title: si-hPAF1-flu

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
Ivan_A549_NS1_siPAF_plus_flu_2011_05_19.bowtie.bam.bed: hg18

tag: transfected with

value: siRNA pools targeted to human PAF1

value: anti-Flag

tag: antibody vendor

value: Sigma

tag: antibody cat. #

value: crosslinked-DNA


title: si-CHD1-flu

status: Public on Jul 01 2013

type: SRA

city: new york

first: ivan

last: marazzi

state: ny

address: 1230 York Avenue

country: USA

institute: rockefeller univeristy

library_source: genomic

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
Ivan_A549_NS1_siCHD1_plus_flu_2011_05_19.bowtie.bam.bed: hg18

molecule: genomic DNA

organism: Homo sapiens

source_name: A549 cells

growth_protocol: Standard culture techniques

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions

treatment_protocol: For siRNA treatments, cells were transfected using Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen) according to the manufacturer’s instructions. siRNA pools targeted to either human PAF1 (L-020349-01, Dharmacon), CHD1 (L-008529-00, Dharmacon) or a control non-targeting pool (D-001810-10-05, Dharmacon) were transfected at a final siRNA concentration of 50 nM. Transfected cells were stimulated with the appropriate stimuli 48 hours post transfection. Gene knockdown efficiency was determined by quantitative PCR and/or Western blotting. For infections, the Flag-NS1 or Flag-∆PAF influenza virus was used at MOI 3.

tag: cell line

value: siRNA pools targeted to human CHD1

tag: infected with

value: Flag-NS1 virus

tag: time post infection

tag: antibody

tag: molecule type


title: Normal Brain 2

city: Philadelphia

first: Paul

last: Ryvkin

state: PA

address: 423 Guardian Dr, 1404 Blockley Hall

department: Pathology

institute: University of Pennsylvania

description: rRNA-depleted RNA

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adapter sequence using cutadapt v0.9 with options "-e 0.06 -O 6 -m 14 -n 2"
Reads were mapped to the genome (hg19) using bowtie with options "--best --strata -v 2 -k 100" and non-unique mappers were removed. Reads with a mismatch rate > 6% were discarded.
Reads mapping to known ribosomal RNA sequences via Bowtie were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files containing read counts for each trimmed, rRNA-masked sequence

molecule: total RNA

source_name: Dorsolateral prefrontal cortex

extract_protocol:
RNA was harvested from frozen brain tissue using Trizol reagent.
Illumina small RNA Sample Prep kit (#FC-102-1009) was used to construct libraries from 30ug total RNA. Instead of initial size fractionation, rRNAs were depleted by one round of Ribominus (Invitrogen).

tag: tissue

value: brain

tag: Sex

value: female

tag: pathology

value: normal


title: si-CTRL-flu

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
Ivan_A549_NS1_siCon_plus_flu_2011_05_19.bowtie.bam.bed: hg18

value: control non-targeting siRNA pool


title: PAF1C 12h

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
Ivan_A549_PAF_12h_2011_04_13_fastq.bowtie.bam.bed: hg18

value: Bethyl laboratories


title: PAF1C 0h

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
Ivan_A549_PAF_0h_2011_04_13_fastq.bowtie.bam.bed: hg18

value: none (uninfected)


title: meDIP-Seq untreated 12hr

status: Public on Jun 30 2013

city: Vancouver

first: Martin

last: Hirst

state: BC

address: 675 West 10th Avenue

department: Epigenomics

country: Canada

institute: BCCA Genome Sciences Centre

data_processing:
Base-calling software: Illumina RTA 1.12.4.2 <default>
Read Alignment Software: BWA v0.5.7 <default>
Read Sorting: Samtools
Mark Duplicates: Picard 1.60
Wiggle Track Generation: Findpeaks 4.01 <unthresholded>
Genome_build: genome build: mm9
Supplementary_files_format_and_content: Unthreasholded Wiggle Files

organism: Mus musculus

source_name: Embryonic stem cells, untreated

growth_protocol: ES cells were cultured on 0.1% gelatin coated plates in N2B27 medium supplemented with the MEK inhibitor PD0325901 (1μM, Stemgent), and the GSK3β inhibitor CHIR99021 (3μM, Selleck Chemicals), and LIF (1000U/ml, Millipore).

extract_protocol:
Phenol-chloroform-isoamyl alcohol extraction
For each sample, 12μg of genomic DNA was isolated, split into 3 replicates of 4ug each and sonicated to ~100-500 bp on a Covaris E210 platform (75s, 10% duty cycle; Covaris Inc.;). Sheared DNA was end-repaired, A-tailed, and ligated to custom paired-end adapters as described <Morin et al., Nature 2011>.    Ligated gDNA was size selected by 8% PAGE to remove unligated adapters (100-300bp), replicates pooled and subjected to qPCR using truncated PE1.0/2.0 PCR primers to assess ligation efficiency and quantified (quBit).   Adapter-ligated DNA from each sample was split into three equal replicates (0.5-1.5ug) and immunoprecipitation using mouse monoclonal anti-methylcytidine antibody (1 mg/ml, Eurogentec, catalog # BI-MECY-0100),  mouse monoclonal anti-hydroxymethylcytidine (hmC) antibody (Diagenode, EF-131-0050) or a nonspecific mouse IgG IP (Jackson Immunoresearch) as a negative control.  Synthetic hmC containing DNA was spiked into the hmC replicates to monitor immunoprecipitation efficiency. Adapted DNA was heat denatured at 95 ° C for 10 minutes, rapidly cooled on ice, and immunoprecipitated with 1 μl primary antibody per microgram of DNA overnight at 4° C with rocking agitation in 500 μl IP buffer (10 mM sodium phosphate buffer, pH 7.0, 140 mM NaCl, 0.05% Triton X-100). To recover the immunoabsorbed DNA fragments, 1 μl of rabbit anti-mouse IgG secondary antibody (2.5 mg/ml, Jackson Immunoresearch) and 100 μl Protein A/G beads (Pierce Biotechnology) were added and incubated for an additional 2 hr at 4° C with agitation. After immunoprecipitation a total of 6 IP washes were performed with ice cold IP buffer.  Washed beads were resuspended in TE with 0.25% SDS and 0.25 mg/ml proteinase K for 2 hrs at 55° C and then allowed to cool to room temperature. Immunoprecipitated and supernatant DNA were purified using Qiagen MinElute columns and eluted in 16 μl EB (Qiagen, USA). Fifteen cycles of PCR were performed on 5 μl of the immunoprecipitated DNA using the single end Illumina PCR primers. The resulting reactions are purified over Qiagen MinElute columns, after which a final size selection (192 -392 bp) was performed by electrophoresis in 2% agarose. Libraries were QC’d by spectrophotometry and Agilent DNA Bioanalyzer analysis.  An aliquot of each indexed library was pooled by sample and sequenced 2 per lane on an Illumina Hiseq2000 platform (2X76nt + 7nt) following the manufacturer’s recommended protocol and V3 chemistry (Illumina Inc.).

