title: RC3

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

data_processing:
Reads were mapped to the reference genome (GRCm38) using the software package Tophat (v2.0.13).
Mapping sequencing reads: a maximum of 2 mismatches were allowed and reads that mapped equally well to more than 40 genomic locations were discarded.
Cufflinks (v2.2.1) was used to reconstruct transcript models from alignments.
The tool cuffmerge (Cufflinks v2.2.1) was used for merging together each of the assemblies with the reference mouse annotation file in order to combine novel isoforms with known isoforms.
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty) developed by Simon Anders at EMBL.
Genome_build: Mouse genome assembly: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files including locus, number of mapped reads, gene name, and chromosome location.

source_name: Mammary gland

extract_protocol:
Total RNA was extracted from mammary gland tissues following the TRI-Reagent (Molecular Research) protocol. The quality and concentration of the extracted RNA was assessed using Agilent Bioanalyzer chips.
Libraries were prepared following the Illumina mRNA-Seq protocol. Sequencing libraries were created from 50 ng samples and sequenced with Illumina’s HiSeq 2000 at the University of Wisconsin-Madison Biotechnology Center.

value: Mammary gland

tag: treatment

value: Tph1 knock-out dams injected daily with 5-HTP


title: H111 s54 mutant

status: Public on Apr 29 2015

type: SRA

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

library_source: transcriptomic

data_processing:
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer
Sequencing reads were mapped to the Bc H111 genome using CLC Genomics Workbench v7.0 (CLCbio) allowing up to 2 mismatches per read
RNA-Seq count data were subsequently analyzed with the DESeq software (Anders & Huber 2010)
Genome_build: H111 genome sequence (accession no. HG938370, HG938371, and HG938372)
Supplementary_files_format_and_content: tab-delimited text files include RPKM and mean values for each sample

molecule: total RNA

organism: Burkholderia cenocepacia H111

source_name: Bc H111 planktonic cells

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using hot phenol protocol (Pessi et al 2007) . Ds cDNA was produced and nugen librairies obtained.
RNA libraries were prepared using Ovation® Complete Prokaryotic RNA-Seq Library System

tag: strain

value: s54 mutant

tag: growth

value: planktonic cells, OD600 equal 0.4

tag: medium

value: minimal medium shift experiment (15 mM to 0.3 mM)


title: KO4

status: Public on Apr 28 2015

country: USA

organism: Mus musculus

tag: tissue

value: Tph1 knock-out dams


title: human C6 (IL3Ra-high)

city: Amsterdam

first: yanling

last: xiao

address: Plesmanlaan 121

country: Netherlands

institute: NKI

data_processing:
Sequence reads were mapped to NCBI build 37 using tophat version 2.0.6 with parameters --bowtie1, --library-type fr-unstranded, --no-coverage-search, --mate-inner-dist, --mate-std-dev, -M, -G, --transcriptome-index, Ensembl GTF version 66
Readcounts were calcultated using HTSeq-count with default parameters
Genome_build: GRCh37
Supplementary_files_format_and_content: The file genecounts.txt contains the absolute gene expression values for each of the samples.

organism: Homo sapiens

source_name: Bone marrow

growth_protocol: human BM IL3Ra-high- or IL3Ra-low hematopoietic progenitor cells were sorted from three different healthy individuals

extract_protocol:
sorted cells were immediately put in 1ml trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were sorted from direct ex-vivo cryo-preserved human BM samples, sorted cells were without additional treatment

tag: date of birth

tag: bm sample date

tag: cell sorting date

value: 15-May-2013 (BD FACS Aria)

tag: cell type

value: BM progenitor

tag: cell population

value: IL3Ra-high progenitor cells


title: RC1


title: suvh456_H3K23ac_ChIP_rep

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

library_source: genomic

data_processing:
ChIP-seq: Reads were mapped to the TAIR10 genome by allowing up to 2 mismatches, and only retaining uniquely mapping reads using Bowtie (Langmead et al., 2009). Reads mapping to identical locations were collapsed in to one read.
Genome_build: TAIR10
Supplementary_files_format_and_content: ChIP-seq: Column 1 is chromosome. Column 2 is the genomic strand(+/-) the read mapped to. Column 3 is the genomic coordinate the read mapped to.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 3 wk leaves

growth_protocol: Plants were grown under continuous light

extract_protocol:
ChIP-seq:One gram of tissue was ground in liquid nitrogen, and ChIP was performed as previously described (Law et al., 2013) using the following antibodies: H3K9me2 (Abcam 1220), H3 (Abcam 1791), H3K9me1 (Upstate 07-450), and H3K23ac (Millipore 07-355).
Libraries were generated and sequenced following manufacturer instructions (Illumina).

tag: ecotype

tag: age

value: 3 wk

value: leaves


title: RC2


title: suvh456_H3_ChIP_rep


title: drm12cmt23_H3K23ac_ChIP_rep


title: KO1


title: KO3


title: KO2


title: suvh456_H3K9me2_ChIP_rep


title: drm12cmt23_H3K9me2_ChIP_rep


title: WT4

value: wild-type dams


title: WT3


title: drm12cmt23_H3_ChIP_rep


title: RC4


title: WT2


title: WT_H3K9me2_ChIP_rep


title: WT_H3K23ac_ChIP_rep


title: MINUS rep5

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

data_processing:
The quality of raw sequence data was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ).   No additional processing of the primary data was required.
Paired end sequences for the two sample groups (plus, minus) were aligned to the Tbb genome (obtained from ftp://ftp.sanger.ac.uk/pub/project/pathogens/gff3/CURRENT/ on 19 Feb 2015 ) using bowtie2 (parameters: --very-sensitive; version: 2.2.4), piped through samtools (parameters: -bhS; version: 0.1.18), and stored in indexed BAM format.
The annotated Tbb genome was viewed using Artemis software (http://www.sanger.ac.uk/resources/software/artemis/ ; http://ukpmc.ac.uk/abstract/MED/11120685), and coding segment (CDS) region coordinates extracted prior to conversion to bedtools bedfile format.  Bedtools (paramters: multicov -bams ; version: bedtools 2.15.0) was used to generate coverages for each CDS for each sample replicate.  RPKM-like values were calculated by dividing coverage by CDS size.
Statistical analyses of the two sample groups were undertaken in the R environment (www.R-project.org) using Bioconductor (www.bioconductor.org) packages.  Differential expression was explored using linear models and empirical Bayes methods, using the limma package (Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3, No. 1, Article 3. (Online, Tech Report PDF)).  RPKM-like values were offset by 1, logged, and quantile normalised prior to group-wise comparison.  Post-comparison,  data were filtered to remove loci whose normalised mean RPKM-like values were below the 10% quantile for all samples.
Genome_build: ftp://ftp.sanger.ac.uk/pub/project/pathogens/gff3/CURRENT/ ; retrieved 19Feb2015.
Supplementary_files_format_and_content: Annotated raw tag counts

organism: Trypanosoma brucei brucei

source_name: Whole organism_minus_tetracycline

growth_protocol: RNAi lines of TbNMD3 were created using the stem loop vector pALC14. For stable transfection 1x108 procyclic form  cells were subjected to nucleofection with Nucleofector system (Amaxa) using program X-014. Stable transformants were grown in SDM79 medium.

extract_protocol:
QIA RNA prep column with on column DNAse treatment
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNAi was induced by addtion of 1 microgram/ml tetracycline (“plus” group).  Controls (“minus” group) had no tetracycline addition. RNAs were isolated after 72h culture.

tag: group

value: MINUS

value: whole organism


title: WT1


title: WT_H3_ChIP_rep


title: MINUS rep4


title: MINUS rep1


title: PLUS rep3

source_name: Whole organism_plus_tetracycline

value: PLUS


title: PLUS rep2


title: MINUS rep3


title: PLUS rep1


title: R008_6gl_SO2

city: Legnaro (PD)

first: Chiara

last: Nadai

address: Viale dell'Università, 16

department: DAFNAE

country: Italy

institute: University of Padova

description: Sample 1

data_processing:
SOLiD reads were aligned using PASS software; only those uniquely aligned on the genome were considered
The number of reads aliged on each gene for each strain and sample was determined using a self-written perl script and an input file for DEGseq was generated
Differentially expressed genes were determined using DEGseq software 2.11.1
Genome_build: APIP00000000
Genome_build: GCA_000218975.1
Genome_build: ScVL3_v01
Genome_build: ScAWRI796_v01
Supplementary_files_format_and_content: tab-delimited text file includes the RKPM value for each strain and sample normalized considering R008_noSO2 sample as a reference and considering the total number of reads aligned for each experiment

organism: Saccharomyces cerevisiae

source_name: Yeast culture

growth_protocol: Yeast cultures were grown in 100 ml YPD medium at 25 °C in agitation for 18 hours. Each culture have been centrifuged and the pellet was resuspended into the volume of synthetic must MS300 required to obtain an OD600 of 0.5 of the 1:10 diluted solution (5x10^6 cells/ml). 100 ml of this pre-inoculum have been added to 900 ml of MS300, a synthetic medium that mimics the composition of a white wine must. Fermentation was performed at 25°C in 1 l bioreactors (Multifors, Infors HT) monitoring the temperature, the pH, and the CO2 flux in a range of 1-20 ml/min (red-y mod. GSM-A95A-BN00). SO2 concentration was determined by iodometric titration at different stages of the fermentation. Yeast cells were collected at the beginning of the process, when the CO2 produced by the cells was 6 g/l (middle exponential growth phase).

extract_protocol: Total RNA has been extracted from each sample using the PureLink® RNA Mini Kit (Ambion). Starting from 10 μgs of total RNA, 18S and 26S rRNAs were removed using the RiboMinusTM Transcriptome Isolation Kit (Invitrogen). Genomic DNA was removed using the DNA-free™ kit from Applied Biosystems. The RNA was used to prepare the libraries using the SOLiD 4 Whole Transcriptome Analysis Kit protocol.

treatment_protocol: For each strain the fermentation has been performed with 0mg/l or 25 mg/l of total SO2 added.

tag: strain type

value: vineyard strain (wild type)

tag: growth phase

value: mid exponential phase

tag: co2 produced before cell collection [g/l]

value: 25 mg/l


title: EC1118_6gl_SO2

description: Sample 2

value: enological strain


title: AWRI796_6gl_noSO2

description: Sample 5

value: 0 mg/l


title: VL3_6gl_SO2

description: Sample 4


title: VL3_6gl_noSO2

description: Sample 3


title: Control_ePCR1_IL_smRNA

city: Bolpur

first: Jolly

last: Basak

state: West Bengal

address: Santiniketan

department: Biotechnology

country: India

institute: Visva-Bharati, Siksha Bhavana

description: 3' adapter:CGATGT

data_processing:
The quality reads from the sequencing data were extracted and the adapter sequences were removed using cutadapt
The sequences smaller than 14 nucleotides were removed.
The reads were made unique for easy analysis by using fastx_collapser
The predicted miRNAs of P. vulgaris were blast searched against the sequencing data to validate the predictions.
Supplementary_files_format_and_content: comma delimited files which includes the TPM values for each miRNA

organism: Phaseolus vulgaris

source_name: Leaf

growth_protocol: Healthy seeds of Anupam cultivar of P. vulgaris were surface sterilized with 0.5% Sodium hypochlorite and germinated in dark at 28°C for 2 days. Germinated seeds were allowed to grow in soilrite in BOD at 24°C for 10days.

extract_protocol:
RNA has been isolated and cDNA has been synthesized.
Library preparation was performed at Genotypic Technology’s Genomics facility following certified protocols from NEXT Flex.

