title: Yra2_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71142.gif
Genotype: Yra2

source_name: total rna extract

tag: total rna extract

source_name: affinity purified RNA

tag: affinity purified RNA


title: Untagged_BY4741_(1)_oligo_Mg _RBP40paper

status: Public on Oct 28 2008

type: RNA

city: Stanford

first: Daniel

last: Hogan

state: CA

address: 279 Campus Dr B439

country: USA

institute: Stanford University

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71138.gif
Genotype: control

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)

molecule: total RNA

organism: Saccharomyces cerevisiae

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


title: Khd1_(3)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65972.gif
Genotype: Khd1

source_name: affinity purified rna

tag: affinity purified rna


title: Nrd1_(3)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71049.gif
Genotype: Nrd1


title: Mex67_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71145.gif
Genotype: Mex67


title: Pin4_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71131.gif
Genotype: Pin4


title: Untagged_BY4741_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71137.gif
Genotype: control


title: Hrb1_(3)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71135.gif
Genotype: Hrb1


title: Khd1_(1)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65970.gif
Genotype: Khd1


title: Nab6_(2)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71011.gif
Genotype: Nab6


title: Pbp2_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67881.gif
Genotype: Pbp2

source_name: PBP2-TAP total RNA from extract

tag: PBP2-TAP total RNA from extract

source_name: PBP2-TAP affinity purified RNA

tag: PBP2-TAP affinity purified RNA


title: Rna15_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71140.gif
Genotype: Rna15


title: Atg8_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71149.gif
Genotype: Atg8


title: Untagged_BY4741_(12)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71008.gif
Genotype: control


title: Untagged_BY4741_(11)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71044.gif
Genotype: control


title: Untagged_BY4741_(2)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69221.gif
Genotype: control

source_name: total RNA from extract

tag: total RNA from extract


title: Ypl184c_(4)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67900.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: Hrb1_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71133.gif
Genotype: Hrb1


title: Ssd1_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71132.gif
Genotype: Ssd1


title: Pab1_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69223.gif
Genotype: Pab1


title: Untagged_BY4741_(8)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69218.gif
Genotype: control


title: Untagged_BY4741_(13)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71009.gif
Genotype: control


title: Ski2_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71143.gif
Genotype: Ski2


title: Cbc2_(3)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71045.gif
Genotype: Cbc2


title: Scp160_(3)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67870.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_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67908.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: Nab6_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71047.gif
Genotype: Nab6


title: Untagged_BY4741_(9)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69217.gif
Genotype: control


title: Nop56_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67892.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: Aco1_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67852.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: Atg8_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71148.gif
Genotype: Atg8


title: Upf1_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67912.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: Bfr1_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67889.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: Pab1_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69222.gif
Genotype: Pab1

source_name: affinity purified RNA

tag: affinity purified RNA


title: Yra2_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71141.gif
Genotype: Yra2

source_name: total rna extract

tag: total rna extract


title: Pbp2_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67883.gif
Genotype: Pbp2

source_name: PBP2-TAP total RNA from extract

tag: PBP2-TAP total RNA from extract

source_name: PBP2-TAP affinity purified RNA

tag: PBP2-TAP affinity purified RNA


title: Rna15_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71139.gif
Genotype: Rna15


title: Nop13_(2)_cDNA_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60211.gif
Genotype: Nop13

source_name: affinity purified rna

tag: affinity purified rna


title: Vts1_(1)_cDNA_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49179.gif
Genotype: Vts1

source_name: VTS1 TAP extract

tag: VTS1 TAP extract

source_name: VTS1 TAP affinity isolated RNA

tag: VTS1 TAP affinity isolated RNA


title: Nce102_(1)_cDNA_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50202.gif
Genotype: Nce102

source_name: Nce102 tot. RNA extract (1)

tag: Nce102 tot. RNA extract (1)

source_name: Nce102 RNA-IP (1)

tag: Nce102 RNA-IP (1)


title: Nop13_(1)_cDNA_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52036.gif
Genotype: Nop13

source_name: NOP13  TAP cell extract

tag: NOP13  TAP cell extract

source_name: NOP13  TAP affinity isolated RNA

tag: NOP13  TAP affinity isolated RNA


title: Ypl184c_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67891.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: Pab1_(3)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71050.gif
Genotype: Pab1


title: Sgn1_(1)_cDNA_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49173.gif
Genotype: Sgn1

source_name: SGN1 TAP extract

tag: SGN1 TAP extract

source_name: SGN1 affinity isolated RNA

tag: SGN1 affinity isolated RNA


title: Yfl023w_(2)_cDNA_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58723.gif
Genotype: Yfl023w

source_name: YFL023W  -TAP total RNA from extract

tag: YFL023W  -TAP total RNA from extract

source_name: YFL023W -TAP affinity isolated RNA

tag: YFL023W -TAP affinity isolated RNA


title: Dhh1_(2)_cDNA_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71151.gif
Genotype: Dhh1

source_name: total RNA extract

tag: total RNA extract

source_name: affinity purified RNA

tag: affinity purified RNA


title: Dhh1_(1)_cDNA_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71150.gif
Genotype: Dhh1


title: Nce102_(2)_cDNA_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71152.gif
Genotype: Nce102


title: Yll032c_(1)_cDNA_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50724.gif
Genotype: Yll032c

source_name: YLL032c tot. RNA extract (1)

tag: YLL032c tot. RNA extract (1)

source_name: YLL032c RNA-IP (1)

tag: YLL032c RNA-IP (1)


title: CD4+ T cell H3K27me3

status: Public on Oct 20 2008

type: SRA

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

description: Chromatin IP against histone H3K27me3

library_source: genomic

data_processing: Sequence reads were mapped to the human genome (hg18) using the Solexa Analysis Pipeline. The mapped CTCF reads were processed using the SISSRs algorithm (Jothi et al, Nucl Acids Res 2008) to identify genome-wide binding sites locations. The mapped H3K27me3 reads were first grouped into 1000 bp summary windows, following which “islands” of summary windows enriched with H3K27me3 tags were identified as domains using an approach similar to that used in our earlier study (Barski et al, Cell 2007). A CTCF binding site, denoted by genomic coordinate x, is defined as a barrier site relative to an H3K27me3 domain d of length l, only if the distance between x and the domain boundary is at most the smaller of l/10 and 1000 bp.

molecule: genomic DNA

organism: Homo sapiens

source_name: CD4+ T cells

growth_protocol: CD4+ T cells were purified from human blood using human CD4+ T cell isolation kit II kits (Miltenyi). Hela cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum and 1 mM glutamine. Jurkat cells were maintained in RPMI supplemented with 10% fetal bovine serum and 1 mM glutamine.

extract_protocol: For chromatin immunoprecipitation (ChIP) using a CTCF antibody (upstate 07-729), the formaldehyde cross-linked cells were sonicated to obtain DNA fragments ranging in size from ~200 bp. Cluster generation and sequencing were performed as described earlier (Barski et al Cell, 2007) . MNase digested, mononucleosome sized DNA fragments were used for H3K27me3 and H2AK5ac ChIPs .

tag: primary T cell

tag: antibody

value: H3K27me3  cell type:CD4+ T cells


title: Jurkat CTCF

description: Chromatin IP against CTCF

source_name: Jurkat cells

value: CTCF  cell type:Jurkat cells


title: HeLa CTCF

description: Chromatin IP against CTCF

source_name: HeLa cells

value: CTCF  cell type:HeLa cells


title: Untagged_BY4741_(4)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69210.gif
Genotype: control

source_name: total RNA from extract

tag: total RNA from extract


title: Pub1_(3)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67995.gif
Genotype: Pub1

source_name: Affinity purified RNA

tag: Affinity purified RNA


title: Hrb1_(2)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71134.gif
Genotype: Hrb1

source_name: total rna extract

tag: total rna extract


title: Nab2_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67885.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: Pin4_(1)_oligo_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71130.gif
Genotype: Pin4


title: Input_DNA in NB4

status: Public on Oct 02 2008

city: New Haven

first: Flora

last: Vaccarino

state: CT

address: 230 South Frontage Road

department: Child Study Center

institute: Yale University

description: Input DNA

data_processing: Enriched peak regions corresponding to transcription factor binding sites were identified by first extending all the uniquely mapped tags reads (mapped against NCBI36) 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 human 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)

source_name: Input DNA

growth_protocol: NB4 cells were grown in RPMI media containing 10% FBS

extract_protocol: Nuclei were isolated from cross-linked (1% formaldehyde for 10 minutes at room temperature) K562 cells. Nuclei were lysed in RIPA buffer and extracted chromatin was sonicated using Branson Sonifier 250. ChIP DNA was prepared using Pol II antibody (Covance: MMS-126R), adapters were ligated to ChIP DNA and sequenced using Illumina Genome Analyzer.

tag: NB4 cells


title: HeLa H3K27me3

description: Chromatin IP against histone H3K27me3

value: H3K27me3  cell type:HeLa cells


title: CD4+ T cell CTCF

description: Chromatin IP against CTCF

value: CTCF  cell type:CD4+ T cells


title: PolII_ChIP-Seq in NB4

description: ChIP DNA prepared using RNA Pol II antibody

source_name: Chromatin IP against Pol II


title: Sgn1_(2)_cDNA_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51608.gif
Genotype: Sgn1

source_name: SGN1 TAP total RNA from cell extract

tag: SGN1 TAP total RNA from cell extract

source_name: SGN1  TAP affinity isolated RNA

tag: SGN1  TAP affinity isolated RNA


title: Vts1_(2)_cDNA_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53042.gif
Genotype: Vts1

source_name: VTS1 TAP total RNA

tag: VTS1 TAP total RNA

source_name: VTS1 TAP affinity isolated RNAs

tag: VTS1 TAP affinity isolated RNAs


title: Untagged_BY4741_(1)_oligo_EDTA_RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69213.gif
Genotype: control

source_name: affinity purified RNA


title: Yfl023w_(1)_cDNA_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50208.gif
Genotype: Yfl023w

source_name: YFL023 tot. RNA extract (1)

tag: YFL023 tot. RNA extract (1)

source_name: YFL023 RNA-IP (1)

tag: YFL023 RNA-IP (1)


title: MAQC human human cell lines

status: Public on Oct 01 2008

city: Hayward

first: Shujun

last: Luo

address: 25861 Industrial Blvd

institute: Illumina inc

library_source: transcriptomic

data_processing:
not applicable

realign.txt column headers (7) and header descriptions:
Column I: tag sequence
Column II: alignment score, for 32 bp, 16000 = perfect match, 14593 = 1bp mismatch, 13906 = 2bp mismatch
Column III: # of hit in the genome, 1 = unique hit
Column IV:  Chr position
Column V: Chr direction
Column VI: matched genome sequence
Column VII: next best possible alignment score

source_name: Human MAQC human cell lines 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: mixed human brain


title: MAQC UHR

source_name: Human cell lines

tag: mixed human cell lines


title: T47D

source_name: Human T47D cell line

tag: human T47D cell line


title: MB435

source_name: Human MB435 cell line

tag: human MB435 cell line


title: MCF-7

source_name: Human MCF-7 cell line tissue

tag: human MCF-7 cell line


title: Yll032c_(2)_cDNA_Mg _RBP40paper

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60207.gif
Genotype: Yll032c

source_name: total RNA extract

tag: total RNA extract

tag: affinity purified RNA


title: NematostellaPeriodate1

city: Cambridge

first: andrew

last: grimson

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

description:
small RNA sequencing
15-30 nt size selection

data_processing: The processed files are collapsed to unique sequences (1 line per sequence); the second (numeric) value in each column is the number of times each unique sequence was sequenced.

