying


title: ago1-25 biological replicate 1

description: ago1-25 biological replicate 1

tag: Col-0 ecotype, ago1-25 homozygous plants


title: Nce102_(4)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67913.gif
Genotype: Nce102

source_name: NCE102-TAP total RNA from extract

tag: NCE102-TAP total RNA from extract

source_name: NCE102-TAP affinity purified RNA

tag: NCE102-TAP affinity purified RNA


title: Col-0 biological replicate 1

description: Col-0 biological replicate 1


title: S2R+ (biological replicate 2)

description: Small RNA data.

source_name: Drosophila melanogaster S2R+ cells

tag: S2R+ cells


title: mid-L3 hermaphrodites

status: Public on Dec 01 2008

city: New Haven

first: Frank

middle: J

last: Slack

department: MCDB

institute: Yale University

description: RNA enriched for small RNA species (<200nt)

data_processing: Sequences were read and raw counts reported.

growth_protocol: Wild-type N2 strains were cultured under standard conditions at 20dC and used to prepare RNAs from each developmental stage (time after staged L1; mid-L3 (4hrs), mid-L3 (14hrs), mid-L3 (25hrs), mid-L4 (36hrs) and young adult (48hrs). For library preparation from males and spermatogenesis-hermaphrodites, dpy-28;him-8 double mutants and spe-9 mutants were cultured at 23dC, respectively, and  RNAs were prepraed from these two strains at 40hrs after staged L1.

extract_protocol: RNAs enriched for small RNA species (less than 200nt) were prepared using the mirVana miRNA Isolation kit (Ambion) with small RNA enrichment procedure. cDNA libraries for small RNAs were made from 10 µg of RNA using the DGE-Small RNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

tag: strain

value: wild-type N2_hermaphrodites

tag: developmental stage

tag: growth condition


title: Ypl184c_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67879.gif
Genotype: Ypl184c

source_name: YPL184C-TAP total RNA from extract

tag: YPL184C-TAP total RNA from extract

source_name: YPL184C-TAP affinity purified RNA

tag: YPL184C-TAP affinity purified RNA


title: young adult spe-9 hermaphrodites

source_name: young adult spe-9

growth_protocol: Wild-type N2 strains were cultured under standard conditions at 20dC and used to prepare RNAs from each developmental stage (time after staged L1; young adult (4hrs), young adult (14hrs), young adult (25hrs), young adult (36hrs) and young adult (48hrs). For library preparation from males and spermatogenesis-hermaphrodites, dpy-28;him-8 double mutants and spe-9 mutants were cultured at 23dC, respectively, and  RNAs were prepraed from these two strains at 40hrs after staged L1.

value: young adult


title: young adult hermaphrodites

source_name: young adult_hermaphrodites


title: RNAP2_mES_rep1

first: Stuart

last: Levine

address: Nine Cambridge Center

institute: Whitehead Institute

description:
V6.5 murine ES cells were cultured as described in Boyer et al., Nature 2006.
Antibody:RNAP2 8WG16

data_processing: Images analysis and base calling was done using solexa pipeline and reads aligned to both mouse NCBI build 36 using ELAND.  For ChIP-Seq, sequences from all lanes were extended 200bp (maximum fragment length accounting for ~100bp of primer sequence), and allocated into 25 bp bins.  Genomic bins containing statistically significant ChIP-seq enrichment were identified by comparison to a Poissonian background model, using a p-value threshold of 10-9.  Additionally, we used an empirical background model obtained from identical Solexa sequencing of DNA from whole cell extract (WCE) from matched cell samples (>5X normalized enrichment across the entire region).

source_name: RNAP2 IP

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs).  For location analysis, cells were grown for one passage off of MEFs, on gelatinized tissue-culture plates. Mouse embryonic fibroblasts were prepared and cultured from DR-4 strain mice.