treatment_protocol: ES cells were cultured in the presence or absence of Vitamin C (L-ascorbic acid 2-phosphate, 100 μg/ml) for 12 or 72 hours.  Vitamin C was added to ES cells one day after seeding.  Medium with or without Vitamin C supplementation was replaced daily.

tag: cell type

value: Oct4-GiP ES cells

tag: treatment

value: untreated

tag: time point

tag: antibody target

value: mouse monoclonal anti-5-methylcytosine

value: Eurogentec

tag: antibody cat#

tag: antibody lot#


title: meDIP-Seq vitamin C treated 12hr

source_name: Embryonic stem cells, vitamin C treated

value: vitamin C treated


title: meDIP-Seq vitamin C treated 72hr


title: hmeDIP-Seq untreated 12hr

value: Diagenode


title: hmeDIP-Seq untreated 72hr


title: hmeDIP-Seq vitamin C treated 12hr


title: meDIP-Seq untreated 72hr


title: si-CTRL-ui

data_processing:
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read.
GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling
Genome Build:
Ivan_A549_NS1_siCon_2011_05_19.bowtie.bam.bed: hg18

tag: transfected with

value: anti-Flag


title: DmS2DRSC_ChIP_FSH_ID173

city: Basel

first: Christian

last: Beisel

address: Mattenstrasse 26

department: Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

data_processing: ChIP-seq reads were quality filtered (FASTX Toolkit 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html), fastq_quality_filter, parameters -Q 33-q 30 -p 75) and subsequently aligned with bowtie (default parameters) (Langmead2009) to the Flybase Drosophila melanogaster reference genome r5.22. For alignment file manipulation, Samtools were used LiSamtools2009.

organism: Drosophila melanogaster

source_name: DRSC-S2 cell line

growth_protocol: Drosophila S2-DRSC cells were grown in Schneiderâs Drosophila Medium (Invitrogen) supplemented with 10 % FBS (Hyclone) at 25Â°C.

extract_protocol: Chromatin fixation and immunoprecipitation were performed essentially as described in (Orlando V et al. (1997) Methods 11:205â214.). Cells (1x109) were fixed in 200-ml medium with 1% formaldehyde for 10 min at room temperature. Cross-linked cells were sonicated to produce chromatin fragments of an average size of 200â400 bp. Soluble chromatin was separated from insoluble material by centrifugation. The supernatant containing chromatin of 5x107 cells was taken for immunoprecipitation. Polyclonal rabbit antibodies for two different epitopes in Ash1 were a gift from Frank Sauer, Riverside. Polyclonal rabbit antibodies for FSH were a gift from Igor Dawid. The antibody ID173 was raised against protein 4.1 (recognizes FSH-L only) and ID166 was raised against the N-terminal, common part of FSH-S and FSH-L, protein 1.2. The cDNAs used for the expression of both antigenes have been described in (Haynes et al. (1989) Dev.Biol. 134)   Libraries for sequencing were prepared with the ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illumina's instructions. After adapter ligation library fragments of ~250 bp were band isolated from an agarose gel. The DNA was PCR amplified with Illumina primers for 18 (ChIP-seq) cycles, purified and loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

value: DRSC-S2 cell line

tag: chip antibody

value: FSH_ID173 [raised against protein 4.1 (recognizes FSH-L only)]

tag: chip antibody supplier

value: gift from Igor Dawid


title: DmS2DRSC_ChIP_Ash1C

tag: cell line

value: gift from Frank Sauer, Riverside


title: DmS2DRSC_ChIP_FSH_ID166

value: FSH_ID166 [raised against the N-terminal, common part of FSH-S and FSH-L, protein 1.2]


title: AngII_H3K4me3_ChIPseq

city: Duarte

first: Amy

last: Leung

address: 1500 E. Duarte Rd

department: Diabetes/Cancer

institute: Beckman Research Institute, City of Hope

data_processing:
ChIP-seq: Reads were aligned to the rn4 version of the rat genome using Bowtie. RSEG was used to identify regions of enriched H3K4me3 and H3K36me3.
Genome_build: rn4
Supplementary_files_format_and_content: ChIP-seq: RSEG output file: bed file with score.

organism: Rattus norvegicus

source_name: vascular smooth muscle cells, AngII-stimulated, H3K4me3 ChIP

growth_protocol: Primary VSMCs were isolated from thoracic aortas and cultured in M199 media supplemented with antibiotics and fetal bovine serum.

extract_protocol: Standard phenol/chloroform was used to extract DNA. DNA was end repaired (Epicentre #ER81050), A-tailed (NEB #m0212l), ligated to Illumina adapters (Promega Cat#M8221), and PCR amplified (NEB Cat# M0531L). Adapter-ligated, amplified fragments were selected from an agarose gel.

treatment_protocol: Cells were starved overnight of fetal bovine serum and treated with AngII (0.1uM) for 3 hours.

tag: strain

value: Sprague-Dawley

value: cultured primary vascular smooth muscle cells (VSMCs)

value: angiotensin II (AngII)

tag: antibody vendor

value: Millipore

tag: antibody catalog #


title: AngII_RNAseq

data_processing:
RNA-seq: Reads were aligned to the rn4 version of the rat genome using Tophat. Cufflinks was used to identify transcripts and Cuffdiff was used to identify differentially expressed genes.
Genome_build: rn4
Supplementary_files_format_and_content: RNA-seq: Cuffdiff output file: fpkm_tracking.

source_name: vascular smooth muscle cells, AngII-stimulated

extract_protocol: RNA-seq: Ribo-minus (Invitrogen Cat. No A10837-08) and Illumina RNA-seq library preparation (Illumina Cat No. FC-122-1002).


title: AngII_H3K36me3_ChIPseq

source_name: vascular smooth muscle cells, AngII-stimulated, H3K36me3 ChIP

value: Abcam


title: DmS2DRSC_ChIP_Ash1N


title: Control_H3K4me3_ChIPseq

source_name: vascular smooth muscle cells, H3K4me3 ChIP


title: AngII_Input_ChIPseq

data_processing:
ChIP-seq: Reads were aligned to the rn4 version of the rat genome using Bowtie. RSEG was used to identify regions of enriched H3K4me3 and H3K36me3.
Genome_build: rn4

source_name: vascular smooth muscle cells, AngII-stimulated, input


title: EXP_6_Pool_RNA_HF_LP_9_10.14.09

status: Public on Jun 29 2013

city: St Louis

first: Federico

middle: E

last: Rey

state: MO

address: 4444 Forest Park Blvd

institute: Washington University

description: Fecal pellet from a mouse (NMRI) colonized with 9-gut bacteria. Mouse was fed a HF/HS diet from Harlan Teklad (09055)

data_processing:
Splitting barcodes - Sequence runs were split into their respective experiments using the 4-bp/8bp barcode at the beginning of each sequencing read.
Mapping reads - After dividing sequence runs by barcode, we mapped the reads to the relevant genomes using the ssaha2 algorithm
Handling ties - Reads that map non-uniquely were added to each gene in proportion to each gene’s fraction of unique-match counts (e.g., a non-unique read that maps equally well to gene A with 18 unique reads and gene B with 2 unique reads will be scored as 0.9 count to gene A and 0.1 count to gene B). We added a pseudocount (i.e. added 1) to each gene count prior to normalization to account for differences in sampling depth.