organism: Nematostella vectensis

source_name: mixed developmental stages, RNA periodate-treated

extract_protocol: Trizol extracted whole RNA

treatment_protocol: Stored at -80


title: breast

source_name: Human breast tissue

tag: individual human breast


title: HME

source_name: Human HME cell line tissue

tag: human HME cell line


title: lymph node

source_name: Human lymph node tissue

tag: individual human lymph node


title: BT474

source_name: Human BT474 cell line tissue

tag: human BT474 cell line


title: testes

source_name: Human testes tissue

tag: individual human testes


title: PolII_ChIP-Seq in K562

source_name: Chromatin IP against Pol II

growth_protocol: K562 cells were grown in RPMI media containing 10% FBS

tag: K562 cells


title: heart

source_name: Human heart tissue

tag: individual human heart


title: liver

source_name: human liver

tag: individual human liver


title: skeletal muscle

source_name: Human skeletal muscle tissue

tag: individual human skeletal muscle


title: Input_DNA in K562

description: Input DNA

source_name: Input DNA


title: colon

source_name: Human colon tissue

tag: individual human colon


title: adipose

source_name: Human adipose tissue

tag: individual human adipose


title: brain

source_name: Human brain tissue

tag: individual human brain


title: IFN_gamma_Input_DNA in HeLa S3

status: Public on Sep 16 2008

description:
IFN Gamma stimulated HeLa S3 Input DNA
Treatment: Stimulated with IFN gamma

source_name: IFN Gamma stimulated HeLa S3 Input 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: STAT1 ChIP DNA samples were prepared from HeLa S3 cells following stimulation with IFN gamma (R&D systems #285-IF) for 30 min as previously described (Hartman et al. 2005; Euskirchen et al. 2007). Lysates were clarified from sonicated nuclei and STAT1-DNA complexes were isolated with anti-STAT1 alpha p91 (C-24) rabbit polyclonal antibody (sc-345 from Santa Cruz Biotechnology). The corresponding Input DNA samples were prepared from the same clarified lysates of the gamma interferon-stimulated, formaldehyde-crosslinked, sonicated HeLa S3 nuclei as were used for the STAT1 ChIP samples. 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 (32 to 52 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.

treatment_protocol: For STAT1 cells were then stimulated at these same growth conditions with 1000 U/ml (final) of Interferon alpha [PBL Biomedical Laboratories Product #11100-1, Recombinant human IFN alpha (Hu-IFN-alpha-A; Hu-IFN-alpha-2a)].

tag: HeLa S3 cells (ATCC/Snyder Lab)

tag: growth properties

value: Suspension Morphology:epithelial Treatment:IFN gamma


title: AmphimedonPeriodate1

organism: Amphimedon queenslandica

source_name: adult tissue, RNA periodate-treated

tag: adult tissue, RNA periodate-treated


title: AmphimedonEmb1

source_name: mixed embryos

tag: mixed embryos


title: 10 dpp Dnmt3L-KO MILI

city: Cold Spring Harbor

first: Alexei

last: Aravin

state: NY

address: 1 Bungtown Rd

institute: Cold Soring Harbor Lab

description: MILI-associated small RNA isolated from testes of 10 dpp Dnmt3L-deficient males

data_processing:
sequential ligation of 3' and 5' linkers using T4 RNA ligase follwed by PCR amplification
small RNA
Reads were aligned to the reference genome allowing zero mismatches. Number of mapping in the genome and genomic annotation were extracted.

organism: Mus musculus

source_name: testes

extract_protocol: total RNA was size selected (24-33nt) or MILI and MIWI2 complexes were immunoprecipitated from extarct using specific polyclonal antibodies

tag: 10 dpp Dnmt3L KO mice


title: AmphimedonPeriodateMock

source_name: adult tissue, RNA mock-treated

tag: adult tissue, RNA mock-treated


title: small RNAs from adult female head

status: Public on Sep 30 2008

city: New York

first: Nicolas

last: Robine

address: 1275 York Avenue, Box 252

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description: Small RNA data.

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

organism: Drosophila melanogaster

source_name: Drosophila melanogaster adult female head

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

tag: adult female head


title: NematostellaPeriodateMock

source_name: mixed developmental stages, RNA mock-treated


title: NematostellaPeriodate2

source_name: mixed developmental stages, RNA periodate-treated


title: 10 dpp MILI-KO total

description: 24-33nt RNA isolated from testes of 10 dpp MILI-deficient males

tag: 10 dpp MILI KO mice


title: AmphimedonPeriodate2


title: small RNA from 2-4 day old pupae (2)

description: Small RNA data.

source_name: Drosophila melanogaster 2-4 day old pupae

extract_protocol: total RNA from 2-4 day old pupae, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: 2-4 day old pupae


title: PolII_ChIP-Seq in HeLa S3

description: Chromatin IP against Pol II

data_processing: Enriched peak regions corresponding to transcription factor binding sites were identified by first extending all the uniquely mapped tags reads (mapped against NCBI36) 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 human 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.

source_name: Chromatin IP against Pol II

extract_protocol: Purified ChIP and Input DNA samples from 2 x 10^8 cells were size-selected on agarose gels for fragments 120 to 350 bp prior to library preparation. RNA polymerase II ChIP DNA samples were prepared according to the same protocol as used for the STAT1 samples except that the cells were not stimulated prior to formaldehyde fixation. RNA Pol II-DNA complexes were isolated with the mouse monoclonal antibody 8WG16 (Covance). 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 (32 to 52 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.

value: Suspension Morphology:epithelial

tag: antibody

value: Pol II (Covance 8WG16) Cellular Condition:Normal


title: Input_DNA in HeLa S3

description: Input DNA

tag: cellular condition

value: Normal


title: 10 dpp total

description: 24-33nt RNA isolated from testes of 10 dpp males (MILI heterozygous)

tag: 10 dpp MILI heterozygotes


title: 10 dpp MILI

description: MILI-associated small RNA isolated from testes of 10 dpp males (Dnmt3L heterozygous)

tag: 10 dpp Dnmt3L heterozygotes


title: Nematostella1524

description:
small RNA sequencing
15-24 nt size selection

source_name: mixed developmental stages

tag: mixed developmental stages


title: Ovary total

description: 24-33nt RNA isolated from ovaries of 4-6 week old females

source_name: ovaries

tag: 4-6 week old mice


title: AmphimedonEmb2


title: AmphimedonAdult2

source_name: adult tissue

tag: adult tissue


title: Nematostella1530


title: AmphimedonAdult3


title: cid14-deletion

status: Public on Sep 02 2008

first: Noah

last: Spies

address: 300 Pasteur Dr

department: Pathology

description: Argonaute-associated small RNAs were sequenced from cid14-deletion fission yeast.

data_processing: We selected 454 reads with matches to the terminal 9 nucleotides of the 5' linker and the first 9 nucleotides of the 3' linker.

organism: Schizosaccharomyces pombe

extract_protocol: Ago1-associated RNAs were recovered from Flag-purified FLAG-Ago1 protein by phenol-chloroform extraction and EtOH precipitation

tag: genotype

value: cid14-deletion Ago1 pull-down


title: Nematostella2530

description:
small RNA sequencing
25-30 nt size selection


title: WCE_mES_rep2

status: Public on Jul 30 2008

first: Whitehead

last: Institute

department: Genome Technology Core

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

data_processing: Images analysis and base calling was done using solexa pipeline and reads aligned to both mouse NCBI build 36 and 37 using ELAND. For miRNA analysis - 5p end defined by start of tag, 3p end defined by 6nt perfect match to 3p linker and . Alignments to build 37 were used for analysis of the mmu-mir-290 cluster only as that cluster is not represented on build 36. 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: ESC

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. Cells harbouring a Dox-repressible Oct4 allele (ZHBT-c4 cells) were treated with 2mg/ml doxycycline (SIGMA, D-9891) for 12hrs or 24hrs. To generate neural precursor cells, ES cells were differentiated along the neural lineage using standard protocols. V6.5 ES cells were differentiated into neural progenitor cells (NPCs) through embryoid body formation for 4 days and selection in ITSFn media for 5–7 days, and maintained in FGF2 and EGF2 (R&D Systems). Mouse embryonic fibroblasts were prepared and cultured from DR-4 strain mice.

extract_protocol: For ChIP-seq samples: 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: Refer to manuscript

tag: Whole cell extract (WCE)


title: H3K36me3_mES_rep1b

tag: Chromatin immunoprecipitation for H3K36me3


title: H3K36me3_mES_repla


title: H3K79me2_mES_rep1b

tag: Chromatin immunoprecipitation for H3K79me2


title: H3K79me2_mES_repla


title: small RNA from 3rd instar larvae (2)

description: Small RNA data.

