title: S2 Cell Nascent RNA 2

status: Public on Dec 01 2011

city: Waltham

first: Yevgenia

middle: L

last: Khodor

address: 415 South St, MS 008

department: Biology

institute: Brandeis University

description: NUN purification of nascent RNA

data_processing: Alignment: raw files were mapped to the Drosophila genome (dm3) by Tophat with Bowtie.

organism: Drosophila melanogaster

source_name: S2 Cells

growth_protocol: S2 cells were grown in Schneider Complete Media (10% FBS, 1% Pennicillin/Streptomycin) in a monolayer in T-75 flasks.  Yw flies were grown under standard conditions.

extract_protocol: Standard Illumina RNA-seq Protocol.  Briefly: RNA was fragmented with Ambion Fragmentation Reagent, reverse transcribed with SuperScript II RTase, and the second strand was synthesized with DNA Pol I.  Ends were repaired with a combination of Klenow Pol, T4 Pol, and PNK.  Overhang A's were ligated with Klenow exo- and adapters were ligated using A-T ligation.  A band of ~250nt was cut from an agarose gel and amplified via PCR.

tag: tissue type

value: Immortalized cells

tag: library source

value: Nascent RNA

tag: stable line

value: S2 cells were harvested and nuclei isolated. Nuclei were treated with NaCl, Urea, and NP-40 buffer (Wuarin and Schibler, 1994), and Nascent RNA was extracted from the pellet.


title: Fly Head Nascent RNA 2

type: SRA

state: MA

country: USA

description: NUN purification of nascent RNA

library_source: transcriptomic

molecule: total RNA

source_name: Heads

value: Adult fly heads

tag: strain

value: yellow-white

tag: treatment

value: Flies were harvested and frozen, and fly heads were isolated.  Heads were homogenized by grinding and nuclei were extracted. Nuclei were treated with NaCl, Urea, and NP-40 buffer (Wuarin and Schibler, 1994), and Nascent RNA was extracted from the pellet.


title: Fly Head Nascent RNA 1

description: NUN purification of nascent RNA


title: S2 Cell RpII215C4 Nascent RNA 2

description: NUN purification of nascent RNA

value: pAc-RpII215C4 integrated

value: 24hrs in alpha-amanitin


title: S2 Cell Nascent RNA 1

description: NUN purification of nascent RNA


title: S2 Cell pA 1

description: NUN purification of nascent RNA

value: pA RNA

value: For pA isolation, S2 cells were harvested using Trizol reagent and RNA extracted according to manufacturer's protocol.  pA RNA was isolated 2x on Invitrogen magnetic dT beads.


title: S2 Cell pA 2

description: NUN purification of nascent RNA


title: S2 Cell RpII215C4 Nascent RNA 1

description: NUN purification of nascent RNA


title: ikk-/- Reverse crosslink 6hr IFNb BMM

city: Huntsville

first: Jason

last: Gertz

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute

description: Input control for IP

library_source: genomic

data_processing:
STAT1 binding sites were identified with the program MACS, using the corresponding reverse cross-link sample as a control.
mm9

molecule: genomic DNA

organism: Mus musculus

source_name: bone marrow macrophages

growth_protocol: Bone marrow from Ikbke+/+ and Ikbke-/- mice was isolated, differentiated into macrophages with macrophage colony-stimulating factor (M-CSF), and either untreated or treated with IFNb or IFNg for six hours before crosslinking for chromatin isolation.

extract_protocol: Standard Illumina library construction

tag: genotype

value: Ikbke-/-

tag: cell type

value: Bone marrow macrophages

tag: chip antibody

value: IFNβ for 6 hour

tag: genetic background


title: ikk-/- Stat1 6hr IFNb BMM

description: Chromatin IP with STAT1 antibody

value: anti-STAT1α (santa cruz:sc-417)

tag: chip antibody manufacturer

value: Santa Cruz

tag: chip antibody catalog #


title: ikk-/- Reverse crosslink 6hr IFNg BMM

description: Input control for IP

value: IFNγ for 6 hour


title: ikk-/- Stat1 6hr IFNg BMM

description: Chromatin IP with STAT1 antibody


title: ikk-/- Stat1 untreated BMM

description: Chromatin IP with STAT1 antibody


title: WT Reverse crosslink 6hr IFNb BMM

description: Input control for IP

value: Ikbke+/+


title: Brg1 KD-Mbd3 ChIP

city: Boston

first: Jui-Hung

last: Hung

address: 24 cummington st

institute: Boston University

data_processing: The alignments are done using Bowtie allowing only one mismatch and unique mapper (*.mapped.txt). The aggregation signals around each TSS (+/- 4000bp) are tabulated in flat format (*.txt)

source_name: Brg1 KD-Mbd3 ChIP

growth_protocol: Feeder-free growth on gelatin coated dishes in standatd ES medium: KO DMEM + 10% FBS, glutamine, LIF, non-essential amino acids, beta-mercaptoethanol.

extract_protocol: ChIP material was  gel purified (100 to 800bp in size) from a 2% TAE agarose gel using  MiniElute columns QiaQuick (Qiagen). Gel purified DNA fragments were blunt ended and phosphorylated with an EPICENTRE End-it-Repair kit (1X buffer, 0.25mM dNTPs,1mM ATP, 1ul/50ul reaction of Enzyme mix) for 1hr at RT and cleaned up with Qiagen MiniElute spin columns. Adenosine nucleotide overhangs were added using EPICENTRE exo- Klenow for 45min at RT (with 0.2mM dATP). Illumina genome sequencing adaptors were then ligated using the EPICENTRE Fast-Link ligation kit: 11.5ul A tailed DNA eluted from a MinElute column was mixed with 1.5ul 10X ligation buffer, 0.75ul 10mMATP, 0.5ul Illumina DNA adaptors and 1ul ligase. The reaction was incubated for 1hr at RT and subsequently supplemented with 7.5 ul water, 1ul 10X buffer, 0.5ul 10mM ATP and 1ul ligase, and incubated overnight at 16C. The ligation reaction was cleaned up with MiniElute columns (with an additional wash step to eliminate all the excess adaptors) and the adaptor ligated fragments were amplified by PCR as follows:0.75 ul of each Illumina genomic DNA sequencing primers, 6ul 10xPfx buffer 1.8ul 10mM dNTPs, 1.2ul 50mM MgSO4 and 1ul Pfx DNA polymerase (Invitrogen) were added to 30ul DNA template in a 100ul reaction.  The cycling parameters were: 1. 94C 2'; 2. 94C 15''; 3. 65C 1'; 4. 68C 30''; 5. repeat from step 2 16 times; 6. 68C 5'. The PCR product (250 to 450bp in size) was gel purified from a 2% TAE agarose gel using the QiaQuick columns (Qiagen). Gel purified fragments were finally precipitated with Sodium acetate and ethanol and pellets were resuspended (25nM final concentration) in TE buffer.

treatment_protocol: In one 10 cm plate, 1.4X10^6 cells were transfected with 2 micrograms of esiRNA using Lipofectamine 2000. After 12-15 hours, the media was replaced and cells were cultured until 48 hours post-transfection.

tag: genotype/variation

value: Brg1 KD

value: embryonic stem (ES) cells

tag: chip antibody vendor & cat.#

value: Abcam (ab3755)


title: Brg1 KD-RNA Polymerase II ChIP

source_name: Brg1 KD-RNA Polymerase II ChIP

value: PolII

value: Santa Cruz (sc-899X)


title: Tet1 KD-Mbd3 ChIP

source_name: Tet1 KD-Mbd3 ChIP

value: Tet1 KD


title: EGFP KD-RNA Polymerase II ChIP

source_name: EGFP KD-RNA Polymerase II ChIP

value: EGFP KD


title: Mbd3 rep2 ChIP

source_name: Mbd3 ChIP

value: WT


title: Mbd3 KD-RNA Polymerase II ChIP

source_name: Mbd3 KD-RNA Polymerase II ChIP

value: Mbd3 KD


title: Mbd3 rep1 ChIP


title: WT Reverse crosslink 6hr IFNg BMM

description: Input control for IP


title: WT Stat1 6hr IFNb BMM

description: Chromatin IP with STAT1 antibody


title: WT Reverse crosslink untreated BMM

description: Input control for IP


title: WT Stat1 6hr IFNg BMM

description: Chromatin IP with STAT1 antibody


title: WT Stat1 untreated BMM

description: Chromatin IP with STAT1 antibody


title: PU.1_ChIPseq

city: Chicago

first: Sebastian

last: Pott

state: Il

address: 920 58th Street

department: Human Genetics

institute: University of Chicago

description: Chromatin IP against PU.1.

data_processing:
The raw images have been processed using the Solexa Pipeline and were mapped to the reference genome (NCBI36/hg18) using Eland software with maximal two-mismatches.

Peak detection was performed using CCAT (Xu et al. 2010). Regions enriched in the specific libraries were tested for significance against the tag distribution in a control library (IgG). Peaks with FDR <0.01 were considered for analysis.

organism: Homo sapiens

source_name: THP-1, PU.1 ChIP-Seq

growth_protocol: THP-1 cells were passaged in suspension prior to treatment; RPMI medium, 10%FBS, Pen/Strep.

extract_protocol:
Genomic DNA was isolated using phenol/chloroform extraction followed by ethanol precipitation.