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

treatment_protocol: Ref. to manuscript

tag: embryonic stem cells


title: Col-0 biological replicate 2

description: Col-0 biological replicate 2

source_name: Inflorescence tissue: flower stages 1-12

tag: Col-0 ecotype


title: ago1-25 biological replicate 3

description: ago1-25 biological replicate 3


title: S2R+ (biological replicate 1)

description: Small RNA data.


title: young adult males

source_name: young adult_males


title: embryo hermaphrodites

growth_protocol: Wild-type N2 strains were cultured under standard conditions at 20dC and used to prepare RNAs from each developmental stage (time after staged L1; mid-L1 (4hrs), mid-L2 (14hrs), mid-L3 (25hrs), mid-L4 (36hrs) and young adult (48hrs). For library preparation from males and spermatogenesis-hermaphrodites, dpy-28;him-8 double mutants and spe-9 mutants were cultured at 23dC, respectively, and  RNAs were prepraed from these two strains at 40hrs after staged L1.

value: Embryo


title: mid-L2 hermaphrodites

growth_protocol: Wild-type N2 strains were cultured under standard conditions at 20dC and used to prepare RNAs from each developmental stage (time after staged L1; mid-L2 (4hrs), mid-L2 (14hrs), mid-L3 (25hrs), mid-L4 (36hrs) and young adult (48hrs). For library preparation from males and spermatogenesis-hermaphrodites, dpy-28;him-8 double mutants and spe-9 mutants were cultured at 23dC, respectively, and  RNAs were prepraed from these two strains at 40hrs after staged L1.


title: Ssd1_(2)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65967.gif
Genotype: Ssd1

source_name: total rna extract

tag: total rna extract

source_name: affinity purified rna

tag: affinity purified rna


title: Gbp2_(2)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67925.gif
Genotype: Gbp2

source_name: GBP2-TAP total RNA from extract

tag: GBP2-TAP total RNA from extract

source_name: GBP2-TAP affinity purified RNA

tag: GBP2-TAP affinity purified RNA


title: Nce102_(3)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67911.gif
Genotype: Nce102


title: Idh1_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67890.gif
Genotype: Idh1

source_name: IDH1-TAP total RNA from extract

tag: IDH1-TAP total RNA from extract

source_name: IDH1-TAP affinity purified RNA

tag: IDH1-TAP affinity purified RNA


title: Scp160_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67904.gif
Genotype: Scp160

source_name: SCP160-TAP total RNA from extract

tag: SCP160-TAP total RNA from extract

source_name: SCP160-TAP affinity purified RNA

tag: SCP160-TAP affinity purified RNA


title: Tdh3_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67896.gif
Genotype: Tdh3

source_name: TDH3-TAP total RNA from extract

tag: TDH3-TAP total RNA from extract

source_name: TDH3-TAP affinity purified RNA

tag: TDH3-TAP affinity purified RNA


title: Pin4_(3)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67888.gif
Genotype: Pin4

source_name: PIN4-TAP total RNA from extract

tag: PIN4-TAP total RNA from extract

source_name: PIN4-TAP affinity purified RNA

tag: PIN4-TAP affinity purified RNA


title: Npl3_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65980.gif
Genotype: Npl3


title: Puf3_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67868.gif
Genotype: Puf3

source_name: PUF3-TAP total RNA from extract

tag: PUF3-TAP total RNA from extract

source_name: PUF3-TAP affinity purified RNA

tag: PUF3-TAP affinity purified RNA


title: Nrp1_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67880.gif
Genotype: Nrp1

source_name: NRP1-TAP total RNA from extract

tag: NRP1-TAP total RNA from extract

source_name: NRP1-TAP affinity purified RNA

tag: NRP1-TAP affinity purified RNA


title: Dhh1_(1)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67922.gif
Genotype: Dhh1

source_name: DHH1-TAP total RNA from extract

tag: DHH1-TAP total RNA from extract

source_name: DHH1-TAP affinity purified RNA

tag: DHH1-TAP affinity purified RNA


title: Scp160_(1)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65973.gif
Genotype: Scp160

source_name: total rna extract

tag: total rna extract

source_name: affinity purified rna

tag: affinity purified rna


title: ago1-25 biological replicate 2

description: ago1-25 biological replicate 2

source_name: Inflorescence tissue: flower stages 1-12

tag: Col-0 ecotype, ago1-25 homozygous plants


title: mid-L1 hermaphrodites

tag: strain

tag: developmental stage

tag: growth condition


title: Nab2_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67848.gif
Genotype: Nab2

source_name: NAB2-TAP total RNA from extract

tag: NAB2-TAP total RNA from extract

source_name: NAB2-TAP affinity purified RNA

tag: NAB2-TAP affinity purified RNA


title: Rna15_(3)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67882.gif
Genotype: Rna15

source_name: RNA15-TAP total RNA from extract

tag: RNA15-TAP total RNA from extract

source_name: RNA15-TAP affinity purified RNA

tag: RNA15-TAP affinity purified RNA


title: Ypl184c_(3)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67849.gif
Genotype: Ypl184c