source_name: Drosophila melanogaster 3rd instar larvae

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

tag: 3rd instar larvae


title: H3K4me3_mES_rep3

tag: Chromatin immunoprecipitation for H3K4me3


title: 16.5 dpc MILI

description: MILI-associated small RNA isolated from testes of 16.5 dpc embryous

tag: 16.5 dpc embryous


title: small RNA from 2-4 day old pupae (1)

description: Small RNA data.

extract_protocol: total RNA from  2-4 day old pupae, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH


title: AmphimedonEmb3

tag: mixed embryos


title: IFN_gamma_STAT1_ChIP-Seq in HeLa S3

description:
Chromatin IP against STAT1 in IFN gamma stimulated HeLa S3 cells
Antibody: STAT1 (Santa Cruz sc-345) Treatment: Stimulated with IFN gamma

tag: HeLa S3 cells (ATCC/Snyder Lab)

tag: growth properties

value: Suspension Morphology:epithelial   Treatment:IFN gamma


title: 16.5 dpc total

description: 24-33nt RNA isolated from testes of 16.5 dpc embryos


title: H3K4me3_mES_rep2


title: AmphimedonAdult1


title: Wild-type

description: Argonaute-associated small RNAs were sequenced from wild-type fission yeast.

source_name: wild-type

value: wild-type Ago1 pull-down


title: 2 dpp total

description: 24-33nt RNA isolated from testes of 2 dpp males

tag: 2 day old mice


title: H3K4me3_mES_rep1


title: H3K4me3_mES_repl


title: Trichoplax

organism: Trichoplax adhaerens

source_name: whole organisms

tag: whole organisms


title: Nanog_mES_rep1

tag: Chromatin immunoprecipitation for Nanog


title: Nanog_mES_rep2


title: oct4_mES_rep1

tag: Chromatin immunoprecipitation for Oct4


title: sox2_mES_rep1

tag: Chromatin immunoprecipitation for Sox2


title: sox2_mES_rep2


title: Tcf3_mES_rep1

tag: Chromatin immunoprecipitation for Tcf3


title: Tcf3_mES_rep2


title: suz12_rep2_1

tag: Chromatin immunoprecipitation for Suz12


title: suz12_mES_repl


title: 16.5 dpc MIWI2

description: MIWI2-associated small RNA isolated from testes of 16.5 dpc embryous


title: ES_H3_ChIPSeq

status: Public on Jul 25 2008

first: Tarjei

middle: S

last: Mikkelsen

address: 7 Cambridge Center

institute: Broad Institute

description: Chromatin IP against Histone H3 (Abcam 1791)

data_processing: Described in Mikkelsen et al., Nature 2007. Briefly, sequence reads from each IP experiment were aligned to the mouse reference genome (mm8), and all uniquely aligned reads (within >2 mismatches) were kept. Read densities were computed by counting the number of reads (extended to 300 bp) overlapping each position in the genome (at 25bp resolution).

source_name: Embyonic Stem Cells (V6.5)

extract_protocol: Described in Mikkelsen et al., Nature 2007. Briefly, chromatin was fixed in 1% formaldehyde, sheared to 200-700bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

tag: Genotype

value: 129SvJae x C57BL/6; Passages 10-15


title: ES_WCE_ChIPSeq

description: Whole cell extract (input DNA)

growth_protocol: Described in Mikkelsen et al., Nature 2007


title: ES_H4K20me3_ChIPSeq

description: Chromatin IP against H4K20me3 (Upstate 07-463)

treatment_protocol: Described in Mikkelsen et al., Nature 2007


title: ES_H3K27me3_ChIPSeq

description: Chromatin IP against H3K27me3 (Upstate 07-449)


title: NP_H3K36me3_ChIPSeq

description: Chromatin IP against H3K36me3 (Abcam 9050)

source_name: ES-derived neural precursor cells

value: 129SvJae x C57BL/6


title: NP_H3K9me3_ChIPSeq

description: Chromatin IP against H3K9me3 (Abcam 8898)


title: ES_H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3 (Abcam 8580)


title: ES_H3K36me3_ChIPSeq


title: NP_H3K4me3_ChIPSeq


title: WCE_mES_rep1

tag: Whole cell extract (WCE)


title: ES_H3K9me3_ChIPSeq


title: NP_H3K27me3_ChIPSeq


title: ES_RPol2_ChIPSeq

description: Chromatin IP against RNA polymerase II (Covance MMS-126R)


title: MEF_H3K36me3_ChIPSeq

source_name: Embryonic fibroblasts

value: 129SvJae x C57BL/6; Timepoint:Embryonic day 13.5; Passages:4-6


title: MEF_H3K9me3_ChIPSeq


title: MEF_WCE_ChIPSeq

description: Whole cell extract (input DNA)


title: MEF_H3K4me3_ChIPSeq


title: ESHyb_H3K36me3_ChIPSeq

source_name: Embyonic Stem Cells (hybrid)

value: 129SvJae x M. m. castaneus F1; Passages 4-6)


title: NP_WCE_ChIPSeq

description: Whole cell extract (input DNA)


title: ESHyb_H3K9me3_ChIPSeq


title: TT_RRBS_MspI

status: Public on Jul 06 2008

type: genomic

description: Bisulfite treated, MspI digestion

data_processing: Full details can be found in Meissner et al. (2008). Briefly, 36bp reads were aligned to a fully bisulfite converted reference sequence database containing all predicted MspI fragments in the 40-220bp range. An alignment was kept if the second best alignment at >= 2 additional mismatches. Methylated CpGs were identified by comparison of the aligned reads to the original reference sequence, and only positions with quality scores >= 20 were kept for analysis.

source_name: Tail-tip fibroblasts

extract_protocol: Full details can be found in Meissner et al. (2008). Briefly, 1-10ug of genomic DNA was digested with MspI, size selected, end-repaired, 3'-terminal A extended and ligated to Illumina adapters containing methylated cytosines, bilsufite converted using the EpiTect Bisulfite Kit (QIAGEN) with 3 extra cycles, PCR amplified with 18-24 cycles and sequenced.

tag: Strain


title: ES_RRBS_MspI

description: Bisulfite treated, MspI digestion

source_name: Embyonic stem cells (V6.5)


title: Analysis of small RNAs in murine neutrophils cultured in vitro by Solexa/Illumina genome analyzer

description: To profile microRNAs in in vitro cultured murine neutrophils, small RNAs were cloned and sequenced by a high-throughput sequencing system (Solexa/Illumina genome analyzer).

data_processing: Solexa/Illumina genome analyzer

source_name: Murine netrophils

growth_protocol: Bone marrow progenitors were isolated from wild-type mice and cultured for 6 days in SILAC-IMDM media with G-CSF and SCF.  To enrich for mature neutrophils, cells were further cultured for 42 hours in SILAC-IMDM media with G-CSF and dead cells were removed.

extract_protocol: Sample RNAs were isolated directly from wild-type murine neutrophils using Tri Reagent protocol.

treatment_protocol: in vitro cultured neutrophils from three-month-old wild-type male mice

tag: Cloning and high-throughput sequencing of small RNAs from neutrophils in vitro cultured from wild-type mice


title: Lung_RRBS_MspI

description: Bisulfite treated, MspI digestion

source_name: Lung


title: Spleen_RRBS_MspI

description: Bisulfite treated, MspI digestion

source_name: Spleen


title: Sox1_NPC_RRBS_MspI

description: Bisulfite treated, MspI digestion

source_name: Neural progenitor cells (Sox1+-derived)


title: Liver_RRBS_MspI

description: Bisulfite treated, MspI digestion

source_name: Liver


title: TcellCD4_RRBS_MspI

description: Bisulfite treated, MspI digestion

source_name: CD4+ T lymphocytes


title: Bcell_RRBS_MspI

description: Bisulfite treated, MspI digestion

source_name: B lymphocytes


title: TKO_RRBS_MspI

description: Bisulfite treated, MspI digestion

source_name: Methylation-deficient ES cells


title: MEF_H3K27me3_ChIPSeq


title: Astro_NPC_p18_RRBS_MspI

description: Bisulfite treated, MspI digestion

source_name: Astrocytes (ES-derived)


title: Brain_RRBS_MspI

description: Bisulfite treated, MspI digestion

source_name: Whole brain


title: NPC_p18_RRBS_MspI

description: Bisulfite treated, MspI digestion

source_name: Neural progenitor cells (ES-derived)


title: Brain_H3K27me3_ChIPSeq

description: Antibody: H3K27me3

data_processing: Described in Meissner et al, 2008. Briefly, sequence reads from each IP experiment were aligned to the mouse reference genome (mm8), and all uniquely aligned reads (within >2 mismatches) were kept. Read densities were computed by counting the number of reads (extended to 300 bp) overlapping each position in the genome (at 25bp resolution).

growth_protocol: ES cells were cultured under standard conditions in the presence of LIF; NPCs were derived dy directed differentiation in the presence of Fgf2 (see Meissner et al., 2008)

tag: Chromatin IP against H3K27me3


title: Brain_H3K4me2_ChIPSeq

description: Antibody: H3K4me2

growth_protocol: ES cells were cultured under standard conditions in the presence of LIF; NPCs were derived dy directed differentiation in the presence of Fgf2  (see Meissner et al., 2008)

tag: Chromatin IP against H3K4me2


title: Astro_primary_p11_RRBS_MspI

description: Bisulfite treated, MspI digestion

source_name: Astrocytes


title: Brain_H3K4me3_ChIPSeq

description: Antibody: H3K4me3

tag: Chromatin IP against H3K4me3


title: TcellCD8_RRBS_MspI

description: Bisulfite treated, MspI digestion

source_name: CD8+ T lymphocytes


title: Astro_primary_p2_RRBS_MspI

description: Bisulfite treated, MspI digestion


title: MEF_RRBS_MspI

description: Bisulfite treated, MspI digestion

source_name: Mouse embryonic fibroblasts (E14.5)


title: small RNA from 3rd instar larvae (1)

description: Small RNA data.

source_name: Drosophila melanogaster 3rd instar larvae

tag: 3rd instar larvae


title: ES_H3K4me1_ChIPSeq

description: Antibody: H3K4me1

tag: Chromatin IP against H3K4me1


title: Sox1_RRBS_MspI

description: Bisulfite treated, MspI digestion

source_name: Sox1+ progenitor cells (ES-derived)


title: NP_H3K4me1_ChIPSeq

description: Antibody: H3K4me1

source_name: Neural progenitor cells (ES-derived, passages 15-18)


title: NP_H3K4me2_ChIPSeq

description: Antibody: H3K4me2


title: ES_H3K4me2_ChIPSeq

description: Antibody: H3K4me2

source_name: Embyonic stem cells (V6.5)


title: ESHyb_H3K4me3_ChIPSeq

source_name: Embyonic Stem Cells (hybrid)


title: ES_Suz12

status: Public on Jun 12 2008

city: Singapore

first: Chia-Lin

last: Wei

address: 60 Biopolis Street #02-01

department: Genome Technology & Biology

country: Singapore

institute: Genome Institute of Singapore

description: Ab12073 (Abcam) antibody was used for ChIP.

data_processing:
The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, mm8) using Eland software with maximal 2 mis-matches. The ChIP-seq data were processed in 3 steps: a) A peak-finding algorithm was applied to identify the candidate binding site, where the cut-off threshold of peak intensity was determined by false discovery rate approximated with a random model; b) The candidate binding sites were further filtered based on the criterion of 5-fold change in relative to negative control library (GFP); c) The cut-off threshold of peak intensity were refined by qPCR validation. The software for the ChIP-seq data processing is available at http://cmb.gis.a-star.edu.sg/ChIPSeq/tools.htm.