10ng of DNA as per manufacturer's protocol. Briefly, using the Solexa ChIP-Seq DNA sample preparation kit, universal linkers were added to the chromatin fragments and DNA was PCR amplified for 15 cycles. DNA was gel-purified and fragments between 200-300bp were selected for sequencing.

treatment_protocol: THP-1 cells were differentiated with 50ng/ml of PMA for 40hrs, followed by treatment with Rosiglitazone for 1.5 hrs.

tag: cell line

value: monocytic cells

tag: treatment 1

value: differentiation with PMA (50ng/ml;40hrs)

tag: treatment 2

value: 1.5 h of 1microM Rosiglitazone

tag: antibody vendor

tag: antibody catalog #


title: PPARg_ChIPseq

description: Chromatin IP against PPARg.

source_name: THP-1, PPARg ChIP-Seq

value: anti-PPARg

value: PPMX

tag: antibody lot #


title: RV_Wt1 (Wildtype sample 1)

status: Public on Dec 09 2011

city: San Francisco

first: Gladstone

last: Bioinformatics

state: CA

address: 1650 Owens St

department: Data Science and Biotechnology

institute: Gladstone Institutes

description: Sample 3

data_processing: RNA expression levels: The raw data paired-end FASTQ files were first aligned to mm9 with TopHat 1.2.0 (with the specific command: tophat-1.2.0.Linux_x86_64/tophat --solexa1.3-quals -o <OUTPUT> --segment-mismatches 2 -m 2 --microexon-search -j dcc13/DSAGE/tables/mm9.juncs --butterfly-search -r 185 --mate-std-dev 75 mm9 <FIRST_FASTQ_FILE_IN_PAIR> <SECOND_FASTQ_FILE_IN_PAIR>). Mapped reads were aggregated into gene-level reads using Cufflinks. Differential expression P-values were calculated using the binomial test.

source_name: wt_heart_right ventricle

extract_protocol: Library construction protocol is described in detail in the following paper: Christodoulou, D. C., Gorham, J. M., Herman, D. S. and Seidman, J. 2011. Construction of Normalized RNA-seq Libraries for Next-Generation Sequencing Using the Crab Duplex-Specific Nuclease. Current Protocols in Molecular Biology. 94:4.12.1–4.12.11.  Short summary excerpt from the paper: "This unit describes the generation of a normalized RNA-seq library for next-generation sequencing by utilizing the preference of the crab duplex nuclease (DSN) for digesting double-stranded, rather than single-stranded DNA (unit 5.12; also see Zhulidov et al., 2004). In this approach (Basic Protocol), polyadenylated RNA is used to generate a complex RNA-seq library. The library is denatured and incompletely renatured, and then digested with DSN. The kinetics of DNA annealing are such that at any given time abundant DNA molecules are more likely to have re-annealed and become double stranded, while rare molecules are more likely to remain single stranded. Thus, preferentially digesting double-stranded DNA with DSN yields a library markedly enriched for more rare DNA species.

value: Mixed background of C57BL/6

tag: genetic variation

value: Wildtype

tag: development stage

value: Adult

tag: tissue

value: Heart, Right ventricle


title: ikk-/- Reverse crosslink untreated BMM

description: Input control for IP

tag: genotype

value: Ikbke-/-

value: Bone marrow macrophages

tag: treatment


title: Control_ChIPseq

description: Chromatin IP using IgG.

source_name: THP-1, control ChIP-Seq

tag: cell type

tag: chip antibody

value: normal mouse IgG

value: Santa Cruz


title: RXR_ChIPseq

description: Chromatin IP against all RXR isoforms.

source_name: THP-1, RXR ChIP-Seq

value: anti-pan-RXR


title: 3'end-seq for sorted sample

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

data_processing: Sequencing reads (72 nt) were first trimmed to 50 nt and then aligned to the WS190 genome using TopHat (Trapnell et al. 2009) allowing 2 mismatches. Only reads uniquely aligned to the genome were used for subsequent analyses.

molecule: nuclear RNA

organism: Caenorhabditis elegans

source_name: sorted nuclei

growth_protocol: Nuclei preparations for microscopy analysis were prepared at small scale (two to four 9 cm NGM plates) and those for flow cytometry experiments at large scale. For large scale assays, mixed stage 150 ml liquid cultures, grown at 25C, were harvested by three washes in M9 buffer (22 mM KH2PO4, 33.71 mM Na2HPO4, 85.56 mM NaCl, 1 mM MgSO4) and incubated for 30-45 min at 25C in M9 buffer for elimination of intestinal bacteria. The worm solution was subsequently passed through a 70 mm cell strainer (BD Biosciences) and the filtrate collected in 10 ml NBP (10 mM Hepes pH 7.6, 10 mM KCl, 1.5 mM MgCl2, 1 mM EGTA, 0.25 mM sucrose) per 250 ml worm slurry (estimated before filtration) for quick buffer exchange and enrichment of adults.

extract_protocol:
The RNA was extracted using Trizol from Invitrogen, following the manufacturer's instructions but adding 20 ug glycogen to each Eppendorf tube as an RNA carrier.
RNA isolated from input or sorted nuclei (about 65 ng) was amplified using the MessageAmp II aRNA amplification kit (Applied Biosystems) to create antisense RNA (aRNA). Briefly, the RNA was reverse transcribed using a primer (R1) containing the T7 promoter sequence and 24 Ts. After 2nd strand synthesis, double-stranded cDNAs were in vitro transcribed by T7 RNA polymerase to give rise to aRNAs. About 30 ng of aRNA per sample was used for ligation with a 3' adapter (Bioo Scientific), which is 5' adenylated and 3' blocked. Ligation was carried out at 22oC for 1 hr using truncated RNA ligase2 (Bioo Scientific). Ligated RNA was then reverse transcribed using Superscript II reverse transcriptase (Invitrogen), followed by 12 cycles of PCR amplification using a three primer mix (P1, P2 and P3). Primers P1 and P2 were used at the ratio of 1:10. P2 and P3 contained sequences for cluster generation on the Illumina flow cell. P3 also contained an index sequence for multiplex sequencing. The amplified PCR product was run in an 8% acrylamide gel, and the product corresponding to insert size of ~50-60 nt were excised from the gel and eluted overnight. Eluted DNA was purified by ethanol precipitation and was checked in an Agilent Bioanalyzer using the high sensitivity DNA kit (Agilent technologies). cDNA were then sequenced on an Illumina GA IIx.

tag: strain

value: intenstine


title: 3'end-seq for input sample

source_name: input nuclei

value: mixed tissues


title: Library L6

city: Magdeburg

first: Israel

last: Barrantes

state: Sachsen-Anhalt

address: Pfälzerstrasse 5

department: Lehrstuhl für Regulationsbiologie

country: Germany

institute: Otto-von-Guericke-Universität

data_processing: The sequencing output was trimmed for quality (Phred score > 15), and assembled de novo, together with a previously available cDNA sequence library from the same strain (Barrantes et al., 2010) using Mira (Chevreux et al., 2004). CAP3 (Huang and Madan, 1999) was used to reduce redundancy in the hybrid assembly. Later, to assess the differential expression, the sequencing output was splitted using the barcode information for each sample. Then the decoded outputs were mapped to the novel assembly with Bowtie (Langmead et al., 2009) and Samtools (Li et al., 2009), to obtain mapped read counts.

molecule: polyA RNA

organism: Badhamia polycephala

source_name: Starved plasmodium exposed to light and collected 6 hours after photoinduction

growth_protocol: Physarum macroplasmodia were cultured as previously described (Barrantes et al., 2010)

extract_protocol: Total RNA was then isolated from frozen plasmodial powders using the mirVana mRNA isolation kit. From this, poly(A)-RNA was prepared for cDNA synthesis, through incubation with calf intestine phosphatase and tobacco acid pyrophosphatase, followed by ligation of a RNA adapter to the 5'-phosphate of decapped mRNAs. cDNA synthesis was then performed with a N6 adapter primer and the MMLV- RNAse reverse transcriptase. The obtained RNAs were PCR-amplified for 22 cycles, including distinctive 4-bp 5'-barcodes for each sample. The resulting cDNAs were then pooled in equivalent amounts. cDNAs in the range of 250 to 450 bp were fractionated from agarose gels and used for Illumina/Solexa sequencing

tag: Stage

value: Macroplasmodium


title: K562 cells with shRNA targeting SRF gene cultured with doxycycline for 48 hours (48 hr), rep2.

first: Anita

last: Bansal

institute: HudsonAlpha Institute for Biotechnology

description: K562-shSRF cells showing decreased expression of SRF gene after induction of shRNA targeting SRF with doxycycline.

data_processing: Bowtie, Cufflinks

growth_protocol: Refer to http://hudsonalpha.org/sites/default/files/pdf/shRNA%20K562%20protocol.pdf for growing conditions for these cell lines

extract_protocol: Standard Illumina RNA-seq library construction

treatment_protocol: Refer to http://hudsonalpha.org/sites/default/files/pdf/shRNA%20K562%20protocol.pdf for culturing conditions for these cell lines

tag: cells

tag: shRNA expression

value: yes targeting SRF

value: Puromycin, doxycycline


title: Library L2

source_name: Plasmodium, 6 hours starvation, 30 minutes of exposure to far red light, and returned to dark and starvation for another 2 hours


title: Library D

source_name: Plasmodium, 6 hours starvation


title: K562 cells with shRNA targeting SRF gene cultured with no doxycycline (uninduced - UI), rep2.

description: Uninduced K562-shSRF cells used as control to measure the change in mRNA expression profile after SRF knock down

value: no

value: Puromycin


title: K562 cells with shRNA targeting SRF gene cultured with doxycycline for 48 hours (48 hr), rep1.

value: yes, targeting SRF


title: 5EL7_YPD_30_O21

status: Public on Nov 30 2011

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University Colege Dublin Conway Institute

data_processing: Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline. Reads were mapped to the Candida parapsilosis genome, All reads mapping only in one location with two or fewer mismatches were retained

organism: Candida parapsilosis

source_name: Total RNA from Candida parapsilosis

growth_protocol: Cells were grown in either YPD (1% Yeast Extract, 2% Peptone, 2% Glucose; FormediumTM), YPGlycerol (YPD with 2% glycerol instead of 2% glucose) or BMW (1.5% Yeast Extract, 1% Peptone, 2% Glucose, 0.2% SC Amino Acid mix, 0.01% Adenine, 0.01% Tryptophan, 0.01% Uracil); Cells were grown at 30°C and 21% O2 unless otherwise noted. Where indicated, cells were grown in 1% oxygen, 99% nitrogen in an InVivo2 400 hypoxic chamber and in two libraries, the temperature used was  either 30 or 37 degree Celsius. In some strains  the transcription factor UPC2 was deleted.

