title: Human-muscle_Normal-3

city: La Jolla

first: Ranjan

last: Batra

state: California

address: 2880 Torrey Pines Scenic Drive

department: Cellular and Molecular Medicine

institute: University of California San Diego

description:
Normal human muscle autopsy
PolyA-seq_sample17
processed data file: Control_pooled.wig.gz

data_processing:
The raw sequencing reads(FASTQ) were mapped to the reference genome (mm10) using the program OLego (Wu and Zhang, in preparation) with a seed size of 13 nt and allowing ≤ two mismatches or insertions or deletions.  Since the antisense strand is sequenced, mapped reads were reverse complemented to obtain the sense strand sequence, and the most 3’ end position was recorded since this position corresponds to the last nucleotide preceding the polyA tail (pA site).
To define robust polyA sites, reads from all samples were pooled and supporting reads for each candidate polyA site were counted. Candidate polyA sites that likely resulted from internal priming from A-rich RNA sequences were then removed using a log-odds model established in a previous study (Derti et al., 2012). These cleaned sites were further filtered to remove those supported by few reads (<10 reads) and then grouped so that sites in each cluster are ≤ 25 nt with each other (Tian et al., 2005)
Finally, unique polyA sites were assigned to overlapping RefSeq and UCSC annotated genes.  If a polyA site did not overlap with a known gene, but overlapped with the extended 3' UTR (1 kb extension) of a transcript, it was assigned to that gene. To identify differential polyA site usage, we considered each pair of polyA sites assigned to the same gene using the number of supporting reads in each group of samples.
Statistical analysis was performed using Fisher’s exact test, followed by Benjamini correction (Benjamini and Hochbergh, 1995) for multiple tests and calculation of proportional change of polyA site usage. To minimize multiple test correction, only those relatively abundant polyA sites were considered (coverage≥20, or {site1_WT+site2_WT≥20, site1_KO+site2_KO≥20, site1_WT+site1_KO≥20, site2_WT+site2_KO≥20}).
For hierarchical clustering and principal component analysis, counts per million (CPM) normalized data was log2(n+1) transformed, filtered to exclude low read number (<log25), centered around the mean, and clustered with Cluster 3.0 or subjected to PCA analysis using R. Hierarchical clustering was visualized with Java Tree view and PCA analysis was plotted with the gplot function and rgl library in R.
For HITS-CLIP FASTQ files were filtered to remove low quality reads by requiring a minimum score of 20 in barcode positions and an average score of 20 in the following 25 nucleotides. The filtered reads were then aligned to the mouse reference genome (mm9) by Novoalign. Potential PCR duplicates, as judged from the starting position of genomic mapping and the barcode sequences, were removed to identify unique CLIP tags.
Genome_build: mm9, mm10, hg19
Supplementary_files_format_and_content: Fastq files were aligned to the UCSC genome build (mm9, mm10, or hg19) using BWA, novoaligner (HITS-CLIP) or Olego (polyA-seq). The resulting .sam files were converted to bed files using samtools (HITS-CLIP) or Olego (PolyA-seq). The resulting .bed files were filtered to remove PCR duplicates (HITS-CLIP) and internal A-stretches (polyA-seq). BedGraph files (wiggles) were generated from bedfiles using bedtools (HITS-CLIP) or tag2profile tool from Olego (polyA-seq). Olego is an open source software by Chaolin Zhang lab from Columbia University.

source_name: Normal human muscle autopsy

growth_protocol: MEFs were grown in DMEM supplemented with 15% FBS

extract_protocol:
Total RNA was extracted using Trizol followed by purification with phenol:chloroform extraction. RNA quality was analyzed using Agilent 2100 bioanalyzer
For HITS-CLIP, Quadriceps muscles from WT FVB mice (3 months, n = 3 each genotype) were dissected, frozen in liquid nitrogen, and crosslinked with UV-light (Stratalinker 1800, Stratagene). For MEFs, 10 cm plates (n = 2 each genotype), were UV-crosslinked followed by scraping cells in ice-cold PBS and centrifugation.
For immunoprecipitation, protein lysates were denatured by adding SDS (1% final concentration), heating (100°C/5 min) and subsequent dilution to a final SDS concentration of 0.1% in PXL lysis buffer (Chi et al., 2009) prior to the addition of anti-Mbnl1 (rpAb A2764), Mbnl2 (mAb 3B4) and Mbnl3 (rpAb Mb3/7G) antibodies (5 µg each)
For PolyA-seq, Reverse transcription was carried out using an oligodT containing reverse primer. DNA libraries of 200-500 bp were obtained and sequenced (Illumina) using an oligo dT-containing sequencing primer for 35 bp reads
RNA tags were generated as described (Charizanis et al., 2012) using RNase A (concentrations of 55 U/ml and 0.55 U/ml for high and low RNase, respectively) and cDNA libraries were generated using RNA linkers and primers as described

treatment_protocol: MEFs were treated with siRNA against Mbnl3 using Dharmacon 4 transfection reagent for 48 hours in DMEM + 10% FBS

value: Normal human muscle autopsy

value: Biceps

tag: molecule subtype

value: oligodT selected total RNA


title: Human-muscle_DM1-2

status: Public on Sep 05 2014

type: SRA

country: USA

description:
DM human muscle autopsy
PolyA-seq_sample19
processed data file: DM_pooled.wig.gz

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: DM human muscle autopsy

tag: genotype/variation

value: DM human muscle autopsy

tag: tissue


title: Human-muscle_DM1-1

description:
DM human muscle autopsy
PolyA-seq_sample18
processed data file: DM_pooled.wig.gz


title: Human-muscle_Normal-2

description:
Normal human muscle autopsy
PolyA-seq_sample16
processed data file: Control_pooled.wig.gz


title: fly_control_rep1

city: Houston

first: hao

last: zhao

address: 1 Baylor Plaza

institute: BAYLOR COLLEGE OF MEDICINE

description: Fly control

data_processing: The raw reads were mapped using Tophat (version 1.12) and Cufflinks. The following parameter settings were used: inner distance (-r) was set to be 150, minimum intron size (-i) to be 40 and maximum intron size (-I) to be 20000. Other parameters were set to be default values. If a read was mapped to multiple locations, only one randomly selected alignment of this read was kept. Reference genomes used were dm3 and mm9.

organism: Drosophila melanogaster

source_name: fly

extract_protocol:
Total RNA was extracted  using Trizol  reagent from invitrogen and RNA was cleaned using Qiagen RNA clean up columns, after total RNA was extracted and clean mRNA was isolated using Dynabeds oligo (dT) 25 kit from invitrogen, when mRNA was isolated and clean double stranded cDNA was synthetized using Superscript double stranded cDNA synthesis Kit from invitrogen. Heads of 1000 animals were used per genotype.
The Sequencing Library was constructed by using 50ng of RNA and the NuGEN Ovation RNA-Seq kit. The double-stranded amplified library was fragmented on a Covaris S2 with end repair, and paired-end adaptor ligation using reagents from New England Biolabs (NEBNextR DNA Sample Prep Master Mix Set 1) for the Illumina platform.
Insert size 300 bp, standard variation 35 of the paired-end data.

value: fly


title: Sox17-XEN_RNA-seq

city: Toronto

first: Angela

middle: C

last: McDonald

state: Ontario

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

description:
Sox17-XEN
4J_dox-indep

data_processing:
Reads were aligned to the mouse genome using TopHat v 2.0.11.
Aligned reads were assembled using Cufflinks v 2.1.2.
Assemblies were merged using Cuffmerge.
Downstream analyses of differentially expressed genes was performed using Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data file was obtained following cuffdiff analysis which includes FPKM values of transcripts for each sample

organism: Mus musculus

growth_protocol: ESCs and XEN cells were cultured according to standard protocols (ESCs on mouse embryonic fibroblasts in serum and LIF and XEN cells in serum and mouse embryonic fibroblast conditioned media).

extract_protocol:
Tizol was used to extract total RNA according to the manufacturer's instuctions.
RNA-seq libraries were constructed using TruSeq RNA Sample Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Sox17-ESCs were grown in standard ESC conditions with the addition of 100ng/ml doxycycline

value: Sox17 overexpression

tag: length of dox treatment

value: 30 days + dox following 30 days without dox


title: KATOIII GATA4

city: Singapore

first: Niantao

last: Deng

state: Singapore

address: Center for Computational Biology, level 6, 8 College Road

country: Singapore

institute: Duke NUS Graduate Medical School

description: Illumina Genome Analyzer IIx

library_source: genomic

data_processing:
CASAVAv1.8 was used to perform base-calling
ChIP-seq sequence reads were mapped to the human genome using bwa version 0.5.7
Enriched peaks were called using MACS version 1.4.1
Genome_build: hg19
Supplementary_files_format_and_content: bed files included peaks called by MACS for KLF5, GATA4, GATA6 in YCC3, AGS, KATOIII cell lines.

molecule: genomic DNA

source_name: KATOIII GATA4

extract_protocol:
Chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using the antibodies
ChIP-seq libraries were constructed using a ChIP-Seq sample prep kit (IP-102-1001, Illumina) and sequenced on a Genome Analyzer IIx instrument (Illumina)

tag: cell line

value: KATOIII

tag: cell type

value: gastric cancer

tag: chip antibody


title: KATOIII GATA6

description: Illumina Genome Analyzer IIx

source_name: KATOIII GATA6


title: KATOIII KLF5

description: Illumina Genome Analyzer IIx

source_name: KATOIII KLF5


title: CT26LacZ-SFV-infected-rep2

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
RNA-Seq results were trimmed to remove 3' A-stretches originating from the library preparation.
Reads were aligned to the mm9 genome using Tophat.
Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://biowhat.ucsd.edu/homer/
Genome_build: mm9
Supplementary_files_format_and_content: Gene expression values (raw tags, RPKM, log2 fold change, P-value) and UCSC Bedgraphs are provided.

source_name: murine colorectal carcinoma

growth_protocol: The cell culture and infections were carried out on approximately 80% confluent cultures in 10 cm dishes with 7 ml of fresh low glucose DMEM (Sigma) supplemented with 10% FCS, L-glutamine and Penicillin/Streptomycin under humified atmosphere in 5% CO2.

extract_protocol:
RNA was purified using RNeasy Mini Kit and enriched for Poly(A)-RNA with MicroPoly(A) Purist Kit.
The RNA was base-hydrolyzed, dephosphorylated with PNK and fragments of 50-400 nts were gel extracted from 10% polyacrylamide TBE-urea gel. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified on a denaturing 10% polyacrylamide TBE-urea gel. The recovered cDNA was circularized, linearized, amplified for 8-10 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina HiSeq 2000 according to the manufacturer's instructions.

treatment_protocol: CT-26 cells were infected with MOI=0.01 and collected 12h post infection. The success of infection 12h p.i. was monitored with fluorescence microscope and by measuring the virus titer from the cell supernatants.