source_name: YPL184C-TAP total RNA from extract

tag: YPL184C-TAP total RNA from extract

source_name: YPL184C-TAP affinity purified RNA

tag: YPL184C-TAP affinity purified RNA


title: Puf1 IP (3)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36821.gif
Genotype: Puf1

source_name: Puf1 tot. RNA extract (3)

tag: Puf1 tot. RNA extract (3)

source_name: Puf1 RNA-IP (3)

tag: Puf1 RNA-IP (3)


title: Rib2_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67918.gif
Genotype: Rib2

source_name: RIB2-TAP total RNA from extract

tag: RIB2-TAP total RNA from extract

source_name: RIB2-TAP affinity purified RNA

tag: RIB2-TAP affinity purified RNA


title: Puf3 IP (3)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36813.gif
Genotype: Puf3

source_name: Puf3 tot. RNA extract (3)

tag: Puf3 tot. RNA extract (3)

source_name: Puf3 RNA-IP (3)

tag: Puf3 RNA-IP (3)


title: Puf4 IP (3)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36826.gif
Genotype: Puf4

source_name: Puf4 tot. RNA extract (3)

tag: Puf4 tot. RNA extract (3)

source_name: Puf4 RNA-IP (3)

tag: Puf4 RNA-IP (3)


title: Puf5 IP (4)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36815.gif
Genotype: Puf5

source_name: Puf5 tot. RNA extract (4)

tag: Puf5 tot. RNA extract (4)

source_name: Puf5 RNA-IP (4)

tag: Puf5 RNA-IP (4)


title: Puf1 IP (2)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36819.gif
Genotype: Puf1

source_name: Puf1 tot. RNA extract (2)

tag: Puf1 tot. RNA extract (2)

source_name: Puf1 RNA-IP (2)

tag: Puf1 RNA-IP (2)


title: Msl5_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65978.gif
Genotype: Msl5

source_name: total rna extract

tag: total rna extract

source_name: affinity purified rna

tag: affinity purified rna


title: Cbf5_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67909.gif
Genotype: Cbf5

source_name: CBF5-TAP total RNA from extract

tag: CBF5-TAP total RNA from extract

source_name: CBF5-TAP affinity purified RNA

tag: CBF5-TAP affinity purified RNA


title: Nsr1_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67862.gif
Genotype: Nsr1

source_name: NSR1-TAP total RNA from extract

tag: NSR1-TAP total RNA from extract

source_name: NSR1-TAP affinity purified RNA

tag: NSR1-TAP affinity purified RNA


title: Npl3_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67917.gif
Genotype: Npl3

source_name: NPL3-TAP total RNA from extract

tag: NPL3-TAP total RNA from extract

source_name: NPL3-TAP affinity purified RNA

tag: NPL3-TAP affinity purified RNA


title: Nop56_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67894.gif
Genotype: Nop56

source_name: SIK1-TAP total RNA from extract

tag: SIK1-TAP total RNA from extract

source_name: SIK1-TAP affinity purified RNA

tag: SIK1-TAP affinity purified RNA


title: Ssd1_(3)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67874.gif
Genotype: Ssd1

source_name: SSD1-TAP total RNA from extract

tag: SSD1-TAP total RNA from extract

source_name: SSD1-TAP affinity purified RNA

tag: SSD1-TAP affinity purified RNA


title: Idh1_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67843.gif
Genotype: Idh1

source_name: IDH1-TAP total RNA from extract

tag: IDH1-TAP total RNA from extract

source_name: IDH1-TAP affinity purified RNA

tag: IDH1-TAP affinity purified RNA


title: Upf1_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67910.gif
Genotype: Upf1

source_name: UPF1-TAP total RNA from extract

tag: UPF1-TAP total RNA from extract

source_name: UPF1-TAP affinity purified RNA

tag: UPF1-TAP affinity purified RNA


title: Untagged_BY4741_(6)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67886.gif
Genotype: control

source_name: MOCK total RNA from extract

tag: MOCK total RNA from extract

source_name: MOCK affinity purified RNA

tag: MOCK affinity purified RNA


title: Bfr1_(2)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67921.gif
Genotype: Bfr1

source_name: BFR1-TAP total RNA from extract

tag: BFR1-TAP total RNA from extract

source_name: BFR1-TAP affinity purified RNA

tag: BFR1-TAP affinity purified RNA


title: Puf4 IP (2)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36825.gif
Genotype: Puf4