organism:
[Clostridium] symbiosum
Bacteroides thetaiotaomicron VPI-5482
Bacteroides ovatus ATCC 8483
Bacteroides caccae ATCC 43185
Collinsella aerofaciens ATCC 25986
Marvinbryantia formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Agathobacter rectalis ATCC 33656
Desulfovibrio piger GOR1

source_name: Fecal

extract_protocol:
Each frozen sample was suspended in a solution containing 500 mL of acid-washed glass beads (Sigma-Aldrich), 500 mL of extraction buffer A (200 mM NaCl, 20 mM EDTA), 210 mL of 20% SDS, and 500 mL of a mixture of phenol:chloroform:isoamyl alcohol (125:24:1, pH 4.5; Ambion), and then lysed by using a bead beater (BioSpec Products; maximal setting; 4 min at room temperature). Cellular debris was removed by centrifugation (8,000 × g; 3 min at 4°C). The extraction was repeated, and nucleic acids were precipitated with isopropanol and sodium acetate (pH 5.5).
DNA libraries were prepared for sequencing using a modified version of Illumina's sample preparation protocol (see  PMID:22030749 for protocol details)

treatment_protocol: Fecal samples obtained from mice  were immediately frozen at -80C and maintained at this temperature prior to processing.

tag: rna subtype

value: rRNA depleted total RNA

tag: source

tag: processed data filename


title: EXP_12_Dp5

description: Fecal pellet from a mouse (NMRI) colonized with 9-gut bacteria. Mouse was fed a high fat/high sugar diet supplemented with 3% chondroitin sulfate (HF/HS+3%CS) TD.110459


title: EXP_6_Pool_RNA_K1_10.14.09

description: Fecal pellet from a mouse (NMRI) colonized with 9-gut bacteria. Mouse was fed a polysaccharide rich diet (BK chow)


title: Control_Input_ChIPseq

source_name: vascular smooth muscle cells, input


title: Control_RNAseq

source_name: vascular smooth muscle cells, untreated


title: macrophages control (IFNAR wt/ko) #5

city: Dresden

first: Tina

last: Schumann

address: Fetscherstraße 74

department: Medical Faculty "Carl Gustav Carus"

country: Germany

institute: Institute of Immunology

description:
S1899_mp_Kontrolle_5
Strand specific RNA-Seq

data_processing:
Read Alignment: pBWA version 0.5.9-r32-MPI-patch2 against mm9 (UCSC)
Counts per feature: Reads per exon were computed using bedtools version 2.11, summarized per gene based on Ensembl Gene 61 annotation.
Normalization of reads per gene: The raw counts (absolute number of reads) were normalized with the DESeq R package (v.1.8.1) and sample to sample correlation (Pearson's correlation coefficient) was computed based on the normalized counts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited 'counts' file with sample size normalized counts per gene (rows) and sample (columns)

source_name: mouse peritoneal macrophages

extract_protocol:
Cells were lysed immediately in µMACS™ mRNA Isolation Kit lysis buffer and cleaned with with LysateClear Columns (Miltenyi Biotec). mRNA was enriched using Oligo(dT) beads.
Poly-dT-enrichment, DNAse treatment, chemical fragmentation, ss-Synthesis, strand specific library prep according to: Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 2009 Jul 20. doi:10.1093/nar/gkp596

tag: age

value: 18 weeks

tag: gender

value: female

value: peritoneal macrophage


title: hmeDIP-Seq vitamin C treated 72hr

tag: cell type

value: Oct4-GiP ES cells

tag: treatment

value: vitamin C treated


title: EXP_12_Dp7

value: Fecal pellet from a mouse (NMRI) colonized with 9-gut bacteria. Mouse was fed a high fat/high sugar diet supplemented with 3% chondroitin sulfate (HF/HS+3%CS) TD.110459


title: EXP_12_NoDp1

description: Fecal pellet from a mouse (NMRI) colonized with 8-gut bacteria. Mouse was fed a high fat/high sugar diet supplemented with 3% chondroitin sulfate (HF/HS+3%CS) TD.110459


title: EXP_12_NoDp2

value: Fecal pellet from a mouse (NMRI) colonized with 8-gut bacteria. Mouse was fed a high fat/high sugar diet supplemented with 3% chondroitin sulfate (HF/HS+3%CS) TD.110459


title: EXP_12_Dp8


title: EXP_12_Dp6


title: EXP_12_NoDp3


title: EXP_12_NoDp4


title: Control_H3K36me3_ChIPseq

source_name: vascular smooth muscle cells, H3K36me3 ChIP


title: EXP_6_Pool_RNA_HF_LP_10_10.14.09

value: Fecal pellet from a mouse (NMRI) colonized with 9-gut bacteria. Mouse was fed a HF/HS diet from Harlan Teklad (09055)


title: EXP_6_Pool_RNA_K4_10.14.09

value: Fecal pellet from a mouse (NMRI) colonized with 9-gut bacteria. Mouse was fed a polysaccharide rich diet (BK chow)


title: BXM 15DAP

city: Tucson

first: Xiangfeng

last: Wang

address: 1140 E. South Campus Drive, Marley Building 541C

department: School of Plant Sciences

institute: University of Arizona

data_processing:
Illumina RTA software used for basecalling.
Sequenced reads were mapped to maize reference genome using tophat2.0.4 with parameters –bowtie1 -r 200 -I 5000 --mate-std-dev 100 -g 5 --max-segment-intron 5000 -n 3 --genome-read-mismatch 4 --read-mismatches 4
Gene expression level was estimated as the sum of all reads mapped to the whole gene region using the intersectBed command implemented in the BEDTools package.
Genome_build: B73_RefGen_v2
Supplementary_files_format_and_content: tab-delimited text files include count-based values for each gene

organism: Zea mays

source_name: maize

extract_protocol:
The total RNA was isolated from the 36 (12 samples × 3 replicates) groups of plant material using the SDS-Phenol method (Shirzadegan et al., 1991) with the following modification: ~1 g of tissue was ground to a fine powder in liquid nitrogen and homogenized with 6 ml of SDS buffer containing 1% SDS, 50 mMTris-Cl (pH8.0), 150 mMLiCl, 5 mM EDTA (pH 8.0), and 10 mM DTT. The homogenate was mixed with 6 ml phenol:chloroform (5:1, pH4.5, Ambion AM9720) and incubated on ice for 5 min. The mixture was transferred to a 50 ml Phase-Lock-Gel (PLG) tube (5 Prime) and centrifuged at 5,000 rpm (SS-34 rotor) for 10 min at 4°C. The aqueous phase was transferred to a new 50 ml PLG tube. The previous step was repeated with phenol:chloroform (1:1) and chloroform alone. The RNA pellet was precipitated with a 2.5 M LiCl on ice for overnight and washed with ice-cold 2M LiCl. The pellet was then dissolved in TE and mixed with a 1/9 volume of 3 M NaAC (pH5.2) and 2.5 volume of ethanol. The mixture was incubated in a -80°C freezer for at least 4 h. The RNA was pelleted by centrifuge at 14,000 rpm for 15 min at 4°C. After rinsing with 75% ethanol and air-drying, the RNA was dissolved in diethylpyrocarbonate-treated water. The genomic DNA was removed by TURBO DNase I (Ambion) and purified using an RNeasy column (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: endosperm