tag: transgene

value: LacZ transgene

value: CT26LacZ tumor

tag: infection

value: SFV


title: KATOIII Input

description: Illumina Genome Analyzer IIx

source_name: KATOIII Input


title: AGS GATA6

description: Illumina Genome Analyzer IIx

source_name: AGS GATA6

value: AGS


title: YCC3 GATA6

description: Illumina Genome Analyzer IIx

source_name: YCC3 GATA6


title: AGS Input

description: Illumina Genome Analyzer IIx

source_name: AGS Input


title: AGS KLF5

description: Illumina Genome Analyzer IIx

source_name: AGS KLF5


title: YCC3 Input

description: Illumina Genome Analyzer IIx

source_name: YCC3 Input


title: AGS GATA4

description: Illumina Genome Analyzer IIx

source_name: AGS GATA4


title: YCC3 GATA4

description: Illumina Genome Analyzer IIx

source_name: YCC3 GATA4


title: Human-muscle_DM1-3

description:
DM human muscle autopsy
PolyA-seq_sample20
processed data file: DM_pooled.wig.gz


title: YCC3 KLF5

description: Illumina Genome Analyzer IIx

source_name: YCC3 KLF5


title: pus9A -CMC

city: Cambridge

first: Thomas

middle: M

last: Carlile

state: Massachusetts

address: 77 Massachusetts Ave

department: Biology

institute: MIT

description:
RNA was fragmented, treated with CMC as indicated, and captured by 3' adaptor ligation. RT was perfromed with enzyme indicated, and truncated CD fragments were selected on a gel, circularized, PCR amplified, and sequenced.
protocol: Pseudo-Seq

data_processing:
Reads were trimmed of adapter sequence
Yeast: Reads were mapped to SacCer3 downloaded from UCSC on 9/2/2011 using TopHat allowing multiply mapping reads
Hela: Reads were mapped to spliced transcripts (see text) of hg19 downloaded from UCSC on 1/8/2012 using bowtie1 requiring uniquely mapping data
Mapped reads were processed using custom bash and python scripts (see text)
Ψ's were identified using custom python scripts (see text)
Genome_build: SacCer3 (9/2/2011), hg19 (1/8/2012)
Supplementary_files_format_and_content: UCSC wiggle files

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: Yeast were grown to mid log phase (OD~1.0) or high density (OD~12-15) in YPD at 30°C

extract_protocol:
yeast: Cells were lysed using hot-acid phenol as described in the text,
Hela: HeLa total RNA was isolated using QIAzol and mechanical distruption with a syringe
OTHER: As described in text.

treatment_protocol: Cells were poured over ice, harvested by centrifugation, and cell pellets were frozen in liquid nitrogen.

tag: strain

tag: rna

value: polyA+

tag: od

tag: cmc use

tag: rt enzyme

value: AMV-RT


title: pus9B +CMC


title: pus9A +CMC


title: pus9B -CMC


title: pus6B +CMC


title: Human-muscle_Normal-1

description:
Normal human muscle autopsy
PolyA-seq_sample15
processed data file: Control_pooled.wig.gz


title: pus6A -CMC


title: pus5B +CMC


title: pus6B -CMC


title: pus5A -CMC


title: pus4B +CMC


title: pus5B -CMC


title: pus4B -CMC


title: pus4A +CMC


title: pus3B +CMC


title: pus4A -CMC


title: pus3B -CMC


title: pus6A +CMC


title: pus3A +CMC


title: pus2B -CMC


title: pus2B +CMC


title: pus3A -CMC


title: pus2A +CMC


title: pus2A -CMC


title: snr49A +CMC

description: RNA was fragmented, treated with CMC as indicated, and captured by 3' adaptor ligation. RT was perfromed with enzyme indicated, and truncated CD fragments were selected on a gel, circularized, PCR amplified, and sequenced.

data_processing:
Reads were trimmed of adapter sequence
Yeast: Reads were mapped to SacCer3 downloaded from UCSC on 9/2/2011 using TopHat allowing multiply mapping reads
HeLa: Reads were mapped to spliced transcripts (see text) of hg19 downloaded from UCSC on 1/8/2012 using bowtie1 requiring uniquely mapping data
Mapped reads were processed using custom bash and python scripts (see text)
Ψ's were identified using custom python scripts (see text)
Genome_build: SacCer3 (9/2/2011), hg19 (1/8/2012)
Supplementary_files_format_and_content: USCS wiggle files, and tab delimited text files for rpkms

growth_protocol:
Yeast: Yeast were grown to mid log phase (OD~1.0) or high density (OD~12-15) in YPD at 30°C
HeLa: Cells were grown at 37°C with 5% CO2 under standard laboratory conditions. For serum starvation cells were plated at a density of 5 x 106 per 150 mm plate in DMEM+10% FBS, 24h prior to the experiment. Cells were then washed three times in PBS, before the addition of either serum-free medium (DMEM, no FBS) or full medium containing FBS (DMEM+10% FBS) for 24h.

extract_protocol:
Yeast: Cells were lysed using hot-acid phenol as described in the text
HeLa: HeLa total RNA was isolated using QIAzol and mechanical distruption with a syringe
OTHER: As described in text.

treatment_protocol: Yeast: Cells were poured over ice, harvested by centrifugation, and cell pellets were frozen in liquid nitrogen.

value: Total RNA

value: exponential


title: snr49B+CMC


title: pus5A +CMC


title: snr43 +CMC


title: WT -CMC


title: WT +CMC


title: pus7B +CMC


title: pus7B -CMC


title: pus7A +CMC


title: pus7A -CMC


title: pus1A +CMC


title: pus1B +CMC


title: satF: WT+CMC


title: pus1A -CMC


title: pus1B -CMC


title: satF: WT-CMC


title: snr81B +CMC


title: satD: WT-CMC


title: snr37B +CMC


title: snr37B -CMC


title: snr81A -CMC


title: snr81A +CMC


title: satD: WT+CMC


title: snr37A -CMC


title: satE: WT +CMC


title: logC: WT+CMC


title: logD: WT+CMC


title: satC: WT +CMC


title: logC: WT -CMC


title: logD: WT -CMC


title: snr37A +CMC


title: logB: WT +CMC longer RT fragments


title: logB: WT -CMC longer RT fragments


title: satC: WT -CMC


title: logB: WT -CMC shorter RT fragments


title: logA: WT -CMC longer RT fragments


title: logA: WT +CMC shorter RT fragments


title: logA: WT -CMC shorter RT fragments


title: satB: WT +CMC shorter RT fragments


title: satB: WT -CMC longer RT fragments


title: satB: WT -CMC shorter RT fragments


title: satB: WT +CMC longer RT fragments


title: snr81B -CMC


title: satA: WT +CMC longer RT fragments


title: satA: WT -CMC longer RT fragments


title: satA: WT +CMC shorter RT fragments


title: 0.4M CMC 100-115nt long RT fragments

value: SuperScript III


title: satA: WT -CMC shorter RT fragments


title: 0.4M CMC 100-115nt short RT fragments


title: satE: WT -CMC


title: 0.2M CMC 100-115nt long RT fragments


title: -CMC 100-115nt long RT fragments


title: -CMC 100-115nt short RT fragments


title: 0.4M CMC 130-145nt long RT fragments


title: -CMC 130-145nt long RT fragments


title: 0.2M CMC 130-145nt short RT fragments


title: logA: WT +CMC longer RT fragments


title: 0.4M CMC 115-130nt short RT fragments


title: 0.4M CMC 130-145nt short RT fragments


title: 0.2M CMC 130-145nt long RT fragments


title: 0.2M CMC 115-130nt long RT fragments


title: logB: WT +CMC shorter RT fragments


title: -CMC 130-145nt short RT fragments


title: 0.2M CMC 115-130nt short RT fragments


title: -CMC 115-130nt long RT fragments


title: 0.4M CMC 115-130nt long RT fragments


title: -CMC 115-130nt short RT fragments


title: Hela +Serum +CMC E

source_name: HeLa

value: HeLa

value: +Serum


title: Hela +Serum -CMC E


title: Hela +Serum +CMC D


title: Hela -Serum +CMC D

value: -Serum


title: Tumor (TNBC)

city: Milan

first: Heiko

last: Muller

address: Via Adamello 16

country: Italy

institute: Italian Institute of Technology

description:
Tumor (TNBC)
small RNA
processed data file: isomir_ALL_RPKM.xlsx

data_processing:
base-calling by Illumina real time analysis software (RTA)
bcl to fastq conversion by Casava 1.8
adapter removal TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC (TrueSeq_RNA_Primer_3_RA3) with Flexible Adapter remover (FAR,  http://sourceforge.net/projects/theflexibleadap/)
Alignment to custom isoform sequence libraries using Bowtie (--best -v 0).  Custom libraries derived from miRBase 20; comprise all possible 3'-, 5'- and trimmed variants.
isoform counting and RPKM normalization using Isomirage
Genome_build: Custom isoform sequence libraries. The miRNAs used for constructing the custom libraries were derived from miRBase 20. Isoforms were created by adding one, two, or three nucleotides either to the 5' end (isomir5prime) or to the 3' end (isomir3prime) of the base miRNA in all possible combinations of A, C, T, and G. The trimming library was produced by removing nucleotides from the 3' end of the base miRNA down to a size of 18 bases.
Supplementary_files_format_and_content: xlsx formatted isoform expression matrix (RPKM normalized isoform counts)

source_name: Breast Epithelium

growth_protocol: primary cells

extract_protocol:
Total RNA, including small species, was isolated through the miRNeasy mini kit (Qiagen)
One microgram of total RNA was used to prepare Small RNA libraries following the Illumina TruSeqTM Small RNA kit instructions

value: primary breast epithelial cells

tag: tumor stage

value: Triple Negative Breast Cancer


title: 0.2M CMC 100-115nt short RT fragments


title: Normal

description:
Normal
small RNA
processed data file: isomir_ALL_RPKM.xlsx

value: Normal Counterpart


title: Hela +Serum -CMC D


title: Hela -Serum +CMC C


title: Hela -Serum -CMC D


title: Hela +Serum -CMC C


title: Hela -Serum -CMC C


title: Hela +Serum +CMC B


title: Hela -Serum +CMC B


title: Hela +Serum -CMC B


title: Hela -Serum -CMC B


title: Hela +Serum +CMC A


title: Hela -Serum +CMC A


title: Hela +Serum -CMC A


title: Hela -Serum -CMC A


title: DKO-MEF_HITS-CLIP_Cpsf6-1

description:
DKO_MEFs_HITS-CLIP
HITS-CLIP_sample15
processed data file: MEF_dko_cpsf_pooled.bedgraph.txt.gz

tag: strain background

value: Mbnl1/2 KO

value: Mouse embryonic Fibroblasts (MEFs)

tag: clip antibody

value: affinity purified Rabbit polyclonal Cpsf6 (CPSF68) antibody

tag: clip antibody vendor

value: Bethyl Labs

tag: clip antibody cat. #

value: Immunoprecipitated RNA


title: Mouse_quad_HITS-CLIP_Mbnl1-3

description:
WT_mouse_Muscle_HITS-CLIP for Mbnl1
HITS-CLIP_sample12
processed data file: Mbnl1_quad_pooled.wig.gz

source_name: WT_mouse_Muscle_HITS-CLIP for Mbnl1

value: FVB

tag: genotype/variation

value: wild type

tag: tissue

value: Quadriceps

value: Affinity purified Rabbit polyclonal Mbnl1

tag: clip antibody info

value: in-house, known as A2764

tag: molecule subtype


title: WT-MEF_HITS-CLIP_Cpsf6-2

description:
WT_MEFs_HITS-CLIP for Cpsf6
HITS-CLIP_sample14
processed data file: MEF_wt_cpsf_pooled.bedgraph.txt.gz

source_name: WT_MEFs_HITS-CLIP for Cpsf6


title: WT-MEF_HITS-CLIP_Cpsf6-1

description:
WT_MEFs_HITS-CLIP for Cpsf6
HITS-CLIP_sample13
processed data file: MEF_wt_cpsf_pooled.bedgraph.txt.gz


title: Hela +Serum +CMC C

tag: cell line

value: polyA+

value: AMV-RT


title: MEF_HITS-CLIP_Mbnl3-2

description:
MEFs_HITS-CLIP for Mbnl3
HITS-CLIP_sample8
processed data file: HITS-CLIP_MEFs_Mbnl3.wig.gz

source_name: MEFs_HITS-CLIP for Mbnl3

value: affinity purified Rabbit polyclonal Mbnl3

value: in-house as published before (PMID:23660517)