extract_protocol: mRNA purified from total RNA using oligo dT Dynabeads (Invitrogen) was fragmented to an average size of 200 nucleotides by a 5 minute heat treatment (70°C) with a buffered zinc solution (Fragmentation Reagent, Ambion). Fragmentation of mRNA was stopped using an EDTA based Stop buffer (Ambion). Fragmented mRNA was incubated with 3 μg Random Hexamer Primers at 65°C for 5 min. First strand cDNA synthesis was carried out using 1 x First Strand Buffer (Invitrogen), 10 mM DTT, 500 μM dNTP mix (Invitrogen), 20 Units RNaseOUT and 200 units SuperScriptTM II Reverse Transcriptase (Invitrogen). For strand-specific library generation, unincorporated dNTPs were subsequently removed using G-50 Micro Columns (GE Healthcare). Second strand cDNA was generated using 1x Second Strand Buffer, 300 μM dNTP mix, 2 units RNaseH, 50 units DNA Polymerase I (NEB), while a 300 μM dUTP mix was used instead of a dNTP mix for the generation of a strand specific library. This material was used for library preparation. For strand-specific libraries, DNA fragments were blunted in an End Repair reaction using T4 DNA Polymerase, Klenow DNA Polymerase and T4 Polynucleotide Kinase, after which a single ‘A’ base was added to the 3’ end using dATP and Klenow Exo Fragment. Illumina adapters were ligated to the ends of the DNA fragments, allowing for the subsequent hybridization to a flow cell. Fragments of approximately 300 base pairs were purified from a 2% Agarose Gel. For the strand-specific libraries, the second strand containing uridine was removed by treatment with 1 unit Uracil N-glycosylase (UNG) in TE Buffer at 37°C for 15 min. In all cases, purified adapter ligated DNA templates were then amplified through PCR enrichment, using PCR primers (Illumina), a dNTP mix, Phusion Polymerase (NEB) and 16 cycles of PCR. All libraries were quantified using a Qubit® Fluorometer (Invitrogen) and assessed on a 2% agarose gel. Amplified libraries were loaded on a flow cell. Sequencing was carried out in-house by running at least 36 cycles on an Illumina Genome Analyzer IIx according to manufacturer’s instructions, resulting in read lengths of approximately 42 bases. In addition, long reads (76 bases) were generated from two libraries by GATC Biotech AG using an Illumina Genome Analyzer IIx.

tag: medium

value: YPD

tag: temperature

value: 30 degree Celsius

tag: oxygen concentration


title: F1 E17.5 Brain RNA-seq Cross 2 (CxB)

city: Toronto

first: Brian

last: DeVeale

state: Ontario

address: 160 College Street, rm 1110

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: Dynabead mRNA Extraction following total RNA extraction with Trizol

data_processing: Alignment: Sequence reads were mapped to mouse genome (July 2007 NCBI 37/mm9) and a collection of all known and predicted splice junctions (Babak et al. 2010) using Novoalign. All uniquely aligning reads were retained for analysis.

source_name: Whole Brain

growth_protocol: Breeding pairs were fed ad libitum on standard chow

extract_protocol: Total RNA was extracted with Trizol followed by mRNA purification with dynabeads. Double stranded cDNA libraries were made using the Illumina mRNA-Seq kit according to the manufacturer's recommendations  (Illumina) and converted into libraries (adapter ligation, PCR, cleanup) using a NEBNext kit according to the manufacturer's recommendations (NEB). Libraries were verified on an Agilent Bioanalyzer and by qRT-PCR before sequencing.

treatment_protocol: Samples were snap chilled with liquid nitrogen immediately after dissection

value: Hybrid:F1 from CastEi/J mother x C57BL/6J father

tag: age


title: F1 E17.5 Brain RNA-seq Cross 1 (BxC)

value: Hybrid:F1 from C57BL/6J mother x CastEi/J father


title: 1E_BMW_30_O21

value: BMW


title: mRNA_male_adult_rep1

city: Beijing

first: Xianyu

last: Piao

address: Dong Dan San Tiao 9

department: Institute of Pathogen Biology

country: China

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing: if the reads contains more than four bases that sequencing quality less than 10 were deemed as low quality reads, low quality reads were removed before further analysis. Then the first 17 base pairs was cut from each reads as the expressed tag.

organism: Schistosoma japonicum

source_name: male adult mRNA

extract_protocol: Extract 6 µg of the total RNA, use Oligo (dT) magnetic beads adsorption to purify mRNA, and then use Oligo (dT) to guide reverse transcription to synthesize double-stranded cDNA. The generation of 5' ends of tags can be recognized with two types of Endonuclease: NlaIII or DpnII (see table 1 for recognition sites). Usually we use NlaIII which recognizes and cuts off the CATG sites on cDNA, then use magnetic beads precipitation to purify cDNA fragments with 3' ends and add Illumina adapter 1 to their 5' ends. The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which is a type of Endonuclease with separated recognition sites and digestion sites. It cuts at 17bp downstream of the CATG site, producing tags with adapter 1. After removing 3' fragments with magnetic beads precipitation, Illumina adapter 2 is introduced at 3' ends of tags, acquiring tags with different adapters at both ends to form a tag library. After 15 cycles of linear PCR amplification, 85 base strips are purified by 6% TBE PAGE Gel electrophoresis. These trips are then digested, and the single-chain molecules are fixed onto the Solexa Sequencing Chip (flowcell). Each molecule grows into a single-molecule cluster sequencing template through Situ amplification. Then add in four types of nucleotides which are labeled by four colors, and perform sequencing with the method of sequencing by synthesis (SBS). Each tunnel will generate millions of raw reads with sequencing length of 35bp.

value: China mainland

tag: developmental stage

value: adult

value: male adult


title: 5EL4_YPD_30_O1_UPC2KO

description: upc2 deletion


title: 4EL8_YPD_30_O21


title: K562 cells with shRNA targeting SRF gene cultured with no doxycycline (uninduced - UI), rep1.


title: 5EL2_YPD_30_O1


title: 4EL1_YPD_30_O1


title: 1E_YPD_30_O21


title: mRNA_female_adult_rep1

source_name: female adult mRNA

value: female adult


title: 3EL6_Mediamix_30_37_O21

description: mix of cDNA originated from different conditions: cells grown at 30 or 37 degree, in YPD or BMW media

value: mix of YPD and BMW medium

value: mix of 30 and 37 degree Celsius


title: 4EL2_YPD_30_O1


title: 4EL5_YPD_30_O1_UPC2KO

description: upc2 deletion


title: 3EL4_YPD_37_O21

value: 37 degree Celsius


title: 3EL2_YPD_30_O1


title: 2E2SL8_YPD_30_O21


title: 2E2SL7_BMW_30_O21


title: 2E2SL3_BMW_30_O21


title: 2E2SL2_YPD_30_O21


title: 2E2SL5_YPD_30_O21


title: 2E2SL6_YPD_30_O21


title: 2E2SL1_BMW_30_O21


title: 2E1SL5_YPD_30_O21


title: 2E1SL3_BMW_30_O21


title: 2E1SL8_YPD_30_O21


title: 2E1SL2_YPD_30_O21


title: 2E1SL1_BMW_30_O21


title: EedWT-CBX7

city: Oxford

first: Stephen

last: Taylor

address: Headington

country: United Kingdom

institute: CBRG

data_processing:
Pooled replicates were aligned using BOWTIE (Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25) using parameter -m 1 --best, visualized using GBrowser
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) using an FDR of <2 and number of tags >100
genome build: mm9

source_name: Embryonic stem cells WT

extract_protocol: ChIP DNA was end-repaired, A-tailed and adapter-ligated using a ChIP-seq DNA Sample prep Kit (Illumina). A Qiagen PCR purification step was performed following each enzymatic reaction. The adapter-ligated material was then PCR amplified, using 18 cycles of PCR before size selection of 200-500 bp fragments on an agarose gel. The library was then extracted using a Qiaquick gel extraction kit and checked for concentration and integrity.

treatment_protocol: Cells (1-2x108 cells) were fixed in PBS with 2 µM EGS (21565, thermofisher) for 1 h at RT. After washing cells were fixed again in ChIP fix buffer (1% formaldehyde, 5 µM EGTA, 10 µM EDTA, 1 mM NaCl and 0.5 mM HEPES in PBS) for 10 min at RT. Fixation was stopped by Glycine to a final concentration of 125 mM. Cell extracts were lysed (1% SDS, 10 mM EDTA pH 8.0, 50 mM Tris-HCl pH 8.1) with complete protease inhibitors (Roche) and sonication was performed using a BioRupter sonicator (Diagenode) to obtain an average DNA fragment size of 300 bp. Chromatin was diluted with 1% Triton X-100, 2 mM EDTA pH 8.0, 150 mM NaCl, 20 mM Tris-HCl pH 8.1 containing complete protease inhibitors. Protein G Sepharose and rProtein A Sepharose (17-0618-01 and 17-1279-01, respectively, GE Healthcare) were blocked for 1 h at 4 oC with 1 mg/ml BSA and 1 mg/ml yeast tRNA (R8759-500UN, Sigma). Chromatin was pre-cleared with blocked beads for 1 h at 4 oC.  150 µg of chromatin were incubated with Ring1B antibodie(Atsuta, T. et al. Production of monoclonal antibodies against mammalian Ring1B proteins. Hybridoma 20, 43-6 (2001)) ON at 4 oC with rotation. Protein-antibody complexes were pulled down by adding beads to the solution for 2 h. Complexes were washed 4 times with 1% SDS, 1% triton X-100, 2 mM EDTA pH 8.0, 150 mM NaCl and 200 mM Tris-HCl pH 8.0, followed by 1 washes in 0.1% SDS, 1% triton X-100, 500 mM NaCl and 20 mM Tris-HCl pH 8.1. The last wash was in TE. Samples were treated with RNase A and Proteinase K and reverse crosslinked ON. DNA was then purified using a PureLink PCR micro column (Invitrogen).