tag: genotype


title: MXB 15DAP


title: MXB 10DAP


title: BXM 7DAP


title: BXM 10DAP


title: BXM 3DAP

value: kernel


title: BXM 0DAP


title: MXB 0DAP


title: MXB 3DAP


title: BXM 5DAP


title: Drn1-TAP CLIP-seq replicate 1

status: Public on Jun 28 2013

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

data_processing:
Reads were aligned to theUCSC sacCer1 genome using bowtie2
BAM alignment files were processed to genome coverage in bedGraph format using bedtools
BedGraph files were coverted to BigWig format for display in the UCSC Genome Browser
Genome_build: sacCer1
Supplementary_files_format_and_content: Genome coverage for positive strand in bedGraph format
Supplementary_files_format_and_content: Genome coverage for negative strand in bedGraph format

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae

growth_protocol: Yeast cells were grown in YEPD at 30 ˚C to an OD600 ~2.0

extract_protocol:
Cells were  frozen in liquid nitrogen and lysed with a SPEX SamplePrep 6870 Freezer Mill (SPEX CertiPrep)
The supernatant was treated with RNase A/T1 cocktail (Ambion) at 37 ˚C for 10 minutes (0.05 unit of RNase A and 2 units of RNase T1 per ml of cell lysate). The treated sample was incubated with IgG resin (GE Healthcare) to capture Drn1-TAP/Dbr1-TAP with covalently bound RNAs. The sample was treated with calf intestinal phosphatase (New England Biolabs) to remove 5’ phosphates on RNAs. A 22 nt RNA linker (5’-phosphate-AAAGAUCGGAAGAGCGGUUCAG) was ligated to the 3’ end of the RNA using T4 RNA ligase (New England Biolabs). The RNA was then radiolabeled at its 5’ end with g-32P-ATP and polynucleotide kinase. The radiolabeled Drn1/Dbr1-RNA was separated on a SDS-PAGE gel to remove co-immunoprecipitated contaminants. The sample was  transferred to a nitrocellulose membrane and exposed to X-ray film to identify crosslinked proteins  A small region of the membrane corresponding to the Drn1/Dbr1-RNA complex (whose migration is slightly slower than Drn1/Dbr1 alone due to the TAP tag and the RNA bound) is excised. Protein was then digested with Proteinase K (Fermentas) and another RNA linker (ACACGACGCTCTTCCGATCTAC) was ligated to the 5’ end of the RNA using T4 RNA ligase. The resulting product was amplified with RT-PCR using primers containing sequence from the RNA linker as well as sequence to be used for high throughput sequencing by the Illumina sequencer. The sequences of these primers are: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT and CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT. The final CLIP RT-PCR product was sequenced using the Illumina sequencing platforms.

treatment_protocol: Cells were irradiated  with 254 nm UV light  at 800mJ/cm2 using a Stratalinker Model 1800 (Stratagene).

value: MATa his3 1 leu2 0 met15 0 ura3 0 YGR093W::TAP-his3MX

tag: sample type

value: Drn1-TAP CLIP-seq

tag: genetic background


title: Dbr1-TAP CLIP-seq replicate 1

value: MATa his3 1 leu2 0 met15 0 ura3 0 YKL149C:TAP-:his3MX

value: Dbr1-TAP CLIP-seq


title: Amborella opened female flowers_sRNA-seq

city: St. Louis

first: Blake

middle: C.

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
small RNA profiles (sRNA-seq)
AmOFFs

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides by custom Perl scripts developed in Blake Meyer's laboratory. Small RNA reads were mapped to the Amborella genome (Amborella Genome Database).
PARE-seq: the adapter sequences were trimmed from raw sequence reads, and then the PARE sequences were trimmed to the lengths between 18 and 21 nucleotides by custom Perl scripts developed in Blake Meyer's laboratory. PARE reads were mapped to the Amborella genome (Amborella Genome Database).
Genome_build: Amborella Genome Database (http://www.amborella.org/)
Supplementary_files_format_and_content: Text containing distinct small RNAs or PARE RNAs with their raw abundance after removing the adapter sequences

organism: Amborella trichopoda

source_name: opened female flower tissue

extract_protocol:
Small RNA libraries were constructed from total RNA isolated from leaf tissue and opened female flower tissue of Amborella trichopoda using Plant RNA Reagent (Invitrogen, Life Technologies, USA). The sRNA library preparation protocol is based on Illumina’s sRNA Sequencing Sample Preparation Guide (Illumina, San Diego, CA). The libraries were sequenced on an Illumina HiSeq at the Delaware Biotechnology Institute (Newark, DE).
Degradome libraries (Parallel Analysis of RNA Ends; PARE libraries) constructed from total RNA isolated from leaf tissue and opened female flower tissue of Amborella trichopoda using Plant RNA Reagent (Invitrogen, Life Technologies, USA). The libraries were constructed as previously described (German et al. 2009 PMID: 19247285). The libraries were sequenced on an Illumina HiSeq at the Delaware Biotechnology Institute (Newark, DE).

value: opened female flower tissue


title: MXB 7DAP


title: Amborella leaf_sRNA-seq

description:
small RNA profiles (sRNA-seq)
AmLs

source_name: leaf tissue

value: leaf tissue


title: U1_1

city: New York

first: Xuebing

last: Wu

state: NY

address: 630 West 168th Street

department: Medicine/Systems Biology

institute: Columbia University

data_processing:
Reads mapping. Raw reads were processed with the program cutadapt to trim the adaptor sequence (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCAC) from the 3’ end. Reads longer than 15 nts after adaptor trimming are mapped to the mouse genome (mm9) with bowtie requiring unique mapping with at most two mismatches (options: -n 2 -m 1 --best --strata). Mapped reads were collapsed by unique 3’ end positions.
Internal priming filter. Reads that have 1) more than 10 As in the first 20 nt window or 2) more than 6 As in the first 10 nt window downstream the 3’ end are removed
PAS filter. Reads without any PAS variants within 41 bases upstream of the 3' ends were discarded.
Genome_build: mm9
Supplementary_files_format_and_content: BED file with appended columns: column 1-6: BED6 format of unique cleavage sites passing internal priming filter and PAS filter. Column 7 is the number of reads ending at this site. Column 8 is the number of As within 20 bases downstream the cleavage site. Column 9 is the distance between an assigned PAS and the cleavage site. Column 10 is the assigned PAS hexamer.

