title: MB_shKap1_RNAseq_replicate2

data_processing:
Raw reads were mapped to the human genome (mm9) using Tophat 2.0.11 without asking for novel novel junctions nor indels in sensitive mode
Count per gene were obtained with htseq-count
Genome_build: mm9
Supplementary_files_format_and_content: csv containing the raw counts table with rows as genes and columns as samples.

molecule: polyA RNA

extract_protocol:
cytoplasmic RNA was extracted with Qiagen miRNeasy kit + on column DNAse treatment. The quality was assessed on a bioanalyzer, analyzed by RT-qPCR with positive and negative controls, selected for polyA+ RNA and sequenced.
Libraries were prepared according to Illumina's instructions

tag: genotype/variation

value: LV sh-Kap1 transduced


title: MB_shKap1_RNAseq_replicate1

status: Public on Feb 02 2015

type: SRA

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

library_source: transcriptomic

organism: Mus musculus

source_name: C2C12 myoblasts

growth_protocol: C2C12 myoblasts were routinely grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum (FCS) and penicillin/streptomycin.

treatment_protocol: For differentiation, cells were placed in media containing Dulbecco's Modified Eagle Medium (DMEM) supplemented with 2% horse serum, penicillin/streptomycin and insulin-Transferrin-selenium-A.

tag: strain

tag: developmental stage

value: proliferating myoblasts


title: MB_Kap1_ChIPSeq

library_source: genomic

data_processing:
Raw reads were mapped to the human genome (mm9) using Bowtie 2.2.1 in sensitive mode
Peaks were called using MACS
Genome_build: mm9
Supplementary_files_format_and_content: bedfiles contain the results of the peakcalled using MACS

molecule: genomic DNA

extract_protocol:
C2C12 cells at various stages were washed 2x (in PBS + Protease inhibitor), counted to normalize by cell number, cross-linked (ten minutes rotation in 1% formaldehyde), quenched with glycine (at 125mM on ice), washed 3x (PBS+PI) and pelleted at 10e7 cells per eppendorf. Pellets were lysed, resuspended in 1ml sonication buffer on ice (10mM Tris pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% NaDOC, 0.25% NLS and protease inhibitors), transferred to glass 12x12mm tubes (Covaris: 520081) and sonicated (Covaris settings: 5% duty cycle, PIP 140, 200cyles/ burst, 25 minutes). Sonication was then assessed by reverse cross-linking overnight in the presence of proteinase K and RNase, followed by DNA extraction and quantification on a Bioanalyzer (Agilent 2100 machine). Libraries were prepared according to Illumina's instructions.
Libraries were prepared according to Illumina's instructions

tag: chip antibody (epitope/name)

value: Kap1 - homemade rabbit polylconal antibody


title: MT_shKap1_RNAseq

value: 48-hours differentiating myoblasts


title: wild-type S phase

status: Public on Feb 03 2015

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

country: United Kingdom

institute: Earlham Institute

data_processing:
Sequence reads were mapped to the S. pombe reference genome using stampy.
Sequence reads mapping to a single genomic location were summed in 1 kb bins. Windows where fewer than 250 reads were mapped in either sample were excluded.
Normalised copy numbers were generated by dividing the sequence read counts from the replicating sample by counts from the non-replicating 45 min post-elutriation.
The resulting absolute ratios reflect the read numbers; therefore data was normalized by dividing by an empirically determined factor. This resulted in >95% of the data points lying between 1 and 2 (a biologically imposed restraint).
Genome_build: ASM294v2
Supplementary_files_format_and_content: Wig & bedgraph files containing analysed datasets.

organism: Schizosaccharomyces pombe

source_name: Genomic DNA from S phase FACS sorted cells

extract_protocol:
Library preparation and sequencing was carried out according to Illumina instructions.
DNA was prepared using the QIAGEN 100/G Genomic-tip"

tag: relevant genotype

tag: growth protocol

value: Cells were harvested from mid-log phase cultures grown in rich medium.

tag: treatment protocol

value: Cells were sorted by DNA content, selecting S phase cells.


title: MB_shCtrl_RNAseq_replicate 1

value: LV sh-Luc transduced


title: MB_shCtrl_RNAseq_replicate 2


title: MB_H3K9me3_ChIPSeq

value: H3K9me3 diagenode pAb-056-050


title: MT_shCtrl_RNAseq


title: wild-type S phase (5 min)

data_processing:
Sequence reads were mapped to the S. pombe reference genome using stampy.
Sequence reads mapping to a single genomic location were summed in 1 kb bins. Windows where fewer than 250 reads were mapped in either sample were excluded.
Normalised copy numbers were generated by dividing the sequence read counts from the replicating sample by counts from the non-replicating 45 min post-elutriation.
The resulting absolute ratios reflect the read numbers; therefore data were normalized for read number and the fraction of bulk genome replication (determined by flow cytometry).  This resulted in >95% of the data points lying between 1 and 2 (a biologically imposed restraint).
Genome_build: ASM294v2
Supplementary_files_format_and_content: Wig & bedgraph files containing analysed datasets.

source_name: Genomic DNA from cells 55 minutes post-elutriation

value: Cells were synchronised in G2 by elutriation, concentrated into a volume of 200 mls, grown in fresh media at 27 °C and a sample taken after 55 min.

value: None.


title: wild-type non-replicating

source_name: Genomic DNA from cells 45 minutes post-elutriation

value: Cells were synchronised in G2 by elutriation, concentrated into a volume of 200 mls, grown in fresh media at 27 °C and a sample taken after 45 min.


title: PE2_flocculate_18hrs

city: campinas

first: Osmar

last: Netto

address: UNICAMP

country: Brazil

institute: Genomic and Expression Laboratory

data_processing:
Libraries were validated on an Experion DNA chip (Bio-Rad) and quantified using a Qubit fluorometer (Invitrogen).
Each RNA-seq library was sequenced in one lane of an Illumina Genome Analyzer II sequencer, which produced ~20-30 million reads (36 bp single-end).
For each RNA-seq library, reads were aligned against a reference gene database constituted by S. cerevisiae S288C genes (www.yeastgenome.org).
The alignment was performed by SOAPaligner version 2.20 allowing up to 2 base mismatches and discarding repeat reads.
After that, a Perl script was made to calculate the number of reads aligned by genes for each RNA-seq library. The output file was analyzed by DEGSeq package (R Bioconductor) for identification of differentially expressed (DE) genes between libraries.
Gene expression levels were determined using RPKM formula.
Gene ontology (GO) terms of DE genes were obtained by SGD database (http://www.yeastgenome.org/cgi-bin/GO/goSlimMapper.pl) using Yeast GO-Slim Process parameters and cutoff p-value < 0.01.
Genome_build: S. cerevisiae S288c
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: Yeasts were collected directly from industrial fermentation tanks of sugarcane ethanol production

extract_protocol:
Pools of biological material were obtained mixing the three biological replicates for each time-point. Total RNA of 13 fermentation time-points was extracted using phenol and chloroform.
RNA-seq libraries were prepared from 1 µg total RNA following the manufacturer`s protocol (Illumina). Briefly, mRNA was isolated using oligo(dt) magnetic beads and fragmented in the presence of divalent zinc ions. Fragmented RNA was then used for first and second strands cDNA synthesis. Double-stranded cDNA was end-repaired and 3` adenylated for ligation of sequence adapters. After ligation of adapters, fragments of approximately 250 bp were isolated by gel electrophoresis and PCR amplified.

tag: fermentation time

value: 18 hours of fermentation

tag: fermentation condition

value: flocculate industrial fermentation


title: PE2_flocculate_21hrs

value: 21 hours of fermentation


title: PE2_flocculate_15hrs

value: 15 hours of fermentation


title: PE2_flocculate_9hrs

value: 9 hours of fermentation


title: PE2_flocculate_12hrs

value: 12 hours of fermentation


title: PE2_typical_12hrs

value: typical industrial fermentation


title: PE2_typical_15hrs


title: PE2_typical_10hrs

value: 10 hours of fermentation


title: PE2_flocculate_6hrs

value: 6 hours of fermentation


title: PE2_flocculate_3hrs

value: 3 hours of fermentation


title: PE2_typical_7hrs

value: 7 hours of fermentation


title: PE2_typical_4hrs

value: 4 hours of fermentation


title: 35_NC_Input

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

description:
Normal Colon Close to tumor
SLX-3738.607.s_4
hmeDIP-seq
SLX-3738.607.s_4

data_processing:
Alignments: Illumina reads were aligned to the Human Reference Genome (assembly hg18, NCBI Build 36.3, March 2008) using BWA
Wap counting: counts of overlapping reads in 300bp windows centered around Inifinium array probes (overlapping windows merged), with overlapping reads in control subtracted
Wide promoter counting: counts of overlapping reads in 3500bp windows, 3000bp upstream of TSSs and 500 bp downstream (overlapping windows merged), with overlapping reads in control subtracted
Narrow promoter counting: counts of overlapping reads in 1500bp windows,1000bp upstream of TSSs and 500 bp downstream (overlapping windows merged), with overlapping reads in control subtracted
Gene counting: counts of overlapping reads in windows from TSS to TES (overlapping windows merged), with overlapping reads in control subtracted
Genome_build: hg18
Supplementary_files_format_and_content: *.counts.bed: bed file with score set to number of reads overlapping a feature (minimum 1)
Supplementary_files_format_and_content: *.rpkm.bed: bed file with score set to RPKM based on reads overlapping a feature (minimum reads 1)

organism: Homo sapiens

source_name: Colon primary tissue

growth_protocol: not applicable

extract_protocol:
For hmeDIP-seq, Illumina libraries were prepared from sonicated genomic DNA followed by immunoprecipitation with anti-5hmC antibody (Active Motif, 39791) and sequenced.
For TET2 ChIP-seq, formaldehyde cross-linked material was immunoprecipitated with anti-TET2 antibody (SantaCruz sc-136926) followed by Illumina adapter ligation and sequencing.

treatment_protocol: not applicable

tag: sample id

tag: fraction

value: Input

tag: antibody

tag: tissue

value: Normal Colon Close to tumor


title: PE2_typical_1hr

value: 1 hour of fermentation


title: Control 1

city: Leiden

first: Anastasios

last: Mastrokolias

address: LUMC, Building 2 Einthovenweg 20 2333 ZC Leiden

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Illumina GA Pipeline Software (version 1.5.1) was used for data sequence processing.
The FASTQ files were analyzed using the open source GAPSS_B pipeline.
All sequences were trimmed to 17 base pairs and the NlaIII recognition site (CATG) was added to the 5’ end of the sequence to create the complete 21 mer.
Sequences were aligned using the Bowtie short read aligner (version 0.12.7) against the UCSC hg19 reference genome.
A custom Perl script was used to obtain gene annotations from Biomart.
A custom python script was used to count the tags in each Ensembl gene using the sam output files from bowtie.
Normalization steps:
library(limma)
library(edgeR)
library("org.Hs.eg.db")
library(biomaRt)
#Remove HBA1,HBA2,HBB genes
sumrow=apply(Data,1,sum)
sumroworder=order(sumrow,decreasing=T)
head(sumroworder)
Data=Data[-c(26806,12722,10749),]
#Remove low abundance genes
Data=Data[rowSums(Data)>123,]
#Get HGNC symbols from ensembl
mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
ann <- getGene(id = rownames(Data), type = "ensembl_gene_id", mart = mart)
m <- match(rownames(Data),ann[,9])
genes <- ann[m,1:8]
#Make the limma design matrix
design=model.matrix(~Metadata$Motor_Score+Metadata$HB_Percentage+Metadata$Gender+Metadata$Age)
design=model.matrix(~Metadata$ TFC_Disease_Stage+Metadata$HB_Percentage+Metadata$Gender+Metadata$Age)
#Do Limma
nf=calcNormFactors(Data)
y=voom(Data,design,plot=TRUE,lib.size=colSums(Data)*nf)
y$genes <- genes
fit=lmFit(y,design)
fit=eBayes(fit)
summary(decideTests(fit))
#Make a table of the genes and export it
Topmodel=topTable(fit,coef=2,n=20,sort.by="p")[,c(1,2,3,9,13)]
write.table(Topmodel, file="Topmodel.txt")
Genome_build: hg19
Supplementary_files_format_and_content: Data.txt: Tab-delimited text file representing tag counts for all 124 samples and in each Ensembl gene using the sam output files from bowtie.
Supplementary_files_format_and_content: Normalised_data.txt: Tab-delimited text file representing scaled data (log transformed and normalized). Obtained from the y$E function in the voom limma package for RNA-seq data analysis.