source_name: Puf4 tot. RNA extract (2)

tag: Puf4 tot. RNA extract (2)

source_name: Puf4 RNA-IP (2)

tag: Puf4 RNA-IP (2)


title: Nab3_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67887.gif
Genotype: Nab3

source_name: NAB3-TAP total RNA from extract

tag: NAB3-TAP total RNA from extract

source_name: NAB3-TAP affinity purified RNA

tag: NAB3-TAP affinity purified RNA


title: Puf2 IP (4)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36823.gif
Genotype: Puf2

source_name: Puf2 tot. RNA extract (4)

tag: Puf2 tot. RNA extract (4)

source_name: Puf2 RNA-IP (4)

tag: Puf2 RNA-IP (4)


title: BY4741 mock (1)

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36816.gif
Genotype: control

source_name: BY4741 tot. RNA extract (1)

tag: BY4741 tot. RNA extract (1)

label_protocol:
Gerber et al. (2004) PLoS Biology; The protocol can be accessed from the web-site; Protocol Type = Extract preparation; Performer: Andre,,Gerber
Gerber et al. (2004) PLoS Biology; The protocol can be accessed from the web-site; Protocol Type = Extract preparation; Performer: Andre,,Gerber


title: BY4741 mock (2)

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36817.gif
Genotype: control

source_name: BY4741 tot. RNA extract (2)

tag: BY4741 tot. RNA extract (2)


title: Nrp1_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67899.gif
Genotype: Nrp1

source_name: NRP1-TAP total RNA from extract

tag: NRP1-TAP total RNA from extract

source_name: NRP1-TAP affinity purified RNA

tag: NRP1-TAP affinity purified RNA


title: Sof1_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67872.gif
Genotype: Sof1

source_name: SOF1-TAP total RNA from extract

tag: SOF1-TAP total RNA from extract

source_name: SOF1-TAP affinity purified RNA

tag: SOF1-TAP affinity purified RNA


title: Npl3_(3)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67897.gif
Genotype: Npl3

source_name: NPL3-TAP total RNA from extract

tag: NPL3-TAP total RNA from extract

source_name: NPL3-TAP affinity purified RNA

tag: NPL3-TAP affinity purified RNA


title: Untagged_BY4741_(5)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67884.gif
Genotype: control

source_name: MOCK total RNA from extract

tag: MOCK total RNA from extract

source_name: MOCK affinity purified RNA

tag: MOCK affinity purified RNA


title: Aco1_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67914.gif
Genotype: Aco1

source_name: ACO1-TAP total RNA from extract

tag: ACO1-TAP total RNA from extract

source_name: ACO1-TAP affinity purified RNA

tag: ACO1-TAP affinity purified RNA


title: Mex67_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71076.gif
Genotype: Mex67

source_name: total rna extract

tag: total rna extract

source_name: affinity purified RNA

tag: affinity purified RNA


title: Nab3_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67845.gif
Genotype: Nab3

source_name: NAB3-TAP total RNA from extract

tag: NAB3-TAP total RNA from extract

source_name: NAB3-TAP affinity purified RNA

tag: NAB3-TAP affinity purified RNA


title: Bfr1_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67853.gif
Genotype: Bfr1

source_name: BFR1-TAP total RNA from extract

tag: BFR1-TAP total RNA from extract

source_name: BFR1-TAP affinity purified RNA

tag: BFR1-TAP affinity purified RNA


title: Nab2_(1)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67926.gif
Genotype: Nab2

source_name: NAB2-TAP total RNA from extract

tag: NAB2-TAP total RNA from extract

source_name: NAB2-TAP affinity purified RNA

tag: NAB2-TAP affinity purified RNA


title: Gbp2_(1)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67924.gif
Genotype: Gbp2

source_name: GBP2-TAP total RNA from extract

tag: GBP2-TAP total RNA from extract

source_name: GBP2-TAP affinity purified RNA

tag: GBP2-TAP affinity purified RNA


title: Puf5 IP (3)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36814.gif
Genotype: Puf5

source_name: Puf5 tot. RNA extract (3)

tag: Puf5 tot. RNA extract (3)

source_name: Puf5 RNA-IP (3)

tag: Puf5 RNA-IP (3)


title: BY4741 mock (3)