The final processed peak list is linked as a supplementary file at the foot of this record. The file contains Chromosome number, Peak_location (mm8), and Count (abundance).  BED files are also available (mm8).

source_name: Embryonic stem cells

growth_protocol: E14 mouse ES cells, cultured under feeder-free conditions were maintained in Dulbecco's Modified Eagle-Medium (DMEM, GIBCO), with 15% heat-inactivated ES qualified fetal bovine serum (FBS, GIBCO), 0.055 mM beta-mercaptoethanol (GIBCO), 2mM L-glutamine, 0.1 mM MEM non-essential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Chemicon).

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. ChIP-enriched DNA from multiple ChIP experiments was pooled and quantified using PicoGreen dsDNA quantitation kit (Invitrogen). The ChIP-enriched DNA was processed for Solexa sequencing using ChIP-Seq Sample Prep Kit (Illumina).

treatment_protocol: The ES cells were fixed in 1% formaldehyde for 10 minutes at room temperature. The formaldehyde was quenched using 0.1 M glycine before harvest for extract preparation.

tag: E14 ES cells

tag: Chromatin immunoprecipitation for Suz12 transcription factor


title: ES_p300

description: sc-585 (Santa Cruz) antibody was used for ChIP.

tag: Chromatin immunoprecipitation for p300 transcription factor


title: ES_Klf4

description: Custom made antibody was used for ChIP.

tag: Chromatin immunoprecipitation for Klf4 transcription factor


title: ES_c-Myc

description: Custom made antibody was used for ChIP.

tag: Chromatin immunoprecipitation for c-Myc transcription factor


title: ES_Esrrb

description: Custom made antibody was used for ChIP.

tag: Chromatin immunoprecipitation for Esrrb transcription factor


title: ES_n-Myc

description: Custom made antibody was used for ChIP.

tag: Chromatin immunoprecipitation for n-Myc transcription factor


title: ES_GFP

description: sc-8334 (Santa Cruz) antibody was used for ChIP.

data_processing:
The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, mm8) using Eland software with maximal 2 mis-matches. The ChIP-seq data were processed in 3 steps: a) A peak-finding algorithm was applied to identify the candidate binding site, where the cut-off threshold of peak intensity was determined by false discovery rate approximated with a random model; b) The candidate binding sites were further filtered based on the criterion of 5-fold change in relative to negative control library (GFP); c) The cut-off threshold of peak intensity were refined by qPCR validation. The software for the ChIP-seq data processing is available at http://cmb.gis.a-star.edu.sg/ChIPSeq/tools.htm.

This the negative control sample - there is no peak list binding site information associated with it.

tag: Chromatin immunoprecipitation for GFP transcription factor


title: ES_E2f1

description: 05-379 (Upstate) antibody was used for ChIP.

tag: Chromatin immunoprecipitation for E2f1 transcription factor


title: ES_Tcfcp2I1

description: Custom made antibody was used for ChIP.

tag: Chromatin immunoprecipitation for Tcfcp2I1 transcription factor


title: ES_CTCF

description: 07-729 (Upstate) antibody was used for ChIP.

tag: Chromatin immunoprecipitation for CTCF transcription factor


title: ES_Smad1

description: sc-7965 (Santa Cruz) antibody was used for ChIP.

tag: Chromatin immunoprecipitation for Smad1 transcription factor


title: ES_Zfx

description: Custom made antibody was used for ChIP.

tag: Chromatin immunoprecipitation for Zfx transcription factor


title: ES_STAT3

description: sc-482 (Upstate) antibody was used for ChIP.

tag: Chromatin immunoprecipitation for STAT3 transcription factor


title: mEFsmallrna_rep1

description: MEFs were prepared as described in Tucker et al., Nucleic Acids Res 1997.

source_name: MEF

extract_protocol: For miRNA, Single-stranded cDNA libraries of short transcripts were generated using size selected RNA.  RNA extraction was performed using Trizol, followed by RNeasy purification (Qiagen). 5µg of  RNA was size selected and gel purified.  3’ Adaptor was ligated to RNA with T4 RNA ligase and also, separately with RNA Ligase. Ligation products were gel purified and mixed. 5’ adaptor was ligated with T4 RNA Ligase. RT-PCR (Superscript II, Invitrogen) was performed with 5’ primer. Splicing of overlapping ends PCR (SOEPCR) was performed (Phusion, NEB) with 5’ primer and 3’ PCR primer, generating cDNA with extended 3’ adaptor sequence. PCR product was denatured and the differently sized strands were purified.

tag: miRNA (small RNA)


title: NPC_p9_RRBS_MspI

description: Bisulfite treated, MspI digestion

tag: Strain


title: ZHBT-c40hsmallrna_rep1

description: ZHBT-c4 cells were described in Niwa et al., Nature Genetics 2000.  They are cultured in standard ES cell medium +/- doxycycline.

source_name: ZHBTc4 cells (with doxycycline treatments)


title: ES_Sox2

description: sc-17320 (Santa Cruz) antibody was used for ChIP.

tag: Chromatin immunoprecipitation for Sox2 transcription factor


title: ES_Nanog

description: REC-RCAB0002PF (Cosmo Bio) antibody was used for ChIP.

tag: E14 ES cells

tag: Chromatin immunoprecipitation for Nanog transcription factor


title: NPCsmallrna_rep1

description: NPCs were derived as described in Okabe et al., Mech Dev 1996.

source_name: neural precursor cells


title: ES_Oct4

description: sc-8628 (Santa Cruz) antibody was used for ChIP.

tag: Chromatin immunoprecipitation for Oct4 transcription factor


title: ZHBT-c424hsmallrna_rep1


title: MCV81_H3K4me3_ChIPSeq

status: Public on May 28 2008

description: Antibody: H3K4me3 (Abcam ab8580)

data_processing: Described in Mikkelsen et al, 2008. Briefly, sequence reads from each IP experiment were aligned to the mouse reference genome (mm8), and all uniquely aligned reads (within >2 mismatches) were kept. Read densities were computed by counting the number of reads (extended to 300 bp) overlapping each position in the genome (at 25bp resolution).

source_name: MEF-derived iPS cell line MCV8.1

growth_protocol: MCV6, MCV8, MCV8.1 and BIV1 were cultured under standard mouse ES cell contitions in the prescence of LIF (see Mikkelsen, 2008)

tag: Derived using consititutive Oct4, Klf4, c-Myc, Sox2 retrovirus

tag: Antibody

value: H3K4me3 (Abcam ab8580)


title: BIV1_H3K4me3_ChIPSeq

description: Antibody: H3K4me3 (Abcam ab8580)

source_name: B lymphocyte-derived cell line BIV1

tag: Doxycycline induced Oct4, Klf4, c-Myc, Sox2 lentivirus


title: BIV1_H3K27me3_ChIPSeq

description: Antibody: H3K27me3 (Upstate 07-449)


title: MCV8_H3K27me3_ChIPSeq

description: Antibody: H3K27me3 (Upstate 07-449)

source_name: MEF-derived cell line MCV8

tag: Consititutive Oct4, Klf4, c-Myc, Sox2 retrovirus


title: ZHBT-c412hsmallrna_rep1


title: MEF_H3K27me3_ChIPSeq

description: Antibody: H3K27me3 (Upstate 07-449)

source_name: Mouse embryonic fibroblasts

tag: Wild-type


title: MEF_H3K4me3_ChIPSeq

description: Antibody: H3K4me3 (Abcam ab8580)


title: MCV6_H3K4me3_ChIPSeq

description: Antibody: H3K4me3 (Abcam ab8580)

data_processing: Described in Mikkelsen et al, 2008. Briefly, sequence reads from each IP experiment were aligned to the mosue reference genome (mm8), and all uniquely aligned reads (within >2 mismatches) were kept. Read densities were computed by counting the number of reads (extended to 300 bp) overlapping each position in the genome (at 25bp resolution).

source_name: MEF-derived cell line MCV6


title: MCV6_H3K27me3_ChIPSeq

description: Antibody: H3K27me3 (Upstate 07-449)


title: mESv6.5smallrna_rep1

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

source_name: ESC


title: MCV8_H3K4me3_ChIPSeq

description: Antibody: H3K4me3 (Abcam ab8580)


title: MCV81_H3K27me3_ChIPSeq

description: Antibody: H3K27me3 (Upstate 07-449)


title: ein5-6abh1-1-floral-smRNA-seq-rep1

status: Public on May 15 2008

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: smRNA high-throughput sequencing

data_processing:
Sequence information was extracted from the image files with the Illumina Firecrest and Bustard applications and mapped to the Arabidopsis (Col-0) reference genome sequence (TAIR 7) with the Illumina ELAND algorithm. ELAND aligns 32 bases or shorter reads, allowing up to two mismatches to the reference sequence. For reads longer than 32 bases, only the first 32 bases will be used for alignment, while the remaining sequence will be appended regardless of similarity to the reference sequence.
Prior to alignment of the smRNA reads, a custom Perl script was used to identify the first seven bases of the 3' adapter sequence, and the read was truncated up to the junction with the adaptor sequence. Each of the reads was then mapped to the genome with BLAST using a word size of 10 and expectation value of 10. Only perfect matches were accepted, as these shorter reads will have a higher tendency to falsely map than longer reads. No further analysis was performed on reads that do not contain the adapter sequence, as their size class could not be determined precisely.