source_name: Whole blood, control

extract_protocol:
 Whole blood was drawn into PAX gene tubes and total RNA was isolated using the PAX RNA isolation kit following the manufacturer's instructions, including DNAse treatment
SAGE libraries were produced according to the Illumina 3' Digitial Gene Expression NlaIII protocol

value: peripheral whole blood

tag: age

tag: gender [0=male, 1=female]

value: control

tag: motor_score [higher score indicates greater disease severity]

tag: hb_percentage [a proxy for the reticulocyte content of each sample measured as the ratio of hemoglobin tags versus total aligned tags per sample (0-100%)]


title: Carrier 90

source_name: Whole blood, carrier

value: carrier

tag: presymptomatic hd patient (yes, if motor score is 5 or less)

value: no


title: Carrier 75


title: Carrier 79


title: Carrier 86


title: Carrier 91


title: Carrier 77


title: Carrier 85


title: Carrier 78


title: Carrier 80


title: Carrier 74


title: Carrier 81


title: Carrier 72


title: AkgR_RSP_0981_3xMyc_ChIP_Seq

city: Madison

first: Timothy

middle: J

last: Donohue

state: WI

address: 1552 University Avenue

department: Bacteriology

country: USA

institute: University of Wisconsin - Madison

data_processing:
Mapping was done to the R. sphaeroides reference genome using SOAP version 2.21 allowing for 2 mismatches for 50bp reads
Peaks were identified using MOSAiCS at a false discovery rate of 0.05 using a two-sample analysis with Input DNA or mock chip used as control.
Genome_build: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Rhodobacter_sphaeroides_2_4_1_uid57653/
Supplementary_files_format_and_content: Processed data files are provided as wig files with scores representing the normalized ratio of reads between a sample ChIP and INPUT DNA

organism: Cereibacter sphaeroides

source_name: Bacteria culture (SIS - Photo)

growth_protocol: R. sphaeroides strains that were grown in 500 ml cultures in roux bottles either photosynthetically (bubbling with 95% N2, 5% CO2) or aerobically (bubbling with 69% N2, 30% O2, 1% CO2) on Sistrom's minimal media and harvested at exponential phase. Where necessary 1 to 5μL of IPTG was added at the start of the culture to induce protein expression.

extract_protocol:
At midexponential phase (~2×108 colony-forming units/ml), formaldehyde and sodium phosphate were added to a final concentration of 1% and 10 mM, respectively. This mixture was incubated at 30 °C for 4 min before glycine was added to 100 mM, and the solution was placed on ice for 30 min with gentle agitation to quench excess formaldehyde. Cells were centrifuged at 3000g, washed twice with chilled phosphate buffered saline, centrifuged, and flash-frozen at −80 °C. About 2×1010 cells were suspended in 0.5 ml of 100 mM Tris (pH 8.0), 300 mM NaCl, 2% Triton X-100, RNase A (0.5 μg) and 1 mM phenylmethylsulfonyl fluoride, and sonicated in a Misonix water bath for 8 mins with 10s pulses and intervals. Cell debris was removed by centrifugation for 10 min at 12,000g, and an aliquot was removed to analyze DNA fragmentation by agarose gel eletrophoresis (desired size of ~200–1000 bp with enrichment for ~500-bp molecules). The resulting supernatant was incubated with gentle mixing with 20 μl of Staphylococcus aureus protein A Sepharose beads (Sigma-Aldrich, St. Louis, MO) for 3 h at 4 °C as pretreatment to remove potential nonspecific binding to the beads. After the beads had been removed by centrifugation (5 min at 3000g), one-tenth of the sample was removed and used as non-antibody-treated control. Five microlitre of Myc epitope antibody (ab9132, Abcam plc) was added and the mixture was incubated overnight at 4 °C with gentle mixing before being incubated with protein A Sepharose beads (30 μl) for 3 h at 4 °C. The beads were recovered by centrifugation; washed once (4 °C) with 250 mM LiCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; washed twice with 600 mM NaCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; washed twice with 300 mM NaCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; and washed twice with TE buffer (10 mM Tris pH 8.0 and 1 mM EDTA). Protein–DNA complexes were eluted from the beads by incubating at 65 °C for 30 min in 50 mM Tris (pH 8.0), 10 nM EDTA, and 1% sodium dodecyl sulfate. The beads were removed by centrifugation, and protein–DNA cross-linking was reversed by incubating the samples for 12 h at 65 °C. DNA was purified using the QIAquick PCR Purification Kit. Samples were sent to UW-Madison Biotech center for further processing and sequencing.
Libraries were prepared according to Illumina's instructions by UW-Madison biotech center

tag: strain

value: ΔRSP_0981 complemented with 3xMyc tagged RSP_0981 from an IPTG inducible plasmid

tag: chip-antibody


title: Carrier 71


title: Carrier 70


title: CceR_RSP_1663_3xMyc_ChIP_Seq_Photo

value: ΔRSP_1663 complemented with 3xMyc tagged RSP_1663 from an IPTG inducible plasmid

value: Myc epitope antibody (ab9132, Abcam plc)


title: Carrier 69


title: CceR_RSP_1663_3xMyc_ChIP_Seq_Aero

source_name: Bacteria culture (SIS - Aero)


title: Carrier 66


title: Carrier 64


title: 2.4.1_Input_DNA

source_name: Bacteria culture (SIS)

value: None (input)


title: Carrier 63


title: Carrier 83


title: Carrier 60


title: Carrier 62


title: Carrier 67


title: Carrier 68


title: Carrier 59


title: Carrier 58

value: yes


title: Carrier 56


title: Carrier 47


title: Carrier 52


title: Carrier 44


title: Carrier 49


title: Carrier 51


title: Carrier 45


title: Carrier 55


title: Carrier 48


title: Carrier 41


title: Carrier 40


title: Carrier 43


title: Carrier 65


title: Carrier 38


title: Carrier 37


title: Carrier 39


title: Carrier 36


title: Carrier 35


title: Carrier 88


title: Carrier 89


title: Carrier 42


title: Carrier 84


title: Carrier 87


title: Carrier 34


title: Carrier 82


title: Carrier 76


title: Carrier 50


title: Carrier 73


title: Carrier 31


title: Carrier 54


title: Carrier 61


title: Carrier 30


title: Carrier 57


title: Carrier 46


title: Carrier 33


title: Carrier 28


title: Carrier 29


title: Carrier 16


title: Carrier 32


title: Carrier 17


title: Carrier 15


title: Carrier 53


title: Carrier 26


title: Carrier 24


title: Carrier 25


title: Carrier 23


title: Carrier 1


title: Control 29


title: Control 27


title: Carrier 22


title: Control 19


title: Control 23


title: Carrier 21


title: Carrier 20


title: Control 9


title: Control 16


title: Carrier 27


title: Delta_17_18_92_E_2

city: New York

first: Andrea

last: Ventura

state: NY

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description:
Sample 71
RH2

data_processing:
Reads were filtered for pass filter flag.
Filtered reads were aligned to mm9 using STAR v. 2.3.0 with the following flag: --outFilterMatchNmin 5.
Bam files were generated using samtools 0.1.14.
Counts were calculated with featureCounts (subread-1.4.2) using GTF file Mus_musculus.NCBIM37.66.gtf (ENSEMBL).
Genome_build: mm9
Supplementary_files_format_and_content: Text (tab-delimited) table, rows are ENSEMBL gene ids, columns are 71 samples.

source_name: embryo

growth_protocol: MiR-17~92 mutant animals were subjected to timed-mating. At E9.5, females were euthanized and embryos were harvested.

extract_protocol:
Tissue samples were homogenized in TRIZOL and RNA extracted according to manufacturer's instructions.
Libraries were prepared using the TruSeq SBS Kit v3 kit according to Illumina protocol and sequenced as 50 bp long single reads.

treatment_protocol: Embryonic tail buds (corresponding to samples 1-24) and hearts (samples (25-48) were microdissected and collected in 1ml of TRIZOL. The remaining embryo was also collected in 1ml TRIZOL (samples 49-72).

tag: genotype

value: miR-17,miR-20a, miR-18a, and miR-92a-1  deleted

tag: developmental stage

value: whole embryo (- heart and tail bud)


title: Carrier 19


title: Delta_17_18_E_2

description:
Sample 68
RG2

value: miR-17, miR-20a and miR-18a deleted


title: Delta_17_18_E_1

description:
Sample 67
RG1


title: Carrier 18


title: Carrier 14


title: Delta_19_E_2

description:
Sample 65
RE2

value: miR-19a and miR-19b-1 deleted


title: Carrier 9


title: Delta_19_E_1

description:
Sample 64
RE1


title: Carrier 11


title: Carrier 12


title: Carrier 10


title: Delta_18_E_3

description:
Sample 60
RD3

value: miR-18a deleted


title: Delta_18_E_2

description:
Sample 59
RD2


title: Delta_92_E_2

description:
Sample 62
RF2

value: miR-92a-1  deleted


title: Delta_92_E_3

description:
Sample 63
RF3


title: Delta_92_E_1

description:
Sample 61
RF1


title: Delta_17_E_3

description:
Sample 57
RC3

value: miR-17 and miR-20a deleted


title: Delta_17_E_2

description:
Sample 56
RC2


title: Carrier 8


title: Delta_17_18_92_E_1

description:
Sample 70
RH1


title: Delta_19_E_3

description:
Sample 66
RE3


title: Carrier 6


title: Full-KO_E_2

description:
Sample 53
RB2

value: miR-17~92 Knockout


title: Full-KO_E_1

description:
Sample 52
RB1


title: Carrier 5

value: peripheral whole blood


title: Wild-type_E_3

description:
Sample 51
RA3

value: Wild type miR-17-92 locus


title: Carrier 4

value: carrier


title: Wild-type_E_1

description:
Sample 49
RA1


title: Delta_17_18_92_H_3

description:
Sample 48
HH3

value: heart


title: Carrier 3

value: no


title: Control 33

value: control


title: Carrier 2


title: Delta_18_E_1

description:
Sample 58
RD1


title: Delta_17_18_92_H_2

description:
Sample 47
HH2


title: Control 31


title: Delta_17_18_92_H_1

description:
Sample 46
HH1


title: Control 32


title: Delta_17_18_E_3

description:
Sample 69
RG3


title: Carrier 7


title: Delta_17_18_H_3

description:
Sample 45
HG3


title: Control 28


title: Delta_17_18_H_1

description:
Sample 43
HG1


title: Control 30


title: Carrier 13


title: Delta_17_E_1

description:
Sample 55
RC1


title: Full-KO_E_3

description:
Sample 54
RB3


title: Control 26


title: Delta_19_H_3

description:
Sample 42
HE3


title: Control 25


title: Control 24


title: Delta_19_H_2

description:
Sample 41
HE2


title: Wild-type_E_2

description:
Sample 50
RA2


title: Delta_19_H_1

description:
Sample 40
HE1


title: Delta_92_H_3

description:
Sample 39
HF3


title: Control 21


title: Delta_92_H_1

description:
Sample 37
HF1


title: Control 18


title: Delta_18_H_3

description:
Sample 36
HD3


title: Control 17


title: Delta_18_H_2

description:
Sample 35
HD2


title: Delta_92_H_2

description:
Sample 38
HF2


title: Control 20


title: Delta_17_18_H_2

description:
Sample 44
HG2


title: Control 13


title: Delta_17_H_2

description:
Sample 32
HC2


title: Control 14


title: Delta_17_H_3

description:
Sample 33
HC3


title: Delta_18_H_1

description:
Sample 34
HD1


title: Control 15


title: Delta_17_H_1

description:
Sample 31
HC1


title: Control 10


title: Full-KO_H_2

description:
Sample 29
HB2


title: Control 8


title: Control 7


title: Control 22


title: Full-KO_H_1

description:
Sample 28
HB1


title: Wild-type_H_3

description:
Sample 27
HA3


title: T120_2

city: Williamsburg

first: Margaret

last: Saha

state: VA

address: 540 Landrum Drive

institute: College of William and Mary

data_processing:
Basecalling and adapter trimming was performed with Torrent Suite 4.0.2
CLC Genomic Workbench 7.0.4 was used to align reads to a combined M. smegmatis and Kampy genome and calculate an RPKM measure for each gene using the "RNA-seq analysis" tool with default settings, mapping to inter-genic regions as well as gene regions.
Genome_build: NC_018289.1 (M. smegmatis) and KJ510414.1 (Kampy)
Supplementary_files_format_and_content: CSV read count tables for genes in Mycobacterium smegmatis and mycobacteriophage Kampy were produced in CLC Genomic Workbench 7.0.4.