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37361.gif
Genotype: control

source_name: BY4741 tot. RNA extract (3)

tag: BY4741 tot. RNA extract (3)


title: Puf3 IP (4)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36807.gif
Genotype: Puf3

source_name: Puf3 tot. RNA extract (4)

tag: Puf3 tot. RNA extract (4)

source_name: Puf3 RNA-IP (4)

tag: Puf3 RNA-IP (4)


title: Puf4 IP (4)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36827.gif
Genotype: Puf4

source_name: Puf4 tot. RNA extract (4)

tag: Puf4 tot. RNA extract (4)

source_name: Puf4 RNA-IP (4)

tag: Puf4 RNA-IP (4)


title: Puf2 IP (2)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36822.gif
Genotype: Puf2

source_name: Puf2 tot. RNA extract (2)

tag: Puf2 tot. RNA extract (2)

source_name: Puf2 RNA-IP (2)

tag: Puf2 RNA-IP (2)


title: Ssd1_(1)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65966.gif
Genotype: Ssd1

source_name: total rna extract

tag: total rna extract

source_name: affinity purified rna

tag: affinity purified rna


title: Rib2_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67916.gif
Genotype: Rib2

source_name: RIB2-TAP total RNA from extract

tag: RIB2-TAP total RNA from extract

source_name: RIB2-TAP affinity purified RNA

tag: RIB2-TAP affinity purified RNA


title: Nrd1_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67877.gif
Genotype: Nrd1

source_name: NRD1-TAP total RNA from extract

tag: NRD1-TAP total RNA from extract

source_name: NRD1-TAP affinity purified RNA

tag: NRD1-TAP affinity purified RNA


title: Cbc2_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67855.gif
Genotype: Cbc2

source_name: CBC2-TAP total RNA from extract

tag: CBC2-TAP total RNA from extract

source_name: CBC2-TAP affinity purified RNA

tag: CBC2-TAP affinity purified RNA


title: Puf3 IP (2)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/30145.gif
Genotype: Puf3

source_name: tot. RNA Puf3 (ex2)

tag: tot. RNA Puf3 (ex2)

source_name: IP-RNA Puf3 (2)

tag: IP-RNA Puf3 (2)


title: Khd1 IP (1)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29827.gif
Genotype: Khd1

source_name: total RNA Khd1 extract (1)

tag: total RNA Khd1 extract (1)

source_name: Khd1 IP RNA  (1)

tag: Khd1 IP RNA  (1)


title: Puf2 IP (1)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34715.gif
Genotype: Puf2

source_name: Puf2 tot. RNA extract (1)

tag: Puf2 tot. RNA extract (1)

source_name: Puf2 RNA-IP (1)

tag: Puf2 RNA-IP (1)


title: mid-L4 hermaphrodites

description: RNA enriched for small RNA species (<200nt)

growth_protocol: Wild-type N2 strains were cultured under standard conditions at 20dC and used to prepare RNAs from each developmental stage (time after staged L1; mid-L4 (4hrs), mid-L4 (14hrs), mid-L4 (25hrs), mid-L4 (36hrs) and young adult (48hrs). For library preparation from males and spermatogenesis-hermaphrodites, dpy-28;him-8 double mutants and spe-9 mutants were cultured at 23dC, respectively, and  RNAs were prepraed from these two strains at 40hrs after staged L1.

tag: strain

tag: developmental stage

tag: growth condition


title: Puf4 IP (1)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32245.gif
Genotype: Puf4

source_name: Puf4 tot. RNA extract (1)

tag: Puf4 tot. RNA extract (1)

source_name: Puf4 RNA-IP (1)

tag: Puf4 RNA-IP (1)


title: BY4741 mock (4)

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37362.gif
Genotype: control

source_name: BY4741 tot. RNA extract (4)

tag: BY4741 tot. RNA extract (4)


title: Scp160_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67865.gif
Genotype: Scp160

source_name: SCP160-TAP total RNA from extract

tag: SCP160-TAP total RNA from extract

source_name: SCP160-TAP affinity purified RNA

tag: SCP160-TAP affinity purified RNA


title: Nab2_(2)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67927.gif
Genotype: Nab2

source_name: NAB2-TAP total RNA from extract

tag: NAB2-TAP total RNA from extract

source_name: NAB2-TAP affinity purified RNA

tag: NAB2-TAP affinity purified RNA


title: Puf5 IP (2)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34717.gif
Genotype: Puf5

source_name: Puf5 tot. RNA extract (2)

tag: Puf5 tot. RNA extract (2)

source_name: Puf5 RNA-IP (2)