value: Full-fleged 10days old seedlings


title: R2_L4_t5_25C_LD

status: Public on Apr 27 2015

city: Raleigh

first: Brian

last: Howard

state: NC

address: 1428 Sandusky Lane

department: Plant Biology

institute: North Carolina State University

data_processing:
fastq files were generated using the standard Illumina pipeline.
Low quality sequences were filtered using the quality trimmer tool from the FAST-X toolkit. Positions having quality scores lower than 28 were removed from the ends of reads. Furthermore, any trimmed reads having lengths less than 50 nucleotides were discarded altogether.
Filtered reads were used for de novo transcriptome assembly using the Oases assembler with k=71.
Assembled transcripts were next annotated using BLAST2GO, with maximum number of blast hits=20; e-value cutoff=10-6; HSP length cutoff=33; low complexity filter=on.
RNA-Seq reads were aligned to assembled transcriptome using Bowtie, and the resulting alignments were used to compute RPKM values for each assembled locus.
Supplementary_files_format_and_content: AnnotatedTranscripts.fasta contains assembled transcripts annotated using BLAST2GO
Supplementary_files_format_and_content: RPKM_Locus.txt contains RPKM values for each Sample

organism: Dunaliella viridis

source_name: Dunaliella Transcriptome

growth_protocol: The strain used in this study was a Dunaliella viridis strain obtained from the Center for Applied Aquatic Ecology at North Carolina State University.  The growth media was modified from Wang et al. (2007): 1M NaCl, 10 mM Tris, 50 mM NaHCO3, 5 mM KNO3, 5 mM MgSO4, 0.12 mM KH2PO4, 0.12 mM CaCl2, 7 μM MnCl2, 6 μM EDTA, 2 μM FeCl3, 1 μM ZnSO4, 1 μM Co(NO3)2, 1 μM CuSO4 and 1 μM (NH4)6Mo7O24. After adjusting the pH to 7.5, the media was filter sterilized. The cultures used as inoculum were grown for 1 week under a 12:12 photoperiod (fluorescent lights, 3340 lux) in a room maintained at 25°C.

extract_protocol: Trizol was used for RNA extraction. The Illumina ®TruSeqTM RNA Sample Preparation v2 Kit was used to prepare the libraries of template molecules suitable for cluster generation and DNA sequencing using the Illumina Genome Analyzer GA IIx. The quality and concentration of each library was assessed by running each library on a High Sensitivity DNA chip on the Agilent Bioanalyzer.

treatment_protocol: A starter culture at 0.5 million cells/mL was prepared by mixing the inoculum culture with fresh medium. Right after inoculation, the flasks were placed in a growth chamber at 25°C (fluorescent lights, 400 lux). Half of the flasks were subjected to a 12 hr light/ 12 hr dark cycle and the other of the flasks were subjected to continuous light inside the same incubator (for the dark cycles, the flasks were placed in a dark box inside the incubator). The entire experiment was repeated three times. At 5 different time points (T1-T5) after the inoculation of the fresh media (6, 16, 30, 40 and 54 hrs), cells were removed from the flasks and the following performed: cell counts measurements (TC10 Automatic Cell Counter, Bio-Rad) (10 μL), RNA extraction (20 mL), and lipid content evaluation by Nile Red staining and microscopy (1 mL) as well as osmotic lysis (100 mL).

tag: run

tag: lane

tag: time

tag: temperature

tag: light condition

value: light/dark


title: R2_L3_t5_25C_LD


title: R2_L2_t5_25C_LD


title: R2_L1_t5_25C_LD


title: R2_L4_t4_25C_LD


title: AWRI796_6gl_SO2

description: Sample 6

tag: strain


title: R2_L2_t4_25C_LD


title: R2_L1_t4_25C_LD


title: R2_L3_t4_25C_LD


title: R2_L4_t3_25C_LD


title: R2_L3_t3_25C_LD


title: R2_L3_t2_25C_LD


title: MINUS rep2

tag: tissue


title: R2_L2_t2_25C_LD


title: R2_L4_t2_25C_LD


title: R2_L1_t3_25C_LD


title: R2_L3_t1_25C_LD


title: R2_L4_t1_25C_LD


title: R2_L2_t1_25C_LD


title: R2_L1_t1_25C_LD


title: R2_L4_t5_25C_CL

value: continuous light


title: R2_L3_t5_25C_CL


title: Cel1-Exo

city: Qingdao

first: Jian

last: Xu

state: Shandong

address: No.189 Songling Road, Laoshan District

country: China

institute: Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences

description: Sample 11

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to H10 whole genome using SOAP 2.20 with parameters -m 100 -x 1000 -n 5 -v 2 -p 30
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: H10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Ruminiclostridium cellulolyticum

source_name: Clostridium cellulolyticum

growth_protocol: Clostridium cellulolyticum ATCC35319 (H10) was cultured anaerobically in 250 mL flasks with 100 mL working volume of DCB-1 medium at 35oC. Fermentation experiments included three different substrates in separate yet paralleled cultivations: (i) 3.0 g/L of glucose and (ii) 3.0 g/L of cellobiose, and (iii) 5g/L of cellulose. A 1% (v/v) inoculum of culture pre-adapted on various substrates in vials was used for inoculation.

extract_protocol:
Total RNA was isolated from cultures harvested at the mid-log phase using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. Genomic DNA was removed by RNase-Free DNase Set (Qiagen).Two strategies were applied for purification of mRNA from total RNA. One is to remove 16S and 23S rRNA from total RNA using MicrobExpressTM Bacterial mRNA Purification kit (Ambion) (named Hyb). The other is depletion of rRNA of total RNA using Terminator TM 5’-phosphate-dependent exonuclease (TEX) (Epicentre #TER51020).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: carbon source

value: cellulose

tag: purification

value: Exo (digestion by terminator exonuclease)


title: R2_L1_t4_25C_CL


title: Ceb2-Exo

description: Sample 8

value: cellobiose


title: R2_L2_t3_25C_CL


title: Cel2-Hyb

description: Sample 10

value: Hyb (subtractive hybridization)


title: R2_L2_t4_25C_CL


title: R2_L1_t5_25C_CL


title: R2_L3_t3_25C_CL


title: Cel1-Hyb

description: Sample 9


title: Cel2-Exo

description: Sample 12


title: R2_L4_t4_25C_CL


title: Ceb1-Exo

description: Sample 7


title: R2_L2_t5_25C_CL


title: R2_L1_t3_25C_CL


title: R2_L1_t2_25C_LD


title: R2_L2_t3_25C_LD


title: Ceb1-Hyb

description: Sample 5


title: R2_L4_t2_25C_CL


title: Ceb2-Hyb

description: Sample 6


title: Glu2-Exo

description: Sample 4

value: glucose


title: R2_L3_t2_25C_CL


title: R2_L2_t2_25C_CL


title: Glu1-Exo

description: Sample 3


title: R2_L1_t2_25C_CL


title: R2_L4_t1_25C_CL


title: R2_L3_t1_25C_CL


title: Glu1-Hyb

description: Sample 1


title: Glu2-Hyb

description: Sample 2


title: R2_L2_t1_25C_CL


title: R1_L4_t5_25C_LD


title: R2_L1_t1_25C_CL


title: R1_L2_t5_25C_LD


title: R1_L1_t5_25C_LD


title: R1_L4_t5_25C_CL

value: continous light


title: R1_L3_t5_25C_CL


title: R1_L4_t4_25C_LD


title: R1_L3_t4_25C_CL


title: R1_L3_t4_25C_LD


title: R1_L2_t4_25C_LD


title: R1_L4_t4_25C_CL


title: R1_L1_t4_25C_LD


title: R1_L2_t5_25C_CL


title: R1_L1_t5_25C_CL


title: R2_L4_t3_25C_CL


title: R1_L4_t3_25C_LD


title: R1_L2_t3_25C_LD


title: R1_L2_t4_25C_CL


title: R1_L3_t3_25C_LD


title: R1_L1_t3_25C_LD


title: R1_L4_t3_25C_CL


title: R1_L3_t3_25C_CL


title: 10.5dpc_WT2

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

data_processing:
Sequences were aligned to mouse genome mm10 using tophat with default parameters.
Transcript definitions were according to Ensembl 75.
Data was analyzed using Bioconductor package EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: cufflinks gene level results

source_name: Embryos, dpc 10.5

growth_protocol: Normal embryo growth conditions

extract_protocol:
Staged embryos were dissected and homogenized in TRIzo using hand help homogeniozer.RNA was isolated by Directzol RNA miniprep kit( R2052) as per manufacturer's instruction. Quality of RNA were assessed using bioanalyzer and samples with RIN more than 9 were used for library preparation.
For each sample, 250ng of total RNA was used to make libraries. Following manufacturer's directions, short fragment libraries were made using the Illumina TruSeq Stranded Total RNA LT - (with Ribo-Zero TM Gold) - set A and B (Illumina, Cat. No. RS-122-2301 and RS-122-2302). The resulting libraries were quantified using the LabChip GX (Perkin Elmer) and a Qubit Fluorometer (Life Technologies). All libraries were pooled, quantified and run as 50 bp single read on an Illumina HiSeq 2500 instrument using HiSeq Control Software 2.2.58

treatment_protocol:
Feeders were separated by plating freshly trypsinized cells on gelatinized plate for 30 min. After half an hour media was aspirated and centrifuged for 5 min at 1000 rpm.
No treatment

tag: cell type

value: embyos

tag: Stage

tag: passages


title: 10.5dpc_WT1


title: 9.5dpc_7

source_name: Embryos, dpc 9.5


title: 9.5dpc_2


title: R1_L3_t5_25C_LD


title: R2_L3_t4_25C_CL


title: R1_L2_t3_25C_CL


title: R1_L1_t3_25C_CL


title: 36hrs_RA_2

source_name: KH2 cells, 36 hrs RA

growth_protocol: Cells were grown in ES cell media (DMEM + 15% Serum + NAA+ Beta-mercaptoethanol)

extract_protocol:
Cells were lysed in TRIzol and RNA was isolated using Directzol RNA miniprep kit( R2052). Quality of RNA were assessed using bioanalyzer and samples with RIN more than 9 were used for library preparation.
For each sample, 250ng of total RNA was used to make libraries. Following manufacturer's directions, short fragment libraries were made using the Illumina TruSeq Stranded Total RNA LT - (with Ribo-Zero TM Gold) - set A and B (Illumina, Cat. No. RS-122-2301 and RS-122-2302). The resulting libraries were quantified using the LabChip GX (Perkin Elmer) and a Qubit Fluorometer (Life Technologies). All libraries were pooled, quantified and run as 50 bp single read on an Illumina HiSeq 2500 instrument using HiSeq Control Software 2.2.58

treatment_protocol:
Feeders were separated by plating freshly trypsinized cells on gelatinized plate for 30 min. After half an hour media was aspirated and centrifuged for 5 min at 1000 rpm.
ES Cells were differentiated with differentiation media (DMEM + 10% Serum + NAA+ 0.03µM RA) RA supplemented 33nm for requisite length of time.

value: KH2 cells

tag: treatment

value: 36 hrs RA


title: R1_L1_t4_25C_CL


title: R1_L3_t5_35C_LD


title: 24hrs_RA_1

source_name: KH2 cells, 24 hrs RA

value: 24 hrs RA


title: TOX knockout mouse RNA 2

city: Los Angeles

first: Wolf

last: Wiedemeyer

state: California

address: 8700 Beverly Blvd.

department: BMS

institute: Cedars-Sinai

data_processing:
base-calling was performed on Ion Torrent suite software
Raw sequencing reads in FASTQ format were aligned to the UCSC mouse reference genome (mm10)  using TOPHAT21.
Gene expression for each sample was calculated using reference-guided transcript assembly using a gene transfer file (GTF) from UCSC genes (http://genome.ucsc.edu/) and normalized quantification of reads as FPKM (fragments per kilo bases of exons for per million mapped reads) calculated with Cufflinks and finally compiled into a gene counts table for all samples in preparation for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each sample

source_name: sorted isolated bone marrow cell populations

extract_protocol: cDNA sequencing libraries were made from total RNA using ClonTech SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Torrent Ion Xpress Plus Fragment Library Kit per manufacturers' instructions.  RNAseq libraries were assessed for concentration and length using Invitrogen's Qubit® dsDNA HS Assay Kit (Carlsbad, CA) and Agilent High Sensitivity DNA Kit respectively (Santa Clara, CA).  The samples were amplified onto Ion Sphere Particles using the Ion PI™ Template OT2 200 Kit v3 (Ion Torrent) per manufacturer’s instructions.  The libraries were sequenced on the Ion Proton™ System using the Ion PI™ Sequencing 200 Kit v3 (Ion Torrent).   Samples were multiplexed to obtain at least 10 million reads each for sequencing.