molecule: polyA RNA

source_name: embryonic stem cells

growth_protocol: standard ES cell culture conditions

extract_protocol:
Total RNA was extracted from V6.5 mESCs using Ambion’s Ribopure kit (AM1924M)
Poly (A) selected RNA was fragmented using RNase T1 (AM2283). Reverse transcription was performed with an RT oligo (Table S1) at 0.25 uM final concentration using Invitrogen’s Superscript III Reverse Transcriptase (18080-44) according to the manufacturer’s protocol. The resulting cDNA was run on a 6% TBE-Urea polyacrylamide gel (National Diagnostics) and the 100-300 size range of products were gel extracted and eluted overnight. The gel-purified cDNA products were circularized using CircLigase II buffer (CL9025K) according to the manufacturer’s protocol. Circularized cDNA was PCR-amplified using the Phusion High-Fidelity DNA Polymerase (MO530L) for 15-18 cycles using the primer described in Table S1. Amplified products were run on a 1.5 % agarose gel and the 200-400 size range was extracted using Qiagen’s MinElute Gel Extraction Kit (28604). The 3’-end library was  then submitted for Illumina sequencing on the HI-Seq 2000 platform.
3' end RNA sequencing

treatment_protocol: U1 inhibition conditions from Kaida et al., Nature, 2010

value: U1-targeting AMO


title: Amborella leaf_degradome

description:
degradome (PARE-seq) profiles
AmLd


title: SCR_2

value: Scrambled AMO


title: WT_2


title: SCR_1


title: U1_2

value: U1-targeting  AMO


title: Amborella opened female flowers_degradome

description:
degradome (PARE-seq) profiles
AmOFFd


title: MXB 5DAP


title: WT_1


title: UISO

first: Neil

last: Renwick

address: 1230 York Ave

institute: Rockefeller University

description:
Sample name: A36
small RNA sequencing
Barcode: TATCA
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
UISO_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).

source_name: Cell line

extract_protocol: Total RNA was isolated from FFPE tissues for samples A1-20 using the Recoverall Total Nucleic Acid Recover kit (Ambion) and for samples A21-A30 using the Masterpure Complete DNA and RNA Purification Kit (Epicenter Technologies) according to the manufacturer's guidelines.   Total RNA was isolated from cultured cell lines using a modified Trizol protocol (acidic phenol:chloroform:IAA (25:24:1) extraction, precipitated with 2M NaOAc pH 4.2 and Ethanol). Quality of isolated RNA was assessed on a 1% agarose gel based on the relative abundance of 18S and 28S subunits of ribosomal RNA. We used a barcoded small RNA sequencing approach (Hafner 2011). Briefly, in a total reaction volume of 20 μl, 2 μg total RNA was ligated to 100 pmol adenylated 3’ adapter containing a unique pentamer barcode (App-(Barcode)TCGTATGCCGTCTTCTGCTTGT), 1 μg Rnl2(1-249)K227Q (plasmid for expression of recombinant ligase is available at www.addgene.org) in 50 mM Tris-HCl, pH 7.6, 10 mM MgCl2, 10 mM 2-mercaptoethanol, 0.1 mg/ml acetylated BSA (Sigma, St. Louis, MO), and 15% DMSO for 16 h on ice. Barcodes are listed in this table. Following 3’ adapter ligation, 20 barcoded samples were pooled and products were purified on a 15% denaturing polyacylamide gel. Small RNAs, measuring 45-50 nt in length, were excised from the gel, eluted, and ligated to 100 pmol 5’ oligoribonucleotide adapter (GUUCAGAGUUCUACAGUCCGACGAUC) in a 20 μl reaction volume using 1 μg Rnl1 RNA ligase in 50 mM Tris-HCl, pH 7.6, 10 mM MgCl2, 10 mM 2-mercaptoethanol, 0.2 mg/ml acetylated BSA, 0.1 mg/ml acetylated BSA, 0.2 mM ATP, and 15% DMSO for 1 h at 37°C. Ligated small RNAs were purified on a 12% polyacrylamide gel, reverse transcribed using SuperScript III Reverse Transcriptase (Invitrogen, Carlsbad, CA), and amplified by PCR using appropriate primers (forward primer: AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA; RT and reverse primer: CAAGCAGAAGACGGCATACGA). cDNA libraries were sequenced by Solexa technology at the Rockefeller University Genomics Resource Center. To selected samples we added in total 2.5 or 3.4 fmol of a cocktail of 10 calibrator oligoribonucleotides per μg of total RNA (for sequences see (Hafner 2011)).

value: Cell line derived from Merkel Cell Carcinoma


title: NU3

description:
Sample name: A39
small RNA sequencing
Barcode: TTACA
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)
Not used in study but present in fastq file

data_processing:
NU3_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MKL-1c

description:
Sample name: A37
small RNA sequencing
Barcode: TGATG
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MKL-1c_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MKL-2

description:
Sample name: A38
small RNA sequencing
Barcode: TGTGT
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MKL-2_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: NU4

description:
Sample name: A40
small RNA sequencing
Barcode: TTGGT
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)
Not used in study but present in fastq file

data_processing:
NU4_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MCC13

description:
Sample name: A32
small RNA sequencing
Barcode: TAACG
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC13_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: BCC5b

description:
Sample name: A30
small RNA sequencing
Barcode: TCTGA
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
BCC5b_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).

source_name: Skin

value: FFPE Basal Cell Carcinoma


title: NS5b

description:
Sample name: A26
small RNA sequencing
Barcode: TCGAT
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
NS5b_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).

value: FFPE Normal skin


title: MKL-1b

description:
Sample name: A35
small RNA sequencing
Barcode: TAGGA
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MKL-1b_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: NU2

description:
Sample name: A28
small RNA sequencing
Barcode: TCTAG
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)
Not used in study but present in fastq file

data_processing:
NU2_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).

value: FFPE Squamous Cell Carcinoma


title: BCC5a

description:
Sample name: A29
small RNA sequencing
Barcode: TCTCC
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
BCC5a_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: NS5a

description:
Sample name: A25
small RNA sequencing
Barcode: TCCTA
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
NS5a_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MCC14a

description:
Sample name: A23
small RNA sequencing
Barcode: TCCAC
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC14a_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).

source_name: Skin tumor

value: FFPE Merkel Cell Carcinoma


title: NU1

description:
Sample name: A27
small RNA sequencing
Barcode: TCGCG
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)
Not used in study but present in fastq file

data_processing:
NU1_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MCC13b

description:
Sample name: A22
small RNA sequencing
Barcode: TCATC
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC13b_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MCC13a

description:
Sample name: A21
small RNA sequencing
Barcode: TCACT
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC13a_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: BCC4

description:
Sample name: A20
small RNA sequencing
Barcode: TTGGT
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
BCC4_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: BCC3

description:
Sample name: A19
small RNA sequencing
Barcode: TTACA
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
BCC3_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: BCC2

description:
Sample name: A18
small RNA sequencing
Barcode: TGTGT
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
BCC2_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: NS3

description:
Sample name: A15
small RNA sequencing
Barcode: TAGGA
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
NS3_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).