organism: Arabidopsis thaliana

source_name: immature floral tissue

growth_protocol: All plants were grown in potting soil (Metro Mix 250; Grace-Sierra, Boca Raton, FL) at 23C under a 16-hour light/8-hour dark cycle.

extract_protocol:
smRNA-seq library construction protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA). Immediately following RNA precipitation, the flow through from the anion-exchange chromatography column was further precipitated in another 2.5 volumes of 100% ethanol (smRNA fraction). The smRNA fraction was further purified by a phenol-chloroform extraction and an additional ethanol precipitation. Small RNAs were resolved by electrophoresis of 2.5 micrograms of the smRNA fraction and 7.5 micrograms of total RNA on 15% polyacrylamide gels containing 7 M urea in TBE buffer (45 mM Tris-borate, pH 8.0, and 1.0 mM EDTA). A gel slice containing RNAs of 15 to 35 nucleotides (based on the 10 base pair ladder size standard (Invitrogen, Carlsbad, CA)) was excised and eluted in 0.3 M NaCl rotating at room temperature for 4 hours. The eluted RNAs were precipitated using ethanol and resuspended in diethyl pyrocarbonate-treated deionized water. Gel-purified smRNA molecules were ligated sequentially to 5' and 3' RNA oligonucleotide adapters using T4 RNA ligase (10 units/mL) (Promega, Madison, WI). The 5' RNA adapter (5' - GUUCAGAGUUCUACAGUCCGACGAUC - 3') possessed 5' and 3' hydroxyl groups. The 3' RNA adapter (5'-pUCGUAUGCCGUCUUCUGCUUGidT-3') possessed a 5' mono-phosphate and a 3' inverted deoxythymidine (idT). The smRNAs were first ligated to the 5' RNA adapter. The ligation products were gel eluted and ligated to the 3' RNA adapter as described above. The final ligation products were then used as templates in a reverse transcription (RT) reaction using the RT-primer (5' - CAAGCAGAAGACGGCATACGA - 3') and Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA). This was followed by a limited (15 cycle) PCR amplification step using the PCR reverse (5'-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA-3') and forward (5'-CAAGCAGAAGACGGCATACGA-3') primers and Phusion hot-start high fidelity DNA polymerase (New England Biolabs, Cambridge, MA). All oligonucleotides were provided by Illumina (Illumina, San Diego, CA). The amplification products were separated by electrophoresis on a 6% polyacrylamide gel in TBE buffer, eluted in 0.3 M NaCl rotating at room temperature for 4 hours, precipitated using ethanol, and resuspended in nuclease-free water.

treatment_protocol: Immature (unopened) flower buds were collected and frozen in liquid nitrogen.

tag: ein5-6 abh1-1, unopened flower buds


title: ein5-6-floral-smRNA-seq-rep1

description: smRNA high-throughput sequencing

tag: ein5-6, unopened flower buds


title: Col-0-floral-GMUCT-seq-rep1

description: 5'-RACE high-throughput sequencing

data_processing:
Sequence information was extracted from the image files with the Illumina Firecrest and Bustard applications and mapped to the Arabidopsis (Col-0) reference genome sequence (TAIR 7) with the Illumina ELAND algorithm. ELAND aligns 32 bases or shorter reads, allowing up to two mismatches to the reference sequence. For reads longer than 32 bases, only the first 32 bases will be used for alignment, while the remaining sequence will be appended regardless of similarity to the reference sequence.
In order to avoid omitting unannotated transcripts, 36 nucleotide GMUCT reads were aligned to the Arabidopsis reference genome sequence (TAIR 7) with the ELAND algorithm.

extract_protocol: Total RNA from wild-type Col-0 immature flower buds was isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) and treated with RNase-free DNaseI (Qiagen) for 25 min at room temperature. Following an ethanol precipitation, poly(A)+ RNA was column purified from 50 micrograms of the total RNA samples using Oligotex mRNA kit (Qiagen). The poly(A)+ RNA was then depleted for18S and 28S rRNA molecules in two sequential Ribominus (Invitrogen, Carlsbad, CA) reactions as per manufacturer's instructions, using 6 plant-specific biotinylated LNA oligonucleotide rRNA probes supplied by the manufacturer (Invitrogen, Carlsbad, CA). The rRNA-depleted poly(A)+ RNA was then ligated to the Illumina 5' smRNA adapter using T4 RNA ligase (10 units/mL) (Promega, Madison, WI). The 5' RNA adapter (5' - GUUCAGAGUUCUACAGUCCGACGAUC - 3') possessed 5' and 3' hydroxyl groups. The ligated rRNA-depleted poly(A)+ RNA was purified by phenol:chloroform extraction and ethanol precipitation. Oligo(dT) was then used to prime cDNA synthesis using SuperScript II reverse transcriptase(200 units/mL) (Invitrogen, Carlsbad, CA). The cDNA was then subjected to second strand synthesis using Oligo(dT) and the PCR primer specific for the Illumina 5' smRNA adapter (5' -AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA - 3'). The dscDNA was ethanol precipiated, and then fragmented by sonication to 50-500 bp with a Bioruptor (Diagenode Sparta, NJ), followed by end repair and ligation of the genomic DNA (gDNA) adapters provided by Illumina (Illumina, San Diego, CA) as per manufacturer's instructions for gDNA library construction. 100-200 ng of adapter-ligated dscDNA of 195-235 bp was isolated by agarose gel electrophoresis, and subsequently purified using a gel extraction kit (Qiagen, Valencia, CA). This was followed by a limited (16 cycle) PCR amplification step using the PCR primer specific for the Illumina 5' smRNA adapter (5' -AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA - 3') and primer 2.1 that is specific for the gDNA 3' adapter using Phusion hot-start high fidelity DNA polymerase (New England Biolabs, Cambridge, MA). Using this primer combination for the limited amplification enriched for the desired products that had an Illumina 5' smRNA adapted on the 5' end and the 3' gDNA adapter on the 3' end. The enriched library was purified with the PCR purification kit (Qiagen, Valencia, CA) and quantity and quality examined by spectrophotometry, gel electrophoresis, and limited sequencing of cloned library molecules.

tag: Col-0, unopened flower buds


title: ein5-6-floral-GMUCT-seq-rep1

description: 5'-RACE high-throughput sequencing

extract_protocol: Total RNA from ein5-6 immature flower buds was isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) and treated with RNase-free DNaseI (Qiagen) for 25 min at room temperature. Following an ethanol precipitation, poly(A)+ RNA was column purified from 50 micrograms of the total RNA samples using Oligotex mRNA kit (Qiagen). The poly(A)+ RNA was then depleted for18S and 28S rRNA molecules in two sequential Ribominus (Invitrogen, Carlsbad, CA) reactions as per manufacturer's instructions, using 6 plant-specific biotinylated LNA oligonucleotide rRNA probes supplied by the manufacturer (Invitrogen, Carlsbad, CA). The rRNA-depleted poly(A)+ RNA was then ligated to the Illumina 5' smRNA adapter using T4 RNA ligase (10 units/mL) (Promega, Madison, WI). The 5' RNA adapter (5' - GUUCAGAGUUCUACAGUCCGACGAUC - 3') possessed 5' and 3' hydroxyl groups. The ligated rRNA-depleted poly(A)+ RNA was purified by phenol:chloroform extraction and ethanol precipitation. Oligo(dT) was then used to prime cDNA synthesis using SuperScript II reverse transcriptase(200 units/mL) (Invitrogen, Carlsbad, CA). The cDNA was then subjected to second strand synthesis using Oligo(dT) and the PCR primer specific for the Illumina 5' smRNA adapter (5' -AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA - 3'). The dscDNA was ethanol precipiated, and then fragmented by sonication to 50-500 bp with a Bioruptor (Diagenode Sparta, NJ), followed by end repair and ligation of the genomic DNA (gDNA) adapters provided by Illumina (Illumina, San Diego, CA) as per manufacturer's instructions for gDNA library construction. 100-200 ng of adapter-ligated dscDNA of 195-235 bp was isolated by agarose gel electrophoresis, and subsequently purified using a gel extraction kit (Qiagen, Valencia, CA). This was followed by a limited (16 cycle) PCR amplification step using the PCR primer specific for the Illumina 5' smRNA adapter (5' -AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA - 3') and primer 2.1 that is specific for the gDNA 3' adapter using Phusion hot-start high fidelity DNA polymerase (New England Biolabs, Cambridge, MA). Using this primer combination for the limited amplification enriched for the desired products that had an Illumina 5' smRNA adapted on the 5' end and the 3' gDNA adapter on the 3' end. The enriched library was purified with the PCR purification kit (Qiagen, Valencia, CA) and quantity and quality examined by spectrophotometry, gel electrophoresis, and limited sequencing of cloned library molecules.


title: Col-0-floral-smRNA-seq-rep1

description: smRNA high-throughput sequencing


title: abh1-1-floral-smRNA-seq-rep1

description: smRNA high-throughput sequencing

tag: abh1-1, unopened flower buds


title: Female body

status: Public on Jun 02 2008

first: Wei-Jen

last: Chung

address: 430 E 67th St

institute: Sloan-Kettering Institute

description: small RNAs

source_name: Drosophila melanogaster female body

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

tag: Drosophila melanogaster female body


title: Platypus testis 25-33 nt

status: Public on May 21 2008

city: Cold spring Harbor

first: ravi

last: Sachidanandam

address: 1 bungtown road

institute: Cold Spring Harbor Laboratory

data_processing: The 3' linker, CTGTAGGCACCATCAAT, was identified and stripped out of the raw reads using a smith-waterman based alignment algorithm.