tag: genotype

value: TOX knockout


title: TOX knockout mouse RNA 3

value: sorted isolated bone marrow cell populations


title: TOX knockout mouse RNA 4


title: 36hrs_RA_1


title: wildtype mouse RNA 3

value: wild type


title: 24hrs_RA_2


title: wildtype mouse RNA 2


title: wildtype mouse RNA 4


title: R1_L2_t5_35C_LD


title: wildtype mouse RNA 1


title: R1_L1_t5_35C_LD


title: R1_L4_t5_35C_CL


title: 12hrs_RA_1

source_name: KH2 cells, 12 hrs RA

value: 12 hrs RA


title: TOX knockout mouse RNA 1


title: 6hrs_RA_2

source_name: KH2 cells, 6 hrs RA

value: 6 hrs RA


title: R1_L3_t5_35C_CL


title: 6hrs_RA_1


title: 4hrs_RA_1

source_name: KH2 cells, 4 hrs RA

value: 4 hrs RA


title: Uninduced_ES_2

source_name: KH2 cells, uninduced

value: uninduced


title: R1_L4_t4_35C_LD

value: light/dark


title: R1_L2_t5_35C_CL


title: R1_L1_t5_35C_CL


title: R1_L3_t4_35C_LD


title: R1_L4_t5_35C_LD


title: Uninduced_ES_1


title: 12hrs_RA_2


title: Trbp-smallRNA-replicate-3

city: Boston

first: Da-Zhi

last: Wang

state: MA

address: 300 Longwood Ave.

department: Cardiology

institute: Boston Children's Hospital

data_processing:
Base-calling: Illumina's Real Time Analyzer (RTA) version 1.17.21.3.
Demultiplexing and fastq file generation: Illumina's CASAVA version 1.8.2
TruSeq adapter sequence removal: cutadapt 0.9.5
Alignment: bowtie 0.12.9 (mRNA: -m 1 -v 2; miRNA: -m 1 -v 0) SAM to BAM conversion: samtools 0.1.16 Read counting: R 3.0/Bioconductor Genomic
Genome_build: mm10
The processed data file contains:
accession: gene accession number
gene: gene name
description: brief functional description of gene WT raw read: wild type raw read counts in replicates Trbp-cKO raw read: K/O raw read counts in replicates
Ratio: Trbp-cKO/WT ratio
Pvalue: p-value for log2(Ratio) under null-hypothesis of no change
Qvalue: FDR-adjusted p-value (BH method) for log2(Ratio) under null-hypothesis of no change
(Note: because we used BioConductor's edgeR to calculate differential expression, as advised by edgeR's manual we did not use FPKM)

source_name: Heart

extract_protocol:
Heart vetricle tissue samles were harvetsed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2002) was used with 1 ug of total RNA to prepare libraries for sample 1-4. Illumina® TruSeq™ Small RNA Sample Preparation (Cat # RS-930-1012)  was used with 1 ug of total RNA to prepare libraries for sample 5-10.

tag: background strain

value: Heart

tag: age

value: postnatal day 2.5

value: Trbp-cKO


title: Trbp-smallRNA-replicate-2


title: Trbp-smallRNA-replicate-1


title: WT-smallRNA-replicate-2


title: Trbp-mRNA-replicate-1

value: 2 weeks


title: WT-smallRNA-replicate-3


title: R1_L4_t4_35C_CL

value: continous light


title: R1_L1_t4_35C_LD


title: R1_L2_t4_35C_CL


title: Trbp-mRNA-replicate-2


title: WT-mRNA-replicate-2


title: input DNA

city: Urbana

first: Milan

middle: K

last: Bagchi

state: IL

address: 407 S. Goodwin Ave

department: MIP

institute: UIUC

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the human genome (hg18 genome assembly) using BOWTIE v.1
Peaks were called using MACS version 1.4.1 20110627, pvalue cutoff = 1.00e-05, maximum duplicate tags at the same position in control and sample = 2,  Redundant rate in control and samples: 0.01
Filter peaks: false discovery rate < 0.05, enrichment factor >4.5
Genome_build: hg18
Supplementary_files_format_and_content: bed files contain the start and end locations of peaks on chromosomes, excel files contain the location of summits within the peaks, number of tags, fold enrichment and the percentage of false discovery rate

source_name: Endometrial stromal cells

growth_protocol: Growth in DMEM:F12 medium + 5% FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and were incubated with anti-flag M2 affinity gel (Sigma, A2220) to isolate the immune complexes (flag-PGR-A and flag-PGR-B). The immunocomplexes were eluted from the beads using flag-peptide and heated at 65°C for 6 h to reverse the cross-linking. Following digestions with RNAase A and proteinase K, DNA fragments were purified using QIAquick PCR purification kit (Qiagen).
The ChIPseq libraries were prepared with Illumina's 'TruSeq DNAseq Sample Prep kit'.The libraries were quantitated by qPCR, and sequenced for 100 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3 and analyzed with Casava1.8 (pipeline 1.8). Sequence adapters used the make the libraries: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG. Library construction and base-calling were performed by Roy J. Carver Biotechnology Center, UIUC.

treatment_protocol: Treatment in DMEM:F12 medium containing  2% charcoal stripped serum, 48h siRNA transfection, 24h adenovirus transduction to express flag-PGR-A or flag PGR-B , 2h differentiation cocktail treatment composed of E, P and cAMP

value: Endometrial stromal cells

tag: pgr isoform expression

value: pooled

tag: chip antibody

value: none (input)


title: WT-smallRNA-replicate-1


title: 4hrs_RA_2

value: KH2 cells


title: R1_L1_t4_35C_CL

tag: run

tag: lane


title: PGR-B_ChIPSeq

value: PGR-B

value: anti-flag M2 affinity gel (Sigma, A2220)


title: H3K27ac_treated with E2, replicate2

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

description: local id 539

data_processing:
Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm9 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle generated with MACS using parameters --nomodel --shiftsize=120--format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Peaks called with Sicer V1.1 using parameters mm9 1 200 150 0.74 600 0.01
Filter blacklist regions from peaks, and convert to broadpeak format (see UCSC Genome Browser for format specs)
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle file with read coverage, peak file in broad peak format

source_name: G1E -ER4 cells, treated with E2

extract_protocol:
Chromatin immunoprecipitation of H3K27ac occupied segments using anti-H3K27ac (Abcam Cat# Ab4729) using published methods (Welch et al. 2004)
TruSeq ChIP Sample Prep Kit (Illumina)

treatment_protocol: See Treatment column for Samples

value: Estradiol 10nM 24hr

value: Derived by transducing the Gata1 knock out cell line G1E with  virus expressing the hormone-inducible rescue protein GATA1-ER. Induced for 24 hr.

tag: developmental stage

value: model for adult erythropoiesis

tag: antibody


title: H3K27ac_replicate2

description: local id 535

source_name: G1E cells, an  erythroid progenitor model

value: Derived from Gata1 knock out ES cells; immortalized as a model for erythroid progenitors

tag: strain


title: PGR-A_ChIPSeq

value: PGR-A


title: Chicken Stage X blastodermal Cells

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

description: Small ncRNA expression data of chicken blastodermal cells isolated at stage X.

data_processing:
Solexa pipeline used for base-calling clean reads
Raw NGS data were processed to obtain clean reads by removing low-quality reads strictly (Q-value < 13), short read tags (< 18 nt), poly A and adaptor-ligated contaminants
To further identify sequence reads with reliable chromosomal locations, they were mapped onto the reference genome from the NCBI (Gallus gallus v.4) using BLAST, with identity ≥ 90% and HSP coverage ≥ 95%.
Basic annotations of small ncRNAs were performed following standard protocols from Insilicogen. Briefly, to identify miRNAs, sequence reads were aligned with the precursor or mature miRNAs of chickens in miRBase19 using BLASTN with an e-value cutoff of 0.01. Sequence reads from repeat regions were identified by alignment with the reference chicken repeat sequences. To identify rRNAs, tRNAs, snoRNAs, scRNAs and snRNAs, sequence reads were aligned with the reference nucleotides from GenBank records and into the Rfam database using BLASTN with an e-value of 0.01. Sequence reads from exonic or intronic regions were identified based on their genomic locations in 17,767 reference gene sets.
Genome_build: Gallus_gallus-4.0
Supplementary_files_format_and_content: txt files includes size, count, and sequence of small ncRNAs

organism: Gallus gallus

source_name: Blastodermal cells isolated at stage X from White Leghorn eggs

extract_protocol:
Blastodermal cells at Eyal-Giladi and Kochav (EG&K) stage X were collected by gentle dissociation of stage X blastoderms (n = 30) from freshly laid eggs in phosphate buffered saline (PBS) followed by centrifugation at 1,250 rpm for 10 min. Fertilized eggs were incubated at 37.5°C under 50–60% relative humidity. PGCs and GSCs were isolated from the gonads of chicken embryos at E6.0 (mixed sex, n = ~2000) using the magnetic-activated cell-sorter (MACS) method. Gonads were dissociated by gentle pipetting in 0.25% trypsin and 0.05% ethylenediaminetetraacetic acid (EDTA). After adding 10% fetal bovine serum (FBS) to inactivate the trypsin-EDTA and briefly centrifuging at 200 × g for 5 min, total gonadal cells were incubated with anti-stage specific embryonic antigen (SSEA-1) for 20 min at room temperature. Cells were washed with 1 mL MACS buffer (0.5% BSA and 2 mM EDTA in PBS), and the supernatant was completely removed by centrifugation. The pellet was mixed with 100 μL MACS buffer supplemented with 20 μL goat anti-mouse IgM microbeads for 15 min at 4°C. Cells were washed with 500 μL MACS buffer and loaded onto a MACS column (Miltenyi Biotec GmbH). After several batches of cell preparation, the PGC-enriched fraction and GSCs were separated. The survival rate of PGCs purified by MACS were >95%. CEFs were collected by dissociating the embryonic body (E6.0, n = 6) in 0.25% EDTA at 37°C for 20 min. Cells were then cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% FBS and 1% antibiotic–antimycotic in a 5% CO2 atmosphere at 37°C.
Approximately 5 µg total RNA from each test sample (PGCs, stage X blastoderms, GSCs, and CEFs) was used to generate high-throughput NGS data using the Illumina HiSeq (Beijing Genomics Institute, China) following standard protocols from Insilicogen, Korea

tag: breed

value: White Leghorn

tag: cell

value: Dissociated blastoderm cells

value: Pluripotent cells

value: embryonic stage X (E0, freshly laid eggs)


title: Chicken Gonadal Stromal Cells

description: Small ncRNA expression data of chicken gonadal stromal cells isolated from embryonic gonads.

source_name: Gonadal stromal cells isolated from the gonads of White Leghorn chicken embryos

value: GSCs purified by MACS method

value: Somatic cells

value: embryonic day E6.0


title: Chicken Primordial Germ Cells

description: Small ncRNA expression data of chicken primordial germ cells isolated from embryonic gonads.

source_name: Primordial germ cells isolated from the gonads of White Leghorn chicken embryos

value: PGCs purified by MACS method

value: Reproductive cells


title: Chicken Embryonic Fibroblasts

description: Small ncRNA expression data of chicken embryonic fibroblasts cultured until passage 2.