title: MEF_HITS-CLIP_Mbnl3-3

description:
MEFs_HITS-CLIP for Mbnl3
HITS-CLIP_sample9
processed data file: HITS-CLIP_MEFs_Mbnl3.wig.gz


title: Mouse_quad_HITS-CLIP_Mbnl1-2

description:
WT_mouse_Muscle_HITS-CLIP for Mbnl1
HITS-CLIP_sample11
processed data file: Mbnl1_quad_pooled.wig.gz


title: MEF_HITS-CLIP_Mbnl2-3

description:
MEFs_HITS-CLIP for Mbnl2
HITS-CLIP_sample6
processed data file: HITS-CLIP_MEFs_Mbnl2.wig.gz

source_name: MEFs_HITS-CLIP for Mbnl2

value: Mouse monoclonal Mbnl2 antibody (known as 3B4)

value: Santa-cruz


title: MEF_HITS-CLIP_Mbnl3-1

description:
MEFs_HITS-CLIP for Mbnl3
HITS-CLIP_sample7
processed data file: HITS-CLIP_MEFs_Mbnl3.wig.gz


title: MEF_HITS-CLIP_Mbnl1-3

description:
MEFs_HITS-CLIP for Mbnl1
HITS-CLIP_sample3
processed data file: HITS-CLIP_MEFs_Mbnl1.wig.gz

source_name: MEFs_HITS-CLIP for Mbnl1


title: Mouse_quad_HITS-CLIP_Mbnl1-1

description:
WT_mouse_Muscle_HITS-CLIP for Mbnl1
HITS-CLIP_sample10
processed data file: Mbnl1_quad_pooled.wig.gz


title: MEF_HITS-CLIP_Mbnl2-2

description:
MEFs_HITS-CLIP for Mbnl2
HITS-CLIP_sample5
processed data file: HITS-CLIP_MEFs_Mbnl2.wig.gz


title: MEF_HITS-CLIP_Mbnl1-2

description:
MEFs_HITS-CLIP for Mbnl1
HITS-CLIP_sample2
processed data file: HITS-CLIP_MEFs_Mbnl1.wig.gz


title: MEF_HITS-CLIP_Mbnl2-1

description:
MEFs_HITS-CLIP for Mbnl2
HITS-CLIP_sample4
processed data file: HITS-CLIP_MEFs_Mbnl2.wig.gz


title: MEF_HITS-CLIP_Mbnl1-1

description:
MEFs_HITS-CLIP for Mbnl1
HITS-CLIP_sample1
processed data file: HITS-CLIP_MEFs_Mbnl1.wig.gz


title: Adult-HSALR-2

description:
4 weeks old HSA mouse muscle
PolyA-seq_sample14
processed data file: FVB_HSA_pooled.wig.gz

source_name: 4 weeks old HSA mouse muscle

value: HSALR model

tag: age

value: 4 weeks

value: oligodT selected total RNA


title: Adult-WT mouse-2

description:
4 weeks old WT mouse muscle
PolyA-seq_sample12
processed data file: FVB_WT_pooled.wig.gz

source_name: 4 weeks old WT mouse muscle


title: Adult-HSALR-1

description:
4 weeks old HSA mouse muscle
PolyA-seq_sample13
processed data file: FVB_HSA_pooled.wig.gz


title: P1-WT mouse-2

description:
one day old WTmouse muscle
PolyA-seq_sample10
processed data file: FVB_P1_pooled.wig.gz

source_name: one day old WTmouse muscle

value: 1 day


title: Adult-WT mouse-1

description:
4 weeks old WT mouse muscle
PolyA-seq_sample11
processed data file: FVB_WT_pooled.wig.gz


title: DKO-MEF_HITS-CLIP_Cpsf6-2

description:
DKO_MEFs_HITS-CLIP
HITS-CLIP_sample16
processed data file: MEF_dko_cpsf_pooled.bedgraph.txt.gz

value: Mbnl1/2 KO

value: Mouse embryonic Fibroblasts (MEFs)

value: affinity purified Rabbit polyclonal Cpsf6 (CPSF68) antibody

value: Bethyl Labs


title: MEF_Mbnl1/2KO NTsiRNA-2

description:
Mbnl1/2 KO with non-targeting siRNA
PolyA-seq_sample8
processed data file: MEF_DKONTsi_pooled.wig.gz

source_name: Mbnl1/2 KO with non-targeting siRNA

value: Mbnl1/2 KO with non-targeting siRNA


title: MEF_Mbnl1/2KO NTsiRNA-1

description:
Mbnl1/2 KO with non-targeting siRNA
PolyA-seq_sample7
processed data file: MEF_DKONTsi_pooled.wig.gz


title: MEF_Mbnl1/2 KO 3KD-2

description:
Mbnl1/2 KO with Mbnl3 siRNA
PolyA-seq_sample6
processed data file: MEF_DKO3si_pooled.wig.gz

source_name: Mbnl1/2 KO with Mbnl3 siRNA

value: Mbnl1/2 KO with Mbnl3 siRNA


title: MEF_Mbnl1/2 KO (DKO)-1

description:
Mbnl1/2 KO MEFs
PolyA-seq_sample3
processed data file: MEF_DKO_pooled.wig.gz

source_name: Mbnl1/2 KO MEFs


title: MEF_Mbnl1/2 KO 3KD-1

description:
Mbnl1/2 KO with Mbnl3 siRNA
PolyA-seq_sample5
processed data file: MEF_DKO3si_pooled.wig.gz


title: MEF_Mbnl1/2 KO (DKO)-2

description:
Mbnl1/2 KO MEFs
PolyA-seq_sample4
processed data file: MEF_DKO_pooled.wig.gz


title: MEF_WT2

description:
wildtype MEFs
PolyA-seq_sample2
processed data file: MEF_WT_pooled.wig.gz

source_name: wildtype MEFs

value: wild type


title: MEF_WT1

description:
wildtype MEFs
PolyA-seq_sample1
processed data file: MEF_WT_pooled.wig.gz


title: Cortex_control_rep1

description: Control Cortex

source_name: cortex

value: cortex


title: Striatum_Control_rep1

description: Control Stiatum

source_name: striatum

value: striatum


title: Striatum_Htt_rep1

description: Htt Striatum


title: Cortex_Htt_rep1

description: Htt Cortex


title: mTEC R2

status: Public on Sep 04 2014

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

country: United Kingdom

institute: Kennedy Institute of Rheumatology

data_processing:
(1) Alignment: 36bp single end reads were mapped to the mouse genome (mm9) using tophat (version 1.4.1) with the options “ --library-type fr-unstranded --segment-length 18” together with reference junctions and a transcriptome index.
(2) Expression quantitation: FPKM values were calculated using cuffdiff (version 2.0.2) with the options "--upper-quartile-norm --library-type=fr-unstranded --frag-len-mean=200 --frag-len-std-dev=80 --no-effective-length-correction" together with a mask file (ribosomal and mitochondrial rRNA/tRNA) and a gtf file containing the sanitised ensembl 67 reference coding geneset.
Genome_build: mm9
Supplementary_files_format_and_content: A tab-delimited text file containing cuffdiff calculated FPKM values for the seven TEC populations.

source_name: wild type mTEC

growth_protocol: C57BL/6 mice were obtained from Janvier (St Berthevin, France). A novel mouse line, designated AireGFP/+, was generated to target the enhanced green fluorescent protein (EGFP) expression to Aire positive cells. In short, a knock-in targeting vector was used to replace the first exon of the Aire locus with the sequence of EGFP. Following 129/Ola embryonic stem cell (ESC) electroporation and screening for homologous recombinants by Southern blotting and PCR, verified ESC were used for blastocyst injections. Germ-line transmitted heterozygous mice were bred onto a C57BL/6 genetic background. Heterozygous and homozygous mice were born at the expected Mendelian frequency. The transgenic mice displayed a thymic cellularity of lymphoid and stromal cells that were indistinguishable from that of wild type mice. Mice were maintained under specific pathogen-free conditions and according to Swiss federal and institutional regulations.

extract_protocol:
Thymic stromal cells were isolated and sorted according to their cell surface phenotypes. Fragmented thymi were digested repeatedly for 15-20 min at 37 °C with 1mg/ml Collagenase/Dispase (Roche Diagnostic) and 100µg/ml DNaseI (Roche Diagnostic) in HBSS containing 2% FCS (Perbio), to obtain single cell suspensions. After the final digest, cells were pooled and labelled with biotinylated anti-EpCAM for positive enrichment by AutoMACS system (Miltenyi Biotec), and stained using the following directly labelled antibodies and reagents: FITC-anti-IAb (clone AF6-120.1, BioLegend), PE-anti-Ly51 (clone 6C3, BioLegend), PECy7-anti-CD45 (clone 30-F11, BioLegend), APC-Cy7-anti-I-A/E (clone M5/114.15.2, BioLegend), biotinylated anti-EpCAM (clone G8.8, DSHB, University of Iowa), Streptavidin-labelled PerCP-Cy5.5 (BioLegend) and Cy5-UEA1 (Vector Laboratories). The cells were exposed to 4’, 6-diamidino-2-phenylindole (DAPI) to identify dead cells and then sorted by flow cytometry (FACSAira, BD Biosciences) achieving a TEC purity of over 93%. Sorted TEC were pelleted, lysed in the RLT lysis buffer of the RNeasy Micro Kit (Qiagen), or cross-linked for ChIP and kept at -80 °C until use. Total RNA was isolated from sorted TEC using the RNeasy Micro Kit.
PolyA+ selected RNA-seq libraries were generated from 1 µg of total RNA by mRNA-Seq Sample Prep Kit (Illumina).

treatment_protocol: None.

tag: aire locus

value: wildtype

value: 1 week

value: thymus

tag: celltype

value: medullary thymic epithelial cell (mTEC)

tag: facs profile

value: CD45- EpCAM+ MHCII+ Ly51- UEA+


title: mature Aire-knockout mTEC R2

source_name: mature Aire-knockout mTEC

value: GFP/GFP (GFP +ve)

value: 4 weeks

value: CD45- EpCAM+ MHCIIhi Ly51- UEA+ GFP+


title: mTEC R1


title: mature mTEC R2

source_name: wild type mature mTEC

value: CD45- EpCAM+ MHCIIhi Ly51- UEA+


title: P1-WT mouse-1

description:
one day old WTmouse muscle
PolyA-seq_sample9
processed data file: FVB_P1_pooled.wig.gz

value: FVB

value: 1 day

value: Quadriceps

value: oligodT selected total RNA


title: mature mTEC R1


title: FMsgn1_Chipseq

city: Frederick

first: Ravindra B

last: Chalamalasetty

state: MD

address: 1050 Boyles St, Bldg 539,Rm205

department: Cancer and Developmental Biology

institute: National Cancer Institute-Frederick

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using ELAND algorithm
Quality check was carried out using FASTQC on the mapped reads
MACS Version 1.4.1 (Model-based analysis of Chip-seq, Zhang et al., 2008) was used to identify the peak enrichments in Flag-Msgn1 compared to the Input DNA. Peak calling parameters used : p<1e-5, Bandwidth: 300bp, MFOLD=10,30.
Genomic Regions Enrichment of Annotations Tool (GREAT) was used to carry out assessment of motif enrichment
Genome_build: mm9
Supplementary_files_format_and_content: BED format files were generated containing the 4087 peaks identified using MACS. Information include: chromosome name, start position of peak, end position of peak, PeakID, -10*log10(pvalue) for the peak region (e.g. pvalue is 1e-10, then this value should be 100).