organism: Ornithorhynchus anatinus

source_name: Adult testis

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

tag: tissue

value: testis


title: Male heads

description: small RNAs

source_name: Drosophila melanogaster male heads

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

tag: male heads


title: Male body

description: small RNAs

source_name: Drosophila melanogaster male body

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

tag: Drosophila melanogaster male body


title: 6-10hr embryo #1

description: small RNAs

source_name: Drosophila melanogaster 6-10hr embryo

extract_protocol: total RNA from 6-10hr embryo, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: Drosophila melanogaster 6-10hr embryo


title: CE9

status: Public on May 12 2008

city: Brisbane

first: Evgeny

last: Glazov

address: Ipswich Road

department: Diamantina Institute

country: Australia

institute: University of Queensland

description: 9 day embryo

data_processing: Refer to Supplemental Methods of the related manuscript for detail.

organism: Gallus gallus

source_name: 9 day embryo

growth_protocol: Fertilized Ross-308 eggs were incubated in a Multiquip incubator at 37.5 C with rotation every 6 hours. Chick embryos were collected at day 5, 7, and 9 of incubation to represent the embryonic developmental stages 25-27, 30-31, and 35 respectively (Hamburger and Hamilton 1992). After removal of the amnion embryos were rinsed in 1xPBS, and immediately processed for RNA isolation.

extract_protocol: Low molecular weight RNA was extracted using mirVana Isolation Kit (Ambion) folowing the manufacturer's protocol.

tag: breed

value: Ross-308™, Tissue:whole embryo, Stage:9 days of incubation


title: RNA-seq analysis of oligo(dT)- and random-hexamer-primed yeast polyA RNA

status: Public on May 05 2008

first: Zhong

last: Wang

address: 266 Whitney Avn, KBT716

department: MCDB

description: Transcriptome analysis

data_processing:
The processed data on this record (linked in the 'Supplementary file' section below) are derived from raw samples of oligo(dT)-primed and RandomHexamer-primed polyA cDNA, as well as original, biological and technical replicates. Consequently, fastq raw data files are composed of 6 batches of sequences:
RH_bio:SRX000564
RH_ori:SRX000562
RH_tech:SRX000563
dT_bio:SRX000561
dT_ori:SRX000559
dT_tech:SRX000560

After removing adapter and low quality sequences (N-runs, N>=12), short sequence reads were mapped to a recent reference yeast genome assembly (January, 2008) with software SOAP and BLAT. Reads aligning to two different locations in the genome represent splicing junctions and reads have leading Ts and trailing As (hereafter referred as End Tags) represent the 3'ends of mRNA. These reads were also recovered in order to define intron and mRNA ends.

molecule: polyA RNA

source_name: yeast BY4741, mid-exponential phase

growth_protocol: Yeast strain BY4741(leu2D0 ura3D0 met15D0 his3D1) was grown at 30C to mid exponential phase (OD 600=1.0) in YPAD rich medium.

extract_protocol: Total RNA was extracted from Ribopure Yeast kit (Ambion) and treated for 30 min at 37C with RNAse free DNase I (Ambion). Poly(A) RNA was purified with Micro Poly(A) Purist Kit according to the manufacturer's instructions (Ambion), and used to generate double stranded cDNA by reverse transcription with either random hexamers or oligo(dT) primers. The double stranded cDNA was fragmented and subjected to high throughput Illumina sequencing in which 35 bp of sequence was determined from the fragment ends.

tag: strain

value: BY4741(leu2D0 ura3D0 met15D0 his3D1)


title: rdd_RNA-seq

status: Public on Apr 21 2008

description: Sequence information was extracted from the image files with the Illumina Firecrest and Bustard applications and mapped to the Arabidopsis (Col-0) reference genome sequence (TAIR 7) with the Illumina ELAND algorithm. ELAND aligns 32 bases or shorter reads, allowing up to two mismatches to the reference sequence. For reads longer than 32 bases, only the first 32 bases will be used for alignment, while the remaining sequence will be appended regardless of similarity to the reference sequence. A Perl script was used to truncate the appended sequence at the point where the next four bases contain two or more errors relative to the reference sequence.

data_processing: In order to avoid omitting unannotated transcripts, 36 nucleotide transcriptome reads were aligned to the Arabidopsis reference genome sequence (TAIR 7) with the ELAND algorithm.

source_name: Immature floral tissue

extract_protocol:
RNA-seq library construction protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) and treated with DNaseI (Qiagen) for 30 min at room temperature. following ethanol precipitation the 18S and 28S rRNA molecules were depleted from 20 µg of total RNA in three sequential Ribominus (Invitrogen, Carlsbad, CA) reactions as per manufacturer's instructions, using 6 plant-specific biotinylated LNA oligonucleotide rRNA probes supplied by (Invitrogen, Carlsbad, CA). The 5' cap was removed from the rRNA-depleted RNA by treatment with 10 U/µl Tobacco Acid Pyrophosphatase for 1.5 h at 37C. This and all subsequent enzymatic reactions involving RNA used contained 2.5-4 U/µl RNaseOut ribonuclease inhibitor (Invitrogen, Carlsbad, CA). The RNA was purified by phenol:chloroform extraction and ethanol precipitation. This and all subsequent ethanol precipitations contained 20-40 µg/ml nuclease-free glycogen (Ambion, Austin, TX). De-capped RNA was fragmented by metal hydrolysis in 1X fragmentation buffer (Affymetrix, Santa Clara, CA) for 35 min at 94 C then cooled on ice for 2 min and ethanol precipitated. The fragmented RNA was dephosphorylated using 10 U/µl Calf intestinal phosphatase (New England Biolabs, Cambridge, MA) for 1 h at 37C, then 10 µl Gel loading Buffer II (Ambion, Austin, TX) added, heated at 65'C for 5 min, cooled on ice and then separated on a 10% polyacrylamide gel containing 7 M urea in TBE buffer (45 mM Tris-borate, pH 8.0, and 1.0 mM EDTA) by electrophoresis at 150 V for 2 h at 4C. The gel was stained in SYBR Gold (Invitrogen, Carlsbad, CA), and a gel slice containing RNAs of 35 to 50 nucleotides was excised, crushed, and the RNA eluted in 0.3 M NaCl rotating at room temperature for 4 hours. The eluted RNAs were ethanol precipitated and resuspended in nuclease-free water, after which the RNA fragments were heated to 65'C for 5 min, cooled on ice for 5 min and then ligated to the Illumina 3' RNA oligonucleotide adapter (see smRNA library construction above) using 10 U/µl T4 RNA ligase (Promega, Madison, WI) in 10% DMSO, incubated at 20C for 6 h then 4 C for 4 h. Nucleic acids in the ligation reaction were separated by electrophoresis and a gel slice containing 3' adapter-ligated RNA molecules from 50 to 80 nucleotides was excised and the RNA eluted and precipitated as described above. The gel-purified RNA was resuspended in nuclease-free water then phosphorylated in a reaction containing 1 U/µl T4 polynucleotide kinase (New England Biolabs, Cambridge, MA) and 1 mM ATP (Illumina, San Diego, CA) for 1 h at 37 C. After purification by phenol:chloroform extraction and ethanol precipitation the 5' phosphorylated RNA fragments were ligated to the Illumina 5' RNA oligonucleotide adapter (see smRNA library construction above) under the same conditions used for the 3' adapter ligation. Nucleic acids in the ligation reaction were separated by electrophoresis and a gel slice containing 5' and 3' adapter-ligated RNA molecules from 80 to 125 nucleotides was excised and the RNA eluted as described above. The size-selected ligation products were then used as templates in a reverse transcription (RT) reaction, followed by a limited (20 cycle) PCR amplification step (see smRNA library construction above). The amplification products were separated by electrophoresis on a 6% polyacrylamide gel in TBE buffer and the 80 to 125 bp band excised. This cDNA was eluted in 1 X gel elution buffer (Illumina, San Diego, CA) rotating at room temperature for 3 hours, ethanol precipitated and resuspended in 15 µl elution buffer (Qiagen, Valencia, CA).

tag: genotype/variation

value: ros1-3 dml2-1 dml3-1

value: unopened flower buds


title: B cells rep1

status: Public on Jul 03 2008

city: Berlin

first: Marc

last: Sultan

address: Ihnestr. 73

country: Germany

institute: Max Planck Institute for molecular genetics

description: raw sequence 070713_3

data_processing: Reads were aligned to the human genome (hg18, NCBI build 36.1) using Eland software (Gerald module v.1.27, Illumina). The mapping criteria imposed by Eland are the followings: matches should be collinear to the genome allowing up to two mismatches, but no indels. In these conditions, 50% of the reads obtained here matched to unique locations of the human genome, whereas 16-18% of the reads mapped to more than one genomic position. Reads that were found in unique positions in the human genome were further mapped to exons of protein-coding genes retrieved from two independent databases: ENSEMBL v.46 and Eldorado (release 05/2007).  The number of reads that were fully included in exons (which we refer as “number of hits”) was counted. For genes encoding multiple transcripts, the number of hits per gene was determined as the sum of all hits in all possible exons.

source_name: Ramos lymphoma B cells

growth_protocol: EK 293T cells were cultured in parallel in 2*150 cm3 flasks with DMEM (penicillin-streptomycin) (Gibco) supplemented with 10% Fetal Calf Serum (FCS) (Biochrom) and Glutamax (1x) (Gibco). At passage 20 (confluent state), cells were  trypsinized, washed off in PBS, pelleted and resuspended in 2 ml lysis solution RLT (Qiagen).  B cells were cultured parallely in 2*150 cm3 flasks with RPMI 1640 (penicillin-streptomycin) (Gibco) supplemented with 10% FCS (Biochrom) and Glutamax (1x) (Gibco). At passage 20 (confluent state), cells were  trypsinized, washed off in PBS, pelleted, and resuspended in 2 ml lysis solution RLT (Qiagen).