source_name: Normal Skin


title: NS4

description:
Sample name: A16
small RNA sequencing
Barcode: TATCA
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
NS4_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MS-1

description:
Sample name: A34
small RNA sequencing
Barcode: TAGAG
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MS-1_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: NS2

description:
Sample name: A14
small RNA sequencing
Barcode: TAGAG
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
NS2_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: BCC1

description:
Sample name: A17
small RNA sequencing
Barcode: TGATG
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
BCC1_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MCC26

description:
Sample name: A33
small RNA sequencing
Barcode: TAATA
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC26_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MCC12

description:
Sample name: A12
small RNA sequencing
Barcode: TAACG
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC12_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: NS1

description:
Sample name: A13
small RNA sequencing
Barcode: TAATA
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
NS1_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MKL-1a

description:
Sample name: A31
small RNA sequencing
Barcode: TTAAG
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MKL-1a_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MCC10

description:
Sample name: A10
small RNA sequencing
Barcode: TCTGA
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC10_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MCC9

description:
Sample name: A9
small RNA sequencing
Barcode: TCTCC
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC9_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MCC8

description:
Sample name: A8
small RNA sequencing
Barcode: TCTAG
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC8_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MCC7

description:
Sample name: A7
small RNA sequencing
Barcode: TCGCG
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC7_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MCC11

description:
Sample name: A11
small RNA sequencing
Barcode: TTAAG
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC11_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MCC6

description:
Sample name: A6
small RNA sequencing
Barcode: TCGAT
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC6_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MCC1

description:
Sample name: A1
small RNA sequencing
Barcode: TCACT
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC1_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MCC3

description:
Sample name: A3
small RNA sequencing
Barcode: TCCAC
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC3_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MCC5

description:
Sample name: A5
small RNA sequencing
Barcode: TCCTA
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC5_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: MCC2

description:
Sample name: A2
small RNA sequencing
Barcode: TCATC
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC2_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: Excyst_8h_1

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

state: CA

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

data_processing:
Primary analysis by SOLiD Instrument Control Software
Colorspace reads were trimmed to 35 bp to remove 3' end
Alignments were performed with Bowtie (version 0.12.7) with the parameters: -v 3 -m 1
FPKM values were calculated with Cufflinks (version 2.0.0)
Genome_build: Entamoeba invadens version 1.3 (http://amoebadb.org)
Supplementary_files_format_and_content: FPKM (Fragments Per Kilobase of transcript per Million mapped reads) data for all genes in each sample are listed in a single file

organism: Entamoeba invadens

source_name: E. invadens 8h excysting parasties

growth_protocol: E. invadens was grown in LYI under standard axenic culture conditions

extract_protocol:
At each time point, parasites were harvested by chilling on ice, spun down, and washed 1x in cold PBS.  All samples were lysed using a French press at 400psi. Following lysis, RNA was isolated using Trizol (Invitrogen) following the manufacturer's protocol.
5µg total RNA was treated with Terminator enzyme (Epicentre) to degrade uncapped RNAs (60min at 30°C in 20µl total reaction), followed by heat inactivation for 10min at 65°C. Samples were diluted to 100µl in 1x DNAse buffer, and treated with DNAseI (Life Technologies) for 20min at room temperature. Samples were then purified using the Ribominus cleanup protocol (Life Technologies) and reanalyzed by the BioAnalyzer to determine the level of enrichment of mRNA. First-strand cDNA synthesis was performed using a modified version of the SMART porticol and 30ng of mRNA-enriched RNA as a template. Adaptors containing restriction sites for SfiI were incorporated into the cDNA using a template switching mechanism at the 5’ end of the RNA transcript. For SMART PCR amplification of first-strand cDNA, a SMART PCR primer was used to anneal to identical sequence regions on both the 3’ and 5’ adaptors. Following 20-24 cycles of PCR amplification using Advantage Taq (Clontech) according to manufacturer’s instructions samples were digested with SfiI (New England Biolabs) to remove the majority of adaptor sequences. Samples were purified using a nucelospin column (Macherey Nagel) to remove digested adaptors. Amplified, double stranded cDNA was used to prepare SOLiD fragment libraries according to the manufacturer's protocols (Life Technologies). Briefly, cDNA was fragmented by sonication on a Covaris S2 sonicator (Covaris ) and end-repaired in preparation for P1 and P2 adaptor ligation. Adaptors were ligated and the samples size selected and amplified by standard PCR. DNA was bound to SOLiD P1 beads and amplified by emulsion PCR, followed by enrichment for templated beads.
All libraries were sequenced on a SOLiD 4 sequencer (Life Technologies), to produce 50bp reads.

treatment_protocol: Encystation was induced by transfer of trophzoites to 47% LG (low glucose) media, and incubating for specified time (8, 24, 48 or 72 hours) at 25°C. Excystation was induced by harvesting mature (72 hour) cysts and incubating overnight in distilled water at 4°C. Cysts were then transferred to excysatation media (Mitra, B.N, et al.  (2010). Int J Parasitol 40, 751-760) for 2 or 8h at 25°C.

tag: isolation method

value: Lysis by French Press; RNA isolated using Trizol (Invitrogen)

tag: mrna enrichment

value: Terminator treatment (Epicentre), followed by cleanup on RiboMinus column (Invitrogen)

tag: Stage

value: 8 hour excysting parasites


title: Excyst_2h_2

source_name: E. invadens 2h excysting parasties

tag: strain

value: 2 hour excysting parasites


title: MCC4

description:
Sample name: A4
small RNA sequencing
Barcode: TCCGT
A1-20.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC4_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: Cyst_48h_2

source_name: E. invadens 48h cysts

value: Pre-treatment with 0.1% sarkosyl for 30 min, Lysis by French Press; RNA isolated using Trizol (Invitrogen)

value: 48 hour cysts


title: Cyst_72h_1

source_name: E. invadens 72h cysts

value: 72 hour cysts


title: Cyst_48h_1


title: Excyst_2h_1


title: Cyst_72h_2


title: Cyst_8h_2

source_name: E. invadens 8h cysts

value: 8 hour encysting parasites


title: Dbr1-TAP CLIP-seq replicate 2

data_processing:
Reads were aligned to theUCSC sacCer1 genome using bowtie2
BAM alignment files were processed to genome coverage in bedGraph format using bedtools
BedGraph files were coverted to BigWig format for display in the UCSC Genome Browser
Genome_build: sacCer1
Supplementary_files_format_and_content: Genome coverage for positive strand in bedGraph format
Supplementary_files_format_and_content: Genome coverage for negative strand in bedGraph format

value: MATa his3 1 leu2 0 met15 0 ura3 0 YKL149C:TAP-:his3MX

value: Dbr1-TAP CLIP-seq


title: Cyst_8h_1


title: Drn1-TAP CLIP-seq replicate 2

value: MATa his3 1 leu2 0 met15 0 ura3 0 YGR093W::TAP-his3MX

value: Drn1-TAP CLIP-seq


title: MCC14b

description:
Sample name: A24
small RNA sequencing
Barcode: TCCGT
A21-40.fastq.txt.gz (raw data file subsequently demultiplexed by barcode)

data_processing:
MCC14b_geo.txt; genome build: hg19
We processed all samples by 3’-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 9,379,544 sequence reads were present in A1-20.fastq.txt.gz and 9,730,961 sequence reads were present in A21-40.fastq.txt.gz. These reads were mapped to the genome [hg19] allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion. We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).