organism:
Mycolicibacterium smegmatis
Mycobacterium phage Kampy

source_name: Infected culture

growth_protocol: Mycobacterium smegmatis strain mc2155 was grown in Middlebrook 7H9 media with AD supplement (10%), carbenicillin (50 μg/mL), cyclohexamide (10 μg/mL), and calcium chloride (1 mM), in a 37°C shaking incubator.

extract_protocol:
15 ml of infected M. smegmatis culture was pelleted by centrifugation for 10 minutes at 400 G at 4°C. Pellets were flash frozen in liquid nitrogen and stored at -80°C until further processing. Frozen cell pellets were resuspended in 1 ml TRIzol (Life Technologies). Cells were then disrupted by beadbeating twice for 45 seconds, with one minute on ice between cycles. Total RNA was extracted from the TRIzol solution with bromochloropropane, washed with isopropanol, precipitated with 70% ethanol, and resuspended in nuclease-free water. Total RNA was incubated with recombinant DNase I (Ambion) and RNasin (Promega) for 30 minutes at 37°C. DNase I was inactivated by addition of EDTA (5 mM) and 10 minute incubation at 70°C.
Ribosomal RNA was depleted from prepared samples by subtractive hybridization using the RiboZero kit for gram-positive bacteria (Epicentre) and depleted RNA was checked for integrity and rRNA depletion with the Bioanalyzer 2100 (Aligent). Libraries for sequencing were prepared from rRNA-depleted RNA using the Ion Total RNA-Seq Kit v2 (Ion Torrent) and sequenced on an Ion Torrent PGM according to the manufacturer's instructions.

treatment_protocol: Bacteria were infected with mycobacteriophage Kampy at 10:1 MOI. Samples were taken before infection and 5, 15, 30, 60, and 120 minutes after infection.

tag: time

value: 120 minutes

tag: treatment

value: A4 mycobacteriophage


title: T120_1


title: T60_3

value: 60 minutes


title: T60_2


title: Control 5


title: Wild-type_H_2

description:
Sample 26
HA2


title: T30_3

value: 30 minutes


title: Delta_17_18_92_TB_3

description:
Sample 24
MH3

value: miR-17,miR-20a, miR-18a, and miR-92a-1  deleted

value: tail bud


title: Wild-type_H_1

description:
Sample 25
HA1


title: Control 12


title: Control 4


title: Control 11


title: Full-KO_H_3

description:
Sample 30
HB3


title: T30_2


title: Control 2


title: T15_1

value: 15 minutes


title: Delta_17_18_TB_3

description:
Sample 21
MG3

value: miR-17, miR-20a and miR-18a deleted


title: Control 3


title: T5_2

value: 5 minutes


title: Delta_17_18_92_TB_1

description:
Sample 22
MH1


title: Delta_17_18_TB_2

description:
Sample 20
MG2


title: T15_2


title: T5_1


title: Control 6


title: Delta_19_TB_2

description:
Sample 17
ME2

value: miR-19a and miR-19b-1 deleted


title: Delta_19_TB_3

description:
Sample 18
ME3


title: Delta_17_18_TB_1

description:
Sample 19
MG1


title: T0_2

organism: Mycolicibacterium smegmatis

source_name: Uninfected culture

value: 0 minutes

value: uninfected


title: T0_3


title: Delta_92_TB_2

description:
Sample 14
MF2

value: miR-92a-1  deleted


title: Delta_92_TB_3

description:
Sample 15
MF3


title: Delta_19_TB_1

description:
Sample 16
ME1


title: Delta_18_TB_3

description:
Sample 12
MD3

value: miR-18a deleted


title: Delta_18_TB_2

description:
Sample 11
MD2


title: Delta_17_18_92_TB_2

description:
Sample 23
MH2


title: Delta_18_TB_1

description:
Sample 10
MD1


title: Delta_17_TB_3

description:
Sample 9
MC3

value: miR-17 and miR-20a deleted


title: Delta_17_TB_2

description:
Sample 8
MC2


title: Full-KO_TB_3

description:
Sample 6
MB3

value: miR-17~92 Knockout


title: Delta_17_TB_1

description:
Sample 7
MC1


title: Full-KO_TB_1

description:
Sample 4
MB1


title: Drosophila_4-7d_ovary_nbr null; pCaSper-nbr (WT)

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

description: Sample name: MA4

data_processing:
For base-calling Illumina Casava version 1.8.2 was used
Sequenced reads were trimmed for adapter sequence, then mapped to dm3 genome assembly for drosophila melanogaster using the RUM v1.11 pipeline by setting Bowtie to allow 0 mismatches and Blat to require 100% sequence identity
The uniquely mapping sequences with length between 16-35 nt were checked for overlap with the miRNAs, piRNAs and esiRNAs
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited files containing the read counts corresponding to each uniquely mapping sequence read with length between 16-35 nt

organism: Drosophila melanogaster

source_name: 4-7d nbr null; pCaSper-nbr (WT) fly ovaries

growth_protocol: Flies were raised at 25˚C

extract_protocol:
Total RNA was extracted and purified using TRIzol reagent (Invitrogen).
The small RNAs between ~16 to ~29 nt in size were purified from 15% TBE-urea gel (#EC6885BOX, Life Technologies, Carlsbad, CA).
Libraries were prepared according to Illumina's TruSeq small RNA sample preparation kit (#RS-200-0012, Illumina, Inc. San Diego, CA) except 40ug of total RNA was used for each library.

treatment_protocol: Female flies were collected and aged to 4-7d on yeasted food, then ovaries dissected.

value: ovary

tag: genotype/variation

value: nbr null; pCaSper-nbr (WT)

tag: sample description

value: rescue of nbr null with wild-type nbr


title: Drosophila_4-7d_ovary_nbr null (nbrf02257/Df(2L)BSC312)

description: Sample name: MA3

source_name: 4-7d nbrf02257/Df(2L)BSC312 fly ovaries

value: nbr null


title: Drosophila_4-7d_ovary_Df(2L)BSC312/+

description: Sample name: MA2

source_name: 4-7d Df(2L)BSC312/+ fly ovaries

value: nbr/+ heterozygote


title: Drosophila_4-7d_ovary_nbr null; pCaSper-nbr (D435A,E437A)

description: Sample name: MA5

source_name: 4-7d nbr null; pCaSper-nbr (D435A,E437A) fly ovaries

value: nbr null; pCaSper-nbr (D435A,E437A)

value: rescue of nbr null with catalytically-mutated nbr


title: Wild-type_TB_2

description:
Sample 2
MA2

value: Wild type miR-17-92 locus

value: tail bud


title: 8-oxoG challenge - 120 min

city: Galveston

first: Istvan

last: Boldogh

state: Texas

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

description: Sample type: test

data_processing:
Base call conversion to sequence reads was done with Casava-1.8.2 software (Illumina).
Sequence data were analyzed with the Bowtie 2.
Splice junction mapping was performed with TopHat.
Assembly and estimation of abundance was performed with GFOLD.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: *RPKM.txt: Tab-delimited text files that include abundance measurements (RPKM values) for each Sample.
Supplementary_files_format_and_content: All_samples_fold_change.txt: Tab-delimited text file that includes fold changes (test/control).

source_name: Lung, 8-oxoG, 120min

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit (Qiagen) followed by DNase I treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice (5 per group) were intranasally challenged with 8-oxoguanine (1 µM, 60 µl) for 30, 60 and 120 min. Control group mice were intranasally challenged with saline (60 µl).

tag: strain/background

value: Balb/cJ

value: wild type

tag: gender

value: female

value: 8 weeks

value: lung

tag: time point


title: Wild-type_TB_3

description:
Sample 3
MA3

tag: tissue


title: Drosophila_4-7d_ovary_wild type

description: Sample name: MA1

source_name: 4-7d 5905 (wild-type) fly ovaries

tag: age

value: 5905 (wild-type)

value: wild-type control


title: Wild-type_TB_1

description:
Sample 1
MA1


title: 8-oxoG challenge - 30 min

description: Sample type: test

source_name: Lung, 8-oxoG, 30min


title: Pristionchus pacificus Sample 21

status: Public on Feb 01 2015

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

institute: Imperial College London

description: 5' monophosphate only

data_processing:
Adapter trimming using Cutadapt v1
fastq to fasta conversion, selection for small RNAs of 15-33nt in length using custom Perl scripts using Perl v5.12.4
fasta collapsed using FastX toolkit fastx_collapser module
Supplementary_files_format_and_content: Fasta header: id_number of reads

organism: Pristionchus pacificus

source_name: Total RNA whole animal

extract_protocol:
Total RNA extracted using Trisure (BioLine) or Trizol (Invitrogen) according to manufacturer's instructions
Illumina Truseq small RNA according to manufacturer's instructions

value: Mixed

tag: blaxter clade

value: V


title: Pristionchus pacificus Sample 22

description: 5' polyphosphatase treated


title: Saline challenge

description: Sample type: control

source_name: Lung, saline

value: saline


title: Delta_92_TB_1

description:
Sample 13
MF1

value: miR-92a-1  deleted


title: Bb2860_menadione_3h

city: Tianjin

first: Liu

last: Qian

address: Xi 7 Dao No.32 Airport Economic Area

country: China

institute: TIB CAS

data_processing:
Illumina HiSeq™ 2000 used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 49 bp tag fragments were mapped to the sequenced genome of Bb2860 or M. robertsii ARSEF23 with the precision of no more than two nucleotide mismatch.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Bb2860 and M. robertsii ARSEF23
Supplementary_files_format_and_content: Excel files include GeneID, gene_length, RPKM values and false discovery rate (FDR)  for each Sample

organism: Beauveria bassiana

source_name: BbWT

growth_protocol: Conidia suspension (100 μl,107 conidia ml-1) of WT and ΔMsn2 of Beauveria bassiana and Metarhizium robertsii were  inoculated into 50ml Sabouraud dextrose broth (SDB) at 25 °C for 2-day with shaking (180 r.p.m) growth to exponential phase.

extract_protocol: Total RNA was isolated from frozen mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA), double-stranded cDNA were prepared with the Illumina gene expression sample prep kit for Illumina arrays

treatment_protocol: Resultant mycelia of each strain were harvested and washed in sterile water twice. For thermal stress, mycelia of each sample were transferred to fresh SDB exposed to 40 °C with shaking for 3-h response. For oxidative stress, mycelia transferred to fresh SDB containing 2 mM menadione for 3-h.