extract_protocol: Total RNA was then extracted from ~ 20 x 106 cells per sample (2*HEK and 2*B cells samples) using RNeasy Midi extraction kit (Qiagen) by following the manufacturer’s instructions. DNA was removed using the “on column digestion” protocol of the RNeasy Midi extraction kit (Qiagen).  Total RNA quality was assessed by spectrophotometry (Nanodrop) and gel electrophoresis (1% agarose). Then, mRNA was extracted from 120 µg of each total RNA sample, using Dynabeads mRNA purification kit (Invitrogen) and following the manufacturer’s instructions. The mRNA was eluted in 10,5 µl 10 mM Tris-HCl.  First strand cDNA was directly generated from the eluted mRNA using random hexamers (Invitrogen) and superscript RT kit (Invitrogen), following the manufacturer’s instructions. The final volume was 20 µl. The second strand cDNA synthesis was generated immediately after the first strand synthesis. Briefly, 1x Second strand buffer (Invitrogen), 200 nM final dNTPs (Invitrogen), 20 Units of E. coli DNA ligase (Invitrogen), 40 Units of E. coli polymerase (Invitrogen), and 4 Units of E. coli RNase H (Invitrogen) were added to the first strand cDNA and incubated for 2 hours at 16°C. Double stranded cDNA was then purified using QIA quick PCR purification kit, following the manufacturer’s instructions. The generated cDNA was quantified by UV spectrophotometry (Nanodrop). For the digital expression libraries, about 250 ng of the double-stranded cDNA of each sample  was fragmented by sonication on the UTR200 (Hielscher Ultrasonics GmbH, Germany) under following conditions: 1 hour, 50% pulse, 100% power, and continuous cooling by 0°C water flow-through. In brief the library preparation consisted of the following steps: end-repair, A-tailing, ligation of adapter primers, size selection and pre-amplification. For all samples, the libraries were prepared using the DNA sample kit (#FC-102-1002, Illumina), following the manufacturer’s instructions, but with the following modifications: five times reduced amount of all enzymes were used and adapters were ligated to the DNA fragments using 2 µl of ‘Adapter oligo mix’ in a total reaction volume of 25 µl. For the digital expression library, 250 ng of the sheared double stranded cDNA (see above) were used and 170-220bp fragments were selected at the gel size fractionation step.


title: S2 and KC cells

status: Public on May 01 2008

description: small RNAs

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

source_name: Drosophila melanogaster S2 and KC cell

extract_protocol: total RNA from S2 and KC cell, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: mix of 4 populations:

tag: 1. S2 cells

tag: 2. S2 cells treated with ecdysone for 48 hrs.

tag: 3. KC cells

tag: 4. KC cells treated with ecdysone for 48 hrs.


title: CE7

description: 7 day embryo

source_name: 7 day embryo

value: Ross-308™, Tissue:whole embryo, Stage:7 days of incubation


title: Col-0_RNA-seq


title: met1_RNA-seq


title: rdd_smRNA-seq

data_processing: Prior to alignment of the smRNA reads, a custom Perl script was used to identify the first seven bases of the 3? adapter sequence, and the read was truncated up to the junction with the adaptor sequence. Each of the reads was then mapped to the genome with BLAST using a word size of 10 and expectation value of 10. Only perfect matches were accepted, as these shorter reads will have a higher tendency to falsely map than longer reads. No further analysis was performed on reads that do not contain the adapter sequence, as their size class could not be determined precisely.

extract_protocol:
smRNA-seq library construction protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA). Immediately following RNA precipitation, the flow through from the anion-exchange chromatography column was further precipitated in another 2.5 volumes of 100% ethanol (smRNA fraction). The smRNA fraction was further purified by a phenol-chloroform extraction and an additional ethanol precipitation. Small RNAs were resolved by electrophoresis of 2.5 mg of the smRNA fraction and 7.5 mg of total RNA on 15% polyacrylamide gels containing 7 M urea in TBE buffer (45 mM Tris-borate, pH 8.0, and 1.0 mM EDTA). A gel slice containing RNAs of 15 to 35 nucleotides (based on the 10 base pair ladder size standard (Invitrogen, Carlsbad, CA)) was excised and eluted in 0.3 M NaCl rotating at room temperature for 4 hours. The eluted RNAs were precipitated using ethanol and resuspended in diethyl pyrocarbonatetreated deionized water. Gel-purified smRNA molecules were ligated sequentially to 5' and 3' RNA oligonucleotideadapters using T4 RNA ligase (10 units/mL) (Promega, Madison, WI). The 5' RNA adapter (5' - GUUCAGAGUUCUACAGUCCGACGAUC - 3') possessed 5' and 3' hydroxyl groups. The 3' RNA adapter (5'-pUCGUAUGCCGUCUUCUGCUUGidT-3') possessed a 5' mono-phosphate and a 3' inverted deoxythymidine (idT). The smRNAs were first ligated to the 5' RNA adapter. The ligation products were gel eluted and ligated to the 3' RNA adapter as described above. The final ligation products were then used as templates in a reverse transcription (RT) reaction using the RT-primer (5' - CAAGCAGAAGACGGCATACGA - 3') and Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA). This was followed by a limited (15 cycle) PCR amplification step using the PCR reverse (5'-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA-3') and forward (5'-CAAGCAGAAGACGGCATACGA-3') primers and Phusion hot-start high fidelity DNA polymerase (New England Biolabs, Cambridge, MA). All oligonucleotides were provided by Illumina (Illumina, San Diego, CA). The amplification products were separated by electrophoresis on a 6% polyacrylamide gel in TBE buffer, eluted in 0.3 M NaCl rotating at room temperature for 4 hours, precipitated using ethanol, and resuspended in nuclease-free water

tag: ros1-3 dml2-1 dml3-1, unopened flower buds


title: 6-10hr embryo

description: small RNAs


title: B cells rep2

description: raw sequence 070713_4


title: dcl2,3,4 inflorescence rep2 SBS

status: Public on Jun 10 2008

city: Newark

first: Marcelo

middle: Ariel

last: German

state: DE

address: 15 Innovation Way

institute: Delaware Biotechnology Institute

description: low molecular weight RNA used

data_processing: Raw abundances were normlazed according to the formula: normalized abundance (TP10M)= raw/(total genome match - (t/r/sn/snoRNA)*10,000,000.

source_name: inflorescence whole

extract_protocol: A conventional Trizol extraction was used for total RNA extraction, followed by oligo (dT) columns for polyA RNA extraction.

treatment_protocol: tissues and cells were harvested on ice

tag: floral tissue (up to stage 11/12)


title: Col-0_smRNA-seq

tag: Columbia-0, unopened flower buds


title: met1_smRNA-seq

tag: met1-3, unopened flower buds


title: rdr2 inflorescence rep1 SBS

description: low molecular weight RNA used


title: HEK293T cells rep2

description: raw sequence 070612_4

source_name: Human embryonic kidney cells


title: Imaginal disc

description: small RNAs

source_name: Drosophila melanogaster imaginal disc

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

tag: Drosophila melanogaster imaginal disc


title: KC cells

description: small RNAs

source_name: Drosophila melanogaster KC cell

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

tag: D. melanogaster KC cells


title: rdd_methylC-seq

data_processing: When mapping reads generated from bisulfite converted genomic DNA, converted cytosines will score as a mismatch and will adversely affect the ELAND alignment ability. Therefore reads were mapped against computationally bisulfite converted and non-converted genome sequences. As bisulfite conversion of cytosine to thymidine results in non-complementarity of the two strands of a DNA duplex, reads were mapped against two converted genome sequences, one with cytosine changed to thymidine to represent a converted Watson strand, and a second with guanine changed to adenosine to represent the converted Crick strand. For reads that aligned to multiple positions in the reference genome at 32 bases we utilized version (1.080214) of the cross_match algorithm (P. Green personal communication) to map these non-unique reads to a reference sequence that was repeat-masked for 50 bp perfect repeat sequence. To reduce clonal bias, short read sequences that mapped to the same start position were collapsed into a single consensus read. Where a base call within the consensus was contentious, the base to be retained was randomly selected.

growth_protocol: All plants were grown in potting soil (Metro Mix 250; Grace-Sierra, Boca Raton, FL) at 23?C under a 16-hour light/8-hour dark cycle.

extract_protocol: MethylC-seq library construction protocol: Genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen, Valencia, CA), and 5 µg of was fragmented by sonication to 50-500 bp with a Bioruptor (Diagenode Sparta, NJ), followed by end repair and ligation of methylated adapters provided by Illumina (Illumina, San Diego, CA) as per manufacturer?s instructions for gDNA library construction. 100-200 ng of adapter-ligated gDNA of 120-170 bp was isolated by agarose gel electrophoresis, and subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen, Valencia, CA), using the subsequent FFPE purification step, as outlined in the manufacturer?s instructions. The reaction was then purified once more using the PCR purification kit (Qiagen, Valencia, CA). Five ng of bisulfite-converted, adapter-ligated DNA molecules were enriched by 18 cycles of PCR with the following reaction composition: 2.5 U of uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Stratagene), 5 µl 10X PfuTurbo reaction buffer, 25 µM dNTPs, 1 µl Primer 1.1, 1 µl Primer 2.1 (50 µl final). The thermocyling was as follows: 95?C 2 min, 98?C 30 sec, then 18 cycles of 98?C 10 sec, 65?C 30 sec and 72?C 30 sec, completed with one 72?C 5 min step. The enriched library was purified with the PCR purification kit (Qiagen, Valencia, CA)and quantity and quality examined by spectrophotometry, gel electrophoresis, and limited sequencing of cloned library molecules.


title: HEK293T cells rep1

description: raw sequence 070612_3


title: HEK ChIP DNA rep2

description: raw sequence 070929_4

data_processing: After mapping of the reads to the genome, the replicates were pooled and resulted in 3,198,755 unique reads for two lanes of the RNA Pol II experiment and in 8,017,459 unique reads for three lanes of the control input DNA. The reads were sorted by their position on the chromosome and the start positions were used for the analysis. The RNA-Seq reads were analyzed for clusters of 10 reads in an initial window of  100 base pairs. 198 of the Pol-II clusters were overlapping with one of the input control clusters and thus were discarded.

source_name: Polymerase II ChIP DNA

growth_protocol: HEK 293T cells were cultured in parallel in 2*150 cm3 flasks with DMEM (penicillin-streptomycin) (Gibco) supplemented with 10% Fetal Calf Serum (FCS) (Biochrom) and Glutamax (1x) (Gibco). In short, 5-10 ? 107 293T/17 cells were cross-linked with 1% formaldehyde for 10 min and the reaction stopped by adding 1/20 volume of 2.5 M glycine. The cross-linked material was washed with PBS, lysed, and sonicated to an average size of 300 bp.