value: embryonic stem cells

tag: genotype/variation

value: wild type

tag: chip antibody vendor

value: Abcam

tag: chip antibody catalog #


title: EedKO-CBX7

value: Eed -/-


title: 2E1SL6_YPD_30_O21


title: 2E1SL7_BMW_30_O21


title: pancreas_flox_pool1

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: wild-type pool 1

library_source: non-genomic

data_processing: The sequence tags were aligned to the mouse (mm9) genome with Bowtie 3.

source_name: pancreas, flox

growth_protocol: To generate the tamoxifen-inducible cre Lrh1 deletion, mice with floxed Lrh1 alleles (Lee et al. 2008) were crossed with a ROSA26 Tam-ERCre strain (no. 004847, Jackson Laboratories). This line was backcrossed to generate a mixed strain, homozygous Lrh1 floxed, and heterozygous ROSA26 Tam-ERCre line. From this line, adult male mice with or without ROSA26 Tam-ERCre (3–5 mo old) were treated with 0.25 mg/g tamoxifen (T5648, Sigma-Aldrich) in corn oil by oral gavage for two consecutive days followed by sacrifice after 5 d. Mice were kept on a 12-h light–dark cycle from 6:00 am to 6:00 pm with free access to water and standard chow diet (TD.2016, Harland-Teklad Laboratories).

extract_protocol: Ten micrograms of total RNA from two separate pools of three Flox or two LRHt-/- pancreas RNA preparations was subjected to the Illumina RNA-seq protocol (Illumina). DNA (0.7 fmol) from each amplified library was analyzed with an Illumina Genome Analyzer.

tag: gender

value: male

tag: tissue

value: pancreas

value: wild-type


title: pancreas_LRHt-/-_pool1

description: LRH KO pool 1

source_name: pancreas, LRHt-/-

tag: genotype

value: LRHt-/-


title: Eed WT Input DNA replicate 3

data_processing:
Pooled replicates were aligned using BOWTIE (Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25) using parameter -m 1 --best, visualized using GBrowser
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) using an FDR of <2 and number of tags >100
BAM index file for Eed WT = Eed_WT.bam
BAM index file for pooled Eed KO replicates = Eed_KO.bam
BAM index file for pooled Input replicates = Input.bam
GFF Peak calls using MACS = Eed_WT.gff3
GFF Peak calls using MACS = Eed_KO.gff3

source_name: Embryonic stem cells

growth_protocol: All cells were cultured in KO DMEM supplemented with 10% FCS, 5% KO serum replacement (Invitrogen), Leukemia-Inhibitor factor, 50 µg/ml penicillin/streptomycin, 2 mM L-glutamine, 1x non-essential amino-acids and 50 µM 2-mercaptoethanol.

treatment_protocol:
Cells (1-2x108 cells) were fixed in PBS with 2 µM EGS (21565, thermofisher) for 1 h at RT. After washing cells were fixed again in ChIP fix buffer (1% formaldehyde, 5 µM EGTA, 10 µM EDTA, 1 mM NaCl and 0.5 mM HEPES in PBS) for 10 min at RT. Fixation was stopped by Glycine to a final concentration of 125 mM. Cell extracts were lysed (1% SDS, 10 mM EDTA pH 8.0, 50 mM Tris-HCl pH 8.1) with complete protease inhibitors (Roche) and sonication was performed using a BioRupter sonicator (Diagenode) to obtain an average DNA fragment size of 300 bp. Chromatin was diluted with 1% Triton X-100, 2 mM EDTA pH 8.0, 150 mM NaCl, 20 mM Tris-HCl pH 8.1 containing complete protease inhibitors. Protein G Sepharose and rProtein A Sepharose (17-0618-01 and 17-1279-01, respectively, GE Healthcare) were blocked for 1 h at 4 oC with 1 mg/ml BSA and 1 mg/ml yeast tRNA (R8759-500UN, Sigma). Chromatin was pre-cleared with blocked beads for 1 h at 4 oC. 150 µg of chromatin were incubated with Ring1B antibodies (Atsuta, T. et al. Production of monoclonal antibodies against mammalian Ring1B proteins. Hybridoma 20, 43-6 (2001)) ON at 4 oC with rotation. Protein-antibody complexes were pulled down by adding beads to the solution for 2 h. Complexes were washed 4 times with 1% SDS, 1% triton X-100, 2 mM EDTA pH 8.0, 150 mM NaCl and 200 mM Tris-HCl pH 8.0, followed by 1 washes in 0.1% SDS, 1% triton X-100, 500 mM NaCl and 20 mM Tris-HCl pH 8.1. The last wash was in TE. Samples were treated with RNase A and Proteinase K and reverse crosslinked ON. DNA was then purified using a PureLink PCR micro column (Invitrogen).
Antibody was received from Atsuta, T. et al. Production of monoclonal antibodies against mammalian Ring1B proteins. Hybridoma 20, 43-6 (2001)

tag: cell type

value: no IP


title: Eed WT Input DNA replicate 2

tag: chip antibody


title: Eed WT Input DNA replicate 1

tag: strain


title: EedKO-Ring1B replicate 3

source_name: Embryonic stem cells knockout for Eed


title: EedKO-Ring1B replicate 1


title: EedWT-Ring1B


title: pancreas_flox_pool2

description: wild-type pool 2


title: cDNA from reproductive Petromyzon marinus olfactory epithelia

city: East Lansing

first: Scot

last: Libants

state: MI

address: 13 Natural Resources Bldg.

department: Fisheries and Wildlife

institute: Michigan State University

description: total RNA from sea lamprey olfactory epithelia

data_processing: The TIGR SeqClean sequence trimming pipeline was used to remove low quality, low complexity, polyA/T and adapter sequences from the cDNA sequences prior to any analyses. Clustering and consensus assembly of the cDNA sequences was performed using the TIGR Gene Indices clustering tools (TGICL) The stringent filtering threshold was set for 95% sequence identity and 90% coverage of the cDNA sequence.  Clusters were generated ab initio and by using known full or partial cDNA sequences to seed the clustering. Contigs were used as queries in BLASTX searches against the NCBI protein and nucleotide nr databases to putatively identify their function.

organism: Petromyzon marinus

source_name: olfactory epithelia, reproductive phase, adult

growth_protocol: tissues collected from free-living animals

extract_protocol:
Total RNA was extracted using Perfect Pure RNA Tissue Kit (5 Prime, Gaithersburg, MD, USA) according to the manufacturer?s protocol, with an additional round of DNase treatment and wash. The quality of the extracted RNA was verified by gel electrophoresis and RNA concentration was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
1ug of total RNA was used as template for first strand cDNA synthesis using the SMART™ cDNA Synthesis Kit (Clontech Laboratories, Mountain View, CA, USA). 13 cycles of LD-PCR was performed to amplify single-strand cDNA using the Advantage® 2 PCR Kit (Clontech Laboratories) according to manufacturer’s instructions.

treatment_protocol: Adult (Library 1) animals captured  on spawning habitat in early June. Parasite (Library 2) animals were captured in Northern Lake Huron attached to fish caught by commercial fisherman and recreational anglers. Animals euthanized by overdose of the anesthetic tricaine methanesulfonate (MS-222).

value: adult (reproductive)

tag: behavioral phase

value: spawning

value: olfactory epithelium

tag: collection site

value: Lake Huron and Lake Michigan

tag: collection date

value: June

tag: library


title: cDNA from parasitic Petromyzon marinus olfactory epithelia

source_name: olfactory epithelia, parasitic phase, adult

value: adult (parasitic)

value: feeding

value: February and March


title: CSHL_RnaSeq_GM12878_cell_total

status: Public on Nov 29 2011

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlLongRnaSeq

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

tag: rnaextract

value: total

tag: rnaextract description

value: Total RNA extract (longer than 200 nt)

tag: biorep

tag: labexpid

tag: replicate

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: localization

value: cell

tag: localization description

value: Whole cell

tag: replicate description

value: tier 1


title: CSHL_RnaSeq_K562_cell_total

tag: cell karyotype

value: cancer


title: TKO2_H3K36me2_rep2

first: kaifu

last: chen

address: 1 Baylor plaza, suite 450A

description: Lauring J et al. Blood. 2008 Jan 15; 111 (2): 856-64.

data_processing: Reads are mapped to genome (hg18) using ELAND. Reads that are uniquely mapped and have no more than 2 mismatches are selected for future analysis. MACS is used to call peaks with p value 1e-8, DANPOS is used to calculated ChIP intensity.

extract_protocol: ChIP was performed using the corresponding antibodies and protein A-conjugated magnetic beads (Invitrogen). Briefly, cells were cross-linked with 1% formaldehyde and lysed with the buffer containing 50mM Tris-HCl pH=8.0, 10mM EDTA, 1% SDS and protease inhibitors. Cell lysate was sonicated with Branson Digital Sonifier (Branson) and diluted with RIPA buffer by 10 fold (v/v) before incubated overnight with antibody-protein A-magnetic beads complexes. In the next day, beads were washed three times with RIPA buffer and twice with TE buffer. IP   ed DNA was eluted from beads, de-crosslinked at 68    and purification by MinElute PCR Purification Kit (Qiagen). Purified DNA was subject to ChIP-sequencing analysis.

tag: cell line

tag: tissue type

value: blood

tag: genotype/variation

value: t(4;14)-associated NSD2 allele knocked-out

tag: gender

value: Female

tag: chip antibody

tag: chip antibody vendor

value: Active Motif

tag: chip antibody lot#

tag: chip antibody catalog#


title: TKO2_input


title: KMS11_Input


title: KMS11_H3K36me2_rep2


title: TKO2_H3K36me2_rep1


title: KMS11_H3K36me2_rep1


title: Input ChIP-seq

city: Detroit

first: Houtan

last: Noushmehr

address: 2799 W. Grand Blvd

institute: Henry Ford Health System

data_processing:
PEAKS: FindPeaks algorithm version 4.0 (http://sourceforge.net/apps/mediawiki/vancouvershortr/index.php?title=FindPeaks)
hg18

extract_protocol: Libraries for ChIP-seq were prepared following protocols recommended by Illumina.