tag: culture time

value: 2 days

value: mycelia

value: 2 mM menadione for 3-h


title: ΔBbMsn2_menadione_3h


title: ΔBbMsn2_40°C_3h

value: 40 °C for 3-h


title: Bb2860_40°C_3h


title: Full-KO_TB_2

description:
Sample 5
MB2

value: miR-17~92 Knockout


title: bqsR deletion, after Fe(II) shock, replicate 2

city: Pasadena

first: Dianne

middle: K

last: Newman

state: CA

address: 1200 E California Blvd

department: BBE and GPS

institute: Caltech

data_processing:
Base calling, de-multiplexing, and conversion of sequencing to fastq format were carried out by Illumina software on the Hi Seq 2500 machine.
Reads were trimmed and filtered based on their quality scores using the Trimmomatic package v 0.32 (Bolger et al, Bioinformatics published online April1 2014). Leading and trailing quality cutoffs were set to 27, and a cutoff of 20 was set for a sliding window of 4 bases. Reads shorter than 35 bp after trimming were discarded.
The trimmed reads were mapped to the genome using Bowtie 1.0.1 (Langmead B, Trapnell C, Pop M, Salzberg S. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.) and sorted mapped reads  to indexed .sam file and converted to .bam file with .Samtools v. 0.1.19 (Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Subgroup GPDP. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079.),
Read counts per gene or transcriptional unit were calculated using Easy RNASeq package (Delhomme N, Padioleau I, Furlong EE, Steinmetz LM. 2012. easyRNASeq: a bioconductor package for processing RNA-Seq data. Bioinformatics 28:2532-2533.) in R, using .gff gene description files generated from the curated genome hosted by NCBI (NC_008463.1) and .gff transcriptional units files modifying the curated genome hosted by NCBI (NC_008463.1) by the results of the single nucleotide resolution sequencing study published by Wurtzel et al (Wurtzel O, Yoder-Himes DR, Han K, Dandekar AA, Edelheit S, Greenberg EP, Sorek R, Lory S. 2012. The single-nucleotide resolution transcriptome of Pseudomonas aeruginosa grown in body temperature. PLoS Pathog 8:e1002945.)
Normalization, ratios, significance were determined using Degust web-interface (Law C, Chen Y, Shi W, Smyth G. 2014. voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol 15:R29.)
Genome_build: gi|116048575|ref|NC_008463.1|
Supplementary_files_format_and_content: 2 mapping schemes: gene mapping and transcriptional unit mapping. The files will be in .csv format which contains average log2 fold change values normalized to the WT before shock condition for all samples/conditions, as well as the raw counts for all 12 samples.
150126_FDR_1_all_conditions_normalized_wt_0_txn_unit_analysis.txt: abundance count, calculated fold change
150126_FDR_1_all_conditions_normalized_wt_0_gene_analysis.txt: abundance count, calculated fold change
BqsR_regulon_txn_unit.txt: Transcription units in Fe(II) shocked cells that wt was over 2 fold change greater or less than ∆bqsR with an FDR < 0.01
BqsR_regulon_genes.txt: Genes in Fe(II) shocked cells that wt was over 2 fold change greater or less than ∆bqsR with an FDR < 0.01

organism: Pseudomonas aeruginosa

source_name: planktonic cells

growth_protocol: Triplicate aerobic cultures of P. aeruginosa WT-pMQ72 and ∆bqsR-pMQ72 were grown in MOMM + 100 µg ml-1 gentamycin at 37 oC for 36 hours. Anaerobic cultures were inoculated with 1% inoculum in MOMM + 100 µg ml-1 gentamycin + 1% arabinose. when the cells reached deep stationary phase (OD500 = 0.8).

extract_protocol:
Total RNA was extracted using the RNEasy kit (Qiagen) according to the manufacturer's instructions with minor modifications. Briefly, frozen pellets were resuspeded in 215 ul TE buffer containing 15 mg/ml lysozyme (Sigma) and 1.4 mg/ml proteinase K (Qiagen). Samples were incubated with shaking for 10 minutes at room temperature to disrupt the cell walls.  700 ul buffer RLT and 500 ul 100% ethanol were added and the mixture was applied to the Qiagen column. washing, and elution were carried out according to instructions in 100 µl water. Total RNA was then further treated with the rigoruos treatment Turbo DNAse free kit (Ambion) according to instructions. RNA was concentrated with an ethanol precipitation and 5 ug total RNA was subjected to ribosomal RNA depletion using the Ribo-Zero Magnetic Kit for gram negative bacteria (Epicentre).
Libraries for RNA Seq were constructed from the rRNA-depleted samples using the NEBNext mRNA Library Prep Master Mix Set for Illumina, according to the manufacturer's instructions.

treatment_protocol: when the cells reached deep stationary phase (OD500 = 0.8), 1 ml of culture  was added to 2 ml RNAprotect before and after a 30 min 200 µM (NH4)2Fe(SO4)2 · 6H2O shock. RNAprotect treated cells were pelleted by centrifugation for 10 min. at 5000 x g. the pellets were frozen and stored at -80 degrees C until RNA extraction.

tag: growth phase

value: late stationary

tag: length fe(ii) shock

value: 30 min

tag: fe(ii) concentration

value: 200 µM ferrous ammonium sulfate

tag: medium

value: 100 µg ml-1 gentamycin, 1% arabinose, 40 mM succinate (C4H4Na2O4 · 6H2O), 9.3 mM NH4Cl, 2.2 mM KH2PO4, 25 mM KNO3, 25 mM NaNO3, 25 mM MOPS, 25 mM NaMOPS pH 7.2. Additionally, immediately prior to inoculation 100 µM CaCl2, 1 µM (NH4)2Fe(SO4)2 · 6H2O, 1 mM MgSO4, and trace metals (Kopf SH, Henny C, Newman DK. 2013. Ligand-enhanced abiotic iron oxidation and the effects of chemical versus biological iron cycling in anoxic environments. Environ Sci Technol 47:2602-2611) were added


title: bqsR deletion, after Fe(II) shock, replicate 3

tag: strain

tag: genotype


title: bqsR deletion, after Fe(II) shock, replicate 1


title: 8-oxoG challenge - 60 min

description: Sample type: test

source_name: Lung, 8-oxoG, 60min

value: Balb/cJ

value: wild type

value: female

value: 8 weeks


title: bqsR deletion, before shock, replicate 2

value: 0 min

value: 1 µM ferrous ammonium sulfate


title: bqsR deletion, before shock, replicate 3


title: wild type, after Fe(II) shock, replicate 3


title: bqsR deletion, before shock, replicate 1


title: wild type, after Fe(II) shock, replicate 1


title: wild type,  before shock, replicate 3


title: wild type,  before shock, replicate 1

value: 100 µg ml-1 gentamycin, 1% arabinose. The basic MOMM =  40 mM succinate (C4H4Na2O4 · 6H2O), 9.3 mM NH4Cl, 2.2 mM KH2PO4, 25 mM KNO3, 25 mM NaNO3, 25 mM MOPS, 25 mM NaMOPS pH 7.2. Additionally, immediately prior to inoculation 100 µM CaCl2, 1 µM (NH4)2Fe(SO4)2 · 6H2O, 1 mM MgSO4, and trace metals (Kopf SH, Henny C, Newman DK. 2013. Ligand-enhanced abiotic iron oxidation and the effects of chemical versus biological iron cycling in anoxic environments. Environ Sci Technol 47:2602-2611) were added


title: Caenorhabditis elegans Sample 13

description: 5' monophosphate only

data_processing:
Adapter trimming using Cutadapt v1
fastq to fasta conversion, selection for small RNAs of 15-33nt in length using custom Perl scripts using Perl v5.12.4
fasta collapsed using FastX toolkit fastx_collapser module
Supplementary_files_format_and_content: sequence id + number of reads + sequence

organism: Caenorhabditis elegans

tag: developmental stage

value: V


title: Mr23_40°C_3h

organism: Metarhizium robertsii

source_name: MrWT

value: 2 days

tag: treatment


title: wild type, after Fe(II) shock, replicate 2


title: wild type,  before shock, replicate 2


title: ΔMrMsn2_menadione_3h

value: mycelia


title: Mr23_menadione_3h

value: 2 mM menadione for 3-h


title: ORF57 HITS-CLIP pellet rep2

city: Dallas

first: Tao

last: Wang

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

description: Pellet2 (H2)

data_processing:
Basecalls performed using CASAVA (version 1.8.2)
The trailing Ns, representing adaptor sequences, in the raw sequencing fastq files were trimmed. The trimmed fastq files were aligned by gsnap (version 2014-01-21) with parameters "-A sam --maxsearch 1 -N 1 -t 4 -n 1"
Paired-end read pairs were merged into single-end format and collapsed to unique tags. Then tags from all experiments were simultaneously overlapped to identify CLIP clusters with at least 10 tags from any one or more conditions. Then the CLIP clusters were binned by 20bp and the tag counts and mutation counts on each base were summed for each bin within each experimental condition separately.
The total tag count and characteristic mutation (Del and T2C) count were combined to yield the overall binding intensity for each bin. We used the median intensity value of each condition for normalization and employed DESeq (version 1.8.3) for identifying differentially bound regions between the 3 pellets and the 3 input samples. The analysis was conducted separately for human and virus binding sties. Bins that were more enriched (p-val<0.001 or <0.05) in the pellets compared to the inputs were extracted and neighboring enriched bins were concatenated to form the reliable ORF57 binding sites.
The binding sites were screened to retain only those sites that span at least 3 bins and have on average >4 intensity count in the pellet samples. In addition, the ORF57 binding sites that overlap repeating sequences (rRNAs, tRNAs, low complexity regions, LINEs, SINEs and simple repeats) were discarded.
Genome_build: hg19+U75698.1
Supplementary_files_format_and_content: csv format. Include the location, genomic annotation, and tag counting data of each significant binding site of Orf57

source_name: TREx BCBL1-Rta primary effusion lymphoma (PEL) cell

growth_protocol: TREx BCBL1-Rta cells were carried in RPMI-1640 media (Sigma) supplemented with 10% tetracycline-free fetal bovine serum (FBS, Clontech), penicillin-streptomycin (Sigma), 2 mM L-glutamate, and 100 μg/ml hygromycin (Sigma).

extract_protocol:
Modified HITS-CLIP protocol. The details are given in Sei et al. (2015)
Modified HITS-CLIP protocol and standard Illumina pipeline. The details are given in Sei et al. (2015)
The anti-ORF57 antibody was made by our lab [Sahin BB, Patel D, Conrad NK. 2010. Kaposi's sarcoma-associated herpesvirus ORF57 protein binds and protects a nuclear noncoding RNA from cellular RNA decay pathways. PLoS Pathog 6:e1000799.]

treatment_protocol: Lytic reactivation was induced by addition of 1mg/ml doxycycline and 3 mM sodium butyrate.

tag: cell line

value: TREx BCBL1-Rta cells

value: Lytic reactivation

tag: ip antibody

value: anti-ORF57 (made in-house)


title: ORF57 HITS-CLIP pellet rep1

description: Pellet1 (H1)


title: IgG-CLIP

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

data_processing:
clean reads after getting rid of the adapto
All steps were referred to the method in "Circular RNAs are a large class of animal RNAs with regulatory potency"
Illumina Casava1.7 software used for basecalling.
CLIP-seq reads were aligned to hg19 genome using bowtie2 to get the unmaped reads
Data were filtered using the following specifications
Align the unmaped reads again to get the circular exon-exon junction reads and the information of the circular RNAs
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include circular RNA information for each Sample

source_name: hela cell

growth_protocol: DMEM with 10%FBS grows in 37℃，5%CO2

extract_protocol:
Trizol
CLIP-seq

treatment_protocol: pre-treated with 20 μg/ml α-Amanitin

tag: cell type

value: epithelial

tag: passages

tag: clip antibody

value: IgG

value: HeLa


title: Pol II-CLIP

value: Pol II (Abcam, cat# ab5095)


title: ORF57 HITS-CLIP input rep3

description: Input3 (C3)


title: ORF57 HITS-CLIP input rep2

description: Input2 (C2)


title: ORF57 HITS-CLIP input rep1

description: Input1 (C1)


title: ORF57 HITS-CLIP pellet rep3

description: Pellet3 (H3)


title: Sample_P020

first: Elizabeth

last: Philipone

address: 630 West 168th Street

department: Oral & Maxillofacial Pathology

institute: Columbia University

description:
small RNA (18 to 30nt)
incisional biopsy of an oral leukoplakia that progressed to oral cancer within 5 yrs

data_processing:
3'end adapters were clipped with fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit)
Clipped reads were processed with miraligner (Pantano. NAR 2010)
Genome_build: miRBase v20

source_name: progressive leukoplakias 010

extract_protocol:
Ten 10-mm sections were obtained from archived FFPE tumor tissue samples for all subjects. Total RNA was isolated from tissues using RNeasy FFPE kit (Qiagen Inc., Valencia, CA) following the manufacturer’s protocol and yield was quantitated by Nanodrop, and stored at -80o C.
Total RNA (minimum of 2 mg) ranging from 18 to 30 nt were gel-purified and ligated to 3’ adaptor and 5’adaptor. Ligation products were reverse transcribed, then amplified for 16 cycles using the adaptor primers, and the fragments around 150 bp were isolated from PAGE-gel using TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, CA).