source_name: A2lox FMsgn1 embryonic stem cells

growth_protocol: A2loxFMsgn1 ES cells were grown in DMEM, 15%FBS, Pen/Strep and LIF on mitomycin treated mouse embryonic fibroblasts. For EB differentiation, ESC were plated on 10cm Petri dishes at a density of 2.5 million cells per plate in 15ml of DMEM, 10% FBS, 1x NEAA, Pen/Strep, 2-Mercaptoethanol and 50ug/ml ascorbic acid (Sigma).

extract_protocol:
For Chromatin Immunoprecipitation-sequencing (CHIP-seq), day2 EBs were induced with Dox for 36h and fixed in 1% formaldehyde solution for 15 min and quenched with 0.125M Glycine and flash-frozen. Sonicated nuclear extracts were incubated with anti-Flag M2 antibody (Sigma) and antibody-chromatin complexes were extracted using prepared Staph A cells (Pansorbin, Calbiochem).
Libraries were prepared from immunoprecipitated DNA using illumina Chip-seq DNA sample prep kit (illumina) according to manufacturer’s instructions. Immunoprecipitated enriched DNA was end repaired converting the overhangs into phosphorylated blunt ends, using T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase (PNK). To the blunt phosphorylated 3’ end of DNA Fragments, ‘A’ base was added using Klenow fragment (3’ to 5’ exo minus) allowing the ligation of DNA fragments to adapters, which have a single ‘T’ base overhang at their 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. DNA libraries were sequenced on Genome Analyzer II according to manufacturer’s instructions.

treatment_protocol: After 2 days of differentiation, EBs were then transferred to 6 well ultra low attachment dishes (Corning) and expression of FLAG-Msgn1 was induced using 1ug/ml Dox. Samples were collected at 36h after induction.

tag: strain

tag: timepoint

value: Day2 embryoid bodies induced with dox for another 36h

tag: chip-antibody

value: anti-Flag M2 (Sigma, Cat#F3165)


title: angmgrna_RNAseq

city: Armilla

first: Elena

last: Gómez-Díaz

state: Granada

address: Avda. del Conocimiento, 17

department: Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN)

country: Spain

institute: Spanish National Research Council (CSIC)

data_processing:
Reads were trimmed using FASTX-Toolkit based on quality scores on both ends.
ChIP-seq reads were aligned to the Agam PEST 4.1 genome assembly using Bowtie version 1.0.0 with the following configuration: -t -m 1
Peak calling of H3K27me3 was performed using SICER with the following configuration: window size of 200, gap size 600 and FDR cutoff of 1x10e-5
Peak calling of H3K27ac was performed using MACS version 1.4 with the following configuration: -f SAM -g 2.73e+8 -p 1e-5 -s 50 -w --single-profile.
RNA-seq reads were aligned to the Agam PEST 4.1 genome assembly using TopHat version 2.0.10 with the following configuration: -p 8 --bowtie1 -r 60 --mate-std-dev 47 --segment-length 20 --library-type=fr-firststrand -G
Transcript assembly and quantification was performed using Cufflinks 2.1.1 with the following configuration: -p 8 -g --library-type=fr-firststrand -b --total-hits-norm
Genome_build: AgamP4
Supplementary_files_format_and_content: Wig files were generated using MACS 1.4
Supplementary_files_format_and_content: BED files were generated using MACS1.4 or SICER
Supplementary_files_format_and_content: Combined GTF file generated using CuffCompare on midgut and salivary glands merged transcripts obtained from Cufflinks and that include a provisional list of novel and conserved transcripts relative to the most recent genome annotation for A. gambiae, AgamP4.1.
Supplementary_files_format_and_content: angcuffdiffcombined_genes.fpkm_tracking:  Data processed from Cufflinks/Cuffdiff. Include FPKM values for both novel and conserved transcripts.
Supplementary_files_format_and_content: angcuffdiffconserved_genes.fpkm_tracking: Data processed from Cufflinks/Cuffdiff. Include FPKM values for conserved transcripts based on genome assembly Agam PEST 4.1

organism: Anopheles gambiae

source_name: A. gambiae midgut cells

extract_protocol: Total RNA was extracted from fresh mosquito tissues (~25 midguts and ~ 50 salivary glands) using the mirVana™ RNA Isolation Kit (Ambion®) according to the manufacturer’s protocol. Illumina libraries were prepared and sequenced at the HudsonAlpha Institute for Biotechnology, using an Illumina HiSeq2000 sequencer. Standard directional RNA-seq library construction, 50 bp paired end reads with ribosomal reduction (RiboMinus™ Eukaryote Kit, Ambion®).

treatment_protocol: A. gambiae (strain Kisumu) mosquitoes were maintained at the insectarium under standard rearing conditions (27 ± 1 °C, 70 ± 10 % RH and 16L: 8D photoperiod). Blood- fed adult females were allowed to lay eggs. On the day of hatching, larvae were seeded into plastic trays (25cm x 35cm x 7cm) containing one liter of mineral water at a density of 300 individuals per tray. Larvae were provided with 200 mg of TetraMin® fish flakes the day after hatching, and, from then on, 400 mg TetraMin every two days until pupation. On pupation, trays were placed inside an emergence cage (27 x 40 x 35 cm) and provided with an ad libitum source of 10% sugar solution for the emerged adults. Dissection of the midguts and the salivary glands was performed on adult females aged 6-8 days. Tissues were maintained in ice-cold Schneider’s insect culture medium, and fresh tissues were immediately processed.

value: Midguts

value: KISUMU


title: angmgH3K27me3_ChIPseq

description: Chromatin IP against H3K27me3

extract_protocol: Sequencing libraries were prepared following the protocol described by Bowman et al. BMC Genomics 2013, 14:466  doi:10.1186/1471-2164-14-4662013. ChIP libraries were sequenced at the HudsonAlpha Institute for Biotechnology using an Illumina HiSeq2000 sequencer.

tag: chip antibody

value: H3K27me3 (Millipore 07-449)


title: immature mTEC R1

source_name: wild type immature mTEC

tag: strain background

value: wildtype

value: CD45- EpCAM+ MHCIIlo Ly51- UEA+


title: immature mTEC R2

value: thymus

value: medullary thymic epithelial cell (mTEC)


title: mature Aire-positive mTEC R1

source_name: mature Aire-positive mTEC

value: GFP/Aire (GFP +ve)


title: angmginput_ChIPseq

description: Chromatin IP control


title: angmgH3K27ac_ChIPseq

description: Chromatin IP against H3K27ac


title: mature Aire-knockout mTEC R1

value: GFP/GFP (GFP +ve)

value: 4 weeks


title: mature Aire-positive mTEC R2

value: CD45- EpCAM+ MHCIIhi Ly51- UEA+ GFP+


title: angsgrna_RNAseq

source_name: A. gambiae salivary gland cells

value: Salivary glands


title: MCF7_Deproteinized_DNase

city: Durham

first: Christopher

middle: L

last: Frank

state: NC

address: 101 Science Dr.

institute: Duke University

data_processing:
Basecalls performed using CASAVA v1.8
First 20bp of DNase-seq reads mapped to hg19 with BWA, allowing up to 2 mismatches
Putative PCR artifacts filtered from mapped DNase-seq reads
We counted the number of DNA 6-mers centered at each DNase cleavage site (between the 3rd and 4th bp) and calculated the relative frequency of each 6-mer. These relative frequencies are normalized by the relative frequency of each 6-mer in the human genome and genomic relative frequencies are corrected for regions that are mappable using our DNase-seq protocol.
Genome_build: hg19
Supplementary_files_format_and_content: plain text file with two columns: DNA 6-mer and corresponding cleavage propensity

source_name: cultured MCF7 cells (ATCC HTB-22)

growth_protocol: K562 or MCF7 cells were cultured in RPMI-1640 or DMEM media, respectively, + 10% FBS

extract_protocol:
Deproteinized genomic DNA was isolated from ~20 million K562 or MCF7 cells using a DNeasy Blood and Tissue kit (Qiagen). Isolated total DNA was then subjected to two phenol-chloroform extractions followed by ethanol precipitation to ensure removal of bound protein.
DNase I digestions were performed in 120μL solution with ~50μg of deproteinized DNA. Digestions were punctuated by addition of 50mM EDTA and 15 min incubation at 75°C. Digestions performed with 1.2U and 2.4U total DNase I were selected based on .8% agarose gel sizing to be similar to typical DNase-seq assay digestions and pooled for the two cell lines separately. Libraries were constructed from pooled digests as described (Song and Crawford 2010; PMID:20150147).

value: ATCC HTB-22

tag: cell type


title: mature Aire-negative mTEC R1

source_name: mature Aire-negative mTEC

value: GFP/GFP (GFP -ve)

value: CD45- EpCAM+ MHCIIhi Ly51- UEA+ GFP-


title: K562_Deproteinized_DNase

source_name: cultured K562 cells (ATCC CCL-243)

value: ATCC CCL-243


title: mature Aire-negative mTEC R2


title: cTEC R2

source_name: wild type cTEC

value: 1 week

value: cortical thymic epithelial cell (cTEC)

value: CD45- EpCAM+ MHCII+ Ly51+ UEA-


title: cTEC R1


title: HeLa + PRPF8 RNAi (2)

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

description: 50 bp single end

data_processing:
Basecalling software: Illumina RTA 1.13.48
Alignment: TopHat 1.3.1. for samples 1 and 2, reads are mapped uniquely to genome with 0 to 2 errors
Alignment: TopHat 1.4.1. for samples 3 to 8, trimming by 6 bp, reads are mapped uniquely to genome with 0 to 2 errors
Transcriptome-wide identification of retained introns was performed using our method which is described in the paper.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: 2 tab delimited text files; listing all annotated intronic regions (retained and not retained) with read counts for all samples as described in the paper

source_name: cervical carcinoma

growth_protocol: HeLa cells were growing asynchronously

extract_protocol:
Cells were resuspended in Trizol and total RNA isolated. PolyA containing RNAs were isolated using Dynabeads, and RNA was fragmented and reversely transcribed with Superscript III followed by second strand synthesis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HeLa cells were transfected with siRNAs for 48 hours

value: HeLa Kyoto

tag: bac expression

tag: RNAi

value: PRPF8 RNAi


title: HeLa + PRPF8 RNAi (1)

description: 50 bp single end


title: FMsgn1_Input DNA

value: Day2 embryoid bodies induced with dox for another 36h


title: HeLa + SNW1 RNAi (1)

description: 50 bp single end

value: SNW1 RNAi


title: HeLa + control RNAi (1)

description: 50 bp single end

value: control RNAi


title: HeLa + control RNAi (2)

description: 50 bp single end


title: mhcIIhi4wk-wildtype-cell_B88

description:
mtec_12028_R88
PolyA RNA

data_processing:
(1) Alignment: Reads were aligned using the GSNAP (version 2014-01-21) algorithm with the parameters “ -N1 --maxsearch=1000 -w 500000 --pairexpect=100 --pairdev=200 -n100” to a custom genome based on the mm10 version of the mouse genome and containing the ERCC spike-in sequences.
(2) Expression quantitation: Gene expression was quantitated separately for each cell using Cufflinks (version 2.1.1) against ENSEMBL 74 reference annotations with the parameters “ --multi-read-correct --max-intron-length 500000 --library-type=fr-unstranded --frag-bias-correct --no-effective-length-correction --max-bundle-length 10000000 --max-bundle-frags 2000000 --min-intron-length 50 --max-mle-iterations 10000”
(3) Copy numbers were calculated for protein-coding genes based on per-cell normalisation curves determined from known spike-in copy number and observed spike-in FPKMs. The curves were obtained from a first order polynomial linear model forced through the plot origin for log 10 (x+1) transformed data.
(4) Cells were filtered to retain only those expressing 3,000-10,000 protein-coding genes.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: A tab-delimited text file containing per-cell copy number for protein-coding genes (rows) for each single cell (columns).

source_name: Mature, MHCII-high medullary thymic epithelial cell

growth_protocol: C57BL/6 mice were obtained from Janvier (St. Berthevin, France).

extract_protocol:
Thymic stromal cells were isolated and sorted according to their cell surface phenotypes. Fragmented thymi were digested repeatedly for 15-20 min at 37 °C with 1mg/ml Collagenase/Dispase (Roche Diagnostic) and 100µg/ml DNaseI (Roche Diagnostic) in HBSS containing 2% FCS (Perbio), to obtain single cell suspensions. After the final digest, cells were pooled and labelled with biotinylated anti-EpCAM for positive enrichment by AutoMACS system (Miltenyi Biotec), and stained using the following directly labelled antibodies and reagents: FITC-anti-IAb (clone AF6-120.1, BioLegend), PE-anti-Ly51 (clone 6C3, BioLegend), PECy7-anti-CD45 (clone 30-F11, BioLegend), APC-Cy7-anti-I-A/E (clone M5/114.15.2, BioLegend), biotinylated anti-EpCAM (clone G8.8, DSHB, University of Iowa), Streptavidin-labelled PerCP-Cy5.5 (BioLegend) and Cy5-UEA1 (Vector Laboratories). The cells were exposed to 4’, 6-diamidino-2-phenylindole (DAPI) to identify dead cells and then sorted by flow cytometry (FACSAira, BD Biosciences). Mature, MHCII-high mTEC were sorted into media+FCS and stored on ice for 2-3 hours before Fluidigm C1 analysis.
Single cells were isolated and amplified on the Fluidigm C1 platform at the Sanger Institute/EBI Single Cell Genomics Centre. Briefly, a pool of FACS-sorted TECs (220K cells/ml) were loaded on two (denoted by the prefixes "A" and "B") medium chips (designed for capture of cells between 10-17 µM in diameter). After loading and capture, chips were inspected under the microscope and the presence of a single cell at capture sites was confirmed. Cell lysis, cDNA synthesis and subsequent PCR amplification was performed using the SMARTer Ultra Low RNA Kit (Clontech) for the C1 platform as per the manufacturer’s instructions (Clontech/Fluidigm). The cell lysis buffer (20 µL) was supplemented with 1 µL of a 1:400 dilution of the External RNA Controls Consortium (ERCC) spike-in Mix 1 (Invitrogen). Indexed Libraries from the 96 samples harvested from each chip were prepared using the Nextera XT kit (Illumina). Multiplexed libraries from each chip were sequenced over two lanes on a HiSeq 2500 (Illumina) at the Wellcome Trust Sanger Institute run in fast mode to generate 100bp paired-end reads.

tag: strain/background

value: wildtype

value: thymus

value: medullary thymic epithelial cell

value: CD45- EpCAM+ MHCIIhi Ly51- UEA+


title: mhcIIhi4wk-wildtype-cell_B95

description:
mtec_12028_R95
PolyA RNA

value: 4 weeks

tag: tissue


title: mhcIIhi4wk-wildtype-cell_B90

description:
mtec_12028_R90
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B91

description:
mtec_12028_R91
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B85

description:
mtec_12028_R85
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B84

description:
mtec_12028_R84
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B92

description:
mtec_12028_R92
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B82

description:
mtec_12028_R82
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B86

description:
mtec_12028_R86
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B81

description:
mtec_12028_R81
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B87

description:
mtec_12028_R87
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B79

description:
mtec_12028_R79
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B75

description:
mtec_12028_R75
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B77

description:
mtec_12028_R77
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B80

description:
mtec_12028_R80
PolyA RNA


title: HeLa + SNW1 RNAi (2)

description: 50 bp single end


title: HeLa + SNW1 RNAi

description: 100 bp paired end


title: HeLa + mSnw1-LAP + SNW1 RNAi

description: 100 bp paired end

value: Mus musculus Snw1-LAP


title: mhcIIhi4wk-wildtype-cell_B89

description:
mtec_12028_R89
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B69

description:
mtec_12028_R69
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B67

description:
mtec_12028_R67
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B71

description:
mtec_12028_R71
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B72

description:
mtec_12028_R72
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B66

description:
mtec_12028_R66
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B96

description:
mtec_12028_R96
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B74

description:
mtec_12028_R74
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B70

description:
mtec_12028_R70
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B73

description:
mtec_12028_R73
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B68

description:
mtec_12028_R68
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B78

description:
mtec_12028_R78
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B53

description:
mtec_12028_R53
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B51

description:
mtec_12028_R51
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B52

description:
mtec_12028_R52
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B59

description:
mtec_12028_R59
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B60

description:
mtec_12028_R60
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B56

description:
mtec_12028_R56
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B61

description:
mtec_12028_R61
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B63

description:
mtec_12028_R63
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B65

description:
mtec_12028_R65
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B57

description:
mtec_12028_R57
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B62

description:
mtec_12028_R62
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B54

description:
mtec_12028_R54
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B64

description:
mtec_12028_R64
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B55

description:
mtec_12028_R55
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B50

description:
mtec_12028_R50
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B33

description:
mtec_12028_R33
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B34

description:
mtec_12028_R34
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B36

description:
mtec_12028_R36
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B44

description:
mtec_12028_R44
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B48

description:
mtec_12028_R48
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B40

description:
mtec_12028_R40
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B47

description:
mtec_12028_R47
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B49

description:
mtec_12028_R49
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B45

description:
mtec_12028_R45
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B42

description:
mtec_12028_R42
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B41

description:
mtec_12028_R41
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B35

description:
mtec_12028_R35
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B37

description:
mtec_12028_R37
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B32

description:
mtec_12028_R32
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B43

description:
mtec_12028_R43
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B39

description:
mtec_12028_R39
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B24

description:
mtec_12028_R24
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B38

description:
mtec_12028_R38
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B46

description:
mtec_12028_R46
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B29

description:
mtec_12028_R29
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B26

description:
mtec_12028_R26
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B30

description:
mtec_12028_R30
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B31

description:
mtec_12028_R31
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B28

description:
mtec_12028_R28
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B27

description:
mtec_12028_R27
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B25

description:
mtec_12028_R25
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B22

description:
mtec_12028_R22
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B21

description:
mtec_12028_R21
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B20

description:
mtec_12028_R20
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B23

description:
mtec_12028_R23
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B18

description:
mtec_12028_R18
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B19

description:
mtec_12028_R19
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B06

description:
mtec_12028_R6
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B10

description:
mtec_12028_R10
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B13

description:
mtec_12028_R13
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B08

description:
mtec_12028_R8
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B16

description:
mtec_12028_R16
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B14

description:
mtec_12028_R14
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B15

description:
mtec_12028_R15
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B17

description:
mtec_12028_R17
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B05

description:
mtec_12028_R5
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B11

description:
mtec_12028_R11
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B07

description:
mtec_12028_R7
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B12

description:
mtec_12028_R12
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B09

description:
mtec_12028_R9
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B01

description:
mtec_12028_R1
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B02

description:
mtec_12028_R2
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B03

description:
mtec_12028_R3
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_B04

description:
mtec_12028_R4
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A95

description:
mtec_12027_R95
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A96

description:
mtec_12027_R96
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A94

description:
mtec_12027_R94
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A93

description:
mtec_12027_R93
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A88

description:
mtec_12027_R88
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A91

description:
mtec_12027_R91
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A89

description:
mtec_12027_R89
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A86

description:
mtec_12027_R86
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A87

description:
mtec_12027_R87
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A85

description:
mtec_12027_R85
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A92

description:
mtec_12027_R92
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A82

description:
mtec_12027_R82
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A79

description:
mtec_12027_R79
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A81

description:
mtec_12027_R81
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A78

description:
mtec_12027_R78
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A76

description:
mtec_12027_R76
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A74

description:
mtec_12027_R74
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A84

description:
mtec_12027_R84
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A70

description:
mtec_12027_R70
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A71

description:
mtec_12027_R71
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A72

description:
mtec_12027_R72
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A73

description:
mtec_12027_R73
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A77

description:
mtec_12027_R77
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A69

description:
mtec_12027_R69
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A64

description:
mtec_12027_R64
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A66

description:
mtec_12027_R66
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A68

description:
mtec_12027_R68
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A65

description:
mtec_12027_R65
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A75

description:
mtec_12027_R75
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A62

description:
mtec_12027_R62
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A67

description:
mtec_12027_R67
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A56

description:
mtec_12027_R56
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A50

description:
mtec_12027_R50
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A48

description:
mtec_12027_R48
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A52

description:
mtec_12027_R52
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A51

description:
mtec_12027_R51
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A55

description:
mtec_12027_R55
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A47

description:
mtec_12027_R47
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A58

description:
mtec_12027_R58
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A46

description:
mtec_12027_R46
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A49

description:
mtec_12027_R49
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A45

description:
mtec_12027_R45
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A44

description:
mtec_12027_R44
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A61

description:
mtec_12027_R61
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A36

description:
mtec_12027_R36
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A42

description:
mtec_12027_R42
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A41

description:
mtec_12027_R41
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A40

description:
mtec_12027_R40
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A37

description:
mtec_12027_R37
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A39

description:
mtec_12027_R39
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A60

description:
mtec_12027_R60
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A30

description:
mtec_12027_R30
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A34

description:
mtec_12027_R34
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A38

description:
mtec_12027_R38
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A31

description:
mtec_12027_R31
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A32

description:
mtec_12027_R32
PolyA RNA


title: WT Sperm sRNA

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

data_processing:
Adapter sequences were removed from raw sequence reads using crossmatch with a minimum match parameter of 5.
siRNA sequencing frequencies for 100 base windows along all five chromosomes were calculated by summation of the per-library sequencing frequencies of 21 and 24 nt siRNAs matching with 100% identity within the window by the number of times they matched the genome as a whole. Because the results of these calculations are on different scales, on the basis of the depth of each sequence library, a layer of per-library normalization based on the sum values of all small RNAs matching the genome was implemented.
Genome_build: TAIR8
Supplementary_files_format_and_content: UCSC wiggle format coverage files

organism: Arabidopsis thaliana

source_name: Sperm

extract_protocol: Small RNAs of 19-28nt were size selected by denaturing 15% PAGE, and cloned as previously described (Brennecke et al., 2007). Following ligation, small RNA libraries were reverse transcribed, PCR-amplified using the forward PCR primer (5’AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACG 3’) and the reverse PCR primer (5’ CAAGCAGAAGACGGCATACGATTGATGGTGCCT ACAG3’) for 22 cycles using proofreading Taq polymerase, and the products of 105 to 120bp were isolated.

tag: genotype

value: wild type

value: sperm

tag: cultivar

value: Columbia


title: mhcIIhi4wk-wildtype-cell_A28

description:
mtec_12027_R28
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A33

description:
mtec_12027_R33
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A27

description:
mtec_12027_R27
PolyA RNA


title: ddm1 Inflorescence sRNA

source_name: Inflorescence

value: inflorescence


title: mhcIIhi4wk-wildtype-cell_A43

description:
mtec_12027_R43
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A25

description:
mtec_12027_R25
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A23

description:
mtec_12027_R23
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A24

description:
mtec_12027_R24
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A18

description:
mtec_12027_R18
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A17

description:
mtec_12027_R17
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A16

description:
mtec_12027_R16
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A15

description:
mtec_12027_R15
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A13

description:
mtec_12027_R13
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A29

description:
mtec_12027_R29
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A12

description:
mtec_12027_R12
PolyA RNA


title: Col20GC3

city: Harpenden

first: Dana

middle: Reid

last: MacGregor

state: Hertfordshire

address: Rothamsted Research

department: Biointeractions and Crop Protection

institute: Rothamsted Research

data_processing:
Samples are pre-filtered using Bowtie to remove reads matching PhiX control sequence.
Samples were then filtered using the fastq-mcf program from the ea-utils package (http://code.google.com/p/ea-utils/)
Spike-in reads were removed using Bowtie and the lower limit of detection quantified using custom scripts.
The remaining reads were aligned using Tophat v1.4.1 and the following parameters -I 10000 -r 50 --mate-std-dev 100 –library-type fr-unstranded.
The Cufflinks package was used to quantify gene and isoform abundance using the -G flag. The 17 cuffcompare and cuffdiff components of Cufflinks were used to quantify gene and isoform differential expression (Trapnell et al., 2012).
All other settings were as per the default settings.  Further analysis was performed using the cummeRbund package (Trapnell et al., 2012).
Genome_build: TAIR9: GCF_000001735.2
Supplementary_files_format_and_content: TopHat output files accepted_hits.bam and CuffLinks output files _genes.fpkm_tracking

source_name: Col green cotyledon stage seeds

growth_protocol: Plants were grown until flowering at 22°C under standard long days using fluorescent white light at 80 to 100 μmolm−2s−1 until anthesis of the first flowers. Once flowering, plants were transferred to growth cabinets running the same conditions, but with the indicated seed maturation temperatures and left until harvesting at CT5 - CT7

extract_protocol:
150 mg of seed (based on dry seed weight) was ground and extracted with 1 ml of frozen XT buffer (0.2M sodium borate, 30 mM EGTA, 1% SDS, 1% sodium deoxycholate, 2% polyvinylpyrollidone, 10 mM DTT, and 1% IGEPAL [pH 9.0]) in a pestle and mortar. This was allowed to thaw and was treated with 40 μl proteinase K (PCR grade, Roche, UK) for 90 min at 42°C; precipitation on ice followed for 1 hr with 80 μl 2M potassium chloride. The supernatant was collected after centrifugation at 4°C. The RNA was precipitated from the supernatant at −20°C for 2 hr with 360 μl 8M lithium chloride. The RNA was collected by centrifugation at 4°C and redissolved in 100 μl water. The RNA was further purified via the clean-up protocol of the RNeasy Plant RNA isolation kit (Qiagen) according to the manufacturer's protocol.
5 μg RNA was submitted to sequencing using standard protocols for Illumina TruSeq™ technologies RS-122-2001 | TruSeq™ RNA Sample Prep Kit v2. Data were generated on Illumina HiSeq 2000. The input material contains 1-2% PhiX which is used as a control.

tag: ecotype

value: Col

tag: Stage

value: Green cotyledon stage developing seed

tag: maturation temperature

tag: time point

value: 5-7hrs after dawn


title: Col20GC2


title: mhcIIhi4wk-wildtype-cell_A11

description:
mtec_12027_R11
PolyA RNA

tag: age

tag: aire locus

tag: facs profile


title: mhcIIhi4wk-wildtype-cell_A08

description:
mtec_12027_R8
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A10

description:
mtec_12027_R10
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A07

description:
mtec_12027_R7
PolyA RNA


title: iSPCH 8h rep2

city: Stanford

first: On Sun

last: Lau

address: 371 Serra Mall, Rm 210

institute: Stanford University

data_processing:
Basecalls were performed using CASAVA version 1.8.
Reads were aligned to the TAIR10 genome assembly via Tophat, where an initial alignment is followed by mapping to known exon junctions.
Differential expression between SPCH induction samples and their WT counterparts was identified via DESeq
Genome_build: TAIR10.18
Supplementary_files_format_and_content: Tab-delimited text file include mean normalized counts for each sample

source_name: Whole seedlings

extract_protocol:
Total RNA from seedlings was extracted using RNeasy Plant Mini Kit with DNaseI digestion (QIAGEN)
Barcoded mRNA libraries were constructed using Illumina Poly-A Purification TruSeq library reagents and protocols.

tag: genotype/variation

tag: developmental stage

value: 4-day-old light grown seedlings

tag: treatment

value: Incubated in 10 uM beta-estradiol for 8h


title: Col15GC3


title: Col20GC1


title: mhcIIhi4wk-wildtype-cell_A06

description:
mtec_12027_R6
PolyA RNA

tag: cell type


title: iSPCH 8h rep1


title: Col15GC2


title: mhcIIhi4wk-wildtype-cell_A09

description:
mtec_12027_R9
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A05

description:
mtec_12027_R5
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A21

description:
mtec_12027_R21
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A04

description:
mtec_12027_R4
PolyA RNA


title: mhcIIhi4wk-wildtype-cell_A19

description:
mtec_12027_R19
PolyA RNA


title: iSPCH 6h rep2

value: Incubated in 10 uM beta-estradiol for 6h


title: mhcIIhi4wk-wildtype-cell_A03

description:
mtec_12027_R3
PolyA RNA


title: iSPCH 0h rep2

value: Not treated


title: mhcIIhi4wk-wildtype-cell_A02

description:
mtec_12027_R2
PolyA RNA

value: wildtype


title: Col15GC1


title: iSPCH 6h rep1


title: iSPCH 0h rep1


title: WT 8h rep2

value: Col (WT control)


title: WT 8h rep1


title: WT 6h rep1


title: WT 6h rep2


title: WT 0h


title: Treg CNS2 wt Foxp3 high rep1

last: Benner

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: PolyA+, unstranded RNA-Seq (SE100)

data_processing:
Reads from all libraries were mapped to the mouse genome (mm9) using STAR (v2.2.0c). To calculate gene expression, read counts in the exons of RefSeq transcripts where calculated using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: rpkm.txt.gz - tab-delimited text file with RPKM values from all experiments and gene annotation information for RefSeq transcripts

source_name: Treg CNS2 wt Foxp3 high

growth_protocol: Total CD4+ T cells were purified from mouse lymph nodes and spleens with the Dynabeads FlowComp Mouse CD4 kit (Invitrogen). Foxp3GFP+ CD4+ T cells and naive CD4+ T cells (CD62L+ CD44- CD4+) were further purified from total CD4+ T cells by sorting on a BD FACSAria cell sorter. Intracellular staining for cytokines and Foxp3 used the Foxp3 staining kit (eBiosciences). Cells were stimulated for 4 h with PMA (phorbol 12-myristate 13-acetate; 50 ng/ml; Sigma) and ionomycin (1 µg/ml; Sigma) and treated with for an additional 1 h with Golgi-Plug (BD Biosciences) before intracellular staining for cytokines.

extract_protocol:
RNA was extracted with the TRIzol Reagent (Life Technologies) from Foxp3hi CD4+ and Foxp3lo CD4+ Treg cells FACS-purified from male CNS2- mice and age-matched male Foxp3GFP mice.
Multiplexed libraries were constructed using the Illumina TruSeq RNA Sample Prep Kit. Libraries were sequenced on the Illumina HiSeq 2500 according to the manufacturer's instructions.

tag: strain

value: Regulatory T (Treg) cells

tag: fox3 expression

value: high


title: Treg CNS2 wt Foxp3 low rep1

description: PolyA+, unstranded RNA-Seq (SE100)

source_name: Treg CNS2 wt Foxp3 low

value: low


title: Treg CNS2 wt Foxp3 high rep2

description: PolyA+, unstranded RNA-Seq (SE100)


title: Treg CNS2-/- Foxp3 low rep2

description: PolyA+, unstranded RNA-Seq (SE100)

source_name: Treg CNS2-/- Foxp3 low


title: wildtype-input-2

data_processing:
(1) Alignment: 50bp, paired-end reads were mapped to the mouse genome (mm9) using bwa (version 0.5.9) with the options "aln -l 25 -k 2 -n 0.1 -q 20 "
(2) Duplicate read pairs were removed using Picard with the command "MarkDuplicates REMOVE_DUPLICATES=true"
(3) Normalised Bedgraph files were prepared for ChIP and input samples using the macs2 (https://github.com/taoliu/MACS/) algorithm with the "callpeak -B --SPMR" options.
(4) For each sample, enrichment over input was calculated using the macs2 algorithm with the "bdgcmp -m FE" options.
(5) After conversion to Wig format, the average enrichment over replicates was caclulated using the "wigmath.Average" function provided by java-genomics-toolkit
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files containing the (average) enrichment over input for the ChIP'ed histone modifications.

source_name: wildtype-input

growth_protocol: C57BL/6 mice were obtained from Janvier (St Berthevin, France). Mice were maintained under specific pathogen-free conditions and according to Swiss federal and institutional regulations.

extract_protocol:
Mature mTEC were isolated and sorted according to their cell surface phenotype. Fragmented thymi were digested repeatedly for 15-20 min at 37 °C with 1mg/ml Collagenase/Dispase (Roche Diagnostic) and 100µg/ml DNaseI (Roche Diagnostic) in HBSS containing 2% FCS (Perbio), to obtain single cell suspensions. After the final digest, cells were pooled and labelled with biotinylated anti-EpCAM for positive enrichment by AutoMACS system (Miltenyi Biotec), and stained using the following directly labelled antibodies and reagents: FITC-anti-IAb (clone AF6-120.1, BioLegend), PE-anti-Ly51 (clone 6C3, BioLegend), PECy7-anti-CD45 (clone 30-F11, BioLegend), APC-Cy7-anti-I-A/E (clone M5/114.15.2, BioLegend), biotinylated anti-EpCAM (clone G8.8, DSHB, University of Iowa), Streptavidin-labelled PerCP-Cy5.5 (BioLegend) and Cy5-UEA1 (Vector Laboratories). The cells were exposed to 4’, 6-diamidino-2-phenylindole (DAPI) to identify dead cells and then sorted by flow cytometry (FACSAira, BD Biosciences) achieving a TEC purity of over 93%. Chromatin immunoprecipitation (ChIP) was performed as previously described (Adli M, Bernstein BE. 2011. Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. Nat Protoc 6(10): 1656-1668)  with the following modifications: protein G magnetic beads (Dynabeads, Life Technologies) were used to capture antibody-chromatin complexes. The captured complexes were washed four times with wash buffer (0.1 % SDS, 1 % Triton X-100, 0.1 % deoxycholate, 20 mM Tris- HCl (pH 8), 1 mM EDTA, 0.5 mM EGTA) containing 150 mM NaCl, once with wash buffer containing 500 mM NaCl, and finally once with LiCl wash buffer (250 mM LiCl, 1 % NP-40, 1%  deoxycholate, 10 mM Tris- HCl (pH 8), 1 mM EDTA).  Antibodies used were anti-H3K4me3 (ab8580, Abcam) and anti-H3K27me3 (#9733, Cell Signalling).
ChIP-seq libraries were prepared with TruSeq ChIP Sample Preparation Kit (Illumina) and 50bp, paired-end reads were sequenced on an Illumina-HiSeq. For more information contact the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics, Oxford.

tag: strain background

value: 4 weeks

value: thymus

value: mature mTEC

value: CD45- EpCAM+ MHCIIhi Ly51- UEA+


title: Col ChIP-Seq

description: Sample 2

data_processing:
Basecalls were performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the TAIR10.18 genome assembly using SOAP2 with default setting.
Only uniquely mapped reads were retained.
Peaks were called using CSAR with default setting.
Genome_build: TAIR10.18
Supplementary_files_format_and_content: wig file was generated using CSAR

extract_protocol:
Six large-scale ChIPs were performed with a modified protocol based on general procedures. Briefly, a much larger amount of starting materials was used in our assay than in standard ChIP protocols (~24 g vs. ~1.5 g of plant materials). However, samples were processed in smaller-sized aliquots starting from cross-linking, through nuclei isolation and chromatin fragmentation to maintain efficacy in these steps. The fragmented chromatin extracts from the smaller aliquots were then combined for immunoprecipitation.
ChIPed DNA from the 6 large-scale ChIPs were pooled for library construction. Sequencing libraries were constructed with the Ovation® Ultralow Library System (NuGEN), according to manufacturer’s protocol.

tag: antibody

value: Anti-Myc (Cell Signaling Technology, catalog# 71D10, lot# 5)


title: SPCH ChIP-Seq

description:
Read length is 51 for this sample. Needs to trim the last base.
Sample 1

value: SPCHp:SPCH2-4A-MYC in spch3


title: wildtype-h3k4me3-2

description: processed data file: wildtype-h3k4me3-average.enrich.bw

value: wild type

tag: tissue

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: wildtype-h3k4me3-1


title: wildtype-h3k27me3-2

description: processed data file: wildtype-h3k27me3-average.enrich.bw

value: Cell Signalling


title: wildtype-h3k27me3-1


title: T_E13_cKO_2

status: Public on Sep 03 2014

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to mm10 whole genome using TopHat v2.0.6 (with Bowtie 2.0.5.0) using default settings.
All samples were modeled using cuffdiff with options -p 6 --no-update-check and the UCSC mm10 genes.gtf file from the Illumina iGenomes site
Raw cuffdiff output files were loaded into the R package cummeRbund
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by cuffdiff and output by cummeRbund
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: fpkm-replicates-cKO.txt: FPKM abundance measurements for knockout samples.

extract_protocol:
Cortical dissections were performed under RNAse free conditions on ice in PBS or HBSS. Cortices were either used immediately or stored at -80C until use. Isolated neocortices were lysed in polysome extraction buffer (PEB: 20mM Tris-HCl, 100mM KCl, 10mM MgCl2, 0.3% Igepal Sigma-Aldrich #CA-630) supplemented with EDTA free protease inhibitor (Santa Cruz Biotechnology #sc-29131) RNAase inhibitor (Invitrogen #100000840), 20mM DTT (Invitrogen #NP0009), and 0.1mg/ml cycloheximide (Santa Cruz Biotechnology #sc-3508A) immediately before use, for 10 minutes on ice with occasional pipetting to mix and homogenize tissue. Then, lysate was cleared by centrifugation (Sorvall Biofuge fresco) for 10 minutes at 4C. Total lysate RNA level was determined on spectrophotometer (NanoDrop ND-1000). 250ug or 50ug total RNA weight was loaded onto 11ml or 2ml columns respectively. Ultracentrifugation for 11ml tubes was performed at 39,000 rpm for 90 minutes (Sorvall Discovery 100 with SW41 rotor and buckets) or for 2ml tubes at 39,000rpm for 50 minutes (Sorvall Discovery M120SE with S-55-S rotor and buckets). Then, samples were immediately placed in tube piercer (Brandel #621140007) connected to a syringe pump (Brandel syringe pump) and fractionated into 14 equal volume fractions while recording the absorbance (Brandel UA-6 absorbance detector). Fractions were processed for RNA by Trizol-LS extraction according to manufacturer’s protocol. Equal volumes of RNA isolated from polysome fractions 4,5,6 and 7 were pooled together for 40S-60S-80S region RNA. Similarly, equal volumes of RNA extracted from polysome fractions 9,10,11 and 12 were pooled together for polysome RNA.
Sequencing libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 according to the manufacturer's protocol. Libraries were quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems), then diluted and symmetrically pooled. We performed 2x100bp paired-end sequencing on the Illumina Hiseq2500 in rapid run mode.

value: HuR cKO

value: brain neocortex

tag: rna fraction

value: Total


title: T_P0_cKO_2


title: T_P0_cKO_1


title: T_P0_cKO_3


title: Treg CNS2 wt Foxp3 low rep2

description: PolyA+, unstranded RNA-Seq (SE100)


title: mhcIIhi4wk-wildtype-cell_A01

description:
mtec_12027_R1
PolyA RNA

tag: strain/background

value: wildtype

value: medullary thymic epithelial cell


title: T_E13_cKO_1

tag: age


title: P_P0_cKO_2

value: Polysome


title: P_E13_cKO_3


title: P_E13_cKO_2


title: P_P0_cKO_1


title: P_P0_cKO_3


title: Treg CNS2-/- Foxp3 low rep1

description: PolyA+, unstranded RNA-Seq (SE100)

value: Regulatory T (Treg) cells


title: P_E13_cKO_1


title: M_P0_cKO_2

value: Monosome


title: M_P0_cKO_1


title: wildtype-input-1

value: 4 weeks


title: Treg CNS2-/- Foxp3 high rep2

description: PolyA+, unstranded RNA-Seq (SE100)

source_name: Treg CNS2-/- Foxp3 high

value: high


title: M_E13_cKO_2


title: Treg CNS2-/- Foxp3 high rep1

description: PolyA+, unstranded RNA-Seq (SE100)


title: Normal_cloned_group - MeDIP-Seq

city: Wuhan

first: Changchun

last: Li

state: Hu Bei

address: No.1, Shizishan Street · Hongshan District

country: China

institute: Huazhong Agriculture University

description: MeDIP library for the paired-end sequencing in 50 bp read length

data_processing:
Raw sequencing data were processed by Illumina base-calling pipeline. After filtering the low quality reads, the MeDIP-seq data were aligned to the ensembl pig reference genome (Sscrofa9.61) using SOAP2 (Version 2.21). The unique reads were used to scan the peaks (wig file) using MACS1.4.0
Genome_build: Sscrofa9.61
Supplementary_files_format_and_content: The processed data is wig file, which contains chromosome position and tag counts.

organism: Sus scrofa

source_name: Biceps Femoris muscle

growth_protocol: the newborn cloned piglets

extract_protocol:
DNA of each collected tissue was extracted using using the phenol-chloroform method
DNA was sonicated to gain fragments in the range 100–500 bp, dAs were added to the 3' ends of the extracted DNA. The adaptors were then ligated to the two ends of each fragment. The detailed steps can be referenced from the protocol of the Paired-End DNA Sample Prep kit (Illumina). The double-stranded DNA was denatured, and then an antibody that recognizes 5-methylcytosine (5-mc) was used to immunoprecipitate the DNA fragments containing regions of methylated-CpGs (Magnetic Methylated DNA Immunoprecipitation kit; Diagenode). After PCR amplification of the enriched fragments, we selected the 220–320 bp fragments using a Gel Extraction kit (28706; Qiagen). The retracted DNA fragments were quantified using an Agilent 2100 Analyzer.

tag: phenotype

value: normal

value: Biceps Femoris muscle

tag: development stage

value: newborn


title: Normal_cloned_group - RNA-Seq

data_processing:
Original data were transferred into sequence data by base calling.
To obtain clean reads, raw reads were filtered before data analyses. First, the adaptors were removed; second, reads in which unknown bases were > 10% were discarded; third, low-quality reads (the percentage of low-quality bases of quality value ≤ 5 in a read were > 50%) were removed. Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches of no more than 2 bases were allowed in the alignment. The message abundance was calculated using the RPKM method.
Genome_build: Sscrofa9.61
Supplementary_files_format_and_content: contains the GeneID,Uniq_reads_num,Length,Coverage,RPKM,Symbol,Description,Blast nr

extract_protocol:
Total RNA was extracted from samples of biceps femoris muscle using TRIzol Reagent (Invitrogen).
The concentration and quality of RNA was confirmed using an Agilent 2100 system and agarose gel electrophoresis (AGE). Equal amounts of RNA from the tissue samples of three abnormal cloned piglets, three normal cloned piglets were mixed into three pools. The two independent RNA pools were then used for library construction and sequencing by the Beijing Genome Institute. Briefly, after evaluation of the quality of total RNA, mRNA was enriched by using oligo(dT) magnetic beads. After adding the fragmentation buffer, mRNA was interrupted to short fragments (≈200 bp). First-strand cDNA was synthesized using a random hexamer primer using the mRNA fragments as templates. Then buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. Double-strand cDNA was purified with a QiaQuick PCR Extraction kit and washed with Ethidium Bromide buffer for end repair and addition of single nucleotide A (adenine). Finally, sequencing adaptors were ligated to the fragments. Required fragments were purified by AGE and enriched by PCR amplification.


title: M_E13_cKO_1

tag: genotype/variation


title: Abnormal_cloned_group - RNA-Seq

value: developmental failure

tag: developmental stage


title: Genomic DNA of neurodevelopmental disorder patient CD14

city: Cologne

first: Axel

last: HILLMER

address: Kerpener Str. 62

department: Institute of Pathology

country: Germany

institute: University of Cologne

data_processing:
The Solid paired tags designated as R3 and F3 were mapped individually to the reference sequence (NCBI build 36) in color space by the ABI SOLiD pipeline Bioscope v1.0.1 (Applied Biosystems). Contigs of the reference sequence with unresolved location (random_chr) and alternative MHC haplotypes were excluded from the reference for mapping since they caused ambiguous mapping due to high sequence similarity to other sequences in the reference.
The pairing and rescuing was performed according to the ABI SOLiD pipeline to generate paired-end tags (PETs). Based on ABI SOLiD pairing report, we further separated all the PETs into concordant PETs (cPETs) and discordant PETs (dPETs).
cPETs were defined as those where both tags mapped to same chromosome, same strand, in the correct 5’ to 3’ ordering and within expected span range. The span range was determined by a procedure based on the gradient of the insert size distribution. The PETs which were rejected by cPET criteria were classified as dPETs. These were further split into five distinct categories; (i) two tags mapped on different chromosomes, (ii) two tags mapped on the same chromosome, but different strand, (iii) two tags mapped on the same chromosome, but wrong order (5’ downstream of 3’), (iv) two tags mapped on the same chromosome, same strand, correct order, but with larger span distance than 1.1x the maximum library size, (v) two tags mapped on same chromosome, same strand, correct order, but with smaller span distance than the minimum library size. Category (v) was excluded from further analysis.
A form of ‘normalization’ was carried out to convert PETs from one strand to the other, so that all dPETs were perceived to have come from a single strand. For each discordant mapping, both the original mapping and its reverse complement mapping were considered. One of the two mappings was selected according to the following hierarchy of preferences. i) Mapping with the lower chromosome number for the 5’ tag was chosen. ii) If both chromosomes were the same, mapping which results in 5’ tag mapping to the ‘+’ strand was chosen. iii) If no such mapping existed, mapping which resulted in the 5’ tag having the smaller coordinate was chosen.
To cluster different dPETs which span the same fusion point, the following procedure was applied: the mapping location of the 5’ and 3’ tags of a given dPET was extended by the maximum insert size of the respective genomic library in both directions, creating 5’ and 3’ windows. If the 5’ and 3’ tags of a second dPET mapped within the 5’ and 3’ window of the first dPET, the two PETs were defined as a cluster of the size 2 and the 5’ and 3’ windows were adjusted so that they contained the tag extensions (by the maximum library size) of the second dPET. dPETs which subsequently mapped with their 5’ and 3’ tags within the 5’ and 3’ windows, respectively, were assigned to this cluster and the windows were adjusted, if necessary. The number of dPETs clustering together around a fusion point was represented by the cluster size. The genomic region which was covered by the 5’ tags of a cluster was defined as the 5’ anchor and the genomic region which was covered by the 3’ tags of a cluster was defined as the 3’ anchor.
Genome_build: hg18
Supplementary_files_format_and_content: Column 1: cluster ID; Column 2: chromosome of the 5’ anchor mapping location (chr. 23 = chr. X; chr. 24 = chr. Y; chr. 25 = chr. M); Column 3: strand of the 5’ anchor mapping location; Column 4: start coordinate of the 5’ anchor mapping location; Column 5: end coordinate of the 5’ anchor mapping location; Column 6: distance between start and end of the 5’ anchor mapping location; Column 7: chromosome of the 3’ anchor mapping location; Column 8: strand of the 3’ anchor mapping location; Column 9: start coordinate of the 3’ anchor mapping location; Column 10: end coordinate of the 3’ anchor mapping location; Column 11: distance between start and end of the 3’ anchor mapping location; Column 12: dPET cluster size (number of PETs connecting both sides) based on non-redundant PETs; Column 13: dPET cluster size including redundant reads which are likely derived from the same PCR product. For all coordinates, only position 1 of the alignment of a 50 bp and 35 bp sequence tag, respectively, was considered.

source_name: mononuclear blood cells

growth_protocol: primary tissue, no growth conditions

extract_protocol:
genomic DNA from whole blood was isolated using QIAamp DNA Blood Midi Kit (Qiagen ) according to the manufacturer's recommendations
DNA-PET libraries were constructed for each sample, six patients and two family members as follows: genomic DNA was hydrosheared to 7-12 kb DNA fragments. Long Mate Paired (LMP) cap adaptors were ligated to the hydrosheared and end repaired DNA fragments. The cap adaptor-ligated DNA fragments were separated by agarose gel electrophoresis, recovered using the QIAEXII Gel Extraction Kit (QIAGEN) and circularized with a biotinylated adaptor that connects the cap adaptors at both ends of the DNA fragments. Missing 5’ phosphate groups of cap adaptors created a nick on each strand after circularization of the DNA. Both nicks were translated outwards by >50 bp into the circularized genomic DNA fragment by DNA polymerase I (NEB). The nick-translated constructs were then digested with T7 exonuclease and S1 nuclease (NEB), to release paired-end tag (PETs) library constructs. These constructs were ligated with SOLiD sequencing adaptors P1 and P2 (Life Technologies), and amplified using 2x HF Phusion Master Mix (Finnzymes OY) for sequencing.  High throughput sequencing of the 2x50 bp libraries was performed on SOLiD sequencers (v3plus and v4, respectively) according to the manufacturer’s recommendation (Life Technologies). Sample CD15 has been sequenced by 2x35 bp. Sequence tags were mapped to the human reference sequence (NCBI Build 36) and paired using SOLiD System Analysis Pipeline Tool Bioscope, allowing up to 12 color code mismatches per 50 bp tag and up to 4 color code mismatches per 35 bp tag. For sample CD5 and CD8, two DNA size fractions were merged for library construction which resulted in a reduced sensitivity to identify small deletions.

treatment_protocol: no treatment

tag: tissue type

value: non affected tissue

value: blood


title: Genomic DNA of neurodevelopmental disorder patient CD8


title: Genomic DNA of neurodevelopmental disorder patient CD15


title: Genomic DNA of neurodevelopmental disorder patient CD16


title: Genomic DNA of neurodevelopmental disorder patient CD10


title: Genomic DNA of neurodevelopmental disorder patient CD5


title: HeLa_H33_FLAG_Input

city: Shanghai

first: Yang

last: Shi

address: NO. 138, Yi-Xue-Yuan Road

institute: Fudan university

data_processing:
base_calling: CASAVA package (Illumina v1.6)
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie-1.0.0
peaks were called using macs2 with the following setting:--qvalue=0.05 --broad -g hs
Genome_build: hg19
Supplementary_files_format_and_content: peak list

source_name: HeLa cells

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (Hyclone) containing 10% FBS (Hyclone).

extract_protocol:
Chromatin samples were incubated with specific antibodies in ChIP Lysis buffer (50mM HEPES pH7.5, 500mM NaCl, 1mM EDTA, 1%Triton, 0.1%Na-deoxylcholate, 0.3% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on protein A/G beads (10μl per reaction). The bound fractions were washed 3 times with Lysis buffer, and 3 times with RIPA buffer (50mM Hepes, 300mM LiCl, 1mM EDTA, 0.5%NP-40, 0.7%Nadeoxylcholate), and once with TE. Elution and Reverse crosslinking were carried out in Elution buffer (50mM Tris, PH8.0, 1mM EDTA, 1% SDS) 65℃ for 6 hours. After RNase A and protease K digestion, DNA fraction was purified using PCR extraction kit (QIAGEN).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: FLAG-H3.3 stably expressing HeLa cells was established using a retroviral expressing system.

tag: cell line

value: HeLa

tag: cell type

value: C-terminal FLAG-tagged H3.3 stably expressing HeLa


title: Genomic DNA of neurodevelopmental disorder patient CD9


title: HeLa_H33_FLAG_ChIP_seq

value: Santa Cruz Bio., sc-7392


title: Genomic DNA of neurodevelopmental disorder patient CD6


title: 3- FVB_508_TMPRSS2-ERG_HOMOZYGOTE_MOUSE_26

first: Joshua

last: Korn

state: MA

address: 250 Mass Ave

institute: Novartis

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence or low-quality sequence, then mapped to mm10 whole genome and transcriptome based on ucsc knownGene using a modified version of Tophat v1.3
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks version 1.3.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: TMPRSS2:ERG homozygote prostate tissue- mouse#3

growth_protocol: TMPRSS2:ERG transgenic mice were generated using a BAC vector in FVB background.

extract_protocol:
RNeasy Plus kit (qiagen) following the manufacturers instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ventral dorsal prostate lobes from homozygous and wild-type mice.

tag: strain

value: FVB

tag: genotype

value: TMPRSS2:ERG homozygote

tag: erg status

value: positive

value: Ventral dorsal prostate lobes


title: 4- FVB_508_TMPRSS2-ERG_HOMOZYGOTE_MOUSE_29

source_name: TMPRSS2:ERG homozygote prostate tissue- mouse#4

tag: tissue


title: 1- FVB_508_WILDTYPE_MOUSE_27

source_name: Wildtype prostate tissue- mouse#1

value: wildtype

value: negative


title: 2-FVB_508_WILDTYPE_MOUSE_28

source_name: Wildtype prostate tissue- mouse#2


title: M_E13_cKO_3

value: HuR cKO

value: brain neocortex

value: Monosome


title: Breast_468PT_cancer

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

description:
468PT
SRX381621

data_processing:
Illumina Casava1.7 software used for basecalling
Read mapping: Two reference sequences were prepared based on the HG19 reference
The alignment was performed using the bowtie alignment software version  0.12.8
Methylation calls files for C's in the bowtie alignment files were generated using Bismark software
Genome_build: HG19
Supplementary_files_format_and_content: Methylation calls files; each column contrain chromosome, position, methylatedCounts, unmethylatedCounts values.

source_name: Cancer

growth_protocol: Cells were cultured in DMEM at 10% FBS, 5% CO2.

extract_protocol:
DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)
BS-seq library constructing, 10ug genomic DNA was fragmented using a Covaris sonication system (Covaris S2). Following fragmentation, libraries were constructed using the Illumina Paired-End protocol consisting of end repair, <A> base addition and methylated-adaptor ligation. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different insert size were excised from the same lane of a 2% TAE agarose gel. Normally, three bands are excised corresponding to DNA insert sizes of 80-100 bp, 100-120 bp to 120-150bp. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. PCR was carried out in a final reaction volume of 50ul consisting of 20ul purified DNA, 4ul 2.5 mM dNTP, 5 ul 10X buffer, 0.5 ul JumpStart Taq DNA polymerase, 2ul 10uM PCR primers and 37.5 ul ÎœltraPure TM Water and the following thermal cycling program: 94C 30 s, 10 cycles of 94C 30 s, 60C 30 s, 72C 30 s then prolong with 1 min at 72C. PCR products were sequenced with an Illumina genome analyzer. The reads generated by Illumina sequencing were aligned to the reference genome using SOAPaligner2. The alignment and methylation estimation was performed as described before (Li, Y. et al. PLoS Biol 8, e1000533 (2010)).
100 bases Pair-end reads

treatment_protocol: Untreated

tag: sample type

value: Cell line


title: AR-V7(-)Met1

city: Baltimore

first: Jun

last: Luo

address: 411 Marburg Building, 600 N Wolf St.

department: Urology

institute: Johns Hopkins Medical Institutions

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
Abundance measurements were obtained using HTSeq followed by RPKM normalization
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab delimited text files containing RPKM values for each sample

source_name: Metastatic castration resistant prostate cancer

extract_protocol:
Total RNA was extracted using the Trizol protocol, following by the Qiagen RNAeasy protocol
Libraries were prepared for sequencing using standard Illumina TruSeq protocol

tag: ar-v7 status

value: Negative

tag: therapy

value: Castration


title: AR-V7(-)Met2

value: Metastatic castration resistant prostate cancer


title: AR-V7(+)Met2

value: Positive

value: Enzalutamide


title: VEC2

city: Bethesda

first: Kai

last: Ge

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

data_processing:
Illumina Casava v1.8.2 was used for basecalling.
The reads were mapped to mouse genome and ERCC spike-in control transcripts by TopHat (V2.0.10)
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on March 06, 2013) and ERCC spike-in transcripts was enumerated using htseq-count from HTSeq package (V0.5.3p9).
The differential expression between VEC vs. CRE was statistically accessed by R/Bioconductor package DESeq (V1.10.1)
Genes with less than 10 fragments in all the samples were removed before differential expression analysis.
The transcripts in ERCC spike-in control were used to estimate the normalization factors that were passed to DESeq to scale the raw samples sizes through linear regression.
The normalization factor passed to DESeq were: 1.067(CRE1), 1.045(CRE2), 0.872(CRE3), 1.001(VEC1) and 1.014(VEC2).
Genome_build: mm10
Supplementary_files_format_and_content: format of 'differential expression' file: gene (gene symbol), exp_VEC(average normalized tag count estimated by DESeq for VEC group), exp_CRE(average normalized tag count estimated by DESeq for CRE group), log2ratio (log2 ratio of CRE to VEC), pvalue (p-value), FDR(false discovery rate)
Supplementary_files_format_and_content: format of 'expression measurements' file: gene (gene symbol), exp (normalized tag count of the gene, estimated by DESeq)

growth_protocol: The cells grow in DMEM medium containing 10% FBS and antibiotics

extract_protocol:
Total RNAs were purified from 1 million cells, and equal spike-in RNAs were added
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse embryonic fibroblasts

tag: passage

value: immortalized by 3T3 protocol


title: CRE3


title: VEC1


title: AR-V7(+)Met1


title: Abnormal_cloned_group - MeDIP-Seq

value: developmental failure

value: Biceps Femoris muscle

value: newborn


title: Breast_468LN_metastasis

description:
468LN
SRX381611

source_name: Metastasis


title: CRE1


title: CRE2


title: VEC_H3K9ac

data_processing:
Illumina Casava v1.8.2 was used for basecalling.
Illumina Casava v1.8.2 was used to align the reads. Reads mappable to multiple locations were discarded and at most one read per genomic location (defined by chromosome, start, end and strand) were kept for furthur analysis.
SICER v1.1 was used to call peaks and filter the reads with parameters: W=200, G=200, FDR=1e-3
H3K9ac ChIP-Seq wig files were generated based on the SICER-filtered reads, and rpkm value are used.
Normalized read counts (RPKM) were calculated at promoters (TSS±500bp)
Genome_build: mm9
Supplementary_files_format_and_content: Wig file scores represent RPKM values; wig files for H3K9ac were generated based on SICER-filtered reads and Wig files for input ChIP-Seq were generated based on preprocessed reads.
Supplementary_files_format_and_content: Read counts of H3K9ac are recorded in tab delimited text files; three columns represent gene name (Refseq), read count, and RPKM.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: chip antibody

value: H3K9ac (Epitomics, 1328-1)


title: CRE_Input


title: HeLa_BS69_ChIP_seq

value: HeLa

value: Home-made


title: CRE_H3K9ac


title: HeLa_BS69_Input


title: HeLa_H3K36me3_Input


title: HeLa_H3K36me3_ChIP_seq

value: Active Motif, 61101