value: none - input DNA


title: resistant biological replicate pool 3

city: Madison

first: Bart

middle: M. G.

last: Smits

address: 1400 University Avenue

department: Oncology

institute: University of Wisconsin-Madison

description: Gene expression data from rat primary T-cell samples

data_processing: The raw sequencing reads were processed into a list of unique seq reads and their respective counts in the 6 sample pools.

organism: Rattus norvegicus

source_name: splenic T-cells from 2 mammary carcinoma resistant congenic rat (carrying the Mcs5a resistance allele in susceptible control background)

growth_protocol: The rats were maintained at an AAALAC approved facility at the University of Wisconsin-Madison.

extract_protocol: A total of 10 mg RNA per sample pool was submitted to Illumina. Digital Gene Expreission (DGE) sample preparation using the NlaIII-based DGE kit and next-generation sequencing were performed by Illumina

treatment_protocol: Primary splenic T-cells were obtained from untreated rats

tag: cell type

value: splenic T-cells

tag: genotype

tag: genetic background

value: mixed Wistar Furth and Wistar Kyoto


title: pancreas_LRHt-/-_pool2

description: LRH KO pool 2

value: male

tag: developmental stage

value: adult

tag: tissue

value: pancreas

value: LRHt-/-


title: resistant biological replicate pool 2

source_name: splenic T-cells from 3 mammary carcinoma resistant congenic rat (carrying the Mcs5a resistance allele in susceptible control background)


title: Runx2 ChIP-seq

value: Runx2 Flag tagged

tag: chip antibody manufacturer

value: Sigma

tag: chip antibody catalog #

tag: chip antibody lot #


title: Cassava_not_infected

city: Montpellier

first: Alvaro

middle: Luis

last: Pérez-Quintero

state: Montpellier

address: 911 Avenue Agropolis

department: RBP

country: France

institute: IRD

description: small RNA

data_processing:
Redundant reads were collapsed and counted non redundant reads using unix scripts
Details: Redundant reads were collapsed and counted using unix commands (uniq -c). Various quality filters were applied to raw reads data. Sequences having less than 0.6 chastity value (measured by sequencing software) in the first 25 bases were removed. Adapter sequences were then removed with an in-house C++ program; this program removed any sequence fragments larger than 10nt from the original sequence matching the adapter sequence used in the libraries (5?-ATCTCGTATGCCGTCTTCTGCTTG-3?) and sequence fragments shorter than 10nt were only removed if they started after the 15thnt in the original sequence. The program used the EMBOSS wordfinder tool (Rice et al., 2000) to find adapter fragments (parameters: minimun match score =70, alignment width = 6, gap opening 0.0 + gap extension 10 or gap opening 500 + gap extension 10). Sequences shorter than 15nt, as well as low-complexity and low-quality sequences, were then removed using UNIX commands.

organism: Manihot esculenta

source_name: Leaves and stem tissues

growth_protocol: Cassava plants (variety MBRA685) were grown form cuttings and kept at a greenhouse at 26-30°C and 80% humidity up to six weeks

extract_protocol: RNA extractions were made using a LiCl-acid phenol:chloroform method. For library construction, adapters were added to total RNA (150µg/mL) and cDNA was synthesized using a Superscript Double-Stranded cDNA Synthesis kit (Invitrogen). cDNA was enriched through PCR and the small RNA fraction (10-50nt) was then separated on a denaturing polyacrylamide gel.

treatment_protocol: Leaves were inoculated by piercing six holes in the mesophyll and placing a 5µL drop of a liquid Xam-MgCl2 culture calibrated at OD600nm = 0.002 (1 x108cfu/ml). Two leaflets per leaf and three leaves per plant were inoculated. Stems were inoculated by puncture in the stems as described previously (24). At least three plants per collection time were inoculated. Leaves and stems were collected from inoculated plants (0 hours post inoculation -hpi, 6hpi, 24hpi, 2 days post-inoculation -dpi, 5dpi, 7dpi and 15dpi) and non-inoculated plants. RNA extractions were made using a LiCl-acid phenol:chloroform method.

tag: infection

value: control

tag: strain

tag: time post-inoculation


title: CSHL_RnaSeq_K562_cytosol_longPolyA (superseded by GSE90220)

description:
****************************
GSM840137 record metadata submitted on Nov 29 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90220
****************************

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: rnaextract

value: longPolyA

tag: rnaextract description

value: Poly(A)+ RNA longer than 200 nt

tag: biorep

tag: labexpid

tag: labversion

value: iIDR

tag: readtype

tag: readtype description

value: Paired 76 nt directed reads

tag: replicate

tag: spikeinpool

tag: localization description

value: The fluid between the cells outer membrane and the nucleus

value: Paired 76 n.t. directed reads

tag: replicate description


title: susceptible biological replicate pool 3

source_name: splenic T-cells from 3 mammary carcinoma susceptible congenic control rat

tag: cell type

value: splenic T-cells

tag: genotype

tag: genetic background


title: Cassava_xam_infected

description: small RNA

tag: infection

value: Xanthomonas axonopodis. pv manihotis

tag: strain

value: Xam CIO151

tag: time post-inoculation

value: 0 hours post inoculation -hpi, 6hpi, 24hpi, 2 days post-inoculation -dpi, 5dpi, 7dpi and 15dpi


title: susceptible biological replicate pool 2

value: mixed Wistar Furth and Wistar Kyoto


title: susceptible biological replicate pool 1

source_name: splenic T-cells from 3 mammary carcinoma susceptible congenic control rats


title: BL41_Input

status: Public on Nov 28 2011

city: Berlin

first: Volkhard

last: Seitz

address: Hindenburgdamm 30

department: Institute of Pathology

institute: Charité Universitätsmedizin

description:
Input control
Solexa (Ilumina) quality format: 1.3

data_processing:
The resulting sequence reads were mapped to the human reference genome (hg19 GRCh37) using Bowtie. Only reads that mapped uniquely with the Bowtie default setting (http://bowtie-bio.sourceforge.net/manual.shtml#the--n-alignment-mode) for mismatches were considered for further analysis (Bowtie option -m 1).
The detection of genomic regions enriched by ChIP vs. input control was conducted with Homer (v2.6) for each experiment individually . Unique reads were directionally extended in the 3' direction to a length of 300 base pairs. HOMER fits a local Poisson distribution to the input tags and tests the sequence depth corrected tag counts for being differentially expressed. This effectively removes peaks with low tag counts for which there is a chance the differential enrichment is found simply due to sampling error. Only ChIP regions with a p-value of less than 1e-6 under this local Poisson distribution were considered as putative peaks.

growth_protocol: Five human Burkitt lymphoma (BL) cell lines (Raji, CA46, Blue1, BL41, Ramos), were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) and supplemented with 10% Sera Plus (PAN Biotech, Aidenbach, Germany) at 37Â°C.

extract_protocol: Approximately 200 ng of ChIP-DNA was used as template for establishing an Illumina sequence library (Illumina, San Diego, CA, USA). The DNA was not further size fractionated and directly taken for adaptor ligation reactions, using a standard Illumina genomic library preparation kit.  In short, DNA was end-repaired using a mix 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 and dATP to yield a protruding 3-'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-350 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. These libraries were submitted to high-throughput sequencing on the Illumina Genome Analyzer II (GAII).

treatment_protocol: No treatment

value: B-cell  lymphoma cell line

value: B-cell

tag: chip antibody

value: No antibody (Input control)


title: Blue1_Input


title: CA46_Input


title: Raji_Input

description:
Input control
Solexa (Ilumina) quality format: 1.0

source_name: Raji


title: NRG1_grown_at 30C

city: Shanghai

first: Li

last: Qun

state: Shanghai

address: 300 Fenglin Road

department: National Key Laboratory of Plant Molecular Genetics

institute: Institute of plant physiology & ecology, SIBS, CAS

description: Solexa gene sequencing

data_processing: The 18-30nt tags from Solexa sequencing will go through the primary analysis first, which includes getting rid of the 5' adaptor, low quality tags and summarise the length distribution of the clean tags.

organism: Arabidopsis thaliana

source_name: NRG1_grown_at 30℃

growth_protocol: Arabidopsis Col-0 and NRG1 transgenic plants were grow at 22°C or 30°C for 4 weeks.

extract_protocol: Small RNAs were prepared from Arabidopsis seedings, 16-28 nt size fractionation was separated from total RNA and ligated to a 5' and a 3' adaptor sequentially, and then RT-PCR amplified. PCR products were provided for sequencing.

treatment_protocol: Total RNA was isolated from 4-week-old 22ºC or 30ºC-grown plants.

tag: ecotype

value: transgene Bri1-Xa21 plant

tag: cultivation temperature

tag: age

tag: tissue

value: seedlings


title: Ramos_ChIP

description:
Chromatin IP against c-MYC
Solexa (Ilumina) quality format: 1.3

source_name: Ramos

value: MYC antibody (N-262 Santa Cruz, CA, USA)

tag: chip antibody lot#

tag: chip antibody catalog#


title: Col-0_grown_at 30C

description: Solexa gene sequencing

source_name: Col-0_grown_at 30℃

value: wildtype


title: NRG1_grown_at 22C

description: Solexa gene sequencing

source_name: NRG1_grown_at 22℃


title: CA46_ChIP


title: Blue1_ChIP


title: Raji_ChIP

description:
Chromatin IP against c-MYC
Solexa (Ilumina) quality format: 1.0


title: NRG1_grown_from 30C to 22C

description: Solexa gene sequencing

source_name: NRG1_grown_from 30℃ to 22℃

value: 30℃ to 22℃


title: BL41_ChIP


title: Input_ES

status: Public on Nov 24 2011

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

description: genomic DNA derived from the chromatin input

data_processing: Reads (36bp) were aligned to the NCBI build 37 (mm9) with BWA v0.5.8 allowing 0/1 mismatches and unique mapped reads were converted to BED format. The aligned reads for MethylCap-seq_medium and MethylCap-seq_high were merged in an unique bed file.