extract_protocol: The sheared chromatin was incubated with 10 µg specific antibody to RNA polymerase II (ab5408, recognizing the hypophosphorylated form of RNA pol II) coupled to protein G magnetic beads (Invitrogen) for 16 h at 4°C. An aliquot of the input DNA was saved prior to immunoprecipitation as reference sample. The DNA was finally recovered, after washing (wash buffer: 50 mM Hepes-KOH, pH 7.6), 500 mM LiCl;1mM EDTA; 1% NP-40; 0.7% Na-Deoxycholate)  and elution, by reversing the cross-linking overnight at 65° C in the elution buffer (50 mM Tris-HCl, pH 8.0; 10mM EDTA; 1% SDS). 80 ng of input DNA and 10 ng of ChIP DNA (see above) were taken for library preparation. The amplification was performed prior to gel size fractionation. 18 cycles of PCR with Illumina PCR primers were performed using an elongation time of 45 seconds. PCR-products were size fractionated and 150-300bp fragments were excised.


title: HEK Input DNA rep1

description: raw sequence 070710_4

source_name: Input DNA


title: met1_methylC-seq


title: ddc_methylC-seq

tag: drm1-2 drm2-2 cmt3-11, unopened flower buds


title: rdr2 inflorescence rep2 SBS

description: low molecular weight RNA used


title: Col-0_methylC-seq


title: HEK Input DNA rep3

description: raw sequence 070929_6


title: ddc_RNA-seq

tag: tissue


title: ddc_smRNA-seq


title: dcl2,3,4 inflorescence rep1 SBS

description: low molecular weight RNA used


title: HEK Input DNA rep2

description: raw sequence 070929_5


title: CE5

description: 5 day embryo

source_name: 5 day embryo

value: Ross-308™, Tissue:whole embryo, Stage:5 days of incubation


title: Platypus testis 18-24 nt

source_name: Adult testis


title: Drosophila melanogaster S2-GMR, first biological replicate

description: small RNAs

source_name: Drosophila melanogaster S2 cell

extract_protocol: total RNA from S2 cell, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: D. melanogaster S2 cells from Gerard Rubin's lab


title: HEK ChIP DNA rep1

description: raw sequence 070824_2


title: 0-1hr embryo #1

description: small RNAs

source_name: Drosophila melanogaster 0-1hr embryo

extract_protocol: total RNA from 0-1hr embryo, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: Drosophila melanogaster 0-1hr embryo


title: Echidna testis 18-24 nt

organism: Tachyglossus aculeatus

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


title: Female heads

status: Public on Apr 23 2008

description: Quality scores in the supplementary file for GSM240749 are undefined.  Quality of the bases assessed by (1) identifying for the sequenced linker, which is a known sequence, and (2) mapping the clipped sequence to the genome and taking only perfect hits.

source_name: Drosophila melanogaster female heads

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

value: female heads


title: Wild type inflorescence SBS

description: low molecular weight RNA used


title: ago2_non-beta-eliminated

status: Public on Apr 11 2008

type: other

city: Worcester

first: Hervé

last: Seitz

address: 364 Plantation Street

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

description:
This RNA sample was not beta-eliminated before adapter ligation.
This sample was not used in Ghildiyal et al. (2008) Science, where a better dataset (with optimized deep-sequencing protocol) was available (GEO sample #GSM278704).

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing:
Small RNA sequences were extracted from the deep-sequencing reads by the following procedure:
For n=29 nt, identify all the reads whose 5´ n-mer is immediately followed by the first trinucleotide (CTG) of the 3´ adapter, and whose 5´ n-mer perfectly maps on the Drosophila melanogaster genome (assembly R5.5 from FlyBase). These inserts are removed from the pool, and flagged as "29 nt-long inserts".
Decrease n iteratively (n=28 nt, n=27 nt, ...) and repeat the above procedure at each step, until n=18 nt.
Pool all 12 sets (29 nt-long inserts, 28 nt-long inserts, ..., 18 nt-long inserts), to generate the list of genome-matching inserts.

Raw data available at SRA under accession SRX000329

label: not applicable

molecule: other

source_name: ago2 mutant heads

label_protocol: not applicable

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

tag: Heads were dissected from ago2 mutant adult flies (ago2^{414} allele described in Okamura et al. (2004) Genes Dev. 18:1655-1666) as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)).


title: WT_males_non-beta-eliminated

description: This RNA sample was not beta-eliminated before adapter ligation.

data_processing:
Small RNA sequences were extracted from the deep-sequencing reads by the following procedure:
For n=29 nt, identify all the reads whose 5´ n-mer is immediately followed by the first trinucleotide (CTG) of the 3´ adapter, and whose 5´ n-mer perfectly maps on the Drosophila melanogaster genome (assembly R5.5 from FlyBase). These inserts are removed from the pool, and flagged as "29 nt-long inserts".
Decrease n iteratively (n=28 nt, n=27 nt, ...) and repeat the above procedure at each step, until n=18 nt.
Pool all 12 sets (29 nt-long inserts, 28 nt-long inserts, ..., 18 nt-long inserts), to generate the list of genome-matching inserts.

Raw data available at SRA under accession SRX000322

source_name: WT male heads

tag: Heads were dissected from Oregon R adult male flies as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)).


title: heterozygous_dcr-2_untreated

description:
This RNA sample was not beta-eliminated before adapter ligation.
This sample was used in Ghildiyal et al. (2008) Science.

data_processing:
Small RNA sequences were extracted from the deep-sequencing reads by the following procedure:
For n=29 nt, identify all the reads whose 5´ n-mer is immediately followed by the first trinucleotide (CTG) of the 3´ adapter, and whose 5´ n-mer perfectly maps on the Drosophila melanogaster genome (assembly R5.5 from FlyBase). These inserts are removed from the pool, and flagged as "29 nt-long inserts".
Decrease n iteratively (n=28 nt, n=27 nt, ...) and repeat the above procedure at each step, until n=18 nt.
Pool all 12 sets (29 nt-long inserts, 28 nt-long inserts, ..., 18 nt-long inserts), to generate the list of genome-matching inserts.

Raw data available at SRA under accession SRX000326

source_name: heterozygous dcr-2 mutant heads

tag: Heads were dissected from dcr-2 heterozygous adult flies (dcr-2^{L811fsX} allele described in Lee et al. (2004) Cell 117(1):69-81, over CyO balancer chromosome) as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)).


title: WT_females_non-beta-eliminated

data_processing:
Small RNA sequences were extracted from the deep-sequencing reads by the following procedure:
For n=29 nt, identify all the reads whose 5´ n-mer is immediately followed by the first trinucleotide (CTG) of the 3´ adapter, and whose 5´ n-mer perfectly maps on the Drosophila melanogaster genome (assembly R5.5 from FlyBase). These inserts are removed from the pool, and flagged as "29 nt-long inserts".
Decrease n iteratively (n=28 nt, n=27 nt, ...) and repeat the above procedure at each step, until n=18 nt.
Pool all 12 sets (29 nt-long inserts, 28 nt-long inserts, ..., 18 nt-long inserts), to generate the list of genome-matching inserts.

Raw data available at SRA under accession SRX000327

source_name: WT female heads

tag: Heads were dissected from Oregon R adult female flies as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)).


title: IR_non-beta-eliminated

data_processing:
Small RNA sequences were extracted from the deep-sequencing reads by the following procedure:
For n=29 nt, identify all the reads whose 5´ n-mer is immediately followed by the first trinucleotide (CTG) of the 3´ adapter, and whose 5´ n-mer perfectly maps on the Drosophila melanogaster genome (assembly R5.5 from FlyBase). These inserts are removed from the pool, and flagged as "29 nt-long inserts".
Decrease n iteratively (n=28 nt, n=27 nt, ...) and repeat the above procedure at each step, until n=18 nt.
Pool all 12 sets (29 nt-long inserts, 28 nt-long inserts, ..., 18 nt-long inserts), to generate the list of genome-matching inserts.

Raw data available at SRA under accession SRX000328

source_name: WT heads expressing an inverted repeat of white exon 3

tag: Heads were dissected from adult flies expressing an inverted repeat directed against white (Lee et al., Cell 117:69-81 (2004); Lee and Carthew, Methods 30


title: dcr-2_beta-eliminated

description:
This RNA sample was beta-eliminated as described in Horwich et al. (2007) Curr. Biol. 17(14):1265-1272 before adapter ligation.
This sample was not used in Ghildiyal et al. (2008) Science.

data_processing:
Small RNA sequences were extracted from the deep-sequencing reads by the following procedure:
For n=29 nt, identify all the reads whose 5´ n-mer is immediately followed by the first trinucleotide (CTG) of the 3´ adapter, and whose 5´ n-mer perfectly maps on the Drosophila melanogaster genome (assembly R5.5 from FlyBase). These inserts are removed from the pool, and flagged as "29 nt-long inserts".
Decrease n iteratively (n=28 nt, n=27 nt, ...) and repeat the above procedure at each step, until n=18 nt.
Pool all 12 sets (29 nt-long inserts, 28 nt-long inserts, ..., 18 nt-long inserts), to generate the list of genome-matching inserts.

Raw data available at SRA under accession SRX000320

source_name: dcr-2 mutant heads

tag: Heads were dissected from dcr-2 mutant adult flies (dcr-2^{L811fsX} allele described in Lee et al. (2004) Cell 117(1):69-81) as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)).


title: IR_beta-eliminated

description: This RNA sample was beta-eliminated as described in Horwich et al. (2007) Curr. Biol. 17(14):1265-1272 before adapter ligation.

data_processing:
Small RNA sequences were extracted from the deep-sequencing reads by the following procedure:
For n=29 nt, identify all the reads whose 5´ n-mer is immediately followed by the first trinucleotide (CTG) of the 3´ adapter, and whose 5´ n-mer perfectly maps on the Drosophila melanogaster genome (assembly R5.5 from FlyBase). These inserts are removed from the pool, and flagged as "29 nt-long inserts".
Decrease n iteratively (n=28 nt, n=27 nt, ...) and repeat the above procedure at each step, until n=18 nt.
Pool all 12 sets (29 nt-long inserts, 28 nt-long inserts, ..., 18 nt-long inserts), to generate the list of genome-matching inserts.

Raw data available at SRA under accession SRX000318