tag: Puf5 RNA-IP (2)


title: Khd1 IP (2)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/30144.gif
Genotype: Khd1

source_name: tot. RNA Khd1 extract (2)

tag: tot. RNA Khd1 extract (2)

source_name: Khd1 IP RNA (2)

tag: Khd1 IP RNA (2)


title: Puf1 IP (1)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34714.gif
Genotype: Puf1

source_name: Puf1 tot. RNA extract (1)

tag: Puf1 tot. RNA extract (1)

source_name: Puf1 RNA-IP (1)

tag: Puf1 RNA-IP (1)


title: Ssd1_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67867.gif
Genotype: Ssd1

source_name: SSD1-TAP total RNA from extract

tag: SSD1-TAP total RNA from extract

source_name: SSD1-TAP affinity purified RNA

tag: SSD1-TAP affinity purified RNA


title: Untagged_BY4741_(3)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67850.gif
Genotype: control

source_name: MOCK total RNA from extract

tag: MOCK total RNA from extract

source_name: MOCK affinity purified RNA

tag: MOCK affinity purified RNA


title: Pub1_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67863.gif
Genotype: Pub1

source_name: PUB1-TAP total RNA from extract

tag: PUB1-TAP total RNA from extract

source_name: PUB1-TAP affinity purified RNA

tag: PUB1-TAP affinity purified RNA


title: Puf3 IP (1)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29828.gif
Genotype: Puf3

source_name: tot. RNA Puf3 (ex)

tag: tot. RNA Puf3 (ex)

source_name: IP RNA Puf3 (1)

tag: IP RNA Puf3 (1)


title: Puf1 IP (4)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36820.gif
Genotype: Puf1

source_name: Puf1 tot. RNA extract (4)

tag: Puf1 tot. RNA extract (4)

source_name: Puf1 RNA-IP (4)

tag: Puf1 RNA-IP (4)


title: Ski2_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71144.gif
Genotype: Ski2

source_name: total rna extract

tag: total rna extract

source_name: affinity purified RNA

tag: affinity purified RNA


title: Gbp2_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67869.gif
Genotype: Gbp2

source_name: GBP2-TAP total RNA from extract

tag: GBP2-TAP total RNA from extract

source_name: GBP2-TAP affinity purified RNA

tag: GBP2-TAP affinity purified RNA


title: Untagged_BY4741_(3)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69220.gif
Genotype: control

source_name: total RNA from extract

tag: total RNA from extract


title: Untagged_BY4741_(7)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69219.gif
Genotype: control


title: Nab6_(3)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69225.gif
Genotype: Nab6


title: Untagged_BY4741_(10)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71043.gif
Genotype: control


title: Puf2 IP (3)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36824.gif
Genotype: Puf2

source_name: Puf2 tot. RNA extract (3)

tag: Puf2 tot. RNA extract (3)

source_name: Puf2 RNA-IP (3)

tag: Puf2 RNA-IP (3)


title: Bfr1_(1)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67920.gif
Genotype: Bfr1

source_name: BFR1-TAP total RNA from extract

tag: BFR1-TAP total RNA from extract

source_name: BFR1-TAP affinity purified RNA

tag: BFR1-TAP affinity purified RNA


title: Khd1 IP (3)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32102.gif
Genotype: Khd1

source_name: total RNA Khd1 extract (3)

tag: total RNA Khd1 extract (3)

source_name: Khd1 IP RNA (3)

tag: Khd1 IP RNA (3)


title: Untagged_BY4741_(4)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67859.gif
Genotype: control

source_name: MOCK total RNA from extract

tag: MOCK total RNA from extract

source_name: MOCK affinity purified RNA

tag: MOCK affinity purified RNA


title: Puf5 IP (1)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32101.gif
Genotype: Puf5

source_name: Puf5 extract tot. RNA

tag: Puf5 extract tot. RNA

source_name: RNA-IP PUF5

tag: RNA-IP PUF5


title: Dhh1_(2)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67923.gif
Genotype: Dhh1

source_name: DHH1-TAP total RNA from extract

tag: DHH1-TAP total RNA from extract

source_name: DHH1-TAP affinity purified RNA

tag: DHH1-TAP affinity purified RNA


title: Sof1_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67847.gif
Genotype: Sof1

source_name: SOF1-TAP total RNA from extract

tag: SOF1-TAP total RNA from extract

source_name: SOF1-TAP affinity purified RNA

tag: SOF1-TAP affinity purified RNA