source_name: E14 stem cells (TNG-A)

growth_protocol: Embryonic stem cells were cultured without feeders in the presence of leukaemia inhibitory factor (LIF) in DMEM containing 10% fetal calf serum.

extract_protocol: MeDIP-/hMeDIP-seq: ESC genomic DNA was purified and sonicated. Illumina adapters were ligated before MeDIP/hMeDIP. Adaptor-ligated DNA was denatured and incubated with 2µg of anti-5mC or 2µg of anti-5hmC antibody  at 4°C overnight. Antibody-DNA complexes were captured by magnetic beads and the immunoprecipitated DNA was purified and sequenced followed by standard Illumina protocols.    MethylCap-seq: ESC genomic DNA was purified and sonicated. Capturing of methylated DNA was done by incubating 2 ug of His6-GST-MBD (Diagenode) with 1 ug of fragmented DNA. GST-MBD-DNA complexs were captured by magnetic GST-beads. Beads-GST-MBD-DNA complexes were washed and eluted using different concentrations of NaCl. The collected eluates were purified using QIAquick PCR purification spin columns (Qiagen), eluted with 100ul elution buffer and prepared following standard Illumina protocols.

tag: sample type

value: Embryonic stem cells carrying the EGFP reporter at the Nanog locus (TNG) from Austin Smith

tag: antibody


title: hMEDIP_ES

description: hydroxymethylated DNA immunoprecipitation and sequencing

source_name: E14 stem cells

value: e14 clones from the sigtr gene-trap library passages:11-14

tag: vendor

value: Active Motif

tag: catalogue no. 39791


title: EedKO-Ring1B replicate 2

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: Eed -/-


title: MethylCap-seq_high

description: methylated DNA immunoprecipitation and sequencing

tag: elution

value: 800mM of NaCl solution


title: MEDIP_ES

value: Diagenode

tag: catalogue no. MAb-081-100


title: MethylCap-seq_medium

value: 600mM of NaCl solution


title: dRNA-seq of White barley plastids without TEX treatment

status: Public on Nov 23 2011

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing: For the mapping of the sequence reads, 5-linker and poly-A-tails clipped reads larger or equal to 18 nt were aligned to the barley chloroplast genome (NC_008590) using WU Blast 2.0 (http://blast.wustl.edu/) with the following parameters: -B=1 -V=1 -m=1 -n=-3 -Q=3 -R=3 -gspmax=1 -hspmax=1 -mformat=2 -e=0.0001. For each library, graphs representing the number of mapped reads per nucleotide were calculated as previously described (Sittka et al.,2008).

organism: Hordeum vulgare

source_name: plastids of primary leaves from 11-day-old white albostrians seedlings

growth_protocol: The barley mutant line albostrians was grown for 11 days in soil at 23 °C in a growth chamber with a photoperiod of 16h (light intensity: 150 mE s-1 m-2). The first leaves from completely green and white seedlings were used for plastid isolation.

extract_protocol: Total RNA from green and white plastids was cleaned from genomic DNA contamination by gDNA Wipeout buffer (QIAGEN). For depletion of processed transcripts, 7 ug of RNA from each sample was treated with TerminatorTM 5’-phosphate-dependent exonuclease (TEX; Epicentre #TER51020) or in buffer alone for 60 min at 30 °C. 1 unit TEX was used per 1 ug total chloroplast RNA. Following organic extraction (25:24:1 v/v phenol/chloroform/isoamyalcohol), RNA was recovered by overnight precipitation with 2.5 volumes of ethanol/0.1M sodium acetate (pH 6.5). RNA was further treated with 1 unit TAP (tobacco acid pyrophosphatase; Epicentre, #T19100) for 1 hour at 37 °C to generate 5’-mono-phosphates for linker ligation, and again purified by organic extraction and precipitation as described above. After addition of specific 5'linkers (with unique tags for each library) and polyA-tailing, the RNA was converted into a cDNA library. The cDNA libraries were sequenced on a Roche FLX sequencer.

tag: strain

value: cv. "Haisa"; albostrians mutant

value: primary leaves of white seedlings

tag: development stage

value: Mixed stage

tag: treatment

value: no TEX


title: dRNA-seq of White barley plastids with TEX treatment

value: TEX


title: dRNA-seq of Green barley plastids with TEX treatment

source_name: plastids of primary leaves from 11-day-old green albostrians seedlings

value: primary leaves of green seedlings


title: dRNA-seq of Green barley plastids without TEX treatment


title: Col-0_grown_at 22C

description: Solexa gene sequencing

source_name: Col-0_grown_at 22℃

tag: ecotype

value: seedlings


title: resistant biological replicate pool 1

value: splenic T-cells

tag: genotype

tag: genetic background

value: mixed Wistar Furth and Wistar Kyoto


city: Farmington

first: Brenton

middle: R

last: Graveley

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=574,Flow cell=B81CG2ABXX,Lane=3,Barcode=GATCAG,Third Instar Larvae, Wandering Stage,Carcass
Third Instar Larvae, Wandering Stage

data_processing:
574_L3_Wand_carcas_B81CG2ABXX_GATCAG_3_pA_plus.gff; genome build: dm3
574_L3_Wand_carcas_B81CG2ABXX_GATCAG_3_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: third instar larvae, wandering stage, carcass

growth_protocol: Oregon R Animals were grown under standard laboratory conditions.

extract_protocol: Total RNA was isolated from tissues dissected from Oregon R animals in biological duplicates. Strand-specific RNA-seq libraries were prepared using pre-release Directional mRNA-seq Library Kits (Illumina). Briefly, poly(A)+ RNA was isolated by oligo-dT selection, fragmented, and treated with phosphatase and polynucleotide kinase to repair the ends. 3’ and 5’ RNA adapters were then sequentially ligated to the RNA fragments and reverse transcribed using a primer complementary to the 3’ linker. The libraries were then PCR amplified. One nanogram of the strand-specific RNA-Seq libraries were reamplified by PCR using a primer complementary to the 5’ adapter and a second primer complementary to the 3’ adapter with six T residues at the 3’ end. After 10 rounds of amplification, the 3’ primer with the T extension was replaced with a 3’ primer complementary to the adapter with a 5’ extension containing a 6 nt index sequence and a sequence complementary to the flow cell primer. After an additional 15 rounds of amplication, the libraries were quantitated, 10-12 libraries were pooled together and sequenced.

treatment_protocol: None.

value: Oregon R

tag: tissue

value: Carcass

value: Third Instar Larvae, Wandering Stage

tag: flow cell

tag: lane

tag: barcode

value: GATCAG


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=583,Flow cell=B81CG2ABXX,Lane=4,Barcode=CGATGT,White Pre-Pupae,Fat
White Pre-Pupae

data_processing:
583_WPP_fat_B81CG2ABXX_CGATGT_4_pA_plus.gff; genome build: dm3
583_WPP_fat_B81CG2ABXX_CGATGT_4_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: WPP, fat body

value: Fat

value: White Pre-Pupae

value: CGATGT


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=577,Flow cell=B81CG2ABXX,Lane=3,Barcode=GGCTAC,Third Instar Larvae,Central Nervous System
Third Instar Larvae

data_processing:
577_L3_CNS_B81CG2ABXX_GGCTAC_3_pA_plus.gff; genome build: dm3
577_L3_CNS_B81CG2ABXX_GGCTAC_3_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: third instar larvae, CNS

value: Central Nervous System

value: Third Instar Larvae

value: GGCTAC


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=506,Flow cell=B81CG2ABXX,Lane=4,Barcode=CAGATC,Adult, Mated Male, Eclosion + 1 day,Head
Adult, Mated Male, Eclosion + 1 day

data_processing:
506_AdMateM_1d_head_B81CG2ABXX_CAGATC_4_pA_plus.gff; genome build: dm3
506_AdMateM_1d_head_B81CG2ABXX_CAGATC_4_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mated male, eclosion + 1 day, heads

value: Head

value: Adult, Eclosion + 1 day

tag: gender

value: Male

tag: mating status

value: Mated

value: CAGATC


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=586,Flow cell=B81CG2ABXX,Lane=4,Barcode=TTAGGC,White Pre-Pupae + 2 days,Central Nervous System
White Pre-Pupae + 2 days

data_processing:
586_Pup_WPP_2d_CNS_B81CG2ABXX_TTAGGC_4_pA_plus.gff; genome build: dm3
586_Pup_WPP_2d_CNS_B81CG2ABXX_TTAGGC_4_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: Pupae, WPP+2d, CNS

value: White Pre-Pupae + 2 days

value: TTAGGC


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=498,Flow cell=B81CG2ABXX,Lane=4,Barcode=ACTTGA,Adult, Virgin Female, Eclosion + 1 day,Head
Adult, Virgin Female, Eclosion + 1 day

data_processing:
498_AdVirF_1d_head_B81CG2ABXX_ACTTGA_4_pA_plus.gff; genome build: dm3
498_AdVirF_1d_head_B81CG2ABXX_ACTTGA_4_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: virgin female, eclosion + 1 day, heads

value: Oregon R

value: Female

value: Virgin

value: ACTTGA


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=580,Flow cell=B81CG2ABXX,Lane=3,Barcode=CTTGTA,White Pre-Pupae,
White Pre-Pupae

data_processing:
580_WPP_saliv_B81CG2ABXX_CTTGTA_3_pA_plus.gff; genome build: dm3
580_WPP_saliv_B81CG2ABXX_CTTGTA_3_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: WPP, salivary glands

value: Salivary Gland

value: CTTGTA


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=516,Flow cell=B81CG2ABXX,Lane=4,Barcode=GATCAG,Adult, Virgin Female, Eclosion + 4 days,Head
Adult, Virgin Female, Eclosion + 4 days