title: Serum P12 (2) BS-Seq

status: Public on Jun 27 2013

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced on either an Illumina GAIIx or an Illumina HiSeq using the default RTA (v1.9) analysis software.
Raw Bisulfite-Seq reads were trimmed to remove both poor quality calls and adapters using Trim Galore (v0.2.2, default parameters; www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Remaining Bisulfite-Seq reads were mapped to the mouse genome (NCBIM37) using Bismark (v0.7.4, default parameters), and CpG methylation calls were extracted using the Bismark methylation extractor (v0.7.4).
RNA-Seq data was mapped to the mouse genome (NCBIM37) assembly using TopHat (v1.4.1, options -g 1) in conjunction with gene models from Ensembl release 61.
Reads were mapped to overlapping transcripts using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and log2 read counts per million reads were calculated for all transcripts. Counts were adjusted by matching distributions between samples.
Genome_build: NCBI37
Supplementary_files_format_and_content: Bismark CpG methylation call files are tab delimited and contain 5 colums: (1) read ID; (2) methylation state, whereby '+' = methylated, and '-' = unmethylated; (3) chromosome; (4) position; (5) context call, whereby 'Z' = methylated CpG, and 'z' = unmethylated CpG
Supplementary_files_format_and_content: Quantitated RNA-Seq data files are delimted and contain the following 7 columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Description (Ensembl); (7) log2 Expression Value

source_name: ES cells

growth_protocol: ESCs were cultured without feeders either in standard serum-containing media (DMEM 4500 mg/L glucose, 4 mM L-glutamine and 110 mg/L sodium pyruvate, 15% fetal bovine serum, 1 U/ml penicillin, 1 μg/ml streptomycin, 0.1mM nonessential amino acids, 50 uM beta-mercaptoethanol, 103 U/ml LIF ESGRO) or under 2i culturing conditions (serum-free N2B27 supplemented with 1000 U/ml LIF and Mek inhibitor PD0325901 (1 uM) and Gsk3 inhibitor CH99021 (3 uM)).

extract_protocol:
Genomic DNA was prepared using QIAamp DNA Micro Kit or AllPrep DNA/RNA mini kit (QIAGEN). RNA was extracted using either the AllPrep DNA/RNA mini kit or RNeasy® mini kit (QIAGEN) and subjected to DNAase treatment using the Ambion DNA-free™ kit according to the manufacturers’ instructions.
mRNA library preparation for RNA-seq was done as previously described (Ficz et al., 2011). For BS-seq library preparation DNA samples were fragmented by sonication (Covaris) and adaptor ligated (using Illumina supplied methylated adaptors and NEBnext library preparation kit). Subsequently, DNA was bisulfite-treated using the Sigma Imprint kit, according to the manufacturer’s instructions (one step protocol). Final library amplification (16 cycles) was done using Pfu Turbo Cx (Agilent), after which the libraries were gel-purified using QIAGEN Minelute kit.

tag: cell line

value: E14 ES

tag: passages


title: Serum P12 (3) BS-Seq


title: 2i P12 (1) BS-Seq


title: 2i P12 (2) BS-Seq


title: 2i P12 (3) BS-Seq


title: Trophozoite_1

source_name: E. invadens Trophozoites

value: trophozoites


title: Serum P12 (1) BS-Seq


title: Excyst_8h_2


title: P0 BS-Seq


title: Bn-N_28_days_old_leaf

city: Yangzhou

first: Jinjin

last: Jiang

address: Wenhui East Road No.12

country: China

institute: Yangzhou University

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Supplementary_files_format_and_content: text files including tag copy numbers and TPM value of distinct sequence tags of each library

organism: Brassica napus

source_name: Brassica napus leaf

growth_protocol: Plants were cultivated in climate chambers at 25 °C, a 16 h light: 8h dark photoperiod, and 70% relative humidity.

extract_protocol:
RNA was extracted with RNAiso Plus reagent (Takara), followed by mRNA purification with oligo-dT-attached magnetic beads, cDNA was synthesized using Oligo (dT) as primer. Quality control was performed with Agilent Bioanalyser.
The DGE libraries were prepared using Illumina Gene Expression Sample Prep Kit

value: 4 weeks

value: leaf


title: Br_28_days_old_leaf

organism: Brassica rapa

source_name: Brassica rapa leaf

value: Aikangqing


title: Bn-F3_28_days_old_leaf

value: resynthesized


title: Bn-F4_28_days_old_leaf


title: Cyst_24h_2

source_name: E. invadens 24h cysts

value: Lysis by French Press; RNA isolated using Trizol (Invitrogen)

value: Terminator treatment (Epicentre), followed by cleanup on RiboMinus column (Invitrogen)

value: 24 hour encysting parasites


title: Trophozoite_2


title: LuCaP_pool_IgG_control

city: Tampere

first: Janne

last: Seppälä

address: Biokatu 8

country: Finland

institute: Institute of Biomedical Technology

data_processing:
Illumina Genome Analyzer II base calling software
The raw reads alignment was carried out with Bowtie and the reads were mapped on the human genome version 19 (hg19). Two mismatches were allowed in the seed region of the read (-n 2), with the default seed length of 28 bp. Only the best alignment was chosen.
The peak detection (i.e., binding site detection) step of the ChIP-seq analysis was performed with the tool MACS 1.3.7. using the default p-value threshold (p=0.00001), high-confidence fold-enrichment of 10 (--mfold 10) for model building and approximately half of the maximum sonication size (--bw 175) for the cell line samples and p-value threshold of 0.0001 and --mfold 5 for the xenograft samples.
Genome_build: hg19
Supplementary_files_format_and_content: "pcDNA3.1/Armo/Arhi_pool_IgG_control" and "LuCaP_pool_IgG_control" were used as controls in peak detection in for cell line and xenograft samples, respectively. The file "high_confidence_ARBSs.bed" was created by using the peaks of ARmo_1nM, ARhi_1nM and pcDNA3.1_100nM

source_name: Normal rabbit immunoglobulin

growth_protocol: The establishment of LNCaP cells overexpressing AR has been described previously (Waltering et al., 2009). Two PC xenografts, LuCaP69 and LuCaP73, grown in intact male mice, were provided by one of the investigators (RLV).