tag: histologic diagnosis

value: hyperkeratosis

tag: source tissue

value: buccal mucosa leukoplakia


title: Sample_P017

source_name: progressive leukoplakias 007

value: tongue leukoplakia


title: Sample_P019

source_name: progressive leukoplakias 009

value: hyperkeratosis with  focus of mild dysplasia

value: gingival leukoplakia


title: Sample_P015

source_name: progressive leukoplakias 005

value: mild dysplasia


title: Sample_P014

source_name: progressive leukoplakias 004


title: Sample_P018

source_name: progressive leukoplakias 008

value: hyperkeratosis w/ atypia & focus of mild dysplasia


title: Sample_P010

description:
small RNA (18 to 30nt)
incisional biopsy of an oral leukoplakia that did not progress to oral cancer

source_name: non-progressive leukoplakias 010

value: benign epithelial hyperplasia & hyperkeratosis


title: ΔMrMsn2_40°C_3h

value: 2 days

tag: tissue

value: mycelia

value: 40 °C for 3-h


title: Sample_P013

source_name: progressive leukoplakias 003

value: hyperkeratosis w atypia


title: Sample_P016

source_name: progressive leukoplakias 006


title: Sample_P009

source_name: non-progressive leukoplakias 009


title: Sample_P012

source_name: progressive leukoplakias 002


title: EPC2_Day6_IL13_2

city: Mason

first: Joe

last: Sherrill

state: Ohio

address: 8700 Mason-Montgomery Rd

institute: Procter and Gamble

data_processing:
The single-end sequencing reads were aligned against the GRCh37 genome model using TopHat 2.04 with Bowtie 2.03 (Trapnell C, et al. Nature protocols 2012; 7(3): 562-78)
The separate alignments were then merged using Cuffmerge (Garber M,et al. Nature methods 2011; 8(6): 469-77) with UCSC gene models as a reference.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated (Garber M, et al. Nature methods 2011; 8(6): 469-77).
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: hTERT-immortalized human esophageal epithelial cell line_ALI_IL13

growth_protocol: EPC2-hTERT cells were grown on semi-permeable membranes submerged (day 8) or at the ALI for 6 days (day 14).

extract_protocol:
RNA was isolated using the RNeasy kit (QIAGEN Incorporated, Germantown, MD) according to the manufacturer’s protocol.
50 base single-end reads

treatment_protocol: EPC2-hTERT cells grown at the ALI (day 14) were left untreated or treated with 100 ng/mL of IL-13 from days 8-14.

tag: growth conditions

value: ALI (day 14)


title: EPC2_Day6_2

source_name: hTERT-immortalized human esophageal epithelial cell line_ALI

value: untreated


title: EPC2_Day6_3


title: EPC2_Day6_IL13_1


title: Sample_P007

source_name: non-progressive leukoplakias 007


title: Sample_P008

source_name: non-progressive leukoplakias 008

value: hyperkeratosis w/ atypia

value: floor of mouth  leukoplakia


title: Sample_P006

source_name: non-progressive leukoplakias 006


title: EPC2_Day6_1


title: Sample_P005

source_name: non-progressive leukoplakias 005


title: Hypsibius dujardini Sample 17

description: 5' monophosphate only

organism: Hypsibius dujardini

source_name: Total RNA whole animal

value: Adult

tag: blaxter clade

value: Tardigrade


title: EPC2_Day0_2

source_name: hTERT-immortalized human esophageal epithelial cell line_submerged

value: submerged (day 8)


title: Sample_P004

source_name: non-progressive leukoplakias 004

value: mild epithelial dysplasia

value: tongue leukoplakia


title: EPC2_Day0_3


title: Sample_P003

source_name: non-progressive leukoplakias 003


title: EPC2_Day0_1


title: EPC2_Day6_IL13_3


title: Sample_P001

source_name: non-progressive leukoplakias 001

value: gingival leukoplakia


title: Hypsibius dujardini Sample 18

description: 5' polyphosphatase treated


title: Sample_P002

source_name: non-progressive leukoplakias 002

value: lip mucosa leukoplakia


title: Globodera pallida Sample 15

description: 5' monophosphate only

organism: Globodera pallida

value: IV


title: Romanomermis culicivorax Sample 6

description: 5' monophosphate only

organism: Romanomermis culicivorax

value: I


title: Globodera pallida Sample 8

description: 5' polyphosphatase treated


title: Qui 2

city: Detroit

first: Maggie

last: Purcell

address: 110 E Warren

institute: Wayne State University

data_processing:
Base-calling performed with CASAVA 1.8.2 software
Alignment performed with Tophat software, aligning to Human Genome Consortium Reference Human Genome hg19
Relative abundances calculated using Cufflinks software
Genome_build: hg19
Supplementary_files_format_and_content: gft files containing relative abundances calculated using Cufflinks software

growth_protocol: Cells were grown in 10 cm tissue culture dishes in Modified Eagles Medium with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
Total RNA was extracted using the QIAGEN Rneasy Kit
RNA libraries were prepared using standard Illumina Protocols in conjunction with the Illumina TruSeq RNA sample preparation kit

tag: tissue origin

value: Skin

value: MDAH041 LFS fibroblasts

tag: treated with

value: Serum-starved

tag: sample group

value: induced into quiescence


title: Qui 1


title: Qui 3


title: H2O2 2

value: induced into senescence


title: Globodera pallida Sample 1

description: 5' monophosphate only


title: H2O2 3


title: Romanomermis culicivorax Sample 12

description: 5' polyphosphatase treated


title: Sample_P011

source_name: progressive leukoplakias 001

value: hyperkeratosis w atypia


title: Bisulfite_seq-Col_2

city: Seattle

first: Christopher

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

department: Pathology

institute: University of Washington

description:
genomic DNA isolated by phenol/chloroform and bisulfite treated; quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane
This is duplicated sample record of GSM1193638 for the convenient retrieval of the complete raw data from SRA.

data_processing:
ChIP-seq -- Reads were filtered for full-length (50bp) reads.  Reads containing adapter were discarded. Reads were mapped with Bowtie (Langmead et al. 2009 Genome Biol) to the nuclear genome, allowing for 1 mismatch and retaining only uniquely mapping reads. Identical reads (potential PCR or optical duplicates) were flattened to 1 read. Samples 5 and 6 are biological replicates of samples 7 and 8 respectively.
miRNA-seq - Reads were demultiplexed (perfect matches to each index were required).  Adapter sequences (identified by at least a 13 nt perfect match) were trimmed and reads >18 nt and <28 nt in length after trimming were retained.  Reads with no identifiable adapter were discarded.  Reads were mapped with Bowtie (Langmead et al. 2009 Genome Biol) to the nuclear genome, allowing for 1 mismatch. Both unique and non-uniquely mapping reads were retained for normalization purposes but only uniquely mapping reads were used for downstream analysis. For downstream analyses up to 100 identical mapping reads were allowed to be counted at any given region, locations with more than 100 siblings were flattened to 100 mapping reads.
BS-seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics), allowing up to 2 mismatches and retaining only uniquely mapping reads. The drm2, drm3, and nrpe1 mutant libraries used in this study were previously published (GSE39901), as were the 2 other Col replicates used (Series:GSE36129-Sample:GSM881756, Series:GSE49090-Sample:GSM1193638).
Genome_build: TAIR10
Supplementary_files_format_and_content: ChIP-seq: Fixed step (25bp) UCSC Genome Browser wiggle format files for each chromosome with the the relative read counts given (reads in 25bp bins /total unique mapping reads)
Supplementary_files_format_and_content: miRNA-seq: Fixed step (25bp) UCSC Genome Browser wiggle format files for each chromosome for 24nt class of small RNAs with each bin given a value corresponding to the relative 24 nt read density at that location (24nt reads in 25bp bins / total mapping small RNA reads of all size classes - unique and non-uniquely mapping)
Supplementary_files_format_and_content: BS-seq: Variable step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level (#methylated cytosines sequenced/#total cytosines sequenced).

organism: Arabidopsis thaliana

growth_protocol: All plants were grown at 22 degrees celsius in constant light.

extract_protocol:
phenol-chloroform extraction followed by bisulfite treatment
converted and fragmented genomic DNA library as described in Stroud et al., Cell 2013

tag: ecotype

value: Columbia

tag: genotype/variation

value: 3 week leaf tissue

tag: molecule subtype

value: Bisulfite-treated genomic DNA


title: Bisulfite_seq-drm3

description:
genomic DNA isolated by phenol/chloroform and bisulfite treated; quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane
This is duplicated sample record of GSM981017 for the convenient retrieval of the complete raw data from SRA.


title: small_RNAseq-nrpe1

description: 18-28nt isolated small RNAs from total RNA Trizol preparation; quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/4 lane

extract_protocol:
Trizol extraction followed by PEG and then urea-PAGE fractionation
Illumina TruSeq small RNA

value: floral tissue

value: Purified small RNAs


title: 5-aza 3


title: Bisulfite_seq-nrpe1

description:
genomic DNA isolated by phenol/chloroform and bisulfite treated; quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane
This is duplicated sample record of GSM981040 for the convenient retrieval of the complete raw data from SRA.


title: 5-aza 2


title: 5-aza 1


title: small_RNAseq-drm2


title: small_RNAseq-drm3


title: Adria 3

value: Adriamycin


title: Adria 2


title: FLAG-NRPE1_ChIPseq-drm3_replicate_2

description: immunoprecipitated formaldehyde-crosslinked flower tissue; quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/5 lane

extract_protocol:
extracted by ChIP followed by phenol-chloroform exctract as described
Illumina TruSeq DNA Prep Kit

value: drm3-1  w/ NRPE1-Flag transgene

tag: chip-seq antibody

value: anti-FLAG antibody

tag: chip-seq antibody vendor

value: Sigma

tag: chip-seq antibody cat #

value: Genomic DNA isolated from immunoprecipitated chromatin using anti-FLAG antibody (Sigma M8823)


title: small_RNAseq-Col

value: Wild type


title: FLAG-NRPE1_ChIPseq-Col_replicate_2

value: Wild type  w/ NRPE1-Flag transgene


title: Bisulfite_seq-drm2

description:
genomic DNA isolated by phenol/chloroform and bisulfite treated; quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane
This is duplicated sample record of GSM981015 for the convenient retrieval of the complete raw data from SRA.


title: Nat 3

value: Skin

tag: cell type

value: MDAH041 LFS fibroblasts

value: None (grown until growth arrest)

value: replicatively senescent


title: FLAG-NRPE1_ChIPseq-drm3_replicate_1


title: Nat 1

tag: passages


title: Nat 2


title: Adria 1

value: induced into senescence


title: H2O2 1


title: LP 3

value: aging cells


title: Bisulfite_seq-Col_1

description:
genomic DNA isolated by phenol/chloroform and bisulfite treated; quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane
This is duplicated sample record of GSM881756 for the convenient retrieval of the complete raw data from SRA.

value: Columbia

value: 3 week leaf tissue


title: Endogenous_NRPE1_ChIPseq-drm3

description: immunoprecipitated formaldehyde-crosslinked flower tissue; quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/4 lane

value: floral tissue

value: NRPE1 antibody

value: Genomic DNA isolated from immunoprecipitated chromatin using anti-NRPE1 endogenous antibody


title: Con rep2

city: Boston

first: Wei

last: Song

email: rocwsong@gmail.com, songw@whu.edu.cn

state: Massachusetts

address: 77 Ave Louis Pasteur, NRB 336

department: Department of Genetics

institute: Harvard Medical School

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Drosophila  genome (flybase genome annotation version r5.51) using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Gene expression was quantified with Cufflinks.
Genome_build: Flybase genome annotation version r5.51
Supplementary_files_format_and_content: csv files include FPKM values for each sample.

extract_protocol:
10 thoraces dissected out from the flies incubated for 8 days at 29°C, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background strain

value: thoracic muscle

tag: developmental stage

value: Adult

tag: days at 29 c

tag: genotype

value: esg-Gal4, tub-Gal80ts, UAS-GFP/+


title: Yki rep1

tag: tissue


title: Yki rep2


title: FLAG-NRPE1_ChIPseq-Col_replicate_1

value: anti-FLAG antibody

value: Sigma

value: Genomic DNA isolated from immunoprecipitated chromatin using anti-FLAG antibody (Sigma M8823)


title: LP 2

value: Skin


title: Endogenous_NRPE1_ChIPseq-drm2


title: Endogenous_NRPE1_ChIPseq-Col

value: Wild type


title: Endogenous_NRPE1_ChIPseq-nrpe1


title: LLP 3

value: MDAH041 LFS fibroblasts

value: young cells


title: LLP 2


title: clf28 flowers

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

data_processing:
FastaQ files of each sample were aligned against Arabidopsis Genome TAIR 10 using TopHat.
Mapped sequences were assembled into transcripts using Cufflinks.
Assembled transcripts of each sample were summarized and merged into transcription units using Cuffcompare.
Expression level of each TU are presented by Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample produced by Cufflinks.

source_name: clf28 flowers

growth_protocol: Arabidopsis plant (Col-0 and clf-28) materials were grown under long day conditions at 22℃. Aerial part and roots were collected from two-week old plants that grew on MS plate. Flowers and siliques were collected from five-week old plants that grew in soil.

extract_protocol: All samples were harvested and frozen immediately in liquid nitrogen until use. Total RNA was extracted and treated with DNase I using RNeasy Plant mini kit (Qiagen). RNA sequence libraries were prepared with TruSeq RNA sample Prep V2 kit according to the instructions (Illumina). Sequences were determined by HiSeq 2000 sequencing system in the genomic center in Rockefeller University.

value: clf-28 mutant


title: clf28 leaves

source_name: clf28 leaves


title: Immortal 3

value: None (spontaneously immortal)

value: spontaneously immortal cells


title: Con rep1


title: clf28 siliques

source_name: clf28 siliques


title: Immortal 1


title: clf28 roots

source_name: clf28 roots


title: wt leaves

source_name: wt leaves

value: wild type


title: Immortal 2


title: wt flowers

source_name: wt flowers


title: wt roots

source_name: wt roots


title: LP 1

value: aging cells


title: ALL65 d3

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Illumina CASAVA pipeline version 1.8.2 used for basecalling
Reads were aligned to the mouse genome by Rsubread version 1.12.6
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI exon annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files were written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

organism: Mus musculus

source_name: ALL65 T-ALL cells

growth_protocol: Spleen cells were isolated from leukemic mice and T-ALL cells were isolated using FACS

extract_protocol:
FACS sorted cell pellets were lysed and RNA prepared using QIAGEN RNeasy plus mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Leukemic mice were untreated or treated with Dox for 3 days, resulting in shutdown of GFP-linked shRNA expression and restoration of endogenous Ikaros expression

tag: immunophenotype

value: GFPmid

tag: treatment

value: 3 days Dox (shRNA shut-off)

tag: cell source

value: splenocytes of leukemic recipient mice

value: T-ALL cells


title: ALL65 untreated

value: GFPhigh

value: untreated


title: wt siliques

source_name: wt siliques


title: HFF-1

city: Stockholm

first: Suvi

middle: Tuulia

last: Asikainen

state: Huddinge

address: Karolinska University Hospital

department: CLINTEC

country: Sweden

institute: Karolinska Institutet

description: Derived from newborn human foreskin

data_processing:
Image analysis was performed using Firecrest (Genome Analyzer IIX)
Basecalling using Bustard
First genome alignment using Gerald
Second genome alignment using Bowtie
Small RNA species extraction using in-house build tools
miRNA and moRNA differential expression analysis using DESeq
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are in tab-delimited .txt format. Every row contains a small RNA read sequence and its count

source_name: Foreskin fibroblast line

growth_protocol: HS401 and HS181 were grown on HFF-1 human fibroblast feeders. Cells were cultured in Knock-out basal growth media which was supplemented with Serum Replacement-supplement (Life Technologies). HFF-1 fibroblast line was cultured in Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted using Trizol protocol.
Small RNA library was constructed using Illumina Small RNA Sample Prep Kit V1 (2008).

treatment_protocol: HS401 and HS181 were harvested usinf TypleE (Invitrogen) avoiding feeder cell contamination. HFF-1 was harvested using Trypsin (Invitrogen).

tag: cell line

tag: passage

tag: pluripotency confirmed using teratoma assay

value: no


title: HS401

description: Derived from human blastocyst

source_name: Embryonic stem cell line

value: yes


title: ALL211 untreated

description: batch date: Apr 22 2014

data_processing:
Illumina CASAVA pipeline version 1.8.2 used for basecalling
Reads were aligned to the mouse genome by Rsubread version 1.14.0
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI exon annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files were written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: ALL211 T-ALL cells


title: LLP 1

tag: tissue origin

value: Skin

tag: treated with

tag: sample group


title: DN-1

city: Marseille

first: Ana

last: Reynders

address: Parc Scientifique de Luminy, 163 Avenue de Luminy

country: France

institute: IBDM

description:
REY4
Processed data files: TMM_Normalized_Counts_3conditions.txt, RPKM_allGenes.txt

data_processing:
Image analyses and basecalling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina).
Demultiplexing was performed using Illumina's sequencing analysis software (CASAVA 1.8.2).
Alignment was performed using the eland_rna module from CASAVA 1.8.2.
The gene counting was performed using the counting module from CASAVA 1.8.2. Raw reads counts and Reads Per Kilobase per Million Mapped Reads (RPKM) were produced. Only first read in pairs have been taken into account during this step.
Differentially expressed genes were identified using the Bioconductor package edgeR (v2.6.2). Only genes having more than 1000 reads in the two replicates of at least one condition were kept for the downstream statistical analysis. Data were normalized using Trimmed Mean of M values (TMM) normalization factors. Genes with adjusted p-value less than 1% (according to the FDR method from Benjamini-Hochberg) were declared differentially expressed.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-separated text files. First column is the gene identifier (Gene symbol|Entrez Gene ID|chromosome|start|end), 6 following columns are normalized abundance measurements for the 6 samples. The 'TMM_Normalized_Counts_3conditions.txt' file contains data normalized according to the Trimmed Mean of M-values (TMM) method (after data filtering). The 'RPKM_allGenes.txt' file contains Reads Per Kilobase per Million Mapped Reads (RPKM) normalized counts.

source_name: Remaining sensory neurons

extract_protocol:
Neurons were sorted directly in RLT-lysis buffer from RNeasy Micro Kit (Qiagen), snap-frozen at -80°C and processed for RNA extraction following manufacturer's recommendations. 50 nanograms of high-quality total RNAs were amplified with the Amino Allyl Message Amp II Amplification kit (Life Technologies, Carlsbad, CA).
RNA-Seq libraries were constructed with the TruSeq RNA sample preparation (Low-throughput protocol) kit from Illumina.

treatment_protocol: FACS-sorting

tag: genotype/variation

value: GINIP+/mcherry

value: dorsal root ganglia (DRG)

tag: sensory neuron subset

value: remaining cells (DN, double-negative=IB4-GINIP-)


title: C-LTMRs-2

description:
REY3_bis
Processed data files: TMM_Normalized_Counts_3conditions.txt, RPKM_allGenes.txt

source_name: C-LTMR sensory neurons

value: C-LTMR (IB4-GINIP+)


title: C-LTMRs-1

description:
REY3
Processed data files: TMM_Normalized_Counts_3conditions.txt, RPKM_allGenes.txt


title: DP-2

description:
REY2_bis
Processed data files: TMM_Normalized_Counts_3conditions.txt, RPKM_allGenes.txt

source_name: Mrgprd+ sensory neurons


title: CEBPA_10K_cells_Biological repl._IV

city: Copenhagen N

first: Janus

middle: Schou

last: Jakobsen

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

description:
ChIP-Seq with 10000 cells
Cross-linked (formaldehyde), sonicated  chromatin for ChIP-seq (fragmented to 200-500 bp)
Lp30 cells generated from floxed p30 using Mx-cre and Poly-IC injection. Tertiary, transplanted leukemia used for examinations
See publication for FACS isolation regimen

data_processing:
Mapping tool: Bowtie v. 0.12.8 with standard settings for unique mapping.
Genome_build: MGSCv37 (UCSC mm9)
Supplementary_files_format_and_content: processed data not provided for this record.

source_name: p30-GMP-blast cells

growth_protocol: whole bone marrow was isolated from a tertiary leukemia initiated (transplanted) from Lp30 mice, GMP population isolated by FACS as previously defined: Kirstetter P, Schuster MB, Bereshchenko O, et al. Modeling of C/EBPalpha mutant acute myeloid leukemia reveals a common expression signature of committed myeloid leukemia-initiating cells. Cancer Cell. 2008;13(4):299-310.

extract_protocol:
Cells were lysed as described previously (Jakobsen JS, Waage J, Rapin N, Bisgaard HC, Larsen FS, Porse BT. Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries. Genome Res. 2013;23(4):592-603.) in 300 μl lysis buffer,12 applying up/down pipetting 10 times using a 100 ul tip low retention tip. Samples were sonicated using a Bioruptor sonicator plus for 30 cycles, 15/30 seconds on/off, high setting, and debris pelleted by centrifuging cold at 14,000g for 10 minutes. Fragmentation of chromatin was evaluated on extracted DNA using either: 1) a c-Kit enriched 500,000 cell sample processed in parallel (one of six tubes sonicated simultaneously) and agarose gel electrophoresis or, 2) direct sample size inspection of a 20 ul aliquot using a Bioanalyzer. ChIP was performed essentially as described previously (Sandmann T, Jakobsen JS, Furlong EE. ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos. Nat Protoc. 2006;1(6):2839-2855) with ca. 125.000 cells for histone mark and ca. 250.000 cells for CEBPA ChIP. Quanta of used antibodies (CEBPA, Santa Cruz sc-61, lot#J0407, 0.2 ug; H3K27me3, Cell signaling #9733S, lot#2, 1 ul; H3K4me3, Cell signaling #9751S,  lot#2, 1 ul) and protein A beads (Sigma, cat#P9424 , 10 ul 50%/50% beads/RIPA-low salt (140 mM)) were optimized for low input amounts, using siliconized tubes (Biozym, cat#1267-2970).
A proprietary protocol for small scale ChIP-seq DNA amplification was used, based on further refining of the standard Illumina amplification and addition of bacterial carrier DNA.  See publication for detailed protocols

tag: sorted cell population

value: GMP

tag: strain/background

value: Tertiary, transplanted leukemia used for examinations; Whole bone marrow, cKIT enriched, FACs isolated

tag: chip antibody

value: anti-CEBPA


title: K4me3_10K_cells_Biological repl._V


title: DP-1

description:
REY2
Processed data files: TMM_Normalized_Counts_3conditions.txt, RPKM_allGenes.txt


title: ALL211 d3

description: batch date: Apr 22 2014

tag: cell type


title: DN-2

description:
REY4_bis
Processed data files: TMM_Normalized_Counts_3conditions.txt, RPKM_allGenes.txt


title: K4me3_CHIP-SEQ_2

description:
K4me3_2
Lp30 cells generated from floxed p30 using Mx-cre and Poly-IC injection. Tertiary, transplanted leukemia used for examinations.
See publication for FACS isolation regimen.
Cross-linked (formaldehyde), sonicated chromatin for ChIP-seq (fragmented to 200-500 bp).

data_processing:
Mapping tool: Bowtie v. 0.12.8 with standard settings for unique mapping.
CEBPA peaks were generated using: MACS2 peak calling, standard settings.
Genome_build: MGSCv37 (UCSC mm9)
Supplementary_files_format_and_content: ALPHA-1-peaks.bed contains CEBPA-1 peak regions in simple bed format (chr_start_end), generated using MACS2 peak calling standard settings, cut-off of fold 30, q-value 50, one outlier filtered out.
Supplementary_files_format_and_content: Mm9_refseq_TSS-positions_pm500bp.bed contains RefSeq TSSs of coding regions in simple bed format (chr_start_end), excluding mitochondrial genes, 1000 bp centered on TSS.

source_name: p30-GMP-blast cells, Biological repl_III, H3K4me3 ChIP

growth_protocol: Whole bone marrow was isolated from a tertiary leukemia initiated (transplanted) from Lp30 mice, GMP population isolated by FACS as previously defined: Kirstetter P, Schuster MB, Bereshchenko O, et al. Modeling of C/EBPalpha mutant acute myeloid leukemia reveals a common expression signature of committed myeloid leukemia-initiating cells. Cancer Cell. 2008;13(4):299-310.

extract_protocol:
Cells were lysed as described previously (Jakobsen JS, Waage J, Rapin N, Bisgaard HC, Larsen FS, Porse BT. Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries. Genome Res. 2013;23(4):592-603) in 300 μl lysis buffer, applying up/down pipetting 10 times using a 100 ul tip low retention tip. Samples were sonicated using a Bioruptor sonicator plus for 30 cycles, 15/30 seconds on/off, high setting, and debris pelleted by centrifuging cold at 14,000g for 10 minutes. Fragmentation of chromatin was evaluated on extracted DNA using either: 1) a c-Kit enriched 500,000 cell sample processed in parallel (one of six tubes sonicated simultaneously) and agarose gel electrophoresis, or 2) direct sample size inspection of a 20 ul aliquot using a Bioanalyzer. ChIP was performed essentially as described previously (Sandmann T, Jakobsen JS, Furlong EE. ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos. Nat Protoc. 2006;1(6):2839-2855) with ca. 125.000 cells for histone mark and ca. 250.000 cells for CEBPA ChIP. Quanta of used antibodies (CEBPA, Santa Cruz sc-61, lot#J0407, 0.2 ug; H3K27me3, Cell signaling #9733S, lot#2, 1 ul; H3K4me3, Cell signaling #9751S, lot#2, 1 ul) and protein A beads (Sigma, cat#P9424 , 10 ul 50%/50% beads/RIPA-low salt (140 mM)) were optimized for low input amounts, using siliconized tubes (Biozym, cat#1267-2970).
A proprietary protocol for small-scale ChIP-seq DNA amplification was used, based on further refining of the standard Illumina amplification and addition of bacterial carrier DNA. See associated publication for detailed protocols.

value: tertiary transplanted leukemia, whole bone marrow, cKIT enriched, FACs isolated

tag: input dna amount


title: K27me3_CHIP-SEQ_1

description:
K27me3-1
Lp30 cells generated from floxed p30 using Mx-cre and Poly-IC injection. Tertiary, transplanted leukemia used for examinations.
See publication for FACS isolation regimen.
Cross-linked (formaldehyde), sonicated chromatin for ChIP-seq (fragmented to 200-500 bp).

source_name: p30-GMP-blast cells, Biological repl_I, H3K27me3 ChIP

tag: tissue


title: CEBPA_CHIP-SEQ_6_50pg

description:
Alpha_6
Lp30 cells generated from floxed p30 using Mx-cre and Poly-IC injection. Tertiary, transplanted leukemia used for examinations.
See publication for FACS isolation regimen.
Cross-linked (formaldehyde), sonicated chromatin for ChIP-seq (fragmented to 200-500 bp).

source_name: p30-GMP-blast cells, from pool of Biological repl_I_II_III, CEBPA ChIP

value: CEBPA


title: K4me3_CHIP-SEQ_1

description:
K4me3_1
Lp30 cells generated from floxed p30 using Mx-cre and Poly-IC injection. Tertiary, transplanted leukemia used for examinations.
See publication for FACS isolation regimen.
Cross-linked (formaldehyde), sonicated chromatin for ChIP-seq (fragmented to 200-500 bp).

source_name: p30-GMP-blast cells, Biological repl_II, H3K4me3 ChIP


title: HS181

description: Derived from human blastocyst


title: CEBPA_CHIP-SEQ_4_100pg

description:
Alpha_4
Lp30 cells generated from floxed p30 using Mx-cre and Poly-IC injection. Tertiary, transplanted leukemia used for examinations.
See publication for FACS isolation regimen.
Cross-linked (formaldehyde), sonicated chromatin for ChIP-seq (fragmented to 200-500 bp).


title: CEBPA_CHIP-SEQ_3_100pg

description:
Alpha_3
Lp30 cells generated from floxed p30 using Mx-cre and Poly-IC injection. Tertiary, transplanted leukemia used for examinations.
See publication for FACS isolation regimen.
Cross-linked (formaldehyde), sonicated chromatin for ChIP-seq (fragmented to 200-500 bp).


title: CEBPA_CHIP-SEQ_2_300pg

description:
Alpha_2
Lp30 cells generated from floxed p30 using Mx-cre and Poly-IC injection. Tertiary, transplanted leukemia used for examinations.
See publication for FACS isolation regimen.
Cross-linked (formaldehyde), sonicated chromatin for ChIP-seq (fragmented to 200-500 bp).

source_name: p30-GMP-blast cells, Biological repl_II, CEBPA ChIP


title: CEBPA_CHIP-SEQ_1_300pg

description:
Alpha_1
Lp30 cells generated from floxed p30 using Mx-cre and Poly-IC injection. Tertiary, transplanted leukemia used for examinations.
See publication for FACS isolation regimen.
Cross-linked (formaldehyde), sonicated chromatin for ChIP-seq (fragmented to 200-500 bp).

source_name: p30-GMP-blast cells, Biological repl_I, CEBPA ChIP


title: ALL101 untreated 3 technical rep 2

description:
4056vt-101xx8INJ-L8
Raw files batch date: Nov 25  2011

data_processing:
Illumina CASAVA pipeline version 1.8.1 used for basecalling
Reads were aligned to the mouse genome by Rsubread version 1.14.0
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI exon annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files were written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: ALL101 T-ALL cells

tag: immunophenotype


title: ALL101 d3 Dox 2 technical rep 2

description:
4056vt-101xx6sortGFP+-L8
Raw files batch date: Nov 25  2011

value: GFPmid

tag: treatment

value: 3 days Dox (shRNA shut-off)


title: ALL101 d3 Dox 1 technical rep 2

description:
4056vt-101xx1sortGFP+-L8
Raw files batch date: Nov 25  2011

tag: cell source

value: splenocytes of leukemic recipient mice

value: T-ALL cells


title: ALL101 d3 Dox 3 technical rep 2

description:
4056vt-101xx9sortGFP+-L8
Raw files batch date: Nov 25  2011


title: BAFF_30hr

city: San Diego

first: Harry

middle: Aaron

last: Birnbaum

state: California

address: 4406 Dawes Street

institute: UCSD Chem and Biochem

data_processing:
Illumina Hiseq 2000 with real time analysis version 1.13.48 was used for basecalling and Casava version 1.8.2 was used to extract reads
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome and searched for splice juntions, with TopHat v2.0.5 and Bowtie v2.0.0.7 with the following parameters to Tophat: --b2-very-sensitive --no-coverage-search
Used Cufflinks v2.0.2 with default parameters to align reads to transcripts and estimate abundances, used cuffmerge to merge the assemblies, and used cuffdiff to calculate differential gene and transcript expression levels
Imported the counts and Fragments per Kilobase of exon per million fragments mapped (FPKM) values calculated by cufflinks to R using the cummeRbund v0.1.3 package
Genome_build: mm10
Supplementary_files_format_and_content: GTF files for each sample containing assembled transcripts, files with fpkm values of genes for each sample, files with fpkm of isoforms for each sample, and one GTF for the merged assemblies

source_name: B cells

extract_protocol:
RNA was extracted and purified as per the manufacturers protocol using the RNeasy kit (QIAGEN). 1 mg of the quantified RNA was reverse transcribed using superscript II RT system (Invitrogen) and poly-dT primers.
cDNA libraries were generated using the IlluminaTruSeq kits and quantitation was performed using the Roche Light Cycler 480

tag: genetic background

value: B cells

value: BAFF

tag: time


title: Both_8hr

value: anti-IgM and BAFF

value: 8 h


title: AntiIGM_30hr

value: anti-IgM


title: Unsimulated_0hr

value: 0 h


title: ALL101 d3 Dox 3 technical rep 1

description:
4056vt-101xx9sortGFP+-L5
Raw files batch date: Nov 25  2011


title: BAFF_8hr


title: ALL101 d3 Dox 2 technical rep 1

description:
4056vt-101xx6sortGFP+-L5
Raw files batch date: Nov 25  2011


title: ALL101 untreated 1 technical rep 2

description:
4056vt-101xx2sortGFP+-L8
Raw files batch date: Nov 25  2011

value: GFPhigh

value: untreated


title: ALL101 untreated 3 technical rep 1

description:
4056vt-101xx8INJ-L5
Raw files batch date: Nov 25  2011


title: ALL101 untreated 2 technical rep 2

description:
4056vt-101xx4sortGFP+-L8
Raw files batch date: Nov 25  2011


title: ALL101 untreated 2 technical rep 1

description:
4056vt-101xx4sortGFP+-L5
Raw files batch date: Nov 25  2011


title: Both_30hr


title: AntiIGM_8hr


title: ALL101 d3 Dox 1 technical rep 1

description:
4056vt-101xx1sortGFP+-L5
Raw files batch date: Nov 25  2011


title: CEBPA_CHIP-SEQ_5_100pg

description:
Alpha_5
Lp30 cells generated from floxed p30 using Mx-cre and Poly-IC injection. Tertiary, transplanted leukemia used for examinations.
See publication for FACS isolation regimen.
Cross-linked (formaldehyde), sonicated chromatin for ChIP-seq (fragmented to 200-500 bp).

value: GMP


title: K27me3_CHIP-SEQ_2

description:
K27me3-2
Lp30 cells generated from floxed p30 using Mx-cre and Poly-IC injection. Tertiary, transplanted leukemia used for examinations.
See publication for FACS isolation regimen.
Cross-linked (formaldehyde), sonicated chromatin for ChIP-seq (fragmented to 200-500 bp).

source_name: p30-GMP-blast cells, Biological repl_II, H3K27me3 ChIP


title: SED-RRBS3

city: Nuthetal

first: Timo

last: Kanzleiter

address: Arthur-Scheunert-Alle 114

department: Experimental Diabetology

country: Germany

institute: DIfE

data_processing:
After adapter clipping (trim_galore_v0.2.5; cutadapt-1.0) , reads were aligned using Bismark (ver 0.7.7; bowtie 0.12.9 ). Parameterts used for alignemnt were /bismark -n 2 -l 20 --phred33 --non_directional. Methylation calls were also made with Bismark using these settings /bismark_methylation_extractor -s -o ../data/Methylation_extrac/ --comprehensive
Methylation calls from Bismark were filtered for CpGs present 2kb upstream and 1kb downstream of UCSC (mm9) annotated transcriptional start sites
Genome_build: mm9 Build 37
Supplementary_files_format_and_content: Data table containing the methylation ratios and genomic position of identified CpGs.

source_name: DNA from quadriceps muscle of sedentary mice

extract_protocol:
Genomic DNA was isolated from quadriceps muscle samples three hours after last training bout.
Full details can be found here Gu H, et al. (2011) Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling Nat Protoc 6: 468–481

treatment_protocol: Exercised (EX) mice were trained for 4 weeks on a motorized treadmill. Sedentary (SED) controls

tag: strain

value: quadriceps muscle


title: SED-RRBS2


title: ALL101 untreated 1 technical rep 1

description:
4056vt-101xx2sortGFP+-L5
Raw files batch date: Nov 25  2011


title: EX_RRBS3

source_name: DNA from quadriceps muscle of exercised mice


title: EX_RRBS2


title: SED-RRBS1


title: EX_RRBS1


title: Waxy apple mRNA extract 3

city: Belvaux

first: Sylvain

last: Legay

address: 41, rue du Brill

department: ERIN department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology

data_processing:
The MiSeq generated FASTQ files were imported in CLC genomics workbench v6.5 discarding reads with poor quality (<Q30). Read duplicates were removed from each sample independently using the duplicate read removal plugin, Illumina adapter residues were then trimmed using the TruSeq adaptor sequence and finally filtered using the following criteria: low sequence quality <0.01, maximum of 2 ambiguous nucleotides, read length between 35 and 80 nucleotides.
The remaining reads were mapped to the predicted apple transcriptome (Velasco et al. 2010) with annotations obtained from Phytozome v.10 beta (http://phytozome.jgi.doe.gov) with the following criteria: mapped reads having multiple hits lower than 5, 90% identity and 50% of coverage with the reference. Expression values were calculated using the RPKM (Reads per kilobase transcript per million reads) method (Mortazavi et al. 2008). Genes with no mapped reads, with no specifically mapped reads and/or with a RPKM value lower than 0.1 in at least one of the libraries were removed from the dataset.
Differentially expressed genes between the russeted exocarp group ('Patte de loup', 'Reinette Parmentier', 'St Edmund's Pippin') and the waxy goup ('CRAW/Ma/AF42', 'CRAW/ma/AG94' ,'Gala') were statistically determined using a Baggerley's 'on proportions' weighted test (Baggerly et al. 2003), a false discovery rate (Benjamini-Hotchberg correction) was set at 0.2 and a fold-change cut-off value at -1>log2 ratio (Russet group/Waxy group))>1.
Genome_build: Malus x domestica V1.0; http://www.ncbi.nlm.nih.gov/assembly/GCF_000148765.1
Supplementary_files_format_and_content: tab-delimited text files include, unique and toal hit reads, RPKM values for each Sample; Log2 transformed fold change for each contig.

organism: Malus domestica

source_name: waxy apple exocarp (WAE)

growth_protocol: 6 apple varieties presenting 3 fully-waxy ('CRAW/Ma/AF42', 'CRAW/ma/AG94' ,'Gala') and 3 fully-russeted phenotypes ('Patte de loup', 'Reinette Parmentier', 'St Edmund's Pippin') were sampled in October 2012 in the orchards of the Walloon Agronomic Research Centre (CRA-W, Gembloux, Belgium)

extract_protocol:
A 5 millimeter (large) longitudinal slice was peeled with scalpels from each quarter, taking care to remove the remaining flesh from the exocarp. The resulting exocarp samples were directly flash-frozen in liquid nitrogen, roughly ground to homogenize the sample and stored at -80°C until RNA extraction. 250 mg samples were ground to a fine powder with mortar and pestle in liquid nitrogen. Total RNA was extracted using an adapted CTAB buffer extraction protocol (Gasic et al. 2004). Total RNAs were cleaned and treated with DNase I using the RNeasy plant mini kit (QIAGEN, Leusden, The Netherlands), following the manufacturer's guidelines. Total RNA integrity was assessed using the RNA Nano 6000 assay (Agilent Technologies, Diegem, Belgium) and a 2100 Bioanalyzer with quality parameters adapted to plant RNA profiles (Agilent Technologies, Santa Clara, CA, USA). Samples with RINs (RNA integrity number) lower than 8 were excluded from the experiment. RNA purity was assessed measuring the absorbance at 230 nm, 260 nm and 280 nm using a Nanodrop ND1000 spectrophotometer (Thermo scientific, Villebon-sur-Yvette, France). Quantification of total RNA was carried out using a Qubit RNA assay kit (Life technologies, Carlsbad, CA, USA).
Libraries were prepared from 3 µg total RNA using the TruSeq RNA Sample Preparation v2 kit according to the manufacturer's guidelines (Illumina, San Diego, CA, USA). After mRNA purification, cDNA synthesis, shearing, Illumina adapters/barcodes ligation and 15-cycles of PCR amplication, libraries were controlled using the Agilent 2100 bioanalyser and the DNA-1000 kit. Quantification of the libraries was performed using the Library Quantification Kit - Illumina/ROX Low (Kapa Biosystems, Boston, MA, USA) on a Viia7 96-well real-time-qPCR instrument (Life Technologies).

tag: apple variety

value: Gala

tag: phenotype

value: fully waxy apple

value: Apple fruit exocarp


title: Waxy apple mRNA extract 1


title: Waxy apple mRNA extract 2


title: Russeted apple mRNA extract 3

source_name: russeted apple exocarp (RAE)

value: Patte de Loup

value: fully-russeted apple


title: Russeted apple mRNA extract 2

description: CRAW4_Reinette Parmentier

value: Reinette Parmentier


title: Brugia malayi Sample 9

city: London

first: Peter

last: Sarkies

address: Du Cane Road

institute: Imperial College London

description: 5' polyphosphatase treated

data_processing:
Adapter trimming using Cutadapt v1
fastq to fasta conversion, selection for small RNAs of 15-33nt in length using custom Perl scripts using Perl v5.12.4
fasta collapsed using FastX toolkit fastx_collapser module
Supplementary_files_format_and_content: sequence id + number of reads + sequence

organism: Brugia malayi

source_name: Total RNA whole animal

extract_protocol:
Total RNA extracted using Trisure (BioLine) or Trizol (Invitrogen) according to manufacturer's instructions
Illumina Truseq small RNA according to manufacturer's instructions

tag: developmental stage

value: Adult

tag: blaxter clade

value: III


title: Brugia malayi Sample 2

description: 5' monophosphate only


title: HT2

city: wuhan

first: Zhou

last: Yingying

address: shizishan street 1#

institute: huazhong agriculture university

data_processing:
Illumina Casava1.7 software used for basecalling
The dirty raw reads were filtered using SolexaQA
Transcriptome de novo assembly is carried out with short reads assembling program-Trinity within each sample. Then unigenes from each sample's assembly can be taken into further process of sequence splicing and redundancy removing to acquire non-redundant unigenes as long as possible
.
Genome_build: Blastx alignment (evalue < 0.00001) between unigenes and protein databases like Nr, Nt, Swiss-Prot, KEGG, COG were performed
Supplementary_files_format_and_content: The 'All-Unigene' includes all unigenes from de novo assembly and annotation.txt file contains the blast annotations for each feature, expression of gene (RPKM) etc.

organism: Isatis tinctoria

growth_protocol: The plants were planted in the greenhouse and irrigated every two days with sunlight .

extract_protocol:
Tender leaves were sampled at seeding stage, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ploidy

value: diploid

value: leaf


title: HT3

value: autotetraploid


title: HT4


title: Paragordius varius Sample 20

description: 5' polyphosphatase treated

organism: Paragordius varius

value: Nematomorpha


title: Trichinella spiralis Sample 16

description: 5' monophosphate only

organism: Trichinella spiralis

value: L1 (muscle)

value: I


title: HT5

value: autotriploid


title: HT6


title: Russeted apple mRNA extract 1

description: CRAW2_St Edmund Pippin

value: St Edmund Pippin


title: Nippostrongylus brasiliensis Sample 14

description: 5' monophosphate only

organism: Nippostrongylus brasiliensis

value: V


title: Trichinella spiralis Sample 3

description: 5' polyphosphatase treated


title: Enoplus brevis Sample 11

description: 5' polyphosphatase treated

organism: Enoplus brevis

value: II


title: Enoplus brevis Sample 4

description: 5' monophosphate only


title: HT1


title: cyto_12_rp2

status: Public on Jan 31 2015

city: Lausanne

last: Marques

address: Rue du Bugnon 27

department: Department of Computational Biology

institute: University of Lausanne

description: cytoplasmic extract from day 12 (replicate 2)

data_processing:
Reads were aligned to the mouse reference genome (mm9) using TopHat [version 2.0.9 (Trapnell et al. 2009)]. Splice junctions from ENSEMBL build 70 (Flicek et al. 2013) were provided to facilitate reads that map across known mouse transcript splice junctions. Pair mates read mapped to distinct chromosomes were discarded.
Gene expression-To account for differences in RNA-sequencing depth, we considered the smallest number of mapped reads (93 million, day 12) and randomly sampled the same number of mapped reads from the remaining samples. Expression levels of protein-coding transcripts and lncRNAs annotated by Guttman and colleagues (Guttman et al. 2011) and ENSEMBl build 70, (Flicek et al. 2013) were estimated using Cufflinks [version 1.3.0, (Trapnell et al. 2010)].
Genome_build: mm9
Supplementary_files_format_and_content: gene expression (FPKMs) as tab delimited file.

source_name: Conditional Dicer mutant mouse Embryonic stem cell (described in Nesterova et al, 2008) 12 days after induction of Dicer LoF

growth_protocol: Mouse DTCM23/49 XY embryonic stem (mES) cell lines (Nesterova et al. 2008) were grown on 0.1% gelatin-coated plates in a culture medium at 37oC in a humidified atmosphere supplemented with 5% CO2, in KnockOut Dulbecco's Modified Eagle Medium (D-MEM, Invitrogen 10829-018) containing 1% antibiotic penicillin/streptomycin (Invitrogen 15140-122), supplemented with 10% Fetal Bovine Serum (FBS, Invitrogen 10108-165), 100 μM non-essential amino acids (Invitrogen 11140-076), 100 μM L-glutamine (Invitrogen 25030-024), 60 μM β-mercaptoethanol (Invitrogen 31350-010) and 0.01% leukemia inhibitory factor (LIF; Millipore; ESG1106).

extract_protocol:
Total cellular extract and cytoplasmic and nuclear fractions-fractionation using the PARIS kit (Ambion AM1921) -was extracted using the miRNeasy kit (Qiagen 217004) Genomic DNA was removed from all RNA extractions using the DNA-free kit (Ambion AM1906).
100 base paired end polyA-selected directional RNA sequencing libraries were prepared by BGI solutions (Hong Kong)

treatment_protocol: mESC cells were seeded at a density of 8.0 x 105 cells/dish were seeded in 10 cm2 dishes and grown for 24h prior to Tamoxifen treatment. In triplicate, deletion of Dicer’s RNAse III domain was induced by culturing the cells in the presence of 800nM Tamoxifen [(Z)-4-HydroxyTamoxifen (4-OHT), Sigma H7904]. Cells treated with 0.1% ethanol were used as control (3 replicates). Dicer-deficient colonies were selected and expanded from 10 cm2 to T-75 75 cm2 tissue culture flasks. Cells were passaged every 2-3 days until 70-80% confluence for 12 days.

tag: days after lof

tag: replicate

tag: subcellular localization

value: cytoplasm


title: cyto_12_rp1

description: cytoplasmic extract from day 12 (replicate 1)


title: cyto_12_rp3

description: cytoplasmic extract from day 12 (replicate 3)


title: nucleus_12_rp2

description: nuclear extract from day 12 (replicate 2)

value: nucleus


title: nucleus_12_rp1

description: nuclear extract from day 12 (replicate 1)


title: nucleus_12_rp3

description: nuclearl extract from day 12 (replicate 3)


title: whole_cell_12_rp3

description: whole cell extract from day 12 (replicate 3)

value: whole cell


title: Odontophora rectangula Sample 5

description: 5' monophosphate only

organism: Odontophora rectangula


title: whole_cell_10_rp3

description: whole cell extract from day 10 (replicate 3)

source_name: Conditional Dicer mutant mouse Embryonic stem cell (described in Nesterova et al, 2008) 10 days after induction of Dicer LoF


title: whole_cell_10_rp2

description: whole cell extract from day 10 (replicate 2)


title: Trichinella spiralis Sample 10

description: 5' polyphosphatase treated


title: Paragordius varius Sample 19

description: 5' monophosphate only


title: whole_cell_4_rp3

description: whole cell extract from day 4 (replicate 3)

source_name: Conditional Dicer mutant mouse Embryonic stem cell (described in Nesterova et al, 2008) 4 days after induction of Dicer LoF


title: whole_cell_8_rp3

description: whole cell extract from day 8 (replicate 3)

source_name: Conditional Dicer mutant mouse Embryonic stem cell (described in Nesterova et al, 2008) 8 days after induction of Dicer LoF


title: whole_cell_8_rp1

description: whole cell extract from day 8 (replicate 1)


title: whole_cell_8_rp2

description: whole cell extract from day 8 (replicate 2)


title: whole_cell_4_rp1

description: whole cell extract from day 4 (replicate 1)


title: whole_cell_4_rp2

description: whole cell extract from day 4 (replicate 2)


title: cyto_0_rp3

description: cytoplasmic extract from day 0 (replicate 3)

source_name: Conditional Dicer mutant mouse Embryonic stem cell (described in Nesterova et al, 2008) before induction of Dicer LoF