data_processing:
516_AdVirF_4d_head_B81CG2ABXX_GATCAG_4_pA_plus.gff; genome build: dm3
516_AdVirF_4d_head_B81CG2ABXX_GATCAG_4_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: virgin female, eclosion + 4 days, heads

value: Adult, Eclosion + 4 days

value: GATCAG


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=575,Flow cell=B81CG2ABXX,Lane=3,Barcode=TAGCTT,Third Instar Larvae, Wandering Stage,Carcass
Third Instar Larvae, Wandering Stage

data_processing:
575_L3_Wand_carcas_B81CG2ABXX_TAGCTT_3_pA_plus.gff; genome build: dm3
575_L3_Wand_carcas_B81CG2ABXX_TAGCTT_3_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

value: Carcass

value: Third Instar Larvae, Wandering Stage

value: TAGCTT


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=589,Flow cell=B81CG2ABXX,Lane=4,Barcode=ACAGTG,White Pre-Pupae + 2 days,Fat
White Pre-Pupae + 2 days

data_processing:
589_WPP_2d_fat_B81CG2ABXX_ACAGTG_4_pA_plus.gff; genome build: dm3
589_WPP_2d_fat_B81CG2ABXX_ACAGTG_4_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: WPP+2d, fat

value: Fat

value: ACAGTG


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=587,Flow cell=B81CG2ABXX,Lane=4,Barcode=TGACCA,White Pre-Pupae + 2 days,Central Nervous System
White Pre-Pupae + 2 days

data_processing:
587_Pup_WPP_2d_CNS_B81CG2ABXX_TGACCA_4_pA_plus.gff; genome build: dm3
587_Pup_WPP_2d_CNS_B81CG2ABXX_TGACCA_4_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

value: Central Nervous System

value: TGACCA


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=581,Flow cell=B81CG2ABXX,Lane=4,Barcode=ATCACG,White Pre-Pupae,Salivary Gland
White Pre-Pupae

data_processing:
581_WPP_saliv_B81CG2ABXX_ATCACG_4_pA_plus.gff; genome build: dm3
581_WPP_saliv_B81CG2ABXX_ATCACG_4_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

value: White Pre-Pupae

value: ATCACG


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=502,Flow cell=B81CG2ABXX,Lane=4,Barcode=GCCAAT,Adult, Mated Female, Eclosion + 1 day,Head
Adult, Mated Female, Eclosion + 1 day

data_processing:
502_AdMateF_1d_head_B81CG2ABXX_GCCAAT_4_pA_plus.gff; genome build: dm3
502_AdMateF_1d_head_B81CG2ABXX_GCCAAT_4_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mated female, eclosion + 1 day, heads

value: Oregon R

value: Head

value: Adult, Eclosion + 1 day

value: Mated

value: GCCAAT


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=532,Flow cell=B81CG2ABXX,Lane=4,Barcode=TAGCTT,Adult, Mated Female, Eclosion + 4 days,Ovaries
Adult, Mated Female, Eclosion + 4 days

data_processing:
532_AdMateF_4d_ovaries_B81CG2ABXX_TAGCTT_4_pA_plus.gff; genome build: dm3
532_AdMateF_4d_ovaries_B81CG2ABXX_TAGCTT_4_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mated female, eclosion + 4 days, ovaries

value: Ovaries

value: Female


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=571,Flow cell=B81CG2ABXX,Lane=3,Barcode=ACTTGA,Third Instar Larvae, Wandering Stage,Digestive System
Third Instar Larvae, Wandering Stage

data_processing:
571_L3_Wand_dig_sys_B81CG2ABXX_ACTTGA_3_pA_plus.gff; genome build: dm3
571_L3_Wand_dig_sys_B81CG2ABXX_ACTTGA_3_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: third instar larvae, wandering stage, digestive system

value: Digestive System

value: ACTTGA


title: Ramos_Input

description:
Input control
Solexa (Ilumina) quality format: 1.3

data_processing:
The resulting sequence reads were mapped to the human reference genome (hg19 GRCh37) using Bowtie. Only reads that mapped uniquely with the Bowtie default setting (http://bowtie-bio.sourceforge.net/manual.shtml#the--n-alignment-mode) for mismatches were considered for further analysis (Bowtie option -m 1).
The detection of genomic regions enriched by ChIP vs. input control was conducted with Homer (v2.6) for each experiment individually . Unique reads were directionally extended in the 3' direction to a length of 300 base pairs. HOMER fits a local Poisson distribution to the input tags and tests the sequence depth corrected tag counts for being differentially expressed. This effectively removes peaks with low tag counts for which there is a chance the differential enrichment is found simply due to sampling error. Only ChIP regions with a p-value of less than 1e-6 under this local Poisson distribution were considered as putative peaks.

source_name: Ramos

value: B-cell  lymphoma cell line

value: B-cell

tag: chip antibody

value: No antibody (Input control)


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=569,Flow cell=B81CG2ABXX,Lane=3,Barcode=CAGATC,Third Instar Larvae, Wandering Stage,Salivary Gland
Third Instar Larvae, Wandering Stage

data_processing:
569_L3_Wand_saliv_B81CG2ABXX_CAGATC_3_pA_plus.gff; genome build: dm3
569_L3_Wand_saliv_B81CG2ABXX_CAGATC_3_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: third instar larvae, wandering stage, salivary glands

value: Salivary Gland

value: Third Instar Larvae, Wandering Stage

value: CAGATC


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=568,Flow cell=B81CG2ABXX,Lane=3,Barcode=GCCAAT,Third Instar Larvae, Wandering Stage,Salivary Gland
Third Instar Larvae, Wandering Stage

data_processing:
568_L3_Wand_saliv_B81CG2ABXX_GCCAAT_3_pA_plus.gff; genome build: dm3
568_L3_Wand_saliv_B81CG2ABXX_GCCAAT_3_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=563,Flow cell=B81CG2ABXX,Lane=3,Barcode=TTAGGC,Third Instar Larvae, Wandering Stage,Fat
Third Instar Larvae, Wandering Stage

data_processing:
563_L3_Wand_fat_B81CG2ABXX_TTAGGC_3_pA_plus.gff; genome build: dm3
563_L3_Wand_fat_B81CG2ABXX_TTAGGC_3_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: third instar larvae, wandering stage, fat body

value: Fat

value: TTAGGC


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=564,Flow cell=B81CG2ABXX,Lane=3,Barcode=TGACCA,Third Instar Larvae, Wandering Stage,Fat
Third Instar Larvae, Wandering Stage

data_processing:
564_L3_Wand_fat_B81CG2ABXX_TGACCA_3_pA_plus.gff; genome build: dm3
564_L3_Wand_fat_B81CG2ABXX_TGACCA_3_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

value: Oregon R

value: TGACCA


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=557,Flow cell=B81CG2ABXX,Lane=3,Barcode=ATCACG,Adult, Mixed Male/Female, Eclosion + 20 days,Digestive System
Adult, Mixed Male/Female, Eclosion + 20 days

data_processing:
557_MixMF_20d_dig_sys_B81CG2ABXX_ATCACG_3_pA_plus.gff; genome build: dm3
557_MixMF_20d_dig_sys_B81CG2ABXX_ATCACG_3_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mixed males and females, eclosion + 20 days, digestive system

value: Adult, Eclosion + 20 days

value: Mixed Male/Female

value: ATCACG


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=551,Flow cell=B81CG2ABXX,Lane=2,Barcode=TAGCTT,Adult, Mated Female, Eclosion + 20 days,Head
Adult, Mated Female, Eclosion + 20 days

data_processing:
551_AdMateF_20d_head_B81CG2ABXX_TAGCTT_2_pA_plus.gff; genome build: dm3
551_AdMateF_20d_head_B81CG2ABXX_TAGCTT_2_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mated female, eclosion + 20 days, heads

value: Head

value: Mated

value: TAGCTT


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=554,Flow cell=B81CG2ABXX,Lane=2,Barcode=GGCTAC,Adult, Mated Male, Eclosion + 20 days,Head
Adult, Mated Male, Eclosion + 20 days

data_processing:
554_AdMateM_20d_head_B81CG2ABXX_GGCTAC_2_pA_plus.gff; genome build: dm3
554_AdMateM_20d_head_B81CG2ABXX_GGCTAC_2_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mated male, eclosion + 20 days, heads

value: Male

value: GGCTAC


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=556,Flow cell=B81CG2ABXX,Lane=2,Barcode=CTTGTA,Adult, Mixed Male/Female, Eclosion + 20 days,Digestive System
Adult, Mixed Male/Female, Eclosion + 20 days

data_processing:
556_MixMF_20d_dig_sys_B81CG2ABXX_CTTGTA_2_pA_plus.gff; genome build: dm3
556_MixMF_20d_dig_sys_B81CG2ABXX_CTTGTA_2_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

value: Digestive System

value: CTTGTA


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=539,Flow cell=B81CG2ABXX,Lane=2,Barcode=TTAGGC,Adult, Mated Male, Eclosion + 4 days,Accessory Gland
Adult, Mated Male, Eclosion + 4 days

data_processing:
539_AdMateM_4d_acc_gland_B81CG2ABXX_TTAGGC_2_pA_plus.gff; genome build: dm3
539_AdMateM_4d_acc_gland_B81CG2ABXX_TTAGGC_2_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mated male, eclosion + 4 days, accessory glands

value: Accessory Gland

value: Adult, Eclosion + 4 days


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=542,Flow cell=B81CG2ABXX,Lane=2,Barcode=ACAGTG,Adult, Mixed Male/Female, Eclosion + 4 days,Digestive System
Adult, Mixed Male/Female, Eclosion + 4 days

data_processing:
542_MixMF_4d_dig_sys_B81CG2ABXX_ACAGTG_2_pA_plus.gff; genome build: dm3
542_MixMF_4d_dig_sys_B81CG2ABXX_ACAGTG_2_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mixed males and females, eclosion + 4 days, digestive system

value: ACAGTG


title: Testes, Adult Miwi -/ADH [MR70]