extract_protocol:
The chromatin was sonicated to reach a fragment size of 150-300 bp with Bioruptor UCD-200TM-EX instrument (Diagenode Inc., Liège, Belgium), diluted 1:10 in 1% Triton-X100, 2 mM EDTA, 20 mM Tris-HCl, 150 mM NaCl containing 2X protease inhibitor and precleared for 1 hour with 100 μg of yeast tRNA (Invitrogen Inc., Carlsbad, California, USA) and 20 μl of preimmune rabbit serum (Santa Cruz Inc., Santa Cruz, California, USA) followed by 1 hour incubation with 40 μl of 50% slurry of Gammabind Sepharose beads (GE Healthcare Bio-Sciences, Piscataway, New Jersey, USA) at 4°C. The beads were precipitated and 10 μg of normal rabbit IgG (Santa Cruz Inc., Santa Cruz, California, USA) or 10 μg of anti-AR (clone N20; Santa Cruz Inc., Santa Cruz, California, USA) or 10 μl of anti-AR polyclonal antibody (AR3) (provided by one of the authors: O. A. J.) (Karvonen et al., 1997, Thompson et al., 2006) were added to the supernatant for overnight incubation. The complexes were then incubated with 70 μl of Gammabind Sepharose beads (GE Healthcare Bio-Sciences, Piscataway, New Jersey, USA) 50% slurry for 4 hours and precipitated. The beads were washed sequentially for 10 min ach in TSE I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, and 150 mM NaCl), TSE II (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, and 500 mM NaCl), and buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, and 10 mM Tris-HCl). Beads were then washed two times with TE buffer. The complexes were then eluted from the beads incubating for 15 minutes at 37°C twice with 1% SDS, 0.1 M NaHCO3. The eluates were pooled and treated for 1 hour at 37°C with RNAase A (Qiagen Inc., California, USA) and 1 hour with proteinase K (Finnzymes Oy, Espoo, Finland), then heated at 65°C for 6 3 hours to reverse the formaldehyde cross-linking. The DNA fragments were purified with a DNA purification kit (QIAquick PCR purification Kit, Qiagen Inc., California, USA) and eluted in 100μl of elution buffer. The libraries of ChIP DNA were prepared and sequenced with Genome analyzer II (Illumina Inc., San Diego, California, USA) according to the manufacturer’s protocol. Each sample was sequenced in one lane. The raw reads were obtained using Illumina analysis pipeline.
Standard illumina protocol
one sample per illumina lane

treatment_protocol: The cells were maintained under geneticin 250 μg/ml (Invitrogen Inc., Carlsbad, CA, USA). Four million cells were plated and hormone-deprived for 4 days and treated with DHT at different concentrations for 2 h. Cells were fixed by adding formaldehyde (Merck KGaA, Darmstadt, Germany) in 1% final concentration for 10 min at room temperature and lysed in 1% sodium dodecyl sulfate, 10 mM EDTA, 50 mM Tris–HCl containing 2X protease inhibitor (Roche Inc., Mannheim, Germany). To perform tissue ChIP, 3 ml of phosphate-buffered saline containing 2X protease inhibitor (Roche Inc.) were added to 40 × 20 μm sections of freshly frozen xenograft specimens. They were first vigorously mixed three times with syringe and 14G needle, then four times with 25G needle. The cells were fixed for 10 min in room temperature by adding 1/10 volume of fixation solution (11% formaldehyde, 0.1 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 50 mM HEPES). Fixation was stopped by adding 1/20 volume of 2.5 M glycine for 5 min at room temperature. The cells were pelleted, washed twice in phosphate-buffered saline containing 2X protease inhibitor (Roche Inc.) and lysed as above. The chromatin was immunoprecipitated with 10 μg of normal rabbit immunoglobulin G (Santa Cruz Inc., Santa Cruz, CA, USA) or 10 μl of anti-AR polyclonal antibody (AR3) (provided by one of the investigators: OAJ).

value: mixed LuCaPs

tag: ar overexpression

value: normal (control)

tag: dht treatment

tag: chip antibody

value: rabbit IgG


title: LuCaP_ARplus

source_name: overexpressed AR xenograft

value: LuCaP69 xenografted tumor tissue

value: 10 fold

value: AR


title: PC8/ARmo/ARhi_pool_IgG_control

source_name: pcDNA3.1 cell line

value: mixed LNCaP lines


title: LuCaP_ARnormal

source_name: normal AR xenograft

value: LuCaP73 xenografted tumor tissue

value: normal


title: PC8_100nM


title: PC8_1nM

value: 1 nM


title: PC8_0M


title: ARhi_1nM

source_name: ARhi cell line

value: LNCaP-ARhi

value: 5 - 6 fold


title: Bj_28_days_old_leaf

organism: Brassica juncea

source_name: Brassica juncea leaf

value: Czern

value: 4 weeks

value: leaf


title: Bg_28_days_old_leaf

organism: Brassica nigra

source_name: Brassica nigra leaf

value: Koch


title: ARhi_0M


title: ARhi_100nM


title: Bc_28_days_old_leaf

organism: Brassica carinata

source_name: Brassica carinata leaf

value: Braun


title: ARmo_1nM

source_name: ARmo cell line

value: LNCaP-ARmo

value: 2 - 4 fold


title: Bo_28_days_old_leaf

organism: Brassica oleracea

source_name: Brassica olerace leaf

value: Zhonghuajielan


title: ARmo_0M


title: Human granulocytes b

city: Camperdown

first: william

last: ritchie

state: NSW

address: Building 93

country: Australia

institute: centenary institute

description: C3.Human.transcripts.gtf.bz2 available on the Series record

data_processing:
Illumina Pipeline 1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm8 whole genome using bowtie v0.12.7
Alternative transcription start sites and gene expression were determined using Cufflinks Version 0.92.
Genome_build: mm9 & hg19
Supplementary_files_format_and_content: GTF file of transcripts

source_name: granulocytes

extract_protocol:
Promyelocytes, myelocytes and granulocytes were purified using fluorescence activated cell sorting. RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peripheral blood


title: Bn-F2_28_days_old_leaf

value: resynthesized


title: Bn-F1_28_days_old_leaf


title: BCBL-1 B

city: Würzburg

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

institute: Julius-Maximilians-Universität Würzburg

description: crosslinked ribonucleoprotein complexes

data_processing:
The 3' sequencing adapter sequence are trimmed from each sequencing read using a specially tailored sequence alignment variant that alignes a prefix of the adapter sequence to a suffix of each sequencing read.
Equal sequences are collapsed and mapped to the human genome (hg19), the KSHV genome (NC_009333.1) and the human transcriptome (Ensembl v60) using Bowtie version 0.12.7
Mapped reads are then submitted to PARma for cluster identification and microRNA assignment
Genome_build: hg19
Supplementary_files_format_and_content: BED files containing cluster positions

source_name: B-cell line

extract_protocol:
A total of 3*10^8 cells per replicate were grown and treated with 4-thiouridine (Sigma) for 14 hours (final concentration 100 uM). Cells were pelleted and washed in cold PBS. Aliquotes of 5*10^7 cells were resuspended in 5 ml of cold PBS, placed in a 15 cm petri dish and irradiated at 365 nm with 100 mJ twice on ice, with 30 s break in between. Crosslinked cells were collected, pelleted and snap-frozen. PAR-CLIP was performed using 11A9 anti-Ago2 monoclonal antibody
PAR-CLIP


title: Human granulocytes a


title: BCBL-1 A

description: crosslinked ribonucleoprotein complexes