source_name: Embryonic fibroblasts isolated from the muscular area of White Leghorn chicken embryos

value: Cultured CEFs


title: R1_L2_t4_35C_LD

source_name: Dunaliella Transcriptome

tag: time

tag: temperature

tag: light condition

value: light/dark


title: H3K27ac_replicate1

description: local id 534

tag: cell type


title: R1_L3_t3_35C_LD


title: R1_L2_t3_35C_LD


title: R1_L1_t3_35C_LD


title: WT-mRNA-replicate-1

tag: tissue

value: Heart

value: 2 weeks

value: wild type


title: R1_L4_t3_35C_CL

value: continous light


title: R1_L3_t3_35C_CL


title: R1_L2_t3_35C_CL


title: TAC Veh H3Ac

status: Public on Apr 25 2015

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

description:
up_in_TAC_VEH_compared_to_SHAM_VEH.bed
down_in_TAC_VEH_compared_to_SHAM_VEH.bed

data_processing:
Illumina pipeline 1.4  was used for base calling
Reads were aligned to the mm9 genome using bwa 0.5.9 with default parameters
A set of peaks were generated for each ChIP condition using MACS 1.4.1
Genome_build: mm9
Supplementary_files_format_and_content: bed files comparing ChIP conditions between samples (SHAM VEH, TAC VEH, TAC TSA)

source_name: TAC Veh H3Ac

growth_protocol: C57BL6 male mice (10-12 week old) that underwent Transverse Aortic Constriciton (TAC) surgery or Sham controls

extract_protocol:
After the incubation, roughly chopped mouse left ventricle were fixed for 10 minutes with 1% formaldehyde. Glycine (0.125 M) solution was then added for another 10 minutes. Pellets were resuspended in SDS lysis buffer containing protease inhibitors. Then cells were sonicated to shear chromatin and ChIP was performed using indicated above antibodies and DynaMag™-2 magnet (Invitrogen).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: C57BL6 male mice (10-12 week old) that underwent TAC/Sham surgery were injected subcutaneously twice daily at 0.6 mg/kg/day of Veh (DMSO) or TSA (dissolved in DMSO) for 4 weeks, as previously described (Chang et al. 2011).

tag: organ

value: Left ventricle

tag: Sex

value: Male

value: Anti-acetyl-Histone H3

tag: antibody vendor

value: Millipore

tag: antibody cat. #

tag: antibody lot#


title: R1_L4_t3_35C_LD

tag: run


title: H3K27ac_treated with E2, replicate1

description: local id 538

tag: treatment

value: Estradiol 10nM 24hr

value: Derived by transducing the Gata1 knock out cell line G1E with  virus expressing the hormone-inducible rescue protein GATA1-ER. Induced for 24 hr.

value: model for adult erythropoiesis


title: Sham TSA H3Ac

description:
GSM1326459
up_in_TAC_TSA_compared_to_SHAM_TSA.bed
down_in_TAC_TSA_compared_to_SHAM_TSA.bed

source_name: Sham TSA H3Ac


title: Sham Veh H3Ac

description:
GSM1326458
up_in_TAC_VEH_compared_to_SHAM_VEH.bed
down_in_TAC_VEH_compared_to_SHAM_VEH.bed

source_name: Sham Veh H3Ac


title: Th17 cells

city: Honolulu

first: Travers

last: Ching

state: HI

address: 701 Ilalo St #600

department: Epidemiology

institute: University of Hawaii Cancer Center

data_processing:
RNA-Seq data were aligned to the Mus Musculus mm10 genome using Tophat2 and default settings
Duplicates aligned reads were removed using samtools rmdup command
FPKM data was generated with Cufflinks software
Genome_build: mm10
Supplementary_files_format_and_content: FPKM comma seperated file

molecule: polyA RNA

source_name: Small Intestine

growth_protocol: The cell populations was obtained in vivo.

extract_protocol:
After removal of the Peyer’s patches, we isolated intraepithelial lymphocytes (IELs) and lamina propria lymphocytes (LPLs) by incubation with 1mM DTT at 37 °C for 30 min (for IEL), followed by further digestion with collagenase IV and DNase at 37 °C for 1 h (for LPL). We then further separated cells with a Percoll gradient. Unless otherwise indicated, we isolated cells from the small intestine (duodenum, ileum and jejunum) of mice treated with antibodies to CD3.
We isolated intestinal lymphocytes from two independent experiments, each using 5 mice injected with anti-CD3 mAb. Th17, exTh17, Tr1 exTh17, Tr1, Foxp3 Treg and Foxp3 IL-10+ Treg cell populations were FACS-sorted from these two independent experiments and the cells of each population were pooled before the analysis. Around 5,000 cells for each population were processed. After sorting, the cells were washed 2 times (1,500rpm, 2min, 4°C) with 1ml phosphate-buffered saline (PBS) and finally suspended in 2.5µl PBS (contain 0.5µl RNaseOut (Invitrogen) and 0.5µl dithiothreitol (DDT) (Invitrogen)). After that, the cytoplasm RNA was isolated as described previously (Guo, S. et al. Cell 156 (4), 649 (2014); Pan, X. et al., Proc Natl Acad Sci U S A 110, 594 (2013).) Briefly, 2.5µl of 2x selected cytoplasm lysis buffer (SCLB) was added and the cells were lysed by pipetting up and down for 5 times. The entire lysate solution was spun at 8000rpm for 5 min in a chilled centrifuge (4°C) and the supernatant (~5µl), which contained the total cytoplasm RNA, was transferred to a PCR tube strip with individually attached dome caps (USA Scientific). The mRNA selection, reverse transcription and cDNA amplification was performed as described previously with some modifications (Guo, S. et al. Cell 156 (4), 649 (2014); Pan, X. et al., Proc Natl Acad Sci U S A 110, 594 (2013). Briefly, 5’-phosphorylated oligo-GdT24 (pGdT24) primer was used to selectively reverse transcribe mRNAs. The first strand cDNA was synthesized with Superscript Reverse Transcriptase III (invitrogen, 10u/µl). Then, the double-stranded cDNA (dscDNA) was generated. The cDNA was purified with the Genomic DNA Clean & Concentrator kit (Zymo). Afterwards, several steps including DNA end-blunting, 5’-end phosphorylation and ligation were performed with The End-It DNA End-Repair Kit (Epicentre) with T4 DNA ligase (Epicentre). The product was directly amplified using REPLI-g UltraFast Mini Kit (QIAGEN) and purified using the same Genomic DNA Clean & Concentrator kit (Zymo) column. Finally, 3 to 5 µg (up to 8 µg) of amplified cDNA derived from mature mRNA was obtained, which was then evaluated by PCR and fragmented to construct sequencing library. We follow the standard Illumina HiSeq2000 protocol to make the library. Briefly, the amplicon was fragmented to an approximately 200-500 bp size range by a Bioruptor Sonicator (Diagenode). After purification with DNA Clean & Concentrator kit (Zymo), end-repairing, 3’-A tailing and ligation with adaptor was performed. Then, a 50bp range DNA (250-300bp) was selected by gel electrophoresis (E-gel EX 2%, invitrogen) and barcode added by PCR using Phusion High-Fidelity DNA polymerase (NEB) for 8 cycles. The product was size selected again and the DNA concentration was quantitated by a Bioanalyzer (Agilent). Multiple samples were mixed and loaded to the Hi-Seq2000 for sequencing performed with 50bp single end reads.

treatment_protocol: Mice were injected with anti-CD3 mAb (2C11,15-50 ug/mouse) intra-peritoneally two times every other day. The mice were sacrificed 4-6 hours after the last injection.

tag: mouse model

value: Fate+ Model

tag: cell population

value: Th17 cells


title: Foxp3 Il10 cells

tag: strain

value: Foxp3 Il10 cells


title: Ex Th17 cells

value: Ex Th17 cells


title: Foxp3 cells

value: Foxp3 cells


title: NU-2

city: Tai An

first: shuaishuai

last: wang

address: daizong street

institute: ShanDong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
To get the clean reads, removing the dirty raw reads is needed before data analysis.Filter steps:1.Remove reads with adaptors;2.Remove reads in which unknown bases are more than 10%;3.Remove low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read).Reads after filtering dirty raw reads, on which all following analysis are based.
Clean reads were mapped to reference sequences using SOAPaligner/soap2.Mismatches no more than 2 bases were allowed in the alignment.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi, A. et al., Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 2008.
Genome_build: maize sequence B73 RefGen_v2 (MGSC)
Supplementary_files_format_and_content: excel file includes Gene ID,Uniq_reads_num,Length,Coverage,RPKM,GO Component, GO Function,GO Process and Blast nr

organism: Zea mays

source_name: nucellus

extract_protocol:
Female gametophytes were isolated by enzymatic immersion of ovule slices, as described in Yang et al. (2006). The female gametophytes and nucellus isolated from ovule slices were frozen in liquid nitrogen quickly and store at -80℃ for RNA extraction.
Total RNA from embryo sacs and nucellus were extracted using an RNeasy plus micro kit (Qiagen, Valencia, CA). At least 500ng RNA were extracted from each materials used for Library Construction. Each sample has two biological replicates. Poly(A) RNAs was isolated using oligo(dT) magnetic beads (Illumina, San Diego, CA). RNA fragmentation, cDNA synthesis, and PCR amplification were carried out using Illumina RNA-seq method (Cat # RS-100-0801).

tag: inbred line

value: nucellus


title: PES-1

source_name: embryo sacs at 14-16h after pollination

value: embryo sacs at 14-16h after pollination


title: ES-2

source_name: embryo sacs

value: embryo sacs


title: NU-1


title: PES-2


title: wildtype total

city: Shanghai

first: Weiwei

last: Qi

address: 333 Nanchen Road

institute: Shanghai University

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 B73 RefGen_v2 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments 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: Ensemble AGPv3.24 equivalent to B73 RefGen_v3 (ftp://ftp.ensemblgenomes.org/pub/plants/release-24/fasta/zea_mays/dna/)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: kernel

extract_protocol:
For isolation of polysomal RNA, pulverized tissue powder was hydrated in two volumes of polysome extraction buffer (PEB), homogenized, filtered through two layers of sterile Miracloth, and cleared by centrifugation. The supernatant was layered over a 1.75 M sucrose cushion, and centrifuged at 170,000 g, at 4 ℃ for 3 h. The polysome pellet was washed with sterile water and resuspended in 700 μl PEB lacking heparin and detergents. Total or polysome-bound RNA was precipitated from total supernatant or ribosome fraction of same amount of sample powder, by addition of 2.5 vol of 8 M guanidine chloride and 3.5 vol of 99% (v/v) ethanol, and extracted by use of Qiagen Plant RNeasy mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: endosperm

tag: age

value: 15 DAP

tag: genotype/variation

value: wild type

tag: rna fraction

value: total RNA


title: rea1 mutant polysome

value: polysome-bound RNA


title: wildtype polysome


title: rea1 mutant total


title: R1_L1_t3_35C_CL

tag: lane

tag: time

tag: temperature

tag: light condition

value: continous light


title: rea1 mutant

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 B73 RefGen_v2 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments 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: Ensemble AGPv2.15 equivalent to B73 RefGen_v2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue


title: wildtype


title: TAC TSA H3Ac

description:
up_in_TAC_TSA_compared_to_TAC_VEH.bed
down_in_TAC_TSA_compared_to_TAC_VEH.bed

source_name: TAC TSA H3Ac

tag: organ

value: Left ventricle

tag: Sex

value: Male

tag: antibody

value: Anti-acetyl-Histone H3

tag: antibody vendor

value: Millipore


title: PC09

status: Public on Apr 24 2015

city: SANTANDER

first: Piero

last: Crespo

state: Cantabria

address: c/Albert Einstein, 22

country: Spain

institute: IBBTEC

data_processing:
Alignment with Tophat
Differential Expression with Cufflinks and DE
Genome_build: hg19
Supplementary_files_format_and_content: The .txt and .csv files include FPKM values for each Sample and Differential Expression

source_name: A375p cells

extract_protocol:
RNeasy mini kit (Qiagen, Germany)
TruSeq Stranded mRNA Illumina

treatment_protocol: 10 μM of either DEL22379, SCH772984 or DMSO as a control for two hours

tag: cell line

value: melanoma cell line A375P

tag: agent


title: PC08


title: PC07


title: PC05


title: R1_L3_t4_35C_CL

tag: run


title: Tr1 cells (ex Th17)

tag: strain

tag: mouse model

value: Fate+ Model

tag: cell population

value: Tr1 cells (ex Th17)


title: PC04


title: Tr1 cells

value: Tr1 cells


title: PC03

value: CONTROL


title: ES-1

tag: inbred line


title: PC01b


title: PC01


title: E17F

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

institute: Murdoch University

data_processing:
Color-space base calling
Mapping, alignment with Lifescope
Lifescope transcriptome workflow
Genome_build: hg19
Supplementary_files_format_and_content: counts data

source_name: skin

growth_protocol: tissue sample from the lesional, non-lesional skin and healthy control skin

extract_protocol:
RNALater and mirVana miRNA Isolation Kit
RNA was amplified with Ovation RNA-Seq System V2 Kit (NuGen, Emeryville, CA, USA) and the output double stranded DNA was used to prepare SOLiD 5500 W System DNA fragment library according to manufacturer’s protocols (Thermo Fisher Scientific Inc, Waltham, MA, USA). The barcoding primers in library preparation and fragment sequencing chemistry was applied (75 bp in forward directions). In case of 12 samples per flowchip lane approximately 33 million mappable reads were expected per one sample, which would be enough for successful whole transcriptome expression pattern analysis.

treatment_protocol: Psoriasis patients and controls, skin biopsies from lesional and non-lesional site

tag: subject

tag: disease

value: C

tag: gender

value: F

tag: age

value: skin


title: E6F


title: R20F


title: R13M

value: M


title: E9F


title: E18M


title: R21M


title: R15M


title: R16M


title: E13M


title: PC06


title: P846TF

value: NLP


title: P856TF


title: P846HF

value: LP


title: P849TF


title: P843HF


title: P856HF


title: P843TF


title: P849HF


title: P853HF


title: PC02


title: P851HM


title: P845TM


title: R19F


title: R24M


title: P840TM


title: P840HM


title: P845HM


title: P851TM


title: P848HM


title: P848TM


title: P652TM


title: P847HM


title: P847TM


title: P844HM


title: O. ochengi nodule fluids

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

data_processing:
Primers were trimmed from the raw fastq format sequence data using cutadapt software (v1.3; parameters -O 6 -m 16 -q 20).
Only trimmed reads that contained the adapter and were present at 2 or more copies per sample were retained.
Simple scripts were used to generate non-redundant sequence sets (collapsed tag counts) in a structured format from each sample.
Genome_build: www.nematodes.org/downloads/959nematodegenomes/blast/db2/Onchocerca_ochengi_nuclear_assembly_nOo.2.0.fna.gz
Genome_build: ftp.ensembl.org/pub/release-71/fasta/bos_taurus/dna/Bos_taurus.UMD3.1.71.dna.toplevel.fa.gz
Genome_build: ftp.sanger.ac.uk/pub/pathogens/Onchocerca/volvulus/OVOC.V3.fa
Supplementary_files_format_and_content: Processed data files contain the non-redundant sequences from each sample.

organism: Bos taurus

source_name: Bovine nodule fluids

extract_protocol:
Total RNA from bovine nodule fluids was purified using miRNeasy kit (Qiagen) and eluted in 50 uL of 0.1 mM EDTA. Total RNA from human serum (200 uL) or plasma (50 uL) was purified using miRCURY RNA Isolation kit - Biofluids (Exiqon) and eluted in 50 uL of 0.1 mM EDTA.
Small RNA libraries were prepared using the Illumina's TruSeq Small RNA library preparation kit (Catalogue RS-200-9002DOC). PCR products were size selected and only the 140-160 bp products were sequenced on an Illumina HiSeq 2500 instrument using v3 reagents in Edinburgh Genomics (http://genomics.ed.ac.uk)

tag: infection

value: Onchocerca ochengi


title: LT_02 Wild Type

city: Paris cedex 15

first: Alain

last: Jacquier

address: 25-28 rue du docteur roux

department: Génomes & génétique

country: France

institute: Institut Pasteur

description: Sample 37

data_processing:
Duplicated reads were first eliminated from the sequences. Then tagged reads were extracted from the unique reads searching the specific 5'-end tag (NNCGCGCGNN or NNCGCCGGNN)
After removal of the tag, the resultant reads were aligned the reference genomes using bowtie2
for 5'end samples, only 5' end extremity of each mapped read was conserved and reported in wig files. For full RNA sample, whole reads were used in wig files
for samples 1 to 24, reads count were normalized using the median reads count of the -50 to -10 nucleotides zone before each annotated ORF as reference value
for samples 25 to 40, reads count were normalized using the total S. pombe mapped read count as reference value
bed files correspond to the application of a peak calling procedure on 5'end samples. We followed the method described by Neil et al (2009). We choose as parameters a distance of 150 nucleotide for the maximal distcane between consecutive TSS and a minimum reads count of 4 in at least one of the samples involved in the procedure
the resultant clusters were associated to annotated features using annotation available on SGD. We used ORFs, tRNAs, snRNAs, snoRNAs, rRNAs, ncRNAs, CUTs, SUTs and XUTs
false-positive clusters were filtered out using two parameters; a proportion of TSSs mapped on a purine preceded by a pyrimidine under 80% and a log2(upf1∆rrp6∆-TAP/upf1∆rrp6∆-No-TAP) below 0.55
Genome_build: S. cerevisiae S88C R64-1-1; S. pombe ASM294 v2.19
Supplementary_files_format_and_content: wig: values correspond to the normalized reads count. Negative values correspond to the reads on reverse strand
Supplementary_files_format_and_content: wig: samples L5p_11.XXX correspond to the sum of L5p_01.XXX, L5p_03.XXX and L5p_04.XXX
Supplementary_files_format_and_content: wig: samples L5p_12.XXX correspond to the sum of L5p_02.XXX, L5p_05.XXX and L5p_06.XXX
Supplementary_files_format_and_content: wig: samples L5p_13.XXX correspond to the sum of L5p_07.XXX, and L5p_08.XXX
Supplementary_files_format_and_content: wig: samples L5p_14.XXX correspond to the sum of L5p_09.XXX, and L5p_10.XXX
Supplementary_files_format_and_content: wig: samples LT_03.XXX correspond to the sum of LT_01.XXX, and LT_02.XXX
Supplementary_files_format_and_content: bed: values correspond to the normalized reads count within the cluster in each sample used to generate clusters

organism: Saccharomyces cerevisiae BY4741

source_name: yeast cells

extract_protocol:
Total RNA was extracted using the hot acid phenol protocol (2). Poly(A)+-RNA were obtained by two successive rounds of purification using oligo (dT)25 magnetic beads (New England Biolabs) following the manufacturer's protocol. RNAs were incubated with TAP (Tobacco Acid Pyrophosphatase) and biotynilated. After fragmentation and elimination of the 5'end RNAs with magnetic beads, POLY(A) RNAs were also removed from the supernatant using oligo (dT)25 magnetic beads. the resultant supernatant was used as body RNAs source
RNA libraries were prepared for sequencing using standard Illumina protocols with only a first step to add a specific tag (NNNNCGCGCGNN or NNNNCGCCGGNN) at the 5'-end of each sequence to eliminates further contamination

tag: genotype

value: Wild Type (BY4741 can1_delta)

tag: internal strain reference


title: LT_02 xrn1∆

description: Sample 39

value: BY4741 can1_delta, xrn1_delta ::KANMX6


title: P652HM

tag: tissue


title: P853TF


title: LT_01 upf1∆xrn1∆

description: Sample 36

value: BY4741 can1_delta, xrn1_delta ::KANMX6, upf1_delta ::HIS3MX6


title: LT_01 upf1∆

description: Sample 34

value: BY4741 can1_delta, upf1_delta ::HIS3MX6


title: LT_02 upf1∆

description: Sample 38


title: LT_02 upf1∆xrn1∆

description: Sample 40


title: LT_01 xrn1∆

description: Sample 35


title: L5p_10 upf1∆set2∆ - TAP

description:
Sample 32
5'-end of RNAs

extract_protocol:
Total RNA was extracted using the hot acid phenol protocol (2). Poly(A)+-RNA were obtained by two successive rounds of purification using oligo (dT)25 magnetic beads (New England Biolabs) following the manufacturer's protocol. RNAs were incubated without TAP (Tobacco Acid Pyrophosphatase) and biotynilated. After fragmentation the 5'-end RNAs were purified using strepavidin magnetic beads
RNA libraries were prepared for sequencing using standard Illumina protocols with only a first step to add a specific tag (NNNNCGCGCGNN or NNNNCGCCGGNN) at the 5'-end of each sequence to eliminates further contamination

value: BY4741 can1_delta, set2_delta ::KANMX6, upf1_delta ::HIS3MX6


title: LT_01 Wild Type

description: Sample 33


title: L5p_09 upf1∆set2∆ - TAP

description:
Sample 30
5'-end of RNAs


title: L5p_10 upf1∆set2∆ + TAP

description:
Sample 31
5'-end of RNAs


title: brain regions, prefrontal cortex

city: Berlin

first: Petar

last: Glazar

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description:
dissected prefrontal cortex
genome build: mm9

data_processing:
Illumina base calling, demultiplexing, and FASTQ conversion with CASAVA-1.8.2
alignment genome reference using bowtie2
20nt anchors from both ends of unaligned reads aligned to genome independently
aligned anchors were extended to find circRNA head-to-tail splice sites (see Suppl. Methods)
Supplementary_files_format_and_content: bed file; circRNA head-to-tail splice sites with number of supporting reads in the score column

source_name: C57BL/6 WT mice

extract_protocol:
TRIZOL
Ribodepletion followed by default Illumina RNA-Seq for HiSeq2500 (TruSeq)

value: brain


title: brain regions, olfactory bulb

description:
dissected olfactory bulb
genome build: mm9


title: brain regions, hippocampus

description:
dissected hippocampus region
genome build: mm9


title: brain regions, cerebellum

description:
dissected cerebellum
genome build: mm9


title: L5p_09 upf1∆set2∆ + TAP

description:
Sample 29
5'-end of RNAs


title: primary neurons, day 21

description:
cortical neurons, day 21 after plating
genome build: mm9

source_name: CD1 mouse embryos (E17.5–E18.5)

growth_protocol: Neurobasal-A medium with 2% B27 and 0.5 mM L-glutamine at 37ºC and 5% CO2

tag: differentiation stage

value: cortical neurons, day 21 after plating


title: P844TM


title: L5p_08 upf1∆rrp6∆ + TAP

description:
Sample 27
5'-end of RNAs

value: BY4741 can1_delta, upf1_delta ::KANMX6, rrp6_delta ::HPHMX6


title: L5p_08 upf1∆rrp6∆ - TAP

description:
Sample 28
5'-end of RNAs


title: primary neurons, day 28

description:
cortical neurons, day 28 after plating
genome build: mm9

value: cortical neurons, day 28 after plating


title: primary neurons, day 14

description:
cortical neurons, day 14 after plating
genome build: mm9

value: cortical neurons, day 14 after plating


title: L5p_07 upf1∆rrp6∆ + TAP

description:
Sample 25
5'-end of RNAs


title: L5p_07 upf1∆rrp6∆ - TAP

description:
Sample 26
5'-end of RNAs


title: primary neurons, day 1

description:
cortical neurons, day 1 after plating
genome build: mm9

value: cortical neurons, day 1 after plating


title: L5p_06 set2∆

description:
Sample 23
5'-end of RNAs

extract_protocol:
Total RNA was extracted using the hot acid phenol protocol (2). Poly(A)+-RNA were obtained by two successive rounds of purification using oligo (dT)25 magnetic beads (New England Biolabs) following the manufacturer's protocol. RNAs were incubated with TAP (Tobacco Acid Pyrophosphatase) and biotynilated. After fragmentation the 5'-end RNAs were purified using strepavidin magnetic beads
RNA libraries were prepared for sequencing using standard Illumina protocols with only a first step to add a specific tag (NNNNCGCGCGNN or NNNNCGCCGGNN) at the 5'-end of each sequence to eliminates further contamination

value: BY4741 can1_delta, set2_delta ::KANMX6


title: L5p_06 upf1∆

description:
Sample 22
5'-end of RNAs

value: BY4741 can1_delta, upf1_delta ::KANMX6


title: L5p_06 Wild Type

description:
Sample 21
5'-end of RNAs


title: L5p_05 upf1∆set2∆

description:
Sample 20
5'-end of RNAs


title: L5p_05 set2∆

description:
Sample 19
5'-end of RNAs


title: Sed8KD_6hr

city: Rochester

first: Laurie

middle: A

last: Steiner

state: New York

address: 601 Elmwood Ave

department: Pediatrics

institute: University of Rochester

data_processing:
CLEANING - seqclean-x86_64 (seqclean & cln2qual), fastqc-0.10.1, fastx_toolkit_0.0.13 (fastq_quality_trimmer)
MAPPING - SHRiMP_2_2_3
DIFFERENTIAL EXP. - cufflinks-2.0.2.Linux_x86_64 (cuffdiff)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and results of differential expression analyses

source_name: shRNA Setd8

growth_protocol: ESREs were derived and maintained as described in "Immature erythroblasts with extensive ex vivo self-renewal capacity emerge from the early mammalian fetus"  England et al. Blood. 2011

extract_protocol:
Qiagen RNA-Easy kit was utilized according to manufacturer's instructions.
Bioo library preparation kit was used according to manufactures instructions.

treatment_protocol: Terminal erythroid maturation was initiated in either knockdown or scramble ESRESs as described in, "Immature erythroblasts with extensive ex vivo self-renewal capacity emerge from the early mammalian fetus" England el al. Blood 2011

tag: prolireating vs maturing

value: maturing cells

tag: transfection

value: shRNA targeting Setd8 and placed in maturation media or 6 hours prior to RNA collection


title: scrESRE_73_KD

value: proliferating cells

value: shRNA targeting Setd8


title: scr_6hr

source_name: scramble control

value: non-targeting shRNA control and placed in maturation media 6 hours before RNA collection


title: scrESRE

value: non-targeting shRNA control


title: SH-SY5Y exp1 day 2

description:
day 2 after retinoic acid treatment
genome build: hg19

source_name: SH-SY5Y cells; CRL-2266 (ATCC)

growth_protocol: DMEM/F12 supplemented with L-glutamine and non-essential amino-acids, 10% FBS

extract_protocol:
TRIZOL
Ribodepletion followed by default Illumina RNA-Seq for HiSeq2000 (TruSeq)

treatment_protocol: retinoic acid induction; 1µM in neurobasal medium, 1X B27

value: day 2 after retinoic acid treatment


title: L5p_05 Wild type

description:
Sample 17
5'-end of RNAs

value: Wild Type (BY4741 can1_delta)


title: L5p_05 upf1∆

description:
Sample 18
5'-end of RNAs


title: SH-SY5Y exp1 day 0

description:
undifferentiated
genome build: hg19

value: undifferentiated


title: L5p_03 upf1∆rrp6∆

description:
Sample 16
5'-end of RNAs


title: L5p_03 rrp6∆

description:
Sample 15
5'-end of RNAs

value: BY4741 can1_delta, rrp6_delta ::hphMX6


title: fractionation, cytoplasm

description:
cytoplasmic fraction
genome build: mm9

source_name: NMRI mouse

value: brain


title: L5p_03 upf1∆

description:
Sample 14
5'-end of RNAs


title: L5p_06 upf1∆set2∆

description:
Sample 24
5'-end of RNAs

value: BY4741 can1_delta, set2_delta ::KANMX6, upf1_delta ::HIS3MX6


title: GFP_ChIPseq_Rep2

city: Durham

first: Timothy

middle: E

last: Reddy

address: 2347 CIEMAS, 101 Science Drive

department: Department of Biostatistics & Bioinformatics

institute: Duke University

data_processing:
Base-calling was performed on instrument using CASAVA software
Reads were aligned to the hg19 version of the human genome using bowtie version 0.12.9, and the  "--best" alignment option
Binding sites were called for each replicate using macs (v1.4) relative to a pooled GFP control library, and with the parameters "-g hs -p 1e-4 --nomodel --shiftsize=65"
Reproducibile binding sites were identified by calculating the Irreproducibility Discovery Rate (IDR) for each pair of replicates, accepting only binding sites with an IDR < 0.05.
Binding sites with IDR < 0.05 in any pairwise comparison were merged into a single set of binding sites per experiment
Binding sites found in the ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz) were removed from further analysis.
The number of sequencing reads in each reproducible binding site in each replicate and each control were tabulated
The counts were loaded into R and analyzed for differential binding relative to control (i.e. HA-ChIP-seq for GFP-transfected cells) using DESeq.
Within DESeq, size factors were set based on total sequencing depth for the replicate; dispersions were estimates using the "pooled" method and a "local" fit; and a False Discovery Rate of 0.1% was used for final reporting.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files of the genome-wide sequenced tag density, split by strand.

source_name: Cultured HEK293T cells

growth_protocol: HEK293T cells were obtained from the American Tissue Collection Center (ATCC) through the Duke University Cancer Center Facilities and were maintained in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
10 million cells were crosslinked for 10 minutes in 1% formaldehyde followed by 5 minutes of quenching in 0.125 M glycine. Cells were then washed with cold PBS pH7.4, and collected in the presence of cold cell lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, and Roche Complete Protease Inhibitor Cocktail Cat #11836145001). Nuclei were pelleted by centrifugation at 2,000 rpm for 5 minutes at 4C, and the supertanant discarded.  Sheared chromatin was then prepared by sonicating the nuclei in the presence of RIPA buffer (1 x PBS pH 7.4, 1% NP-40, 0.5% NaDOC, Roche Protease Inhibitor Cocktail), followed by centrifugation to remove cell debris. The chromatin was then immunoprecipitated with an anti-HA antibody (Covance MMS-101P). After immunoprecipitation, the formaldehyde crosslinks were reversed by heating overnight at 65C, and the DNA was collected using Qiagen PCR cleanup columns.
DNA ends were prepared for Illumina HiSeq sequencing using the NEBNext Uktra DNA Library Prep Kit for Illumina (NEB Cat# E7370L). The adapted DNA was then size selected using SPRI beads for a size of 150-300bp, and PCR-amplified to make the final sequencing library. Samples were sequenced on an Illumina HiSeq 2000.

treatment_protocol: HEK293T cells were transfected with Lipofectamine 2000 (Invitrogen) according to manufacturer’s instructions. Transfection efficiencies were routinely higher than 80% as determined by fluorescence microscopy following delivery of a control eGFP expression plasmid. dCas9-VP64 expression plasmid was transfected at a mass ratio of 3:1 to the total amount of gRNA expression plasmid consisting of a mixture of equal amounts of the four gRNAs.

tag: transfected gene

value: GFP

tag: guide rna

tag: chip antibody

value: anti-HA (Covance MMS-101P)


title: HBG_TALE_VP64_ChIPseq_Rep3


title: GFP_ChIPseq_Rep1


title: HBG_TALE_VP64_ChIPseq_Rep2


title: L5p_02 upf1∆rrp6∆

description:
Sample 12
5'-end of RNAs

tag: strain

value: BY4741 can1_delta, upf1_delta ::KANMX6, rrp6_delta ::HPHMX6


title: fractionation, brain_lysate

description:
whole brain lysate
genome build: mm9


title: primary neurons, day 7

description:
cortical neurons, day 7 after plating
genome build: mm9

value: cortical neurons, day 7 after plating


title: fractionation, synaptoneurosomes

description:
synaptoneurosomic fraction
genome build: mm9


title: L5p_03 Wild type

description:
Sample 13
5'-end of RNAs


title: HBG_TALE_VP64_ChIPseq_Rep1


title: SH-SY5Y exp1 day 4

description:
day 4 after retinoic acid treatment
genome build: hg19

value: day 4 after retinoic acid treatment


title: L5p_02 upf1∆

description:
Sample 10
5'-end of RNAs

value: BY4741 can1_delta, upf1_delta ::KANMX6


title: L5p_02 Wild Type

description:
Sample 9
5'-end of RNAs


title: L5p_04 upf1∆set2∆

description:
Sample 8
5'-end of RNAs


title: P19 exp2 day 12

description:
neurons (day 8 after plating)
genome build: mm9

source_name: P19 cells; ACC316 (DMSZ)

growth_protocol: AlphaMEM-supplemented with L-glutamine and 10% FBS

treatment_protocol: retinoic acid induction; 1µM

value: neuronal culture (day 8 after plating)


title: P19 exp2 day 4

description:
embryoid bodies (day 4)
genome build: mm9

value: embryoid bodies (day 4)


title: HBG_Cas9_VP64_ChIPseq_Rep3


title: HBG_Cas9_VP64_ChIPseq_Rep2


title: P19 exp2 day 0

description:
undifferentiated cells (day 0)
genome build: mm9

value: undifferentiated P19 embryonic carcinoma cells


title: HBG_Cas9_VP64_ChIPseq_Rep1


title: L5p_04 set2∆

description:
Sample 7
5'-end of RNAs

value: BY4741 can1_delta, set2_delta ::KANMX6


title: SH-SY5Y exp2 day 8

description:
day 8 after retinoic acid treatment
genome build: hg19

value: day 8 after retinoic acid treatment


title: P19_Day_12

data_processing:
Illumina base calling, demultiplexing, and FASTQ conversion with CASAVA-1.8.2
alignment to mm9 using bowtie2
20nt anchors from both ends of unaligned reads aligned to mm9 independently
aligned anchors were extended to find circRNA head-to-tail splice sites (see Suppl. Methods)
Genome_build: mm9
Supplementary_files_format_and_content: bed file; circRNA head-to-tail splice sites with num

source_name: P19 cells_induced with RA

growth_protocol: AlphaMEM-supplemented with glutamine

tag: cell line

tag: cell type

value: embryonic carcinoma cells

tag: cell line info

value: DSMZ ACC deposit #316

tag: cell subtype

value: neuronal culture (day 8)


title: GFP_ChIPseq_Rep3

value: GFP'


title: L5p_04 upf1∆

description:
Sample 6
5'-end of RNAs


title: IL1RN_TALE_VP64_ChIPseq_Rep3


title: SH-SY5Y exp2 day 4


title: L5p_02 rrp6∆

description:
Sample 11
5'-end of RNAs

value: BY4741 can1_delta, rrp6_delta ::hphMX6


title: IL1RN_TALE_VP64_ChIPseq_Rep2


title: L5p_04 Wild Type

description:
Sample 5
5'-end of RNAs

value: Wild Type (BY4741 can1_delta)


title: P19_Day_2

value: embryoid bodies (day 2)


title: SH-SY5Y exp2 day 0

description:
undifferentiated
genome build: hg19

value: undifferentiated


title: P19_Day_4


title: Uninfected (Ghanaian) human plasma

source_name: Human blood (Ghana)


title: IL1RN_TALE_VP64_ChIPseq_Rep1

value: anti-HA (Covance MMS-101P)


title: L5p_01 rrp6∆

description:
Sample 3
5'-end of RNAs


title: P19_Day_0

source_name: P19 cells_undifferentiated

value: undifferentiated embryonic carcinoma cells


title: Infected (Ghanaian) human plasma

value: Onchocerca volvulus


title: L5p_01 upf1∆

description:
Sample 2
5'-end of RNAs

value: BY4741 can1_delta, upf1_delta ::KANMX6


title: KLF4_ChIPSeq_KO

city: Charlottesville

first: Gary

last: Owens

state: VA

address: 415 Lane Road MR5 Building Room 1322

institute: University of Virginia

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie version 1.0 with the following configurations - bowtie --sam -q --nomaqround -m 10 --best --strata --chunkmbs 500 --offrate 7 --seedmms 2 -p 12
Data were then converted to bam and duplicates removed using Samtools Version: 0.1.18
Peaks were called using Macs Version 1.4.2 20120305
Genome_build: mm10
Supplementary_files_format_and_content: bed file containing peaks called by Macs

source_name: Atherosclerosis lesion

extract_protocol:
BCA were removed and flash frozen. Lysates were clarified from sonicated nuclei and transcription factor-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals were maintened in a Western Diet

value: Mixture of cell types (SMC, Epithelial, Macrophage, others)

tag: antibody

value: GKLF, Santa Cruz Biotechnology, sc-20691, Lot# J1212


title: Infected (Cameroonian) human serum

source_name: Human blood (Cameroon)


title: IL1RN_Cas9_VP64_ChIPseq_Rep2


title: L5p_01 Wild Type

description:
Sample 1
5'-end of RNAs


title: KLF4_ChIPSeq_WT


title: Uninfected (European) human serum

source_name: Human blood (European)


title: IL1RN_Cas9_VP64_ChIPseq_Rep1


title: RNA-seq HEK293T cytoplasm

status: Public on Apr 23 2015

first: Stirling

last: Churchman

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: RNA

data_processing:
For NET-seq and HEK 293T cytoplasmic RNA-seq libraries, the six 5’ end nucleotides corresponding to the molecular barcode, are trimmed from the reads, but remain associated with the read using a custom python script.
For all samples, reads are aligned using the STAR aligner (v2.4.0) (Dobin et al., 2013) with the following parameters : --clip3pAdapterSeq ATCTCGTATGCCGTCTTCTGCTTG --clip3pAdapterMMp 0.21 --clip3pAfterAdapterNbases 1 –outFilterMultimapNmax 101 –outSJfilterOverhangMin 3 1 1 1 –outSJfilterDistToOtherSJmin 0 0 0 0 –alignIntronMin 11 –alignEndsType EndToEnd. The reference genome used consisted in the human reference genome (hg19), with additional sequences containing the rDNA sequences (genBank U13369.1, genBank U67616.1), and the sequence of processed tRNA (with the additional CCA at their end, and intron removed, when present).
For NET-seq data, to avoid any bias towards favoring annotated regions the alignment was performed without providing transcriptome information, while for RNA-seq data, the GENCODE annotation v16 was used as the transcriptome.
Only uniquely aligned reads are kept to generate the processed data files.
For NET-seq data, only the position corresponding to the 5’ end of the sequencing read (after removal of the barcode), which corresponds to the 3’ end of the nascent RNA fragment, is recorded with a custom python script using HTSeq package (Anders et al., 2014), while the whole read coverage is recorded for RNA-seq data.
For NET-seq and HEK 293T cytoplasmic RNA-seq libraries, reverse transcription mispriming events are identified where barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read. These reads are removed from further analysis.
For NET-seq and HEK 293T cytoplasmic RNA-seq libraries, the few reads that align to the same genomic position and contain identical barcode are considered PCR duplication events and are filtered out.
For NET-seq libraries, evidence of splicing intermediates (Figure S1F) revealed that at sites where intermediates map (exact single bp 3’ ends of introns and exons) it is unclear which reads are due to splicing intermediate contamination and which are due to 3’ ends of nascent RNA. Thus, reads that map precisely at the exact single bp ends of introns and exons are discarded and the single 1 bp genomic positions are removed from subsequent analysis.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph files (http://genome.ucsc.edu/goldenPath/help/bedgraph.html); Column1=chromosome; Column2=start (left most coordinate; 0 based; position included); Column3=end (right most coordinate; 0 based; position not included); Column4=Coverage (3'end nt for NET-seq and whole read for RNA-seq).

source_name: HEK 293T cytoplasm fraction

growth_protocol: HeLa S3 cells (ATCC, CCL-2.2) were grown in DMEM containing 10% FBS, 100 U/ml penicillin and 100 µg/ml streptomycin until 90% confluent.

extract_protocol:
Cell fractionation was performed as described in (Pandya-Jones & Black, RNA, 2009), (Bhatt et al., Cell, 2012) and based on (Wuarin & Schibler, MCB, 1994) with modifications. All subsequent steps have been conducted on ice or at 4°C and in the presence of 25 µM α-amanitin (Sigma, A2263), 50 Units SUPERaseIN (Life Technologies, AM2696) and Protease inhibitors cOmplete (Roche, 11873580001) according to manufacturer’s instructions using RNAse free equipment. All buffers have been pre-chilled on ice before use. The cell pellet corresponding to 1x107 cells was gently resuspended in 200 µl cytoplasmic lysis buffer (0.15% NP-40, 10 mM Tris-HCl pH 7.0, 150 mM NaCl). The cell lysate was incubated for 5 min on ice, layered onto 500 µl sucrose buffer (10 mM Tris-HCl pH 7.0, 150 mM NaCl, 25% sucrose) and centrifuged at 16,000 g for 10 min. The supernatant corresponding to the cytoplasmic fraction was carefully removed. For subcellular RNA-seq (described below) the cytoplasmic fraction was mixed with 3.5x volumes of RLT buffer (74104, QIAGEN). RNA purification from the cytoplasmic and following fractions is described below.
Sequencing library preparation was performed as described in (Churchman & Weissman, 2012) with modifications. 3 µg of purified chromatin associated RNA was used to prepare one DNA sequencing library. 3’ ligation of RNA with a DNA linker was performed essentially as originally described, except that a DNA linker with a mixed random hexameric sequence at its 5’ end was used (new DNA linker: 5’-AppNNNNNNCTGTAGGCACCATCAAT/3ddC-3’). The ligation efficiency was monitored by ligating the new DNA linker to a 28 nt long RNA control oligo (oGAB11: 5’-AGUCACUUAGCGAUGUACACUGACUGUG-3’OH). The ligation efficiency as determined by polyacrylamide gel electrophoresis was ≥95%. After ligation the RNA was fragmented by partial alkaline hydrolysis essentially as originally described. The fragmentation time was adjusted so that most RNA molecules were fragmented into the range of 35 to 100 nt, size-selected and converted into cDNA. Reverse transcription was performed with the following modifications to the original protocol. First, for reverse transcription a new RT primer was used (oLSC007: 5’-Phos/ATCTCGTATGCCGTCTTCTGCTTG/iSp18/CACTCA/iSP18/ TCCGACGATCATTGATGGTGCCTACAG-3’). Second, the RT primer was applied at a lower final concentration (1.9 µM instead of 10.9 µM). Next, cDNA was circularized and vectors that contained cDNA corresponding to original mature snRNAs, snoRNAs, rRNAs and mitochondrial tRNAs that were heavily sequenced in first NET-seq experiments were specifically depleted. For specific depletion, biotinylated oligos were designed that were complementary to the 3’ ends of the 19 most heavily sequenced mature RNAs of HeLa S3 cells (see Supplemental Table S1). Depletion was performed similar to the rRNA depletion approach described by (Ingolia et al., Nature Protocols, 2012). Per depletion 5.0 µl circularization reaction was used. 5.0 µl of circularization reaction was combined with 1.0 µl depletion oligo pool (10 µM of each oligo, prepared in 10 mM Tris-HCl, pH 8.0; see Supplemental Table S1), 1.0 µl 20x SSC (Life Technologies, AM9763) and 3.0 µl DNase-free H2O. Tubes were placed in a thermal cycler, denatured for 90 sec at 99°C and then annealed at 0.1°C s-1 to 37°C. Tubes were incubated for 15 min at 37°C. 37.5 µl of MyOne Streptavidin C1 DynaBeads (10 mg/ml, Life Technologies, 65001) were used per depletion reaction. Magnetic beads were washed 3x with 1x bind/wash buffer (1M NaCl, 0.5 mM EDTA, 2.5 mM Tris-HCl pH 7.0, 0.1% (vol/vol) Triton-X-100). After the last wash, magnetic beads were resuspended in 15 µl 2x bind/wash buffer (2 M NaCl, 1 mM EDTA, 5 mM Tris-HCl pH 7.0, 0.2% (vol/vol) Triton-X-100) and incubated at 37°C. 10 µl of the depletion reaction were transferred directly to the bead aliquot, immediately mixed by pipetting and incubated for 15 min at 37°C with mixing at 1000 rpm. Finally, tubes were transferred to a magnetic rack and 20 µl of supernatant were recovered and isopropanol precipitated. After depletion, the circularized DNA served as template for PCR amplification. PCR amplification was performed as originally described (Churchman & Weissman, 2012), using minimal amplification cycles. The concentration, the quality and the size distribution of final DNA libraries were assessed by Qubit 2.0 Fluorometer (Invitrogen) and 2100 Bioanalyzer (Agilent) measurements. 3’ end sequencing was performed on NextSeq 500 (SE 75 nt) and HiSeq 2000 (SE 50 nt) Illumina sequencing platforms using the following custom sequencing primer: oLSC006: 5’-TCCGACGATCATTGATGGTGCCTACAG-3’.

value: HEK 293T

tag: cellular fraction

value: cytoplasm fraction

tag: library type

value: whole RNA fragment sequencing

tag: treatment


title: NET-seq HEK293T Rep2

description:
nascent RNA
library strategy: NET-seq

source_name: HEK 293T cells

value: 3'end RNA fragment sequencing


title: NET-seq HeLa S3 Flavopiridol

description:
nascent RNA
library strategy: NET-seq

source_name: HeLa S3 cells FP

value: HeLa S3

value: FP


title: NET-seq HeLa S3 DMSO

description:
nascent RNA
library strategy: NET-seq

source_name: HeLa S3 cells DMSO

value: DMSO


title: RNA-seq HeLa S3 cytoplasm

description: RNA

source_name: HeLa S3 cytoplasm fraction


title: RNA-seq HeLa S3 nucleoplasm

description: RNA

source_name: HeLa S3 nucleoplasm fraction

value: nucleoplasm fraction


title: L5p_01 upf1∆rrp6∆

description:
Sample 4
5'-end of RNAs

source_name: yeast cells

tag: genotype

value: BY4741 can1_delta, upf1_delta ::KANMX6, rrp6_delta ::HPHMX6

tag: internal strain reference


title: RNA-seq HeLa S3 chromatin

description: RNA

source_name: HeLa S3 chromatin fraction

value: chromatin fraction


title: NET-seq HEK293T Rep1

description:
nascent RNA
library strategy: NET-seq


title: NET-seq HeLa S3 Rep2

description:
nascent RNA
library strategy: NET-seq

source_name: HeLa S3 cells


title: IL1RN_Cas9_VP64_ChIPseq_Rep3

source_name: Cultured HEK293T cells


title: mNET_CMA603_rep2

city: Lisboa

first: Tomás

last: Gomes

address: Av. Professor Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

description: nascent RNA from Ser5 phosphorylated Pol II

data_processing:
For mNET-seq data, adaptor trimming was preformed using Cutadapt (v1.1), only keeping the reads with more than 10 bases.
mNET-seq data was then aligned to the human genome (build hg19) using TopHat (v2.0.9), with a minimum anchor length of 5 bases and allowing only for unique alignments.
For ChrRNA-seq and NucleoplasmRNA-seq data, alignment was preformed using TopHat (v2.0.9) with a minimum anchor length of 5 bases, allowing only for unique alignments and allowing read pairs to be separated by up to 3kb.
To aquire the last nucleotide incorporated by the polymerase in the aligned mNET-seq reads, a combination of SAMtools and inhouse python scripts was used
Then, ChrRNA-seq, NucleoplasmRNA-seq and mNET-seq singe-nucleotide aligned reads were separated by strand using SAMtools, selecting the strands according to the read flag.
To make bedgraphs of the reads aligning in different strands, genomeCoverageBed (v2.17.0) was used.
After that, the values in the bedgraphs were normalized to reads per 108 sequences using an inhouse python script.
Finally, to convert the bedgraphs to bigWig, the program bedGraphToBigWig from UCSC was used.
Genome_build: hg19
Supplementary_files_format_and_content: processed data files are in bigWig format; the scores in the files represent the number of reads per 108 sequences

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in DMEM with 10% fetal bovine serum

extract_protocol: Approximately 1.6x108 cells were used to generate nuclear and chromatin fractions. Isolated chromatin was washed in 1 ml of 1x Micrococcal Nuclease (MNase) buffer (NEB) and then incubated with MNase (40 u/mL) on Thermomixer (eppendorf, 1,400 rpm) at 37oC for 90 sec. MNase was inactivated by EGTA (25 mM) addition immediately after the reaction and soluble digested chromatin was collected by 13,000 rpm centrifuge for 5 min. The supernatant was diluted with 9 ml of NET-2 buffer and add Pol II antibody-conjugated beads. 40 mg of Pol II antibody was used for each mNET-seq experiment. Immuno-precipitation was performed at 4oC for one hour. The beads were washed with 1 ml of NET-2 buffer six times and with 500 ml of 1xPNKT (1xPNK buffer and 0.05 % Triton X-100) buffer once in the cold room. The washed beads were incubated in 100 ml of PNK reaction mix (1xPNKT, 1 mM ATP and 0.05 U/ml T4 PNK 3'phosphatase minus (NEB) ) on Thermomixer (1,400 rpm) at 37oC for 6 min. After the reaction the beads were washed with 1 ml of NET-2 buffer once and RNA was extracted with Trizol reagent. RNA was resolved on 8 % denaturing acrylamide 7 M urea gels for size purification. 35-100 nt fragments were eluted from the gel using RNA elution buffer (1 M NaOAc and 1 mM EDTA) and RNA was precipitated in 75 % Ethanol.

value: HeLa

tag: net-seq antibody


title: mNET_CMA602_rep2

description: nascent RNA from Ser2 phosphorylated Pol II


title: ChrRNA_siXrn2

description: chromatin-bound RNA

extract_protocol:
Chromatin RNA fraction was prepared from ~80% confluent HeLa cells in 100mm Dishes. Approximately 7x106 cells were washed with ice-cold PBS twice. The cells were lysed with ice-cold 4 ml of HLB/NP40 buffer (10 mM Tris-Hcl pH 7.5, 10 mM NaCl, 0.5% NP40 and 2.5 mM MgCl2) and incubated on ice for 5 min. After the incubation, 1 ml of ice-cold HLB/NP40/Sucrose buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.5% NP40, 2.5 mM MgCl2 and 10 % Sucrose) was under-laid and then the nuclei were collected under 1,400 rpm centrifuge at 40C for 5 min. Isolated nuclei were resuspended in 1.25 ml of NUN1 solution (20 mM Tri-HCl pH 8.0, 75mM NaCl, 0.5 mM EDTA, 50% Glycerol and proteinase inhibitor 1xComplete (Roche)) and added 1.2 ml NUN2 buffer (20 mM HEPES-KOH pH 7.6, 7.5 mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1 M Urea, 1% NP40, proteinase inhibitor 1xComplete and phosphatase inhibitor 1xPhosStop (Roche)). 15 min incubation was carried out on ice with mixing by max speed vortex for 5 sec every ~4 min and then chromatin pellets were precipitated under 13,000 rpm centrifuge at 4oC for 10min. Chromatin pellet was resuspended in 200 ml HSB (10mM Tris-HCl pH 7.5, 500 mM NaCl and 10 mM MgCl2) with 0.25 U/ml TURBO DNase (Life technologies) at 37oC for 10 min and then treated with Proteinase K for 10 min. RNA was extracted by Trizol reagent (Life technologies). This extraction steps were repeated three times.
In prior to RNA library preparations, rRNAs were depleted using Ribo-Zero rRNA removal kits (Epicentre) from 5 mg of Chromatin RNA. RNA was also fragmented 150-200 nt by heat treatment (94oC) for 15 min in 1xNEB first strand synthesis buffer. 100 ng or chromatin RNA was used for RNA library preparations. These were carried out according to NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB). Deep sequencing using Hiseq2000 and Hiseq2500 were performed by the Wellcome Trust Centre for Human Genetics (WTCHG) Oxford UK.

treatment_protocol: SMARTpool siRNA against human CPSF73 (CPSF3) and CstF64 (CSTF2) were purchased from Thermo scientific. ON-TARGET plus siRNA against Xrn2 was made by Thermo Scientific as following sequences. Sense: AAGAGUACAGAUGAUCAUGUU, Antisense: 5'-P CAUGAUCAUCUGUACUCUUUU.  Silencer select siRNA against CstF64 tau (CSTF2T) was designed by Life technologies as following sequence, Sense: CCAUUAUUGACUCACCCUAtt, Antisense: UAGGGUGAGUCAAUAAUGGgc. These siRNA (final conc. 30nM) were transfected into HeLa cell using Lipofectamine RNAiMAX reagent (Life technologies) according to the manual and incubated for 72 hours.

value: Xrn2 siRNA


title: mNET_CMA602_siXrn2


title: mNET_CMA602_siCstF64+siCstF64tau

value: CstF64 siRNA + CstF64tau siRNA


title: ChrRNA_siLuc

description: chromatin-bound RNA

extract_protocol: Chromatin RNA fraction was prepared from ~80% confluent HeLa cells in 100mm Dishes. Approximately 7x106 cells were washed with ice-cold PBS twice. The cells were lysed with ice-cold 4 ml of HLB/NP40 buffer (10 mM Tris-Hcl pH 7.5, 10 mM NaCl, 0.5% NP40 and 2.5 mM MgCl2) and incubated on ice for 5 min. After the incubation, 1 ml of ice-cold HLB/NP40/Sucrose buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.5% NP40, 2.5 mM MgCl2 and 10 % Sucrose) was under-laid and then the nuclei were collected under 1,400 rpm centrifuge at 40C for 5 min. Isolated nuclei were resuspended in 1.25 ml of NUN1 solution (20 mM Tri-HCl pH 8.0, 75mM NaCl, 0.5 mM EDTA, 50% Glycerol and proteinase inhibitor 1xComplete (Roche)) and added 1.2 ml NUN2 buffer (20 mM HEPES-KOH pH 7.6, 7.5 mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1 M Urea, 1% NP40, proteinase inhibitor 1xComplete and phosphatase inhibitor 1xPhosStop (Roche)). 15 min incubation was carried out on ice with mixing by max speed vortex for 5 sec every ~4 min and then chromatin pellets were precipitated under 13,000 rpm centrifuge at 4oC for 10min. Chromatin pellet was resuspended in 200 ml HSB (10mM Tris-HCl pH 7.5, 500 mM NaCl and 10 mM MgCl2) with 0.25 U/ml TURBO DNase (Life technologies) at 37oC for 10 min and then treated with Proteinase K for 10 min. RNA was extracted by Trizol reagent (Life technologies). This extraction steps were repeated three times.

value: Luciferase siRNA


title: ChrRNA_siCPSF73

description: chromatin-bound RNA

treatment_protocol: SMARTpool siRNA against human CPSF73 (CPSF3)  (final conc. 30nM) were transfected into HeLa cell using Lipofectamine RNAiMAX reagent (Life technologies) according to the manual and incubated for 72 hours.

value: CPSF73 siRNA


title: mNET_CMA602_siLuc


title: mNET_CMA601

description: nascent RNA from all CTD isoforms Pol II


title: mNET_CMA602_rep1


title: mNET_CMA603_rep1


title: mNET_CMA602_siCPSF73


title: mNET_8WG16_rep1

description: nascent RNA from unphosphorylated Pol II


title: mNET_8WG16_rep2

tag: anet-seq antibody


title: P493 shTert

city: Singapore

first: Julius

last: Müller

address: 61 Biopolis Drive

department: IMCB

country: Singapore

institute: A*Star Singapore

description: Sample 4_P493

data_processing:
Illumina Casava v1.8 used for basecalling.
In order to make the downstream analysis more comparable to the P493 samples, all mouse Eu Myc samples were trimmed to 35Bp long reads using trimmomatic.
Sequences were mapped to hg19 and mm10 using bowtie2 v2.2.3 with parameters -N 0 --sensitive --no-unal -q -U
MACS v2.0.10.20131216 was used for peak calling with parameters --llocal=10000 --bw 200 --shiftsize 100 -q 0.05 --slocal=1000  --keep-dup=3  --nomodel
All MACS output files contain only peaks with a pileup greater than 4, a q-value smaller or equal to 0.05 and a minimum enrichment of 2.
Genome_build: mm10 (Primary lymphoma cells) and hg19 (P493)
Supplementary_files_format_and_content: MACS v2.0.10.20131216 peaks file

source_name: P493 cells

growth_protocol: P493 cells were maintained in RPMI medium 1640 supplemented with 10% FBS, penicillin, penicillin and streptomycin.

extract_protocol:
Cells were treated with 1% formaldehyde for 10 minutes at room temperature to crosslink protein-DNA complexes, and reactions were then quenched using 125 mM glycine for 5 minutes. The cells were then lysed with sodium dodecyl sulfate (SDS) lysis buffer and sonicated for 10 minutes using the Diagenode Bioruptor. The fragmented chromatin was pre-cleared with bovine serum albumin (BSA), protein A Sepharose beads (Millipore) at 4 ˚C for 2 hours before immunoprecipitation with c-MYC or rabbit control IgG antibodies overnight at 4 ˚C. Sepharose beads were washed as described previously and eluted with SDS elution buffer before subjecting to reverse cross-linking at 65 ˚C overnight. Finally samples were purified using the QIAquick PCR Purification Kit (Qiagen) according to the manufacturer’s protocol.
Single read - Illumina

treatment_protocol: P493 cells were stably infected with the following viruses: pLKO shControl, pLKO shTERT and pCMV-GFP-NheI shTerc.

value: P493 cells

value: shTert

value: c-Myc Antibody (N-262) (Santa Cruz, catalog# sc-764, lot# D0413)


title: P493 shControl

description: Sample 2_P493

value: shControl


title: P493 Input

description: Sample 1_P493

value: none (input)


title: ChrRNA_siCstF64+siCstF64tau

description: chromatin-bound RNA


title: Corinpos vMB (Sample 32)

city: Lund

first: Malin

last: Parmar

address: BMC A11

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

data_processing:
Mature and hairpin microRNAs were downladed from mirbase.org 2013-06-22
Preprocessing with fastx, http://hannonlab.cshl.edu/fastx_toolkit/index.html
The adapter TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC was removed
Sequences shorter than 15 nt were removed.
A fasta file with read counts was produced for each sample
Bowtie2 was used for alignment. Reference : Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
Bowtie indices were built using the mature and hairpin files from mirbase.
Alignment was performed for the reads of each sample. Default bowtie2 scores were used
For each sample and micro-RNA, the total count was found. The counts were multiplicatively normalized such that each sample had the same total count. The counts were logarithm tansformed by adding a pseudocount of 1 to all counts and taking the base 2 logarithm.
Genome_build: Mirbase release 19
Supplementary_files_format_and_content: csv file with normalized counts for the microRNAs for each sample

source_name: FACS Corin+ cells from ventral midbrain cells from ES cells d14

growth_protocol: Kirkeby A, Nelander J, Parmar M. Generating regionalized neuronal cells from pluripotency, a step-by-step protocol.  Front Cell Neurosci. 2013 Jan 3;6:64. doi: 10.3389/fncel.2012.00064

extract_protocol: RNA was exracted using the miRNeasy mini kit form Qiagen

treatment_protocol: Kirkeby A, Grealish S, Wolf DA, Nelander J, Wood J, Lundblad M, Lindvall O, Parmar M. Generation of regionally specified neural progenitors and functional neurons from human embryonic stem cells under defined conditions. Cell Rep. 2012 Jun 28;1(6):703-14. doi: 10.1016/j.celrep.2012.04.009. Epub 2012 May 26.

tag: protocol

value: H9 cells were differentiated towards a ventral midbrain fate according to the protocol in Kirkeby et al 2012, Frontiers in Cellular Neuroscience.In addition, cells were further ventralized by adding Purmophamine to the media (StemGent, 5uM) during day0-11 of differentiation.  On day 14 the cells were stained for Corin (R&D 1:200) and FACS sorted.


title: Corinpos vMB (Sample 28)

value: FACS Corin+ cells from ventral midbrain cells from ES cells d14


title: Corinpos vMB (Sample 29)


title: Corinpos vMB (Sample 31)


title: Corinpos vMB (Sample 30)


title: Corinpos vMB (Sample 34)


title: HB (Sample 25)

source_name: Differentiated hindbrain cells from ES cells d14

value: H9 cells were differentiated towards a  hindbrain fate according to the protocol in Kirkeby et al 2012, Frontiers in Cellular Neuroscience.


title: HB (Sample 26)

value: Differentiated hindbrain cells from ES cells d14


title: HB (Sample 27)


title: MB (Sample 23)

source_name: Differentiated midbrain cells from ES cells d14

value: H9 cells were differentiated towards midbrain according to the protocol in Kirkeby et al 2012, Frontiers in Cellular Neuroscience.


title: MB (Sample 22)

value: Differentiated midbrain cells from ES cells d14


title: ME (Sample 19)

source_name: Differentiated mesenchymal cells from ES cells d14

value: The media on confluent H9 cells was changed to RPMI (Mediatech) complemented with Pen/strep, glutamate and Activin A (R&D) for one day. On the sencond day the media was further supplemented with fetal bovine serum.


title: MB (Sample 20)


title: ME (Sample 18)

value: Differentiated mesenchymal cells from ES cells d14


title: MB (Sample 21)


title: ME (Sample 16)


title: ME (Sample 17)


title: FB (Sample 15)

source_name: Differentiated forebrain cells from ES cells d14

value: H9 cells were differentiated towards a forebrain fate according to the protocol in Kirkeby et al 2012, Frontiers in Cellular Neuroscience.