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description:
Adult Library#2
Small RNA Miwi IP
read_length:  36

data_processing: Barcodes where removed, and trimmed reads were mapped to the mouse genome mm9. The software used for processing the data (genomic coordinates etc) from the raw data files are in-house tools from Sachidanandam lab. They are described in a publication: Olson, A.J., Brennecke, J., Aravin, A.A., Hannon, G.J. & Sachidanandam, R. Analysis of large-scale sequencing of small RNAs. Pac Symp Biocomput, 126-36 (2008).

source_name: Testes, Adult Miwi -/ADH

growth_protocol: mice were mated, grown and kept under standard conditions

extract_protocol:
Testes were dissected from male mice washed in and kept until processing in cold phosphate buffered saline solution.
Miwi-associated small RNAs were isolated from mouse testes and libraries prepared by sequential ligation of 5’- and 3’- RNA adapters. Sequencing was for 36 cycles using the Illumina Genome Analyzer IIx.   For RNAseq of round spermatids total RNA was depleted of abundant RNAs like rRNAs using Ribo-Zero kit (Epicentre). Strand-specific RNAseq library was prepared using the ScriptSeq mRNA-seq Library Preparation Kit (Epicentre; Cat no. SS10906). Sequencing was for 76 cycles by the Illumina Genome Analyzer.   For global 5’-RACE library, total RNA from purified round spermatids was depleted of rRNAs using the Ribo-Zero kit (Epicentre). Then Illumina 5’ RNA adapter was ligated to capture pre-existing 5’ ends. After purification using the Absolutely RNA kit (Stratagene), RNA was reverse-transcribed with a random primer and PCR amplified. PCR products of ~200 bp were gel-eluted for sequencing by the Illumina Genome Analyzer (105 cycles).
Most libraries are run in single lanes. Only one is duplexed and barcoded.

tag: developmental stage

value: Adult

value: Testes

value: Miwi -/ADH


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=547,Flow cell=B81CG2ABXX,Lane=2,Barcode=CAGATC,Adult, Virgin Female, Eclosion + 20 days,Head
Adult, Virgin Female, Eclosion + 20 days

data_processing:
547_AdVirF_20d_head_B81CG2ABXX_CAGATC_2_pA_plus.gff; genome build: dm3
547_AdVirF_20d_head_B81CG2ABXX_CAGATC_2_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: virgin female, eclosion + 20 days, heads

value: Oregon R

value: Female

value: Virgin

value: CAGATC


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=566,Flow cell=B81CG2ABXX,Lane=3,Barcode=ACAGTG,Third Instar Larvae, Wandering Stage,Imaginal Disc
Third Instar Larvae, Wandering Stage

data_processing:
566_L3_Wand_imag_disc_B81CG2ABXX_ACAGTG_3_pA_plus.gff; genome build: dm3
566_L3_Wand_imag_disc_B81CG2ABXX_ACAGTG_3_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: third instar larvae, wandering stage, imaginal discs

value: Imaginal Disc

value: Third Instar Larvae, Wandering Stage


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=535,Flow cell=B81CG2ABXX,Lane=2,Barcode=ATCACG,Adult, Mated Male, Eclosion + 4 days,Testes
Adult, Mated Male, Eclosion + 4 days

data_processing:
535_AdMateM_4d_testes_B81CG2ABXX_ATCACG_2_pA_plus.gff; genome build: dm3
535_AdMateM_4d_testes_B81CG2ABXX_ATCACG_2_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mated male, eclosion + 4 days, testes

value: Mated

value: ATCACG


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=531,Flow cell=B81CG2ABXX,Lane=1,Barcode=CTTGTA,Adult, Mated Female, Eclosion + 4 days,Ovaries
Adult, Mated Female, Eclosion + 4 days

data_processing:
531_AdMateF_4d_ovaries_B81CG2ABXX_CTTGTA_1_pA_plus.gff; genome build: dm3
531_AdMateF_4d_ovaries_B81CG2ABXX_CTTGTA_1_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

value: Ovaries


title: Testes, Adult Miwi +/ADH [MR19]

description:
Adult
Small RNA Miwi IP
read_length:  36

source_name: Testes, Adult Miwi +/ADH

tag: genotype/variation

value: Miwi +/ADH


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=544,Flow cell=B81CG2ABXX,Lane=2,Barcode=GCCAAT,Adult, Mixed Male/Female, Eclosion + 4 days,Carcass
Adult, Mixed Male/Female, Eclosion + 4 days

data_processing:
544_MixMF_4d_carcass_B81CG2ABXX_GCCAAT_2_pA_plus.gff; genome build: dm3
544_MixMF_4d_carcass_B81CG2ABXX_GCCAAT_2_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mixed males and females, eclosion + 4 days, carcass

value: Carcass

value: Mixed Male/Female

value: GCCAAT


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=548,Flow cell=B81CG2ABXX,Lane=2,Barcode=ACTTGA,Adult, Virgin Female, Eclosion + 20 days,Head
Adult, Virgin Female, Eclosion + 20 days

data_processing:
548_AdVirF_20d_head_B81CG2ABXX_ACTTGA_2_pA_plus.gff; genome build: dm3
548_AdVirF_20d_head_B81CG2ABXX_ACTTGA_2_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

value: Head

value: Adult, Eclosion + 20 days

value: ACTTGA


title: Testes, Adult Miwi +/+ [MR11]

description:
Adult-WT
Small RNA Miwi IP

source_name: Testes, Adult Miwi +/+

value: Adult

value: Testes

value: wildtype, Miwi +/+


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=541,Flow cell=B81CG2ABXX,Lane=2,Barcode=TGACCA,Adult, Mixed Male/Female, Eclosion + 4 days,Digestive System
Adult, Mixed Male/Female, Eclosion + 4 days

data_processing:
541_MixMF_4d_dig_sys_B81CG2ABXX_TGACCA_2_pA_plus.gff; genome build: dm3
541_MixMF_4d_dig_sys_B81CG2ABXX_TGACCA_2_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

value: Oregon R

value: Digestive System

value: Adult, Eclosion + 4 days

value: TGACCA


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=536,Flow cell=B81CG2ABXX,Lane=2,Barcode=CGATGT,Adult, Mated Male, Eclosion + 4 days,Testes
Adult, Mated Male, Eclosion + 4 days

data_processing:
536_AdMateM_4d_testes_B81CG2ABXX_CGATGT_2_pA_plus.gff; genome build: dm3
536_AdMateM_4d_testes_B81CG2ABXX_CGATGT_2_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

value: Male

value: Mated

value: CGATGT


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=524,Flow cell=B81CG2ABXX,Lane=1,Barcode=GATCAG,Adult, Mated Male, Eclosion + 4 days,Head
Adult, Mated Male, Eclosion + 4 days

data_processing:
524_AdMateM_4d_head_B81CG2ABXX_GATCAG_1_pA_plus.gff; genome build: dm3
524_AdMateM_4d_head_B81CG2ABXX_GATCAG_1_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mated male, eclosion + 4 days, heads

value: GATCAG


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=523,Flow cell=B81CG2ABXX,Lane=1,Barcode=ACTTGA,Adult, Mated Male, Eclosion + 4 days,Head
Adult, Mated Male, Eclosion + 4 days

data_processing:
523_AdMateM_4d_head_B81CG2ABXX_ACTTGA_1_pA_plus.gff; genome build: dm3
523_AdMateM_4d_head_B81CG2ABXX_ACTTGA_1_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.


title: Testes, P14 Miwi +/+ [MR09]

description:
P14-WT
Small RNA Miwi IP
read_length:  36

source_name: Testes, P14 Miwi +/+


title: Testes, Adult Miwi +/ADH [MR67]

description:
Adult
Strand-specific RNASeq
read_length:  76

value: Miwi +/ADH


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=527,Flow cell=B81CG2ABXX,Lane=1,Barcode=TAGCTT,Adult, Virgin Female, Eclosion + 4 days,Ovaries
Adult, Virgin Female, Eclosion + 4 days

data_processing:
527_AdVirF_4d_ovaries_B81CG2ABXX_TAGCTT_1_pA_plus.gff; genome build: dm3
527_AdVirF_4d_ovaries_B81CG2ABXX_TAGCTT_1_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: virgin female, eclosion + 4 days, ovaries

value: Ovaries

value: Female

value: Virgin

value: TAGCTT


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=528,Flow cell=B81CG2ABXX,Lane=1,Barcode=GGCTAC,Adult, Virgin Female, Eclosion + 4 days,Ovaries
Adult, Virgin Female, Eclosion + 4 days

data_processing:
528_AdVirF_4d_ovaries_B81CG2ABXX_GGCTAC_1_pA_plus.gff; genome build: dm3
528_AdVirF_4d_ovaries_B81CG2ABXX_GGCTAC_1_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

value: GGCTAC


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=497,Flow cell=B81CG2ABXX,Lane=1,Barcode=ATCACG,Adult, Virgin Female, Eclosion + 1 day,Head
Adult, Virgin Female, Eclosion + 1 day

data_processing:
497_AdVirF_1d_head_B81CG2ABXX_ATCACG_1_pA_plus.gff; genome build: dm3
497_AdVirF_1d_head_B81CG2ABXX_ATCACG_1_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: virgin female, eclosion + 1 day, heads

value: Head

value: Adult, Eclosion + 1 day

value: ATCACG


description:
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=520,Flow cell=B81CG2ABXX,Lane=1,Barcode=GCCAAT,Adult, Mated Female, Eclosion + 4 days,Head
Adult, Mated Female, Eclosion + 4 days

data_processing:
520_AdMateF_4d_head_B81CG2ABXX_GCCAAT_1_pA_plus.gff; genome build: dm3
520_AdMateF_4d_head_B81CG2ABXX_GCCAAT_1_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.

source_name: mated female, eclosion + 4 days, heads

value: Oregon R

value: